PeerJ
type: channel
link: https://peerj.com/articles/
description: Articles published in PeerJ
publisher: PeerJ Inc.
publication name: PeerJ
issn: 2167-8359
items: Identification, expression, and phylogenetic analyses of terpenoid biosynthesis-related genes in secondary xylem of loblolly pine (Pinus taeda L.) based on transcriptome analyses
items: Blood parasites in Passeriformes in central Germany: prevalence and lineage diversity of Haemosporida (Haemoproteus, Plasmodium and Leucocytozoon) in six common songbirds
items: GRID-independent molecular descriptor analysis and molecular docking studies to mimic the binding hypothesis of γ-aminobutyric acid transporter 1 (GAT1) inhibitors
items: Genome-wide identification and expression analysis of new cytokinin metabolic genes in bread wheat (Triticum aestivum L.)
items: Transcriptome-wide characterization and functional analysis of MATE transporters in response to aluminum toxicity in Medicago sativa L.
items: Recent updates on metabolite composition and medicinal benefits of mangosteen plant
items: A new species of Escallonia (Escalloniaceae) from the inter-Andean tropical dry forests of Bolivia
items: Subjective assessment for super recognition: an evaluation of self-report methods in civilian and police participants
items: Maternal temperature exposure impairs emotional and cognitive responses and triggers dysregulation of neurodevelopment genes in fish
items: Empirical analysis and modeling of Argos Doppler location errors in Romania
items: Taxifolin protects rat against myocardial ischemia/reperfusion injury by modulating the mitochondrial apoptosis pathway
items: Validation of reference genes for gene expression studies in post-harvest leaves of tea plant (Camellia sinensis)
items: High-resolution maps of Swiss apiaries and their applicability to study spatial distribution of bacterial honey bee brood diseases
items: Kelpie: generating full-length ‘amplicons’ from whole-metagenome datasets
items: Urban plums and toads: do fleshy fruits affect the post-metamorphic growth of amphibians?
items: Spatial variability in soil pH and land use as the main influential factor in the red beds of the Nanxiong Basin, China
items: Expression of matrix metalloproteinases to induce the expression of genes associated with apoptosis during corpus luteum development in bovine
items: Extraordinary centromeres: differences in the meiotic chromosomes of two rock lizards species Darevskia portschinskii and Darevskia raddei
items: Age-related differences in flexibility in soccer players 8–19 years old
items: Improving the efficiency of the Fukui trap as a capture tool for the invasive European green crab (Carcinus maenas) in Newfoundland, Canada
items: EGFR deficiency leads to impaired self-renewal and pluripotency of mouse embryonic stem cells
items: Design, optimization and validation of genes commonly used in expression studies on DMH/AOM rat colon carcinogenesis model
items: Designing online species identification tools for biological recording: the impact on data quality and citizen science learning
items: Breast cancer detection using deep convolutional neural networks and support vector machines
items: A new segmentation algorithm for measuring CBCT images of nasal airway: a pilot study
items: Genome-wide identification of long non-coding RNAs in tomato plants irradiated by neutrons followed by infection with Tomato yellow leaf curl virus
items: Gastric Helicobacter pylori infection perturbs human oral microbiota
items: Optimizing influenza vaccine policies for controlling 2009-like pandemics and regular outbreaks
items: A scalable discrete-time survival model for neural networks
items: Diatom ecological response to deposition of the 833-850 CE White River Ash (east lobe) ashfall in a small subarctic Canadian lake
items: Convergent origin of the narrowly lanceolate leaf in the genus Aster—with special reference to an unexpected discovery of a new Aster species from East China
items: Isolation of wheat bran-colonizing and metabolizing species from the human fecal microbiota
items: Prognostic values of GMPS, PR, CD40, and p21 in ovarian cancer
items: Impact assessment of high soil CO2 on plant growth and soil environment: a greenhouse study
items: Nonconventional opponents: a review of malaria and leishmaniasis among United States Armed Forces
items: Increased tooth brushing frequency is associated with reduced gingival pocket bacterial diversity in patients with intracranial aneurysms
items: The complete chloroplast genomes of three Betulaceae species: implications for molecular phylogeny and historical biogeography
items: New material of the ‘microsaur’ Llistrofus from the cave deposits of Richards Spur, Oklahoma and the paleoecology of the Hapsidopareiidae
items: The dynamics of grooming interactions: maintenance of partner choice and the consequences of demographic variation for female mandrills
items: Food-burying behavior in red imported fire ants (Hymenoptera: Formicidae)
items: Effects of Salmonella enterica serovar Enteritidis infection on egg production and the immune response of the laying duck Anas platyrhynchos
items: Sleeping mattress determinants and evaluation: a biomechanical review and critique
items: Effects of different training modalities on phosphate homeostasis and local vitamin D metabolism in rat bone
items: GPs’ motivation for teaching medical students in a rural area—development of the Motivation for Medical Education Questionnaire (MoME-Q)
items: Intraspecific divergences and phylogeography of Panzerina lanata (Lamiaceae) in northwest China
items: Association of TIMP4 gene variants with steroid-induced osteonecrosis of the femoral head in the population of northern China
items: Accessible molecular phylogenomics at no cost: obtaining 14 new mitogenomes for the ant subfamily Pseudomyrmecinae from public data
items: Prioritizing bona fide bacterial small RNAs with machine learning classifiers
items: Dietary analysis of an uncharacteristic population of the Mountain Pygmy-possum (Burramys parvus) in the Kosciuszko National Park, New South Wales, Australia
items: A turiasaurian sauropod dinosaur from the Early Cretaceous Wealden Supergroup of the United Kingdom
items: Transcriptome profiling reveals the role of ZBTB38 knock-down in human neuroblastoma
items: Genome-wide characterization and expression analyses of the MYB superfamily genes during developmental stages in Chinese jujube
items: Exploring wearable sensors as an alternative to marker-based motion capture in the pitching delivery
items: Reproductive pattern and population dynamics of commercial red swamp crayfish (Procambarus clarkii) from China: implications for sustainable aquaculture management
items: Temporal whole field sawtooth flicker without a spatial component elicits a myopic shift following optical defocus irrespective of waveform direction in chicks
items: The use of one-stage meta-analytic method based on individual participant data for binary adverse events under the rule of three: a simulation study
items: GenoDup Pipeline: a tool to detect genome duplication using the dS-based method
items: P-curve accurately rejects evidence for homeopathic ultramolecular dilutions
items: Comparison of automatic airway analysis function of Invivo5 and Romexis software
items: The sensitivity and specificity of methylene blue spray to identify the parathyroid gland during thyroidectomy
items: Shifting faunal baselines through the Quaternary revealed by cave fossils of eastern Australia
items: Antimicrobial susceptibility and virulence genes of clinical and environmental isolates of Pseudomonas aeruginosa
items: Genome-wide analysis of circular RNAs in goat skin fibroblast cells in response to Orf virus infection
items: Effects of dredging on the vegetation in a small lowland river
items: Use of open mobile mapping tool to assess human mobility traceability in rural offline populations with contrasting malaria dynamics
items: Quantitatively estimating main soil water-soluble salt ions content based on Visible-near infrared wavelength selected using GC, SR and VIP
items: Seasonal changes of commercial traits, proximate and fatty acid compositions of the scallop Flexopecten glaber from the Mediterranean Sea (Southern Italy)
items: Genetic variability in a Brazilian apple germplasm collection with low chilling requirements
items: Molecular mechanism of point mutation-induced Monopolar spindle 1 (Mps1/TTK) inhibitor resistance revealed by a comprehensive molecular modeling study
items: Photosynthesis, yield and raw material quality of sugarcane injured by multiple pests
items: Potential surrogate plants for use in semi-field pesticide risk assessment with Megachile rotundata
items: Review of the ant genus Meranoplus Smith, 1853 (Hymenoptera: Formicidae) in the Arabian Peninsula with description of a new species M. mosalahi sp. n. from Oman

Identification, expression, and phylogenetic analyses of terpenoid biosynthesis-related genes in secondary xylem of loblolly pine (Pinus taeda L.) based on transcriptome analyses
type: item
type: AcademicArticle
description: Loblolly pine (Pinus taeda L.) is one of the most important species for oleoresin (a mixture of terpenoids) in South China. The high oleoresin content of loblolly pine is associated with resistance to bark beetles and other economic benefits. In this study, we conducted transcriptome analyses of loblolly pine secondary xylem to gain insight into the genes involved in terpenoid biosynthesis. A total of 372 unigenes were identified as being critical for oleoresin production, including genes for ATP-binding cassette (ABC) transporters, the cytochrome P450 (CYP) protein family, and terpenoid backbone biosynthesis enzymes. Six key genes involved in terpenoid biosynthetic pathways were selected for multiple sequence alignment, conserved motif prediction, and phylogenetic and expression profile analyses. The protein sequences of all six genes exhibited a higher degree of sequence conservation, and upstream genes were relatively more conserved than downstream genes in terpenoid biosynthetic pathways. The N-terminal regions of these sequences were less conserved than the C-terminal ends, as the N-terminals were quite diverse in both length and composition. The phylogenetic analyses revealed that most genes originated from gene duplication after species divergence, and partial genes exhibited incomplete lineage sorting. In addition, the expression profile analyses showed that all six genes exhibited high expression levels during the high-oleoresin-yielding phase.
format: application/pdf
format: text/html
creator: Jipeng Mao
creator: Zidi He
creator: Jing Hao
creator: Tianyi Liu
creator: Jiehu Chen
creator: Shaowei Huang
subject: Bioinformatics
subject: Molecular Biology
subject: Plant Science
description: doi:10.7717/peerj.6124
publisher: PeerJ Inc.
rights: © 2019 Mao et al.
abstract: Loblolly pine (Pinus taeda L.) is one of the most important species for oleoresin (a mixture of terpenoids) in South China. The high oleoresin content of loblolly pine is associated with resistance to bark beetles and other economic benefits. In this study, we conducted transcriptome analyses of loblolly pine secondary xylem to gain insight into the genes involved in terpenoid biosynthesis. A total of 372 unigenes were identified as being critical for oleoresin production, including genes for ATP-binding cassette (ABC) transporters, the cytochrome P450 (CYP) protein family, and terpenoid backbone biosynthesis enzymes. Six key genes involved in terpenoid biosynthetic pathways were selected for multiple sequence alignment, conserved motif prediction, and phylogenetic and expression profile analyses. The protein sequences of all six genes exhibited a higher degree of sequence conservation, and upstream genes were relatively more conserved than downstream genes in terpenoid biosynthetic pathways. The N-terminal regions of these sequences were less conserved than the C-terminal ends, as the N-terminals were quite diverse in both length and composition. The phylogenetic analyses revealed that most genes originated from gene duplication after species divergence, and partial genes exhibited incomplete lineage sorting. In addition, the expression profile analyses showed that all six genes exhibited high expression levels during the high-oleoresin-yielding phase.
bibliographic citation: Mao et al. (2019) Identification, expression, and phylogenetic analyses of terpenoid biosynthesis-related genes in secondary xylem of loblolly pine (Pinus taeda L.) based on transcriptome analyses. PeerJ 7:e6124 https://doi.org/10.7717/peerj.6124
date submitted: 2018-09-10
date accepted: 2018-11-18
issued: 2019-01-31
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Mao
  given name: Jipeng
author list: Agent
  family name: He
  given name: Zidi
author list: Agent
  family name: Hao
  given name: Jing
author list: Agent
  family name: Liu
  given name: Tianyi
author list: Agent
  family name: Chen
  given name: Jiehu
author list: Agent
  family name: Huang
  given name: Shaowei
doi: 10.7717/peerj.6124
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-01-31
copyright: ©2019 Mao et al.
attribution name: Mao et al.

Blood parasites in Passeriformes in central Germany: prevalence and lineage diversity of Haemosporida (Haemoproteus, Plasmodium and Leucocytozoon) in six common songbirds
type: item
type: AcademicArticle
description: Background Avian Haemosporida are vector-borne parasites that commonly infect Passeriformes. Molecular analyses revealed a high number of different lineages and lineage specific traits like prevalence and host-specificity, but knowledge of parasite prevalence and lineage diversity in wild birds in Central Germany is still lacking. Results Blood samples from a total of 238 adult and 122 nestling songbirds belonging to six species were investigated for infections with avian haemosporidian genera and lineages (Haemoproteus spp., Plasmodium spp., Leucocytozoon spp.) and Trypanosoma avium using PCR, targeting the parasite mitochondrial cytochrome b gene and 18S ribosomal RNA. In total, the prevalence in adult birds was 31.3% infected with Haemoproteus, 12.5% with Plasmodium and 71.0% with Leucocytozoon (nestlings excluded). None of the tested birds was infected with Trypanosoma avium. Only in two nestling birds, aged 12–17 days, a Leucocytozoon spp. infection was proven. Among 225 successfully sequenced samples, we found four Haemoproteus, three Plasmodium and 19 Leucocytozoon lineages, including two new Leucocytozoon lineages. Furthermore, we report two new host-lineage associations. Conclusions As first study investigating avian haemosporidian parasites in Central Germany, we provide new information on genetic diversity of Haemosporida infecting Passeriformes. We show that even with a small sample size new lineages as well as previously unknown linkages between certain lineages and host species can be detected. This may help to elucidate the diversity of lineages as well as lineage-host-connections of avian Haemosporida.
format: application/pdf
format: text/html
creator: Yvonne R. Schumm
creator: Christine Wecker
creator: Carina Marek
creator: Mareike Wassmuth
creator: Anna Bentele
creator: Hermann Willems
creator: Gerald Reiner
creator: Petra Quillfeldt
subject: Ecology
subject: Parasitology
subject: Veterinary Medicine
subject: Infectious Diseases
description: doi:10.7717/peerj.6259
publisher: PeerJ Inc.
rights: © 2019 Schumm et al.
abstract: Background Avian Haemosporida are vector-borne parasites that commonly infect Passeriformes. Molecular analyses revealed a high number of different lineages and lineage specific traits like prevalence and host-specificity, but knowledge of parasite prevalence and lineage diversity in wild birds in Central Germany is still lacking. Results Blood samples from a total of 238 adult and 122 nestling songbirds belonging to six species were investigated for infections with avian haemosporidian genera and lineages (Haemoproteus spp., Plasmodium spp., Leucocytozoon spp.) and Trypanosoma avium using PCR, targeting the parasite mitochondrial cytochrome b gene and 18S ribosomal RNA. In total, the prevalence in adult birds was 31.3% infected with Haemoproteus, 12.5% with Plasmodium and 71.0% with Leucocytozoon (nestlings excluded). None of the tested birds was infected with Trypanosoma avium. Only in two nestling birds, aged 12–17 days, a Leucocytozoon spp. infection was proven. Among 225 successfully sequenced samples, we found four Haemoproteus, three Plasmodium and 19 Leucocytozoon lineages, including two new Leucocytozoon lineages. Furthermore, we report two new host-lineage associations. Conclusions As first study investigating avian haemosporidian parasites in Central Germany, we provide new information on genetic diversity of Haemosporida infecting Passeriformes. We show that even with a small sample size new lineages as well as previously unknown linkages between certain lineages and host species can be detected. This may help to elucidate the diversity of lineages as well as lineage-host-connections of avian Haemosporida.
bibliographic citation: Schumm et al. (2019) Blood parasites in Passeriformes in central Germany: prevalence and lineage diversity of Haemosporida (Haemoproteus, Plasmodium and Leucocytozoon) in six common songbirds. PeerJ 6:e6259 https://doi.org/10.7717/peerj.6259
date submitted: 2018-08-22
date accepted: 2018-12-10
issued: 2019-01-31
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Schumm
  given name: Yvonne R.
author list: Agent
  family name: Wecker
  given name: Christine
author list: Agent
  family name: Marek
  given name: Carina
author list: Agent
  family name: Wassmuth
  given name: Mareike
author list: Agent
  family name: Bentele
  given name: Anna
author list: Agent
  family name: Willems
  given name: Hermann
author list: Agent
  family name: Reiner
  given name: Gerald
author list: Agent
  family name: Quillfeldt
  given name: Petra
doi: 10.7717/peerj.6259
volume: 6
issn: 2167-8359
publication name: PeerJ
publication date: 2019-01-31
copyright: ©2019 Schumm et al.
attribution name: Schumm et al.

GRID-independent molecular descriptor analysis and molecular docking studies to mimic the binding hypothesis of γ-aminobutyric acid transporter 1 (GAT1) inhibitors
type: item
type: AcademicArticle
description: Background The γ-aminobutyric acid (GABA) transporter GAT1 is involved in GABA transport across the biological membrane in and out of the synaptic cleft. The efficiency of this Na+ coupled GABA transport is regulated by an electrochemical gradient, which is directed inward under normal conditions. However, in certain pathophysiological situations, including strong depolarization or an imbalance in ion homeostasis, the GABA influx into the cytoplasm is increased by re-uptake transport mechanism. This mechanism may lead to extra removal of extracellular GABA which results in numerous neurological disorders such as epilepsy. Thus, small molecule inhibitors of GABA re-uptake may enhance GABA activity at the synaptic clefts. Methods In the present study, various GRID-independent molecular descriptor (GRIND) models have been developed to shed light on the 3D structural features of human GAT1 (hGAT1) inhibitors using nipecotic acid and N-diarylalkenyl piperidine analogs. Further, a binding hypothesis has been developed for the selected GAT1 antagonists by molecular docking inside the binding cavity of hGAT1 homology model. Results Our results indicate that two hydrogen bond acceptors, one hydrogen bond donor and one hydrophobic region at certain distances from each other play an important role in achieving high inhibitory potency against hGAT1. Our docking results elucidate the importance of the COOH group in hGAT1 antagonists by considering substitution of the COOH group with an isoxazol ring in compound 37, which subsequently leads to a three order of magnitude decrease in biological activity of 37 (IC50 = 38 µM) as compared to compound 1 (IC50 = 0.040 µM). Discussion Our docking results are strengthened by the structure activity relationship of the data series as well as by GRIND models, thus providing a significant structural basis for understanding the binding of antagonists, which may be useful for guiding the design of hGAT1 inhibitors.
format: application/pdf
format: text/html
creator: Sadia Zafar
creator: Ishrat Jabeen
subject: Computational Biology
subject: Neuroscience
subject: Pharmacology
description: doi:10.7717/peerj.6283
publisher: PeerJ Inc.
rights: © 2019 Zafar and Jabeen
abstract: Background The γ-aminobutyric acid (GABA) transporter GAT1 is involved in GABA transport across the biological membrane in and out of the synaptic cleft. The efficiency of this Na+ coupled GABA transport is regulated by an electrochemical gradient, which is directed inward under normal conditions. However, in certain pathophysiological situations, including strong depolarization or an imbalance in ion homeostasis, the GABA influx into the cytoplasm is increased by re-uptake transport mechanism. This mechanism may lead to extra removal of extracellular GABA which results in numerous neurological disorders such as epilepsy. Thus, small molecule inhibitors of GABA re-uptake may enhance GABA activity at the synaptic clefts. Methods In the present study, various GRID-independent molecular descriptor (GRIND) models have been developed to shed light on the 3D structural features of human GAT1 (hGAT1) inhibitors using nipecotic acid and N-diarylalkenyl piperidine analogs. Further, a binding hypothesis has been developed for the selected GAT1 antagonists by molecular docking inside the binding cavity of hGAT1 homology model. Results Our results indicate that two hydrogen bond acceptors, one hydrogen bond donor and one hydrophobic region at certain distances from each other play an important role in achieving high inhibitory potency against hGAT1. Our docking results elucidate the importance of the COOH group in hGAT1 antagonists by considering substitution of the COOH group with an isoxazol ring in compound 37, which subsequently leads to a three order of magnitude decrease in biological activity of 37 (IC50 = 38 µM) as compared to compound 1 (IC50 = 0.040 µM). Discussion Our docking results are strengthened by the structure activity relationship of the data series as well as by GRIND models, thus providing a significant structural basis for understanding the binding of antagonists, which may be useful for guiding the design of hGAT1 inhibitors.
bibliographic citation: Zafar et al. (2019) GRID-independent molecular descriptor analysis and molecular docking studies to mimic the binding hypothesis of γ-aminobutyric acid transporter 1 (GAT1) inhibitors. PeerJ 7:e6283 https://doi.org/10.7717/peerj.6283
date submitted: 2018-10-11
date accepted: 2018-12-14
issued: 2019-01-31
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Zafar
  given name: Sadia
author list: Agent
  family name: Jabeen
  given name: Ishrat
doi: 10.7717/peerj.6283
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-01-31
copyright: © 2019 Zafar and Jabeen
attribution name: Zafar and Jabeen

Genome-wide identification and expression analysis of new cytokinin metabolic genes in bread wheat (Triticum aestivum L.)
type: item
type: AcademicArticle
description: Cytokinins (CKs) are involved in determining the final grain yield in wheat. Multiple gene families are responsible for the controlled production of CKs in plants, including isopentenyl transferases for de novo synthesis, zeatin O-glucosyltransferases for reversible inactivation, β-glucosidases for reactivation, and CK oxidases/dehydrogenases for permanent degradation. Identifying and characterizing the genes of these families is an important step in furthering our understanding of CK metabolism. Using bioinformatics tools, we identified four new TaIPT, four new TaZOG, and 25 new TaGLU genes in common wheat. All of the genes harbored the characteristic conserved domains of their respective gene families. We renamed TaCKX genes on the basis of their true orthologs in rice and maize to remove inconsistencies in the nomenclature. Phylogenetic analysis revealed the early divergence of monocots from dicots, and the gene duplication event after speciation was obvious. Abscisic acid-, auxin-, salicylic acid-, sulfur-, drought- and light-responsive cis-regulatory elements were common to most of the genes under investigation. Expression profiling of CK metabolic gene families was carried out at the seedlings stage in AA genome donor of common wheat. Exogenous application of phytohormones (6-benzylaminopurine, salicylic acid, indole-3-acetic acid, gibberellic acid, and abscisic acid) for 3 h significantly upregulated the transcript levels of all four gene families, suggesting that plants tend to maintain CK stability. A 6-benzylaminopurine-specific maximum fold-change was observed for TuCKX1 and TuCKX3 in root and shoot tissues, respectively; however, the highest expression level was observed in the TuGLU gene family, indicating that the reactivation of the dormant CK isoform is the quickest way to counter external stress. The identification of new CK metabolic genes provides the foundation for their in-depth functional characterization and for elucidating their association w…
format: application/pdf
format: text/html
creator: Muhammad Shoaib
creator: Wenlong Yang
creator: Qiangqiang Shan
creator: Muhammad Sajjad
creator: Aimin Zhang
subject: Genomics
subject: Plant Science
description: doi:10.7717/peerj.6300
publisher: PeerJ Inc.
rights: © 2019 Shoaib et al.
abstract: Cytokinins (CKs) are involved in determining the final grain yield in wheat. Multiple gene families are responsible for the controlled production of CKs in plants, including isopentenyl transferases for de novo synthesis, zeatin O-glucosyltransferases for reversible inactivation, β-glucosidases for reactivation, and CK oxidases/dehydrogenases for permanent degradation. Identifying and characterizing the genes of these families is an important step in furthering our understanding of CK metabolism. Using bioinformatics tools, we identified four new TaIPT, four new TaZOG, and 25 new TaGLU genes in common wheat. All of the genes harbored the characteristic conserved domains of their respective gene families. We renamed TaCKX genes on the basis of their true orthologs in rice and maize to remove inconsistencies in the nomenclature. Phylogenetic analysis revealed the early divergence of monocots from dicots, and the gene duplication event after speciation was obvious. Abscisic acid-, auxin-, salicylic acid-, sulfur-, drought- and light-responsive cis-regulatory elements were common to most of the genes under investigation. Expression profiling of CK metabolic gene families was carried out at the seedlings stage in AA genome donor of common wheat. Exogenous application of phytohormones (6-benzylaminopurine, salicylic acid, indole-3-acetic acid, gibberellic acid, and abscisic acid) for 3 h significantly upregulated the transcript levels of all four gene families, suggesting that plants tend to maintain CK stability. A 6-benzylaminopurine-specific maximum fold-change was observed for TuCKX1 and TuCKX3 in root and shoot tissues, respectively; however, the highest expression level was observed in the TuGLU gene family, indicating that the reactivation of the dormant CK isoform is the quickest way to counter external stress. The identification of new CK metabolic genes provides the foundation for their in-depth functional characterization and for elucidating their association w…
bibliographic citation: Shoaib et al. (2019) Genome-wide identification and expression analysis of new cytokinin metabolic genes in bread wheat (Triticum aestivum L.). PeerJ 7:e6300 https://doi.org/10.7717/peerj.6300
date submitted: 2018-02-21
date accepted: 2018-12-13
issued: 2019-01-31
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Shoaib
  given name: Muhammad
author list: Agent
  family name: Yang
  given name: Wenlong
author list: Agent
  family name: Shan
  given name: Qiangqiang
author list: Agent
  family name: Sajjad
  given name: Muhammad
author list: Agent
  family name: Zhang
  given name: Aimin
doi: 10.7717/peerj.6300
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-01-31
copyright: ©2019 Shoaib et al.
attribution name: Shoaib et al.

Transcriptome-wide characterization and functional analysis of MATE transporters in response to aluminum toxicity in Medicago sativa L.
type: item
type: AcademicArticle
description: Multidrug and toxic compound extrusion (MATE) transporters contribute to multidrug resistance and play major determinants of aluminum (Al) tolerance in plants. Alfalfa (Medicago sativa L.) is the most extensively cultivated forage crop in the world, yet most alfalfa cultivars are not Al tolerant. The basic knowledge of the MATE transcripts family and the characterisation of specific MATE members involved in alfalfa Al stress remain unclear. In this study, 88 alfalfa MATE (MsMATE) transporters were identified at the whole transcriptome level. Phylogenetic analysis classified them into four subfamilies comprising 11 subgroups. Generally, five kinds of motifs were found in group G1, and most were located at the N-terminus, which might confer these genes with Al detoxification functions. Furthermore, 10 putative Al detoxification-related MsMATE genes were identified and the expression of five genes was significantly increased after Al treatment, indicating that these genes might play important roles in conferring Al tolerance to alfalfa. Considering the limited functional understanding of MATE transcripts in alfalfa, our findings will be valuable for the functional investigation and application of this family in alfalfa.
format: application/pdf
format: text/html
creator: Xueyang Min
creator: Xiaoyu Jin
creator: Wenxian Liu
creator: Xingyi Wei
creator: Zhengshe Zhang
creator: Boniface Ndayambaza
creator: Yanrong Wang
subject: Bioinformatics
subject: Evolutionary Studies
subject: Plant Science
description: doi:10.7717/peerj.6302
publisher: PeerJ Inc.
rights: © 2019 Min et al.
abstract: Multidrug and toxic compound extrusion (MATE) transporters contribute to multidrug resistance and play major determinants of aluminum (Al) tolerance in plants. Alfalfa (Medicago sativa L.) is the most extensively cultivated forage crop in the world, yet most alfalfa cultivars are not Al tolerant. The basic knowledge of the MATE transcripts family and the characterisation of specific MATE members involved in alfalfa Al stress remain unclear. In this study, 88 alfalfa MATE (MsMATE) transporters were identified at the whole transcriptome level. Phylogenetic analysis classified them into four subfamilies comprising 11 subgroups. Generally, five kinds of motifs were found in group G1, and most were located at the N-terminus, which might confer these genes with Al detoxification functions. Furthermore, 10 putative Al detoxification-related MsMATE genes were identified and the expression of five genes was significantly increased after Al treatment, indicating that these genes might play important roles in conferring Al tolerance to alfalfa. Considering the limited functional understanding of MATE transcripts in alfalfa, our findings will be valuable for the functional investigation and application of this family in alfalfa.
bibliographic citation: Min et al. (2019) Transcriptome-wide characterization and functional analysis of MATE transporters in response to aluminum toxicity in Medicago sativa L.. PeerJ 7:e6302 https://doi.org/10.7717/peerj.6302
date submitted: 2018-09-04
date accepted: 2018-12-14
issued: 2019-01-31
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Min
  given name: Xueyang
author list: Agent
  family name: Jin
  given name: Xiaoyu
author list: Agent
  family name: Liu
  given name: Wenxian
author list: Agent
  family name: Wei
  given name: Xingyi
author list: Agent
  family name: Zhang
  given name: Zhengshe
author list: Agent
  family name: Ndayambaza
  given name: Boniface
author list: Agent
  family name: Wang
  given name: Yanrong
doi: 10.7717/peerj.6302
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-01-31
copyright: © 2019 Min et al.
attribution name: Min et al.

Recent updates on metabolite composition and medicinal benefits of mangosteen plant
type: item
type: AcademicArticle
description: Background Mangosteen (Garcinia mangostana L.) fruit has a unique sweet-sour taste and is rich in beneficial compounds such as xanthones. Mangosteen originally been used in various folk medicines to treat diarrhea, wounds, and fever. More recently, it had been used as a major component in health supplement products for weight loss and for promoting general health. This is perhaps due to its known medicinal benefits, including as anti-oxidant and anti-inflammation. Interestingly, publications related to mangosteen have surged in recent years, suggesting its popularity and usefulness in research laboratories. However, there are still no updated reviews (up to 2018) in this booming research area, particularly on its metabolite composition and medicinal benefits. Method In this review, we have covered recent articles within the years of 2016 to 2018 which focus on several aspects including the latest findings on the compound composition of mangosteen fruit as well as its medicinal usages. Result Mangosteen has been vastly used in medicinal areas including in anti-cancer, anti-microbial, and anti-diabetes treatments. Furthermore, we have also described the benefits of mangosteen extract in protecting various human organs such as liver, skin, joint, eye, neuron, bowel, and cardiovascular tissues against disorders and diseases. Conclusion All in all, this review describes the numerous manipulations of mangosteen extracted compounds in medicinal areas and highlights the current trend of its research. This will be important for future directed research and may allow researchers to tackle the next big challenge in mangosteen study: drug development and human applications.
format: application/pdf
format: text/html
creator: Wan Mohd Aizat
creator: Ili Nadhirah Jamil
creator: Faridda Hannim Ahmad-Hashim
creator: Normah Mohd Noor
subject: Biotechnology
subject: Food Science and Technology
subject: Plant Science
subject: Evidence Based Medicine
subject: Translational Medicine
description: doi:10.7717/peerj.6324
publisher: PeerJ Inc.
rights: © 2019 Aizat et al.
abstract: Background Mangosteen (Garcinia mangostana L.) fruit has a unique sweet-sour taste and is rich in beneficial compounds such as xanthones. Mangosteen originally been used in various folk medicines to treat diarrhea, wounds, and fever. More recently, it had been used as a major component in health supplement products for weight loss and for promoting general health. This is perhaps due to its known medicinal benefits, including as anti-oxidant and anti-inflammation. Interestingly, publications related to mangosteen have surged in recent years, suggesting its popularity and usefulness in research laboratories. However, there are still no updated reviews (up to 2018) in this booming research area, particularly on its metabolite composition and medicinal benefits. Method In this review, we have covered recent articles within the years of 2016 to 2018 which focus on several aspects including the latest findings on the compound composition of mangosteen fruit as well as its medicinal usages. Result Mangosteen has been vastly used in medicinal areas including in anti-cancer, anti-microbial, and anti-diabetes treatments. Furthermore, we have also described the benefits of mangosteen extract in protecting various human organs such as liver, skin, joint, eye, neuron, bowel, and cardiovascular tissues against disorders and diseases. Conclusion All in all, this review describes the numerous manipulations of mangosteen extracted compounds in medicinal areas and highlights the current trend of its research. This will be important for future directed research and may allow researchers to tackle the next big challenge in mangosteen study: drug development and human applications.
bibliographic citation: Aizat et al. (2019) Recent updates on metabolite composition and medicinal benefits of mangosteen plant. PeerJ 7:e6324 https://doi.org/10.7717/peerj.6324
date submitted: 2018-09-05
date accepted: 2018-12-20
issued: 2019-01-31
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Aizat
  given name: Wan Mohd
author list: Agent
  family name: Jamil
  given name: Ili Nadhirah
author list: Agent
  family name: Ahmad-Hashim
  given name: Faridda Hannim
author list: Agent
  family name: Noor
  given name: Normah Mohd
doi: 10.7717/peerj.6324
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-01-31
copyright: © 2019 Aizat et al.
attribution name: Aizat et al.

A new species of Escallonia (Escalloniaceae) from the inter-Andean tropical dry forests of Bolivia
type: item
type: AcademicArticle
description: Over the last two decades, renewed fieldwork in poorly explored areas of the tropical Andes has dramatically increased the comparative material available to study patterns of inter- and intraspecific variation in tropical plants. In the course of a comprehensive study of the genus Escallonia, we found a group of specimens with decumbent branching, small narrowly elliptic leaves, inflorescences with up to three flowers, and flowers with red petals. This unique combination of traits was not present in any known species of the genus. To evaluate the hypothesis that these specimens belonged to a new species, we assessed whether morphological variation between the putative new species and all currently known Escallonia species was discontinuous. The lack of overlap in tolerance regions for vegetative and reproductive traits combined with differences in habit, habitat, and geographic distribution supported the hypothesis of the new species, which we named Escallonia harrisii. The new species grows in sandstone inter-Andean ridges and cliffs covered with dry forest, mostly on steep slopes between 1,300–2,200 m in southern Bolivia. It is readily distinct in overall leaf and flower morphology from other Escallonia species in the region, even though it does not grow in sympatry with other species. Because E. harrisii is locally common it may not be threated at present, but due to its restricted geographic distribution and the multiple threats of the tropical dry forests it could become potentially vulnerable.
format: application/pdf
format: text/html
creator: Felipe Zapata
creator: Daniel Villarroel
subject: Biodiversity
subject: Taxonomy
description: doi:10.7717/peerj.6328
publisher: PeerJ Inc.
rights: © 2019 Zapata and Villarroel
abstract: Over the last two decades, renewed fieldwork in poorly explored areas of the tropical Andes has dramatically increased the comparative material available to study patterns of inter- and intraspecific variation in tropical plants. In the course of a comprehensive study of the genus Escallonia, we found a group of specimens with decumbent branching, small narrowly elliptic leaves, inflorescences with up to three flowers, and flowers with red petals. This unique combination of traits was not present in any known species of the genus. To evaluate the hypothesis that these specimens belonged to a new species, we assessed whether morphological variation between the putative new species and all currently known Escallonia species was discontinuous. The lack of overlap in tolerance regions for vegetative and reproductive traits combined with differences in habit, habitat, and geographic distribution supported the hypothesis of the new species, which we named Escallonia harrisii. The new species grows in sandstone inter-Andean ridges and cliffs covered with dry forest, mostly on steep slopes between 1,300–2,200 m in southern Bolivia. It is readily distinct in overall leaf and flower morphology from other Escallonia species in the region, even though it does not grow in sympatry with other species. Because E. harrisii is locally common it may not be threated at present, but due to its restricted geographic distribution and the multiple threats of the tropical dry forests it could become potentially vulnerable.
bibliographic citation: Zapata et al. (2019) A new species of Escallonia (Escalloniaceae) from the inter-Andean tropical dry forests of Bolivia. PeerJ 7:e6328 https://doi.org/10.7717/peerj.6328
date submitted: 2018-09-27
date accepted: 2018-12-21
issued: 2019-01-31
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Zapata
  given name: Felipe
author list: Agent
  family name: Villarroel
  given name: Daniel
doi: 10.7717/peerj.6328
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-01-31
copyright: ©2019 Zapata and Villarroel
attribution name: Zapata and Villarroel

Subjective assessment for super recognition: an evaluation of self-report methods in civilian and police participants
type: item
type: AcademicArticle
description: Metacognition about face recognition has been much discussed in the psychological literature. In particular, the use of self-report to identify people with prosopagnosia (“face blindness”) has contentiously been debated. However, no study to date has specifically assessed metacognition at the top end of the spectrum. If people with exceptionally proficient face recognition skills (“super-recognizers,” SRs) have greater insight into their abilities, self-report instruments may offer an efficient means of reducing candidate lists in SR screening programs. Here, we developed a “super-recognizer questionnaire” (SRQ), calibrated using a top-end civilian sample (Experiment 1). We examined its effectiveness in identifying SRs in pools of police (Experiment 2) and civilian (Experiment 3) participants, using objective face memory and matching tests. Moderate effect sizes in both samples suggest limited insight into face memory and target-present face matching ability, whereas the only predictor of target-absent matching performance across all samples was the number of years that an officer had been in the police force. Because the SRQ and single-item ratings showed little sensitivity in discriminating SRs from typical perceivers in police officers and civilians, we recommend against the use of self-report instruments in SR screening programs.
format: application/pdf
format: text/html
creator: Sarah Bate
creator: Gavin Dudfield
subject: Neuroscience
subject: Psychiatry and Psychology
description: doi:10.7717/peerj.6330
publisher: PeerJ Inc.
rights: © 2019 Bate and Dudfield
abstract: Metacognition about face recognition has been much discussed in the psychological literature. In particular, the use of self-report to identify people with prosopagnosia (“face blindness”) has contentiously been debated. However, no study to date has specifically assessed metacognition at the top end of the spectrum. If people with exceptionally proficient face recognition skills (“super-recognizers,” SRs) have greater insight into their abilities, self-report instruments may offer an efficient means of reducing candidate lists in SR screening programs. Here, we developed a “super-recognizer questionnaire” (SRQ), calibrated using a top-end civilian sample (Experiment 1). We examined its effectiveness in identifying SRs in pools of police (Experiment 2) and civilian (Experiment 3) participants, using objective face memory and matching tests. Moderate effect sizes in both samples suggest limited insight into face memory and target-present face matching ability, whereas the only predictor of target-absent matching performance across all samples was the number of years that an officer had been in the police force. Because the SRQ and single-item ratings showed little sensitivity in discriminating SRs from typical perceivers in police officers and civilians, we recommend against the use of self-report instruments in SR screening programs.
bibliographic citation: Bate et al. (2019) Subjective assessment for super recognition: an evaluation of self-report methods in civilian and police participants. PeerJ 7:e6330 https://doi.org/10.7717/peerj.6330
date submitted: 2018-08-28
date accepted: 2018-12-19
issued: 2019-01-31
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Bate
  given name: Sarah
author list: Agent
  family name: Dudfield
  given name: Gavin
doi: 10.7717/peerj.6330
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-01-31
copyright: © 2019 Bate and Dudfield
attribution name: Bate and Dudfield

Maternal temperature exposure impairs emotional and cognitive responses and triggers dysregulation of neurodevelopment genes in fish
type: item
type: AcademicArticle
description: Fish are sensitive to temperature, but the intergenerational consequences of maternal exposure to high temperature on offspring behavioural plasticity and underlying mechanisms are unknown. Here we show that a thermal maternal stress induces impaired emotional and cognitive responses in offspring rainbow trout (Oncorhynchus mykiss). Thermal stress in mothers triggered the inhibition of locomotor fear-related responses upon exposure to a novel environment and decreased spatial learning abilities in progeny. Impaired behavioural phenotypes were associated with the dysregulation of several genes known to play major roles in neurodevelopment, including auts2 (autism susceptibility candidate 2), a key gene for neurodevelopment, more specifically neuronal migration and neurite extension, and critical for the acquisition of neurocognitive function. In addition, our analysis revealed the dysregulation of another neurodevelopment gene (dpysl5) as well as genes associated with human cognitive disorders (arv1, plp2). We observed major differences in maternal mRNA abundance in the eggs following maternal exposure to high temperature indicating that some of the observed intergenerational effects are mediated by maternally-inherited mRNAs accumulated in the egg. Together, our observations shed new light on the intergenerational determinism of fish behaviour and associated underlying mechanisms. They also stress the importance of maternal history on fish behavioural plasticity.
format: application/pdf
format: text/html
creator: Violaine Colson
creator: Morgane Cousture
creator: Danielle Damasceno
creator: Claudiane Valotaire
creator: Thaovi Nguyen
creator: Aurélie Le Cam
creator: Julien Bobe
subject: Animal Behavior
subject: Aquaculture, Fisheries and Fish Science
subject: Developmental Biology
subject: Genomics
subject: Neuroscience
description: doi:10.7717/peerj.6338
publisher: PeerJ Inc.
rights: © 2019 Colson et al.
abstract: Fish are sensitive to temperature, but the intergenerational consequences of maternal exposure to high temperature on offspring behavioural plasticity and underlying mechanisms are unknown. Here we show that a thermal maternal stress induces impaired emotional and cognitive responses in offspring rainbow trout (Oncorhynchus mykiss). Thermal stress in mothers triggered the inhibition of locomotor fear-related responses upon exposure to a novel environment and decreased spatial learning abilities in progeny. Impaired behavioural phenotypes were associated with the dysregulation of several genes known to play major roles in neurodevelopment, including auts2 (autism susceptibility candidate 2), a key gene for neurodevelopment, more specifically neuronal migration and neurite extension, and critical for the acquisition of neurocognitive function. In addition, our analysis revealed the dysregulation of another neurodevelopment gene (dpysl5) as well as genes associated with human cognitive disorders (arv1, plp2). We observed major differences in maternal mRNA abundance in the eggs following maternal exposure to high temperature indicating that some of the observed intergenerational effects are mediated by maternally-inherited mRNAs accumulated in the egg. Together, our observations shed new light on the intergenerational determinism of fish behaviour and associated underlying mechanisms. They also stress the importance of maternal history on fish behavioural plasticity.
bibliographic citation: Colson et al. (2019) Maternal temperature exposure impairs emotional and cognitive responses and triggers dysregulation of neurodevelopment genes in fish. PeerJ 7:e6338 https://doi.org/10.7717/peerj.6338
date submitted: 2018-05-02
date accepted: 2018-12-21
issued: 2019-01-31
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Colson
  given name: Violaine
author list: Agent
  family name: Cousture
  given name: Morgane
author list: Agent
  family name: Damasceno
  given name: Danielle
author list: Agent
  family name: Valotaire
  given name: Claudiane
author list: Agent
  family name: Nguyen
  given name: Thaovi
author list: Agent
  family name: Le Cam
  given name: Aurélie
author list: Agent
  family name: Bobe
  given name: Julien
doi: 10.7717/peerj.6338
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-01-31
copyright: ©2019 Colson et al.
attribution name: Colson et al.

Empirical analysis and modeling of Argos Doppler location errors in Romania
type: item
type: AcademicArticle
description: Background Advances in wildlife tracking technology have allowed researchers to understand the spatial ecology of many terrestrial and aquatic animal species. Argos Doppler is a technology that is widely used for wildlife tracking owing to the small size and low weight of the Argos transmitters. This allows them to be fitted to small-bodied species. The longer lifespan of the Argos units in comparison to units outfitted with miniaturized global positioning system (GPS) technology has also recommended their use. In practice, large Argos location errors often occur due to communication conditions such as transmitter settings, local environment, and the behavior of the tracked individual. Methods Considering the geographic specificity of errors and the lack of benchmark studies in Eastern Europe, the research objectives were: (1) to evaluate the accuracy of Argos Doppler technology under various environmental conditions in Romania, (2) to investigate the effectiveness of straightforward destructive filters for improving Argos Doppler data quality, and (3) to provide guidelines for processing Argos Doppler wildlife monitoring data. The errors associated with Argos locations in four geographic locations in Romania were assessed during static, low-speed and high-speed tests. The effectiveness of the Douglas Argos distance angle filter algorithm was then evaluated to ascertain its effect on the minimization of localization errors. Results Argos locations received in the tests had larger associated horizontal errors than those indicated by the operator of the Argos system, including under ideal reception conditions. Positional errors were similar to those obtained in other studies outside of Europe. The errors were anisotropic, with larger longitudinal errors for the vast majority of the data. Errors were mostly related to speed of the Argos transmitter at the time of reception, but other factors such as topographical conditions and orientation of antenna at the time of the…
format: application/pdf
format: text/html
creator: Laurentiu Rozylowicz
creator: Florian P. Bodescu
creator: Cristiana M. Ciocanea
creator: Athanasios A. Gavrilidis
creator: Steluta Manolache
creator: Marius L. Matache
creator: Iulia V. Miu
creator: Ionut C. Moale
creator: Andreea Nita
creator: Viorel D. Popescu
subject: Biogeography
subject: Ecology
subject: Spatial and Geographic Information Science
subject: Population Biology
description: doi:10.7717/peerj.6362
publisher: PeerJ Inc.
rights: © 2019 Rozylowicz et al.
abstract: Background Advances in wildlife tracking technology have allowed researchers to understand the spatial ecology of many terrestrial and aquatic animal species. Argos Doppler is a technology that is widely used for wildlife tracking owing to the small size and low weight of the Argos transmitters. This allows them to be fitted to small-bodied species. The longer lifespan of the Argos units in comparison to units outfitted with miniaturized global positioning system (GPS) technology has also recommended their use. In practice, large Argos location errors often occur due to communication conditions such as transmitter settings, local environment, and the behavior of the tracked individual. Methods Considering the geographic specificity of errors and the lack of benchmark studies in Eastern Europe, the research objectives were: (1) to evaluate the accuracy of Argos Doppler technology under various environmental conditions in Romania, (2) to investigate the effectiveness of straightforward destructive filters for improving Argos Doppler data quality, and (3) to provide guidelines for processing Argos Doppler wildlife monitoring data. The errors associated with Argos locations in four geographic locations in Romania were assessed during static, low-speed and high-speed tests. The effectiveness of the Douglas Argos distance angle filter algorithm was then evaluated to ascertain its effect on the minimization of localization errors. Results Argos locations received in the tests had larger associated horizontal errors than those indicated by the operator of the Argos system, including under ideal reception conditions. Positional errors were similar to those obtained in other studies outside of Europe. The errors were anisotropic, with larger longitudinal errors for the vast majority of the data. Errors were mostly related to speed of the Argos transmitter at the time of reception, but other factors such as topographical conditions and orientation of antenna at the time of the…
bibliographic citation: Rozylowicz et al. (2019) Empirical analysis and modeling of Argos Doppler location errors in Romania. PeerJ 7:e6362 https://doi.org/10.7717/peerj.6362
date submitted: 2018-09-13
date accepted: 2018-12-30
issued: 2019-01-31
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Rozylowicz
  given name: Laurentiu
author list: Agent
  family name: Bodescu
  given name: Florian P.
author list: Agent
  family name: Ciocanea
  given name: Cristiana M.
author list: Agent
  family name: Gavrilidis
  given name: Athanasios A.
author list: Agent
  family name: Manolache
  given name: Steluta
author list: Agent
  family name: Matache
  given name: Marius L.
author list: Agent
  family name: Miu
  given name: Iulia V.
author list: Agent
  family name: Moale
  given name: Ionut C.
author list: Agent
  family name: Nita
  given name: Andreea
author list: Agent
  family name: Popescu
  given name: Viorel D.
doi: 10.7717/peerj.6362
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-01-31
copyright: © 2019 Rozylowicz et al.
attribution name: Rozylowicz et al.

Taxifolin protects rat against myocardial ischemia/reperfusion injury by modulating the mitochondrial apoptosis pathway
type: item
type: AcademicArticle
description: Background Taxifolin (TAX), is an active flavonoid, that plays an underlying protective role on the cardiovascular system. This study aimed to evaluate its effect and potential mechanisms on myocardial ischemia/reperfusion (I/R) injury. Methods Healthy rat heart was subjected to I/R using the Langendorff apparatus. Hemodynamic parameters, including heart rate, left ventricular developed pressure (LVDP), maximum/minimum rate of the left ventricular pressure rise (+dp/dtmax and −dp/dtmin) and rate pressure product (RPP) were recorded during the perfusion. Histopathological examination of left ventricular was measured by hematoxylin-eosin (H&E) staining. Creatine kinase-MB (CK-MB) and lactate dehydrogenase (LDH) activities in the effluent perfusion, and the levels of malondialdehyde (MDA), superoxide dismutase (SOD), and glutathione peroxidase (GSH-PX) in the tissue were assayed. Apoptosis related proteins, such as B-cell lymphoma-2 (Bcl-2), Bcl2-associated X (Bax), and cytochrome c (Cyt-c) were also assayed by ELISA. Western blot was employed to determine apoptosis-executive proteins, including caspase 3 and 9. Transferase-mediated dUTP-X nick end labeling assay was performed to evaluate the effect TAX on myocardial apoptosis. Results Taxifolin significantly improved the ventricular functional recovery, as evident by the increase in LVDP, +dp/dtmax, −dp/dtmin and RPP, the levels of SOD, GSH-PX were also increased, but those of LDH, CK-MB, and MDA were decreased. Furthermore, TAX up-regulated the Bcl-2 protein level but down-regulated the levels of Bax, Cyt-c, caspase 3 and 9 protein, thereby inhibits the myocardial apoptosis. Discussion Taxifolin treatment remarkably improved the cardiac function, regulated oxidative stress and attenuated apoptosis. Hence, TAX has a cardioprotective effect against I/R injury by modulating mitochondrial apoptosis pathway.
format: application/pdf
format: text/html
creator: Zhenqiu Tang
creator: Chunjuan Yang
creator: Baoyan Zuo
creator: Yanan Zhang
creator: Gaosong Wu
creator: Yudi Wang
creator: Zhibin Wang
subject: Biochemistry
subject: Cardiology
subject: Pharmacology
description: doi:10.7717/peerj.6383
publisher: PeerJ Inc.
rights: © 2019 Tang et al.
abstract: Background Taxifolin (TAX), is an active flavonoid, that plays an underlying protective role on the cardiovascular system. This study aimed to evaluate its effect and potential mechanisms on myocardial ischemia/reperfusion (I/R) injury. Methods Healthy rat heart was subjected to I/R using the Langendorff apparatus. Hemodynamic parameters, including heart rate, left ventricular developed pressure (LVDP), maximum/minimum rate of the left ventricular pressure rise (+dp/dtmax and −dp/dtmin) and rate pressure product (RPP) were recorded during the perfusion. Histopathological examination of left ventricular was measured by hematoxylin-eosin (H&E) staining. Creatine kinase-MB (CK-MB) and lactate dehydrogenase (LDH) activities in the effluent perfusion, and the levels of malondialdehyde (MDA), superoxide dismutase (SOD), and glutathione peroxidase (GSH-PX) in the tissue were assayed. Apoptosis related proteins, such as B-cell lymphoma-2 (Bcl-2), Bcl2-associated X (Bax), and cytochrome c (Cyt-c) were also assayed by ELISA. Western blot was employed to determine apoptosis-executive proteins, including caspase 3 and 9. Transferase-mediated dUTP-X nick end labeling assay was performed to evaluate the effect TAX on myocardial apoptosis. Results Taxifolin significantly improved the ventricular functional recovery, as evident by the increase in LVDP, +dp/dtmax, −dp/dtmin and RPP, the levels of SOD, GSH-PX were also increased, but those of LDH, CK-MB, and MDA were decreased. Furthermore, TAX up-regulated the Bcl-2 protein level but down-regulated the levels of Bax, Cyt-c, caspase 3 and 9 protein, thereby inhibits the myocardial apoptosis. Discussion Taxifolin treatment remarkably improved the cardiac function, regulated oxidative stress and attenuated apoptosis. Hence, TAX has a cardioprotective effect against I/R injury by modulating mitochondrial apoptosis pathway.
bibliographic citation: Tang et al. (2019) Taxifolin protects rat against myocardial ischemia/reperfusion injury by modulating the mitochondrial apoptosis pathway. PeerJ 7:e6383 https://doi.org/10.7717/peerj.6383
date submitted: 2018-09-21
date accepted: 2019-01-03
issued: 2019-01-31
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Tang
  given name: Zhenqiu
author list: Agent
  family name: Yang
  given name: Chunjuan
author list: Agent
  family name: Zuo
  given name: Baoyan
author list: Agent
  family name: Zhang
  given name: Yanan
author list: Agent
  family name: Wu
  given name: Gaosong
author list: Agent
  family name: Wang
  given name: Yudi
author list: Agent
  family name: Wang
  given name: Zhibin
doi: 10.7717/peerj.6383
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-01-31
copyright: © 2019 Tang et al.
attribution name: Tang et al.

Validation of reference genes for gene expression studies in post-harvest leaves of tea plant (Camellia sinensis)
type: item
type: AcademicArticle
description: Tea is one of three major non-alcoholic beverages that are popular all around the world. The economic value of tea product largely depends on the post-harvest physiology of tea leaves. The utilization of quantitative reverse transcription polymerase chain reaction is a widely accepted and precise approach to determine the target gene expression of tea plants, and the reliability of results hinges on the selection of suitable reference genes. A few reliable reference genes have been documented using various treatments and different tissues of tea plants, but none has been done on post-harvest leaves during the tea manufacturing process. The present study selected and analyzed 15 candidate reference genes: Cs18SrRNA, CsGADPH, CsACT, CsEF-1α, CsUbi, CsTUA, Cs26SrRNA, CsRuBP, CsCYP, CselF-4α, CsMON1, CsPCS1, CsSAND, CsPPA2, CsTBP. This study made an assessment on the expression stability under two kinds of post-harvest treatment, turn over and withering, using three algorithms—GeNorm, Normfinder, and Bestkeeper. The results indicated that the three commonly used reference genes, CsTUA, Cs18SrRNA, CsRuBP, together with Cs26SrRNA, were the most unstable genes in both the turn over and withering treatments. CsACT, CsEF-1α, CsPPA2, and CsTBP were the top four reference genes in the turn over treatment, while CsTBP, CsPCS1, CsPPA2, CselF-4α, and CsACT were the five best reference genes in the withering group. The expression level of lipoxygenase genes, which were involved in a number of diverse aspects of plant physiology, including wounding, was evaluated to validate the findings. To conclude, we found a basis for the selection of reference genes for accurate transcription normalization in post-harvest leaves of tea plants.
format: application/pdf
format: text/html
creator: Zi-wei Zhou
creator: Hui-li Deng
creator: Qing-yang Wu
creator: Bin-bin Liu
creator: Chuan Yue
creator: Ting-ting Deng
creator: Zhong-xiong Lai
creator: Yun Sun
subject: Agricultural Science
subject: Biotechnology
subject: Molecular Biology
subject: Plant Science
description: doi:10.7717/peerj.6385
publisher: PeerJ Inc.
rights: © 2019 Zhou et al.
abstract: Tea is one of three major non-alcoholic beverages that are popular all around the world. The economic value of tea product largely depends on the post-harvest physiology of tea leaves. The utilization of quantitative reverse transcription polymerase chain reaction is a widely accepted and precise approach to determine the target gene expression of tea plants, and the reliability of results hinges on the selection of suitable reference genes. A few reliable reference genes have been documented using various treatments and different tissues of tea plants, but none has been done on post-harvest leaves during the tea manufacturing process. The present study selected and analyzed 15 candidate reference genes: Cs18SrRNA, CsGADPH, CsACT, CsEF-1α, CsUbi, CsTUA, Cs26SrRNA, CsRuBP, CsCYP, CselF-4α, CsMON1, CsPCS1, CsSAND, CsPPA2, CsTBP. This study made an assessment on the expression stability under two kinds of post-harvest treatment, turn over and withering, using three algorithms—GeNorm, Normfinder, and Bestkeeper. The results indicated that the three commonly used reference genes, CsTUA, Cs18SrRNA, CsRuBP, together with Cs26SrRNA, were the most unstable genes in both the turn over and withering treatments. CsACT, CsEF-1α, CsPPA2, and CsTBP were the top four reference genes in the turn over treatment, while CsTBP, CsPCS1, CsPPA2, CselF-4α, and CsACT were the five best reference genes in the withering group. The expression level of lipoxygenase genes, which were involved in a number of diverse aspects of plant physiology, including wounding, was evaluated to validate the findings. To conclude, we found a basis for the selection of reference genes for accurate transcription normalization in post-harvest leaves of tea plants.
bibliographic citation: Zhou et al. (2019) Validation of reference genes for gene expression studies in post-harvest leaves of tea plant (Camellia sinensis). PeerJ 7:e6385 https://doi.org/10.7717/peerj.6385
date submitted: 2018-10-13
date accepted: 2018-12-28
issued: 2019-01-31
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Zhou
  given name: Zi-wei
author list: Agent
  family name: Deng
  given name: Hui-li
author list: Agent
  family name: Wu
  given name: Qing-yang
author list: Agent
  family name: Liu
  given name: Bin-bin
author list: Agent
  family name: Yue
  given name: Chuan
author list: Agent
  family name: Deng
  given name: Ting-ting
author list: Agent
  family name: Lai
  given name: Zhong-xiong
author list: Agent
  family name: Sun
  given name: Yun
doi: 10.7717/peerj.6385
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-01-31
copyright: © 2019 Zhou et al.
attribution name: Zhou et al.

High-resolution maps of Swiss apiaries and their applicability to study spatial distribution of bacterial honey bee brood diseases
type: item
type: AcademicArticle
description: Honey bees directly affect and are influenced by their local environment, in terms of food sources, pollinator densities, pathogen and toxin exposure and climate. Currently, there is a lack of studies analyzing these data with Geographic Information Systems (GIS) to investigate spatial relationships with the environment. Particularly for inter-colonial pathogen transmission, it is known that the likelihood of a healthy colony to become infested (e.g., Varroosis) or infected (e.g., American foulbrood—AFB, European foulbrood—EFB) increases with higher colony density. Whether these transmission paths can actually be asserted at apiary level is largely unknown. Here, we unraveled spatial distribution and high-resolution density of apiaries and bacterial honey bee brood diseases in Switzerland based on available GIS data. Switzerland as ‘model country’ offers the unique opportunity to get apiary data since 2010 owing to compulsory registration for every beekeeper. Further, both destructive bee brood diseases (AFB and EFB) are legally notifiable in Switzerland, and EFB has an epizootic character for the last decades. As governmental data sets have to be ameliorated, raw data from the cantonal agricultural or veterinary offices have been included. We found a mean density of 0.56 apiaries per km2, and high resolution spatial analyzes showed strong correlation between density of apiaries and human population density as well as agricultural landscape type. Concerning two bacterial bee brood diseases (AFB, EFB), no significant correlation was detectable with density of apiaries on cantonal level, though a high correlation of EFB cases and apiary density became obvious on higher resolution (district level). Hence, Swiss EFB epizootics seem to have benefited from high apiary densities, promoting the transmission of pathogens by adult bees. The GIS-based method presented here, might also be useful for other bee diseases, anthropogenic or environmental factors affecting bee coloni…
format: application/pdf
format: text/html
creator: Raphael S. von Büren
creator: Bernadette Oehen
creator: Nikolaus J. Kuhn
creator: Silvio Erler
subject: Agricultural Science
subject: Ecology
subject: Zoology
subject: Environmental Impacts
subject: Spatial and Geographic Information Science
description: doi:10.7717/peerj.6393
publisher: PeerJ Inc.
rights: © 2019 von Büren et al.
abstract: Honey bees directly affect and are influenced by their local environment, in terms of food sources, pollinator densities, pathogen and toxin exposure and climate. Currently, there is a lack of studies analyzing these data with Geographic Information Systems (GIS) to investigate spatial relationships with the environment. Particularly for inter-colonial pathogen transmission, it is known that the likelihood of a healthy colony to become infested (e.g., Varroosis) or infected (e.g., American foulbrood—AFB, European foulbrood—EFB) increases with higher colony density. Whether these transmission paths can actually be asserted at apiary level is largely unknown. Here, we unraveled spatial distribution and high-resolution density of apiaries and bacterial honey bee brood diseases in Switzerland based on available GIS data. Switzerland as ‘model country’ offers the unique opportunity to get apiary data since 2010 owing to compulsory registration for every beekeeper. Further, both destructive bee brood diseases (AFB and EFB) are legally notifiable in Switzerland, and EFB has an epizootic character for the last decades. As governmental data sets have to be ameliorated, raw data from the cantonal agricultural or veterinary offices have been included. We found a mean density of 0.56 apiaries per km2, and high resolution spatial analyzes showed strong correlation between density of apiaries and human population density as well as agricultural landscape type. Concerning two bacterial bee brood diseases (AFB, EFB), no significant correlation was detectable with density of apiaries on cantonal level, though a high correlation of EFB cases and apiary density became obvious on higher resolution (district level). Hence, Swiss EFB epizootics seem to have benefited from high apiary densities, promoting the transmission of pathogens by adult bees. The GIS-based method presented here, might also be useful for other bee diseases, anthropogenic or environmental factors affecting bee coloni…
bibliographic citation: von Büren et al. (2019) High-resolution maps of Swiss apiaries and their applicability to study spatial distribution of bacterial honey bee brood diseases. PeerJ 7:e6393 https://doi.org/10.7717/peerj.6393
date submitted: 2018-10-11
date accepted: 2019-01-03
issued: 2019-01-31
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: von Büren
  given name: Raphael S.
author list: Agent
  family name: Oehen
  given name: Bernadette
author list: Agent
  family name: Kuhn
  given name: Nikolaus J.
author list: Agent
  family name: Erler
  given name: Silvio
doi: 10.7717/peerj.6393
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-01-31
copyright: ©2019 von Büren et al.
attribution name: von Büren et al.

Kelpie: generating full-length ‘amplicons’ from whole-metagenome datasets
type: item
type: AcademicArticle
description: Introduction Whole-metagenome sequencing can be a rich source of information about the structure and function of entire metagenomic communities, but getting accurate and reliable results from these datasets can be challenging. Analysis of these datasets is founded on the mapping of sequencing reads onto known genomic regions from known organisms, but short reads will often map equally well to multiple regions, and to multiple reference organisms. Assembling metagenomic datasets prior to mapping can generate much longer and more precisely mappable sequences but the presence of closely related organisms and highly conserved regions makes metagenomic assembly challenging, and some regions of particular interest can assemble poorly. One solution to these problems is to use specialised tools, such as Kelpie, that can accurately extract and assemble full-length sequences for defined genomic regions from whole-metagenome datasets. Methods Kelpie is a kMer-based tool that generates full-length amplicon-like sequences from whole-metagenome datasets. It takes a pair of primer sequences and a set of metagenomic reads, and uses a combination of kMer filtering, error correction and assembly techniques to construct sets of full-length inter-primer sequences. Results The effectiveness of Kelpie is demonstrated here through the extraction and assembly of full-length ribosomal marker gene regions, as this allows comparisons with conventional amplicon sequencing and published metagenomic benchmarks. The results show that the Kelpie-generated sequences and community profiles closely match those produced by amplicon sequencing, down to low abundance levels, and running Kelpie on the synthetic CAMI metagenomic benchmarking datasets shows similar high levels of both precision and recall. Conclusions Kelpie can be thought of as being somewhat like an in-silico PCR tool, taking a primer pair and producing the resulting ‘amplicons’ from a whole-metagenome dataset. Marker regions from the 16…
format: application/pdf
format: text/html
creator: Paul Greenfield
creator: Nai Tran-Dinh
creator: David Midgley
subject: Bioinformatics
subject: Ecology
subject: Genomics
subject: Microbiology
description: doi:10.7717/peerj.6174
publisher: PeerJ Inc.
rights: © 2019 Greenfield et al.
abstract: Introduction Whole-metagenome sequencing can be a rich source of information about the structure and function of entire metagenomic communities, but getting accurate and reliable results from these datasets can be challenging. Analysis of these datasets is founded on the mapping of sequencing reads onto known genomic regions from known organisms, but short reads will often map equally well to multiple regions, and to multiple reference organisms. Assembling metagenomic datasets prior to mapping can generate much longer and more precisely mappable sequences but the presence of closely related organisms and highly conserved regions makes metagenomic assembly challenging, and some regions of particular interest can assemble poorly. One solution to these problems is to use specialised tools, such as Kelpie, that can accurately extract and assemble full-length sequences for defined genomic regions from whole-metagenome datasets. Methods Kelpie is a kMer-based tool that generates full-length amplicon-like sequences from whole-metagenome datasets. It takes a pair of primer sequences and a set of metagenomic reads, and uses a combination of kMer filtering, error correction and assembly techniques to construct sets of full-length inter-primer sequences. Results The effectiveness of Kelpie is demonstrated here through the extraction and assembly of full-length ribosomal marker gene regions, as this allows comparisons with conventional amplicon sequencing and published metagenomic benchmarks. The results show that the Kelpie-generated sequences and community profiles closely match those produced by amplicon sequencing, down to low abundance levels, and running Kelpie on the synthetic CAMI metagenomic benchmarking datasets shows similar high levels of both precision and recall. Conclusions Kelpie can be thought of as being somewhat like an in-silico PCR tool, taking a primer pair and producing the resulting ‘amplicons’ from a whole-metagenome dataset. Marker regions from the 16…
bibliographic citation: Greenfield et al. (2019) Kelpie: generating full-length ‘amplicons’ from whole-metagenome datasets. PeerJ 6:e6174 https://doi.org/10.7717/peerj.6174
date submitted: 2018-09-18
date accepted: 2018-11-24
issued: 2019-01-30
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Greenfield
  given name: Paul
author list: Agent
  family name: Tran-Dinh
  given name: Nai
author list: Agent
  family name: Midgley
  given name: David
doi: 10.7717/peerj.6174
volume: 6
issn: 2167-8359
publication name: PeerJ
publication date: 2019-01-30
copyright: ©2019 Greenfield et al.
attribution name: Greenfield et al.

Urban plums and toads: do fleshy fruits affect the post-metamorphic growth of amphibians?
type: item
type: AcademicArticle
description: Background The main aim of the study was to analyse the influence of fleshy fruits (plums) on the post-metamorphic growth and feeding behaviour of the green toad Bufotes viridis. We tested the following two hypotheses: (1) juveniles of the green toad are characterised by faster growth in conditions involving fallen plums Prunus cerasifera due to the associated presence of more varied food such as invertebrates; (2) green toads exhibit more active feeding behaviour in the presence of fleshy fruits. Methods A total of 120 fresh metamorphs of the green toad were randomly assigned to one of four groups: two experimental groups with fleshy plums and two other groups as controls (without fruits). Each group was kept in an enclosure to which wild invertebrates had free access. Each individual toad was measured for snout-vent length (mm) and body mass (g) every other day for 30 days. In order to determine whether fallen plums influence the feeding behaviour of toads, the number of active and hidden (under an artificial shelter) individuals was also noted. Results The results showed that green toads from both enclosures with plums were characterised by more rapid growth than individuals from the control treatments. Simultaneously, in the enclosure with fleshy fruits, greater species richness of wild invertebrates was observed. No differences in active feeding behaviour were noted between control groups and groups with plums. Discussion Fleshy fruits, upon falling, attract many types of invertebrates; thus they may represent good dietary supplements for fresh amphibian metamorphs. Therefore, the presence of fruit trees close to a breeding site might influences the post-metamorphic growth of amphibians, but not their feeding behaviour. The presence of insects associated with fallen fruit seems to favour the occurrence of amphibian populations, which is particularly important, since, due to political and social pressure, numbers of fruit trees are currently being reduced. To ou…
format: application/pdf
format: text/html
creator: Mikołaj Kaczmarski
creator: Piotr Tryjanowski
creator: Anna Maria Kubicka
subject: Ecology
subject: Ecosystem Science
subject: Zoology
description: doi:10.7717/peerj.6337
publisher: PeerJ Inc.
rights: © 2019 Kaczmarski et al.
abstract: Background The main aim of the study was to analyse the influence of fleshy fruits (plums) on the post-metamorphic growth and feeding behaviour of the green toad Bufotes viridis. We tested the following two hypotheses: (1) juveniles of the green toad are characterised by faster growth in conditions involving fallen plums Prunus cerasifera due to the associated presence of more varied food such as invertebrates; (2) green toads exhibit more active feeding behaviour in the presence of fleshy fruits. Methods A total of 120 fresh metamorphs of the green toad were randomly assigned to one of four groups: two experimental groups with fleshy plums and two other groups as controls (without fruits). Each group was kept in an enclosure to which wild invertebrates had free access. Each individual toad was measured for snout-vent length (mm) and body mass (g) every other day for 30 days. In order to determine whether fallen plums influence the feeding behaviour of toads, the number of active and hidden (under an artificial shelter) individuals was also noted. Results The results showed that green toads from both enclosures with plums were characterised by more rapid growth than individuals from the control treatments. Simultaneously, in the enclosure with fleshy fruits, greater species richness of wild invertebrates was observed. No differences in active feeding behaviour were noted between control groups and groups with plums. Discussion Fleshy fruits, upon falling, attract many types of invertebrates; thus they may represent good dietary supplements for fresh amphibian metamorphs. Therefore, the presence of fruit trees close to a breeding site might influences the post-metamorphic growth of amphibians, but not their feeding behaviour. The presence of insects associated with fallen fruit seems to favour the occurrence of amphibian populations, which is particularly important, since, due to political and social pressure, numbers of fruit trees are currently being reduced. To ou…
bibliographic citation: Kaczmarski et al. (2019) Urban plums and toads: do fleshy fruits affect the post-metamorphic growth of amphibians?. PeerJ 7:e6337 https://doi.org/10.7717/peerj.6337
date submitted: 2018-09-11
date accepted: 2018-12-21
issued: 2019-01-30
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Kaczmarski
  given name: Mikołaj
author list: Agent
  family name: Tryjanowski
  given name: Piotr
author list: Agent
  family name: Kubicka
  given name: Anna Maria
doi: 10.7717/peerj.6337
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-01-30
copyright: © 2019 Kaczmarski et al.
attribution name: Kaczmarski et al.

Spatial variability in soil pH and land use as the main influential factor in the red beds of the Nanxiong Basin, China
type: item
type: AcademicArticle
description: Soil pH is the main factor affecting soil nutrient availability and chemical substances in soil. It is of great significance to study the spatial variability of soil pH for the management of soil nutrients and the prediction of soil pollution. In order to explore the causes of spatial variability in soil pH in red-bed areas, the Nanxiong Basin in south China was selected as an example, and soil pH was measured in the topsoil by nested sampling (0–20 cm depth). The spatial variability characteristics of soil pH were analyzed by geostatistics and classical statistical methods, and the main factors influencing spatial variability in soil pH are discussed. The coefficient of variation in the red-bed areas of Nanxiong Basin was 17.18%, indicating moderate variability. Geostatistical analysis showed that the spherical model is the optimal theoretical model for explaining variability in soil pH, which is influenced by both structural and random factors. Analysis of the spatial distribution and pattern showed that soil pH is relatively high in the northeast and southwest, and is lower in the northwest. These results indicate that land use patterns and topographic factors are the main and secondary influencing factors, respectively.
format: application/pdf
format: text/html
creator: Ping Yan
creator: Hua Peng
creator: Luobin Yan
creator: Shaoyun Zhang
creator: Aimin Chen
creator: Kairong Lin
subject: Agricultural Science
subject: Soil Science
description: doi:10.7717/peerj.6342
publisher: PeerJ Inc.
rights: © 2019 Yan et al.
abstract: Soil pH is the main factor affecting soil nutrient availability and chemical substances in soil. It is of great significance to study the spatial variability of soil pH for the management of soil nutrients and the prediction of soil pollution. In order to explore the causes of spatial variability in soil pH in red-bed areas, the Nanxiong Basin in south China was selected as an example, and soil pH was measured in the topsoil by nested sampling (0–20 cm depth). The spatial variability characteristics of soil pH were analyzed by geostatistics and classical statistical methods, and the main factors influencing spatial variability in soil pH are discussed. The coefficient of variation in the red-bed areas of Nanxiong Basin was 17.18%, indicating moderate variability. Geostatistical analysis showed that the spherical model is the optimal theoretical model for explaining variability in soil pH, which is influenced by both structural and random factors. Analysis of the spatial distribution and pattern showed that soil pH is relatively high in the northeast and southwest, and is lower in the northwest. These results indicate that land use patterns and topographic factors are the main and secondary influencing factors, respectively.
bibliographic citation: Yan et al. (2019) Spatial variability in soil pH and land use as the main influential factor in the red beds of the Nanxiong Basin, China. PeerJ 7:e6342 https://doi.org/10.7717/peerj.6342
date submitted: 2018-08-27
date accepted: 2018-12-24
issued: 2019-01-30
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Yan
  given name: Ping
author list: Agent
  family name: Peng
  given name: Hua
author list: Agent
  family name: Yan
  given name: Luobin
author list: Agent
  family name: Zhang
  given name: Shaoyun
author list: Agent
  family name: Chen
  given name: Aimin
author list: Agent
  family name: Lin
  given name: Kairong
doi: 10.7717/peerj.6342
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-01-30
copyright: ©2019 Yan et al.
attribution name: Yan et al.

Expression of matrix metalloproteinases to induce the expression of genes associated with apoptosis during corpus luteum development in bovine
type: item
type: AcademicArticle
description: Here we investigated the expressions of apoptosis-associated genes known to induce programed cell death through mRNA expressions of two matrix metalloproteinases (MMPs) that are involved in the degradation of collagen and basal membrane in luteal cells cultured in the treatment media. Our results show that the activity of MMP-2 gelatinase was higher in the CL2 and CL1 of luteal phase, was gradually decreased in the CH2 and CH3 of luteal phase. In particular, the expressions of P4-r and survival-associated genes (IGFr, PI3K, AKT, and mTOR) were strongly induced during CL3 stage, whereas the levels of these genes in corpus luteum (CL) were lower during CL2 and CL1 stages. In the cultured lutein cells analyzed, we found that as MMPs increase, genes related to apoptosis (20α-hydroxy steroid dehydrogenase and caspase-3) also increase. In other words, the results for P4-r and survival-related gene expression patterns in the luteal cells were contrary to the MMPs activation results. These results indicate that active MMPs are differentially expressed to induce the expression of genes associated with programed cell death from the degrading luteal cells. Therefore, our results suggest that the MMPs activation may lead to luteal cell development or death.
format: application/pdf
format: text/html
creator: Sang Hwan Kim
creator: Ji Hye Lee
creator: Jong Taek Yoon
subject: Agricultural Science
subject: Developmental Biology
description: doi:10.7717/peerj.6344
publisher: PeerJ Inc.
rights: © 2019 Kim et al.
abstract: Here we investigated the expressions of apoptosis-associated genes known to induce programed cell death through mRNA expressions of two matrix metalloproteinases (MMPs) that are involved in the degradation of collagen and basal membrane in luteal cells cultured in the treatment media. Our results show that the activity of MMP-2 gelatinase was higher in the CL2 and CL1 of luteal phase, was gradually decreased in the CH2 and CH3 of luteal phase. In particular, the expressions of P4-r and survival-associated genes (IGFr, PI3K, AKT, and mTOR) were strongly induced during CL3 stage, whereas the levels of these genes in corpus luteum (CL) were lower during CL2 and CL1 stages. In the cultured lutein cells analyzed, we found that as MMPs increase, genes related to apoptosis (20α-hydroxy steroid dehydrogenase and caspase-3) also increase. In other words, the results for P4-r and survival-related gene expression patterns in the luteal cells were contrary to the MMPs activation results. These results indicate that active MMPs are differentially expressed to induce the expression of genes associated with programed cell death from the degrading luteal cells. Therefore, our results suggest that the MMPs activation may lead to luteal cell development or death.
bibliographic citation: Kim et al. (2019) Expression of matrix metalloproteinases to induce the expression of genes associated with apoptosis during corpus luteum development in bovine. PeerJ 7:e6344 https://doi.org/10.7717/peerj.6344
date submitted: 2018-06-20
date accepted: 2018-12-22
issued: 2019-01-30
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Kim
  given name: Sang Hwan
author list: Agent
  family name: Lee
  given name: Ji Hye
author list: Agent
  family name: Yoon
  given name: Jong Taek
doi: 10.7717/peerj.6344
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-01-30
copyright: © 2019 Kim et al.
attribution name: Kim et al.

Extraordinary centromeres: differences in the meiotic chromosomes of two rock lizards species Darevskia portschinskii and Darevskia raddei
type: item
type: AcademicArticle
description: According to the synthesis of 30 years of multidisciplinary studies, parthenogenetic species of rock lizards of genus Darevskia were formed as a result of different combination patterns of interspecific hybridization of the four bisexual parental species: Darevskia raddei, D. mixta, D. valentini, and D. portschinskii. In particular, D. portschinskii and D. raddei are considered as the parental species for the parthenogenetic species D. rostombekowi. Here for the first time, we present the result of comparative immunocytochemical study of primary spermatocyte nuclei spreads from the leptotene to diplotene stages of meiotic prophase I in two species: D. portschinskii and D. raddei. We observed similar chromosome lengths for both synaptonemal complex (SC) karyotypes as well as a similar number of crossing over sites. However, unexpected differences in the number and distribution of anti-centromere antibody (ACA) foci were detected in the SC structure of bivalents of the two species. In all examined D. portschinskii spermatocyte nuclei, one immunostained centromere focus was detected per SC bivalent. In contrast, in almost every studied D. raddei nuclei we identified three to nine SCs with additional immunostained ACA foci per SC bivalent. Thus, the obtained results allow us to identify species-specific karyotype features, previously not been detected using conventional mitotic chromosome analysis. Presumably the additional centromere foci are result of epigenetic chromatin modifications. We assume that this characteristic of the D. raddei karyotype could represent useful marker for the future studies of parthenogenetic species hybrid karyotypes related to D. raddei.
format: application/pdf
format: text/html
creator: Victor Spangenberg
creator: Marine Arakelyan
creator: Eduard Galoyan
creator: Mark Pankin
creator: Ruzanna Petrosyan
creator: Ilona Stepanyan
creator: Tatiana Grishaeva
creator: Felix Danielyan
creator: Oxana Kolomiets
subject: Cell Biology
subject: Genetics
subject: Zoology
description: doi:10.7717/peerj.6360
publisher: PeerJ Inc.
rights: © 2019 Spangenberg et al.
abstract: According to the synthesis of 30 years of multidisciplinary studies, parthenogenetic species of rock lizards of genus Darevskia were formed as a result of different combination patterns of interspecific hybridization of the four bisexual parental species: Darevskia raddei, D. mixta, D. valentini, and D. portschinskii. In particular, D. portschinskii and D. raddei are considered as the parental species for the parthenogenetic species D. rostombekowi. Here for the first time, we present the result of comparative immunocytochemical study of primary spermatocyte nuclei spreads from the leptotene to diplotene stages of meiotic prophase I in two species: D. portschinskii and D. raddei. We observed similar chromosome lengths for both synaptonemal complex (SC) karyotypes as well as a similar number of crossing over sites. However, unexpected differences in the number and distribution of anti-centromere antibody (ACA) foci were detected in the SC structure of bivalents of the two species. In all examined D. portschinskii spermatocyte nuclei, one immunostained centromere focus was detected per SC bivalent. In contrast, in almost every studied D. raddei nuclei we identified three to nine SCs with additional immunostained ACA foci per SC bivalent. Thus, the obtained results allow us to identify species-specific karyotype features, previously not been detected using conventional mitotic chromosome analysis. Presumably the additional centromere foci are result of epigenetic chromatin modifications. We assume that this characteristic of the D. raddei karyotype could represent useful marker for the future studies of parthenogenetic species hybrid karyotypes related to D. raddei.
bibliographic citation: Spangenberg et al. (2019) Extraordinary centromeres: differences in the meiotic chromosomes of two rock lizards species Darevskia portschinskii and Darevskia raddei. PeerJ 7:e6360 https://doi.org/10.7717/peerj.6360
date submitted: 2018-09-11
date accepted: 2018-12-28
issued: 2019-01-30
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Spangenberg
  given name: Victor
author list: Agent
  family name: Arakelyan
  given name: Marine
author list: Agent
  family name: Galoyan
  given name: Eduard
author list: Agent
  family name: Pankin
  given name: Mark
author list: Agent
  family name: Petrosyan
  given name: Ruzanna
author list: Agent
  family name: Stepanyan
  given name: Ilona
author list: Agent
  family name: Grishaeva
  given name: Tatiana
author list: Agent
  family name: Danielyan
  given name: Felix
author list: Agent
  family name: Kolomiets
  given name: Oxana
doi: 10.7717/peerj.6360
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-01-30
copyright: © 2019 Spangenberg et al.
attribution name: Spangenberg et al.

Age-related differences in flexibility in soccer players 8–19 years old
type: item
type: AcademicArticle
description: Background Muscle flexibility is a main component of health-related fitness and one of the basic components of fitness for the performance in some sports. Sport and health professionals require the flexibility profile of soccer to define quantitative aims in the training of flexibility. The aim of this study was to identify age-related differences in lower extremity flexibility in youth soccer players. Methods Seventy-two young male soccer players (age: 13.0 ± 3.1 y; body mass: 50.5 ± 15.3 kg; stature 158.2 ± 16.8 cm; BMI: 19.6 ± 2.6 kg/m2) completed this study. Measures of eleven passive hip (hip extension (HE), hip adduction with hip flexed 90°(HAD-HF90°), hip flexion with knee flexed (HF-KF) and extended (HF-KE), hip abduction with hip neutral (HAB) and hip flexed 90°(HAB-HF90°), hip external (HER) and internal (HIR) rotation), knee (knee flexion (KF)) and ankle dorsiflexion (ankle dorsiflexion with knee flexed (ADF-KF) and extended (ADF-KE)) ranges of motion (ROM) were taken. Descriptive statistics were calculated for hip, knee and ankle ROM measured separately by leg (dominant and non-dominant) and age-group (U10, U12, U14, U16 and U19). The data was analysed using a one-way analysis of variance (ANOVA) to examine the interaction of 11 ROM in the different players’ age-group. Results Generally, U10 and/or U12 soccer players obtain the highest mean value in almost all ROM evaluated (U10: HAD-HF [39.6° ± 4.3°], ADF-KE [32.3° ± 4.1°], HER [63.5° ± 5.6°] and HAB-HF90°[64.1° ± 7.5°]; U12: HE [17.7° ± 6.2°], HAB [35.6° ± 3.0], HIR [60.8° ± 4.7°] and KF [133.8° ± 7.1°]). Nonetheless, significant differences between the players’ age-groups are just found in HAD-HF90°(p = .042; ES = .136), HAB (p = .001; ES = .252), HIR (p = .001; ES = .251), HER (p < .001; ES = .321) and HAB-HF90°(p < .001; ES = .376) ROM, showing a progressive and irregular decrease in these ROM until the U19 team. Conclusion The findings of this study reinforce the necessity of prescribing exercises …
format: application/pdf
format: text/html
creator: Antonio Cejudo
creator: Francisco Javier Robles-Palazón
creator: Francisco Ayala
creator: Mark De Ste Croix
creator: Enrique Ortega-Toro
creator: Fernando Santonja-Medina
creator: Pilar Sainz de Baranda
subject: Orthopedics
subject: Pediatrics
description: doi:10.7717/peerj.6236
publisher: PeerJ Inc.
rights: © 2019 Cejudo et al.
abstract: Background Muscle flexibility is a main component of health-related fitness and one of the basic components of fitness for the performance in some sports. Sport and health professionals require the flexibility profile of soccer to define quantitative aims in the training of flexibility. The aim of this study was to identify age-related differences in lower extremity flexibility in youth soccer players. Methods Seventy-two young male soccer players (age: 13.0 ± 3.1 y; body mass: 50.5 ± 15.3 kg; stature 158.2 ± 16.8 cm; BMI: 19.6 ± 2.6 kg/m2) completed this study. Measures of eleven passive hip (hip extension (HE), hip adduction with hip flexed 90°(HAD-HF90°), hip flexion with knee flexed (HF-KF) and extended (HF-KE), hip abduction with hip neutral (HAB) and hip flexed 90°(HAB-HF90°), hip external (HER) and internal (HIR) rotation), knee (knee flexion (KF)) and ankle dorsiflexion (ankle dorsiflexion with knee flexed (ADF-KF) and extended (ADF-KE)) ranges of motion (ROM) were taken. Descriptive statistics were calculated for hip, knee and ankle ROM measured separately by leg (dominant and non-dominant) and age-group (U10, U12, U14, U16 and U19). The data was analysed using a one-way analysis of variance (ANOVA) to examine the interaction of 11 ROM in the different players’ age-group. Results Generally, U10 and/or U12 soccer players obtain the highest mean value in almost all ROM evaluated (U10: HAD-HF [39.6° ± 4.3°], ADF-KE [32.3° ± 4.1°], HER [63.5° ± 5.6°] and HAB-HF90°[64.1° ± 7.5°]; U12: HE [17.7° ± 6.2°], HAB [35.6° ± 3.0], HIR [60.8° ± 4.7°] and KF [133.8° ± 7.1°]). Nonetheless, significant differences between the players’ age-groups are just found in HAD-HF90°(p = .042; ES = .136), HAB (p = .001; ES = .252), HIR (p = .001; ES = .251), HER (p < .001; ES = .321) and HAB-HF90°(p < .001; ES = .376) ROM, showing a progressive and irregular decrease in these ROM until the U19 team. Conclusion The findings of this study reinforce the necessity of prescribing exercises …
bibliographic citation: Cejudo et al. (2019) Age-related differences in flexibility in soccer players 8–19 years old. PeerJ 7:e6236 https://doi.org/10.7717/peerj.6236
date submitted: 2018-09-14
date accepted: 2018-12-07
issued: 2019-01-29
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Cejudo
  given name: Antonio
author list: Agent
  family name: Robles-Palazón
  given name: Francisco Javier
author list: Agent
  family name: Ayala
  given name: Francisco
author list: Agent
  family name: De Ste Croix
  given name: Mark
author list: Agent
  family name: Ortega-Toro
  given name: Enrique
author list: Agent
  family name: Santonja-Medina
  given name: Fernando
author list: Agent
  family name: Sainz de Baranda
  given name: Pilar
doi: 10.7717/peerj.6236
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-01-29
copyright: ©2019 Cejudo et al.
attribution name: Cejudo et al.

Improving the efficiency of the Fukui trap as a capture tool for the invasive European green crab (Carcinus maenas) in Newfoundland, Canada
type: item
type: AcademicArticle
description: The European green crab (Carcinus maenas) is a crustacean species native to European and North African coastlines that has become one of the world’s most successful marine invasive species. Targeted fishing programs aimed at removing green crabs from invaded ecosystems commonly use Fukui multi-species marine traps. Improving the efficiency of these traps would improve the ability to respond to green crab invasions. In this study, we developed four distinct trap modifications that were designed to facilitate the successful capture of green crabs, with the goal of improving the performance of the Fukui trap. We tested these modifications in situ during the summer of 2016 at two locations in Placentia Bay, Newfoundland. We discovered that three of our modified Fukui trap designs caught significantly more green crabs than the standard Fukui trap, increasing catch-per-unit-effort (CPUE) by as much as 81%. We conclude that our top-performing modifications have great potential for widespread use with existing Fukui traps that are being used for green crab removal efforts.
format: application/pdf
format: text/html
creator: Jonathan A. Bergshoeff
creator: Cynthia H. McKenzie
creator: Brett Favaro
subject: Aquaculture, Fisheries and Fish Science
subject: Ecology
subject: Marine Biology
description: doi:10.7717/peerj.6308
publisher: PeerJ Inc.
rights: © 2019 Bergshoeff et al.
abstract: The European green crab (Carcinus maenas) is a crustacean species native to European and North African coastlines that has become one of the world’s most successful marine invasive species. Targeted fishing programs aimed at removing green crabs from invaded ecosystems commonly use Fukui multi-species marine traps. Improving the efficiency of these traps would improve the ability to respond to green crab invasions. In this study, we developed four distinct trap modifications that were designed to facilitate the successful capture of green crabs, with the goal of improving the performance of the Fukui trap. We tested these modifications in situ during the summer of 2016 at two locations in Placentia Bay, Newfoundland. We discovered that three of our modified Fukui trap designs caught significantly more green crabs than the standard Fukui trap, increasing catch-per-unit-effort (CPUE) by as much as 81%. We conclude that our top-performing modifications have great potential for widespread use with existing Fukui traps that are being used for green crab removal efforts.
bibliographic citation: Bergshoeff et al. (2019) Improving the efficiency of the Fukui trap as a capture tool for the invasive European green crab (Carcinus maenas) in Newfoundland, Canada. PeerJ 7:e6308 https://doi.org/10.7717/peerj.6308
date submitted: 2018-08-13
date accepted: 2018-12-19
issued: 2019-01-29
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Bergshoeff
  given name: Jonathan A.
author list: Agent
  family name: McKenzie
  given name: Cynthia H.
author list: Agent
  family name: Favaro
  given name: Brett
doi: 10.7717/peerj.6308
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-01-29
copyright: ©2019 Bergshoeff et al.
attribution name: Bergshoeff et al.

EGFR deficiency leads to impaired self-renewal and pluripotency of mouse embryonic stem cells
type: item
type: AcademicArticle
description: Background Self-renewal and pluripotency are considered as unwavering features of embryonic stem cells (ESCs). How ESCs regulate the self-renewal and differentiation is a central question in development and regenerative medicine research. Epidermal growth factor receptor (EGFR) was identified as a critical regulator in embryonic development, but its role in the maintenance of ESCs is poorly understood. Methods Here, EGFR was disrupted by its specific inhibitor AG1478 in mouse ESCs (mESCs), and its self-renewal and pluripotency were characterized according to their proliferation, expression of pluripotency markers, embryoid body (EB) formation, and mRNA expression patterns. We also used another EGFR inhibitor (gefitinib) and RNA interference assay to rule out the possibility of non-specific effects of AG1478. Results EGFR inhibition by AG1478 treatment in mESCs markedly reduced cell proliferation, caused cell cycle arrest at G0/G1 phase, and altered protein expressions of the cell cycle regulatory genes (CDK2 (decreased 11.3%) and proliferating cell nuclear antigen (decreased 25.2%)). The immunoreactivities and protein expression of pluripotency factors (OCT4 (decreased 26.9%)) also dramatically decreased, while the differentiation related genes (GATA4 (increased 1.6-fold)) were up-regulated in mESCs after EGFR inhibition. Meanwhile, EGFR inhibition in mESCs disrupted EB formation, indicating its impaired pluripotency. Additionally, the effects observed by EGFR inhibition with another inhibitor gefitinib and siRNA were consistent with those observed by AG1478 treatment in mESCs. These effects were manifested in the decreased expression of proliferative and pluripotency-related genes and the increased expression of genes involved in differentiation. Moreover, RNA-seq analysis displayed that transcript profiling was changed significantly after EGFR inhibition by AG1478. A large number of differentially expressed genes were involved in cell cycle, apoptotic process, epi…
format: application/pdf
format: text/html
creator: Miaoying Yu
creator: Yinghui Wei
creator: Kui Xu
creator: Shasha Liu
creator: Lei Ma
creator: Yangli Pei
creator: Yanqing Hu
creator: Zhiguo Liu
creator: Xue Zhang
creator: Bingyuan Wang
creator: Yulian Mu
creator: Kui Li
subject: Cell Biology
subject: Molecular Biology
description: doi:10.7717/peerj.6314
publisher: PeerJ Inc.
rights: © 2019 Yu et al.
abstract: Background Self-renewal and pluripotency are considered as unwavering features of embryonic stem cells (ESCs). How ESCs regulate the self-renewal and differentiation is a central question in development and regenerative medicine research. Epidermal growth factor receptor (EGFR) was identified as a critical regulator in embryonic development, but its role in the maintenance of ESCs is poorly understood. Methods Here, EGFR was disrupted by its specific inhibitor AG1478 in mouse ESCs (mESCs), and its self-renewal and pluripotency were characterized according to their proliferation, expression of pluripotency markers, embryoid body (EB) formation, and mRNA expression patterns. We also used another EGFR inhibitor (gefitinib) and RNA interference assay to rule out the possibility of non-specific effects of AG1478. Results EGFR inhibition by AG1478 treatment in mESCs markedly reduced cell proliferation, caused cell cycle arrest at G0/G1 phase, and altered protein expressions of the cell cycle regulatory genes (CDK2 (decreased 11.3%) and proliferating cell nuclear antigen (decreased 25.2%)). The immunoreactivities and protein expression of pluripotency factors (OCT4 (decreased 26.9%)) also dramatically decreased, while the differentiation related genes (GATA4 (increased 1.6-fold)) were up-regulated in mESCs after EGFR inhibition. Meanwhile, EGFR inhibition in mESCs disrupted EB formation, indicating its impaired pluripotency. Additionally, the effects observed by EGFR inhibition with another inhibitor gefitinib and siRNA were consistent with those observed by AG1478 treatment in mESCs. These effects were manifested in the decreased expression of proliferative and pluripotency-related genes and the increased expression of genes involved in differentiation. Moreover, RNA-seq analysis displayed that transcript profiling was changed significantly after EGFR inhibition by AG1478. A large number of differentially expressed genes were involved in cell cycle, apoptotic process, epi…
bibliographic citation: Yu et al. (2019) EGFR deficiency leads to impaired self-renewal and pluripotency of mouse embryonic stem cells. PeerJ 7:e6314 https://doi.org/10.7717/peerj.6314
date submitted: 2018-07-16
date accepted: 2018-12-17
issued: 2019-01-29
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Yu
  given name: Miaoying
author list: Agent
  family name: Wei
  given name: Yinghui
author list: Agent
  family name: Xu
  given name: Kui
author list: Agent
  family name: Liu
  given name: Shasha
author list: Agent
  family name: Ma
  given name: Lei
author list: Agent
  family name: Pei
  given name: Yangli
author list: Agent
  family name: Hu
  given name: Yanqing
author list: Agent
  family name: Liu
  given name: Zhiguo
author list: Agent
  family name: Zhang
  given name: Xue
author list: Agent
  family name: Wang
  given name: Bingyuan
author list: Agent
  family name: Mu
  given name: Yulian
author list: Agent
  family name: Li
  given name: Kui
doi: 10.7717/peerj.6314
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-01-29
copyright: © 2019 Yu et al.
attribution name: Yu et al.

Design, optimization and validation of genes commonly used in expression studies on DMH/AOM rat colon carcinogenesis model
type: item
type: AcademicArticle
description: Colorectal cancer (CRC), also known as colon cancer, is the third most common form of cancer worldwide in men and the second in women and is characterized by several genetic alterations, among them the expression of several genes. 1,2-dimethylhydrazine (DMH) and its metabolite azoxymethane (AOM) are procarcinogens commonly used to induce colon cancer in rats (DMH/AOM rat model). This rat model has been used to study changes in mRNA expression in genes involved in this pathological condition. However, a lack of proper detailed PCR primer design in the literature limits the reproducibility of the published data. The present study aims to design, optimize and validate the qPCR, in accordance with the MIQE (Minimum Information for Publication of Quantitative Real-Time PCR Experiments) guidelines, for seventeen genes commonly used in the DMH/AOM rat model of CRC (Apc, Aurka, Bax, Bcl2, β-catenin, Ccnd1, Cdkn1a, Cox2, Gsk3beta, IL-33, iNOs, Nrf2, p53, RelA, Smad4, Tnfα and Vegfa) and two reference genes (Actb or β-actin and B2m). The specificity of all primer pairs was empirically validated on agarose gel, and furthermore, the melting curve inspection was checked as was their efficiency (%) ranging from 90 to 110 with a correlation coefficient of r2 > 0.980. Finally, a pilot study was performed to compare the robustness of two candidate reference genes.
format: application/pdf
format: text/html
creator: David Bars-Cortina
creator: Antoni Riera-Escamilla
creator: Gemma Gou
creator: Carme Piñol-Felis
creator: María-José Motilva
subject: Food Science and Technology
subject: Molecular Biology
subject: Nutrition
subject: Oncology
description: doi:10.7717/peerj.6372
publisher: PeerJ Inc.
rights: © 2019 Bars-Cortina et al.
abstract: Colorectal cancer (CRC), also known as colon cancer, is the third most common form of cancer worldwide in men and the second in women and is characterized by several genetic alterations, among them the expression of several genes. 1,2-dimethylhydrazine (DMH) and its metabolite azoxymethane (AOM) are procarcinogens commonly used to induce colon cancer in rats (DMH/AOM rat model). This rat model has been used to study changes in mRNA expression in genes involved in this pathological condition. However, a lack of proper detailed PCR primer design in the literature limits the reproducibility of the published data. The present study aims to design, optimize and validate the qPCR, in accordance with the MIQE (Minimum Information for Publication of Quantitative Real-Time PCR Experiments) guidelines, for seventeen genes commonly used in the DMH/AOM rat model of CRC (Apc, Aurka, Bax, Bcl2, β-catenin, Ccnd1, Cdkn1a, Cox2, Gsk3beta, IL-33, iNOs, Nrf2, p53, RelA, Smad4, Tnfα and Vegfa) and two reference genes (Actb or β-actin and B2m). The specificity of all primer pairs was empirically validated on agarose gel, and furthermore, the melting curve inspection was checked as was their efficiency (%) ranging from 90 to 110 with a correlation coefficient of r2 > 0.980. Finally, a pilot study was performed to compare the robustness of two candidate reference genes.
bibliographic citation: Bars-Cortina et al. (2019) Design, optimization and validation of genes commonly used in expression studies on DMH/AOM rat colon carcinogenesis model. PeerJ 7:e6372 https://doi.org/10.7717/peerj.6372
date submitted: 2018-11-23
date accepted: 2018-12-30
issued: 2019-01-29
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Bars-Cortina
  given name: David
author list: Agent
  family name: Riera-Escamilla
  given name: Antoni
author list: Agent
  family name: Gou
  given name: Gemma
author list: Agent
  family name: Piñol-Felis
  given name: Carme
author list: Agent
  family name: Motilva
  given name: María-José
doi: 10.7717/peerj.6372
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-01-29
copyright: ©2019 Bars-Cortina et al.
attribution name: Bars-Cortina et al.

Designing online species identification tools for biological recording: the impact on data quality and citizen science learning
type: item
type: AcademicArticle
description: In recent years, the number and scale of environmental citizen science programmes that involve lay people in scientific research have increased rapidly. Many of these initiatives are concerned with the recording and identification of species, processes which are increasingly mediated through digital interfaces. Here, we address the growing need to understand the particular role of digital identification tools, both in generating scientific data and in supporting learning by lay people engaged in citizen science activities pertaining to biological recording communities. Starting from two well-known identification tools, namely identification keys and field guides, this study focuses on the decision-making and quality of learning processes underlying species identification tasks, by comparing three digital interfaces designed to identify bumblebee species. The three interfaces varied with respect to whether species were directly compared or filtered by matching on visual features; and whether the order of filters was directed by the interface or a user-driven open choice. A concurrent mixed-methods approach was adopted to compare how these different interfaces affected the ability of participants to make correct and quick species identifications, and to better understand how participants learned through using these interfaces. We found that the accuracy of identification and quality of learning were dependent upon the interface type, the difficulty of the specimen on the image being identified and the interaction between interface type and ‘image difficulty’. Specifically, interfaces based on filtering outperformed those based on direct visual comparison across all metrics, and an open choice of filters led to higher accuracy than the interface that directed the filtering. Our results have direct implications for the design of online identification technologies for biological recording, irrespective of whether the goal is to collect higher quality citizen science data…
format: application/pdf
format: text/html
creator: Nirwan Sharma
creator: Laura Colucci-Gray
creator: Advaith Siddharthan
creator: Richard Comont
creator: René van der Wal
subject: Conservation Biology
subject: Taxonomy
subject: Science and Medical Education
subject: Human-Computer Interaction
description: doi:10.7717/peerj.5965
publisher: PeerJ Inc.
rights: © 2019 Sharma et al.
abstract: In recent years, the number and scale of environmental citizen science programmes that involve lay people in scientific research have increased rapidly. Many of these initiatives are concerned with the recording and identification of species, processes which are increasingly mediated through digital interfaces. Here, we address the growing need to understand the particular role of digital identification tools, both in generating scientific data and in supporting learning by lay people engaged in citizen science activities pertaining to biological recording communities. Starting from two well-known identification tools, namely identification keys and field guides, this study focuses on the decision-making and quality of learning processes underlying species identification tasks, by comparing three digital interfaces designed to identify bumblebee species. The three interfaces varied with respect to whether species were directly compared or filtered by matching on visual features; and whether the order of filters was directed by the interface or a user-driven open choice. A concurrent mixed-methods approach was adopted to compare how these different interfaces affected the ability of participants to make correct and quick species identifications, and to better understand how participants learned through using these interfaces. We found that the accuracy of identification and quality of learning were dependent upon the interface type, the difficulty of the specimen on the image being identified and the interaction between interface type and ‘image difficulty’. Specifically, interfaces based on filtering outperformed those based on direct visual comparison across all metrics, and an open choice of filters led to higher accuracy than the interface that directed the filtering. Our results have direct implications for the design of online identification technologies for biological recording, irrespective of whether the goal is to collect higher quality citizen science data…
bibliographic citation: Sharma et al. (2019) Designing online species identification tools for biological recording: the impact on data quality and citizen science learning. PeerJ 6:e5965 https://doi.org/10.7717/peerj.5965
date submitted: 2018-06-22
date accepted: 2018-10-19
issued: 2019-01-28
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Sharma
  given name: Nirwan
author list: Agent
  family name: Colucci-Gray
  given name: Laura
author list: Agent
  family name: Siddharthan
  given name: Advaith
author list: Agent
  family name: Comont
  given name: Richard
author list: Agent
  family name: van der Wal
  given name: René
doi: 10.7717/peerj.5965
volume: 6
issn: 2167-8359
publication name: PeerJ
publication date: 2019-01-28
copyright: © 2019 Sharma et al.
attribution name: Sharma et al.

Breast cancer detection using deep convolutional neural networks and support vector machines
type: item
type: AcademicArticle
description: It is important to detect breast cancer as early as possible. In this manuscript, a new methodology for classifying breast cancer using deep learning and some segmentation techniques are introduced. A new computer aided detection (CAD) system is proposed for classifying benign and malignant mass tumors in breast mammography images. In this CAD system, two segmentation approaches are used. The first approach involves determining the region of interest (ROI) manually, while the second approach uses the technique of threshold and region based. The deep convolutional neural network (DCNN) is used for feature extraction. A well-known DCNN architecture named AlexNet is used and is fine-tuned to classify two classes instead of 1,000 classes. The last fully connected (fc) layer is connected to the support vector machine (SVM) classifier to obtain better accuracy. The results are obtained using the following publicly available datasets (1) the digital database for screening mammography (DDSM); and (2) the Curated Breast Imaging Subset of DDSM (CBIS-DDSM). Training on a large number of data gives high accuracy rate. Nevertheless, the biomedical datasets contain a relatively small number of samples due to limited patient volume. Accordingly, data augmentation is a method for increasing the size of the input data by generating new data from the original input data. There are many forms for the data augmentation; the one used here is the rotation. The accuracy of the new-trained DCNN architecture is 71.01% when cropping the ROI manually from the mammogram. The highest area under the curve (AUC) achieved was 0.88 (88%) for the samples obtained from both segmentation techniques. Moreover, when using the samples obtained from the CBIS-DDSM, the accuracy of the DCNN is increased to 73.6%. Consequently, the SVM accuracy becomes 87.2% with an AUC equaling to 0.94 (94%). This is the highest AUC value compared to previous work using the same conditions.
format: application/pdf
format: text/html
creator: Dina A. Ragab
creator: Maha Sharkas
creator: Stephen Marshall
creator: Jinchang Ren
subject: Data Mining and Machine Learning
description: doi:10.7717/peerj.6201
publisher: PeerJ Inc.
rights: © 2019 Ragab et al.
abstract: It is important to detect breast cancer as early as possible. In this manuscript, a new methodology for classifying breast cancer using deep learning and some segmentation techniques are introduced. A new computer aided detection (CAD) system is proposed for classifying benign and malignant mass tumors in breast mammography images. In this CAD system, two segmentation approaches are used. The first approach involves determining the region of interest (ROI) manually, while the second approach uses the technique of threshold and region based. The deep convolutional neural network (DCNN) is used for feature extraction. A well-known DCNN architecture named AlexNet is used and is fine-tuned to classify two classes instead of 1,000 classes. The last fully connected (fc) layer is connected to the support vector machine (SVM) classifier to obtain better accuracy. The results are obtained using the following publicly available datasets (1) the digital database for screening mammography (DDSM); and (2) the Curated Breast Imaging Subset of DDSM (CBIS-DDSM). Training on a large number of data gives high accuracy rate. Nevertheless, the biomedical datasets contain a relatively small number of samples due to limited patient volume. Accordingly, data augmentation is a method for increasing the size of the input data by generating new data from the original input data. There are many forms for the data augmentation; the one used here is the rotation. The accuracy of the new-trained DCNN architecture is 71.01% when cropping the ROI manually from the mammogram. The highest area under the curve (AUC) achieved was 0.88 (88%) for the samples obtained from both segmentation techniques. Moreover, when using the samples obtained from the CBIS-DDSM, the accuracy of the DCNN is increased to 73.6%. Consequently, the SVM accuracy becomes 87.2% with an AUC equaling to 0.94 (94%). This is the highest AUC value compared to previous work using the same conditions.
bibliographic citation: Ragab et al. (2019) Breast cancer detection using deep convolutional neural networks and support vector machines. PeerJ 7:e6201 https://doi.org/10.7717/peerj.6201
date submitted: 2018-05-23
date accepted: 2018-12-03
issued: 2019-01-28
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Ragab
  given name: Dina A.
author list: Agent
  family name: Sharkas
  given name: Maha
author list: Agent
  family name: Marshall
  given name: Stephen
author list: Agent
  family name: Ren
  given name: Jinchang
doi: 10.7717/peerj.6201
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-01-28
copyright: ©2019 Ragab et al.
attribution name: Ragab et al.

A new segmentation algorithm for measuring CBCT images of nasal airway: a pilot study
type: item
type: AcademicArticle
description: Background Three-dimensional (3D) modeling of the nasal airway space is becoming increasingly important for assessment in breathing disorders. Processing cone beam computed tomography (CBCT) scans of this region is complicated, however, by the intricate anatomy of the sinuses compared to the simpler nasopharynx. A gold standard for these measures also is lacking. Previous work has shown that software programs can vary in accuracy and reproducibility outcomes of these measurements. This study reports the reproducibility and accuracy of an algorithm, airway segmentor (AS), designed for nasal airway space analysis using a 3D printed anthropomorphic nasal airway model. Methods To test reproducibility, two examiners independently used AS to edit and segment 10 nasal airway CBCT scans. The intra- and inter-examiner reproducibility of the nasal airway volume was evaluated using paired t-tests and intraclass correlation coefficients. For accuracy testing, the CBCT data for pairs of nasal cavities were 3D printed to form hollow shell models. The water-equivalent method was used to calculate the inner volume as the gold standard, and the models were then embedded into a dry human skull as a phantom and subjected to CBCT. AS, along with the software programs MIMICS 19.0 and INVIVO 5, was applied to calculate the inner volume of the models from the CBCT scan of the phantom. The accuracy was reported as a percentage of the gold standard. Results The intra-examiner reproducibility was high, and the inter-examiner reproducibility was clinically acceptable. AS and MIMICS presented accurate volume calculations, while INVIVO 5 significantly overestimated the mockup of the nasal airway volume. Conclusion With the aid of a 3D printing technique, the new algorithm AS was found to be a clinically reliable and accurate tool for the segmentation and reconstruction of the nasal airway space.
format: application/pdf
format: text/html
creator: Chen Zhang
creator: Robin Bruggink
creator: Frank Baan
creator: Ewald Bronkhorst
creator: Thomas Maal
creator: Hong He
creator: Edwin M. Ongkosuwito
subject: Dentistry
subject: Otorhinolaryngology
subject: Radiology and Medical Imaging
description: doi:10.7717/peerj.6246
publisher: PeerJ Inc.
rights: © 2019 Zhang et al.
abstract: Background Three-dimensional (3D) modeling of the nasal airway space is becoming increasingly important for assessment in breathing disorders. Processing cone beam computed tomography (CBCT) scans of this region is complicated, however, by the intricate anatomy of the sinuses compared to the simpler nasopharynx. A gold standard for these measures also is lacking. Previous work has shown that software programs can vary in accuracy and reproducibility outcomes of these measurements. This study reports the reproducibility and accuracy of an algorithm, airway segmentor (AS), designed for nasal airway space analysis using a 3D printed anthropomorphic nasal airway model. Methods To test reproducibility, two examiners independently used AS to edit and segment 10 nasal airway CBCT scans. The intra- and inter-examiner reproducibility of the nasal airway volume was evaluated using paired t-tests and intraclass correlation coefficients. For accuracy testing, the CBCT data for pairs of nasal cavities were 3D printed to form hollow shell models. The water-equivalent method was used to calculate the inner volume as the gold standard, and the models were then embedded into a dry human skull as a phantom and subjected to CBCT. AS, along with the software programs MIMICS 19.0 and INVIVO 5, was applied to calculate the inner volume of the models from the CBCT scan of the phantom. The accuracy was reported as a percentage of the gold standard. Results The intra-examiner reproducibility was high, and the inter-examiner reproducibility was clinically acceptable. AS and MIMICS presented accurate volume calculations, while INVIVO 5 significantly overestimated the mockup of the nasal airway volume. Conclusion With the aid of a 3D printing technique, the new algorithm AS was found to be a clinically reliable and accurate tool for the segmentation and reconstruction of the nasal airway space.
bibliographic citation: Zhang et al. (2019) A new segmentation algorithm for measuring CBCT images of nasal airway: a pilot study. PeerJ 7:e6246 https://doi.org/10.7717/peerj.6246
date submitted: 2018-07-23
date accepted: 2018-12-07
issued: 2019-01-28
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Zhang
  given name: Chen
author list: Agent
  family name: Bruggink
  given name: Robin
author list: Agent
  family name: Baan
  given name: Frank
author list: Agent
  family name: Bronkhorst
  given name: Ewald
author list: Agent
  family name: Maal
  given name: Thomas
author list: Agent
  family name: He
  given name: Hong
author list: Agent
  family name: Ongkosuwito
  given name: Edwin M.
doi: 10.7717/peerj.6246
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-01-28
copyright: © 2019 Zhang et al.
attribution name: Zhang et al.

Genome-wide identification of long non-coding RNAs in tomato plants irradiated by neutrons followed by infection with Tomato yellow leaf curl virus
type: item
type: AcademicArticle
description: Long non-coding RNAs (lncRNAs) play an important role in regulating many biological processes. In this study, tomato seeds were first irradiated by neutrons. Eight tomato mutants were then selected and infected by Tomato yellow leaf curl virus (TYLCV). RNA sequencing followed by bioinformatics analyses identified 1,563 tomato lncRNAs. About half of the lncRNAs were derived from intergenic regions, whereas antisense lncRNAs accounted for 35%. There were fewer lncRNAs identified in our study than in other studies identifying tomato lncRNAs. Functional classification of 794 lncRNAs associated with tomato genes showed that many lncRNAs were associated with binding functions required for interactions with other molecules and localized in the cytosol and membrane. In addition, we identified 19 up-regulated and 11 down-regulated tomato lncRNAs by comparing TYLCV infected plants to non-infected plants using previously published data. Based on these results, the lncRNAs identified in this study provide important resources for characterization of tomato lncRNAs in response to TYLCV infection.
format: application/pdf
format: text/html
creator: Yujie Zhou
creator: Won Kyong Cho
creator: Hee-Seong Byun
creator: Vivek Chavan
creator: Eui-Joon Kil
creator: Sukchan Lee
creator: Seung-Woo Hong
subject: Agricultural Science
subject: Bioinformatics
subject: Genomics
subject: Plant Science
description: doi:10.7717/peerj.6286
publisher: PeerJ Inc.
rights: © 2019 Zhou et al.
abstract: Long non-coding RNAs (lncRNAs) play an important role in regulating many biological processes. In this study, tomato seeds were first irradiated by neutrons. Eight tomato mutants were then selected and infected by Tomato yellow leaf curl virus (TYLCV). RNA sequencing followed by bioinformatics analyses identified 1,563 tomato lncRNAs. About half of the lncRNAs were derived from intergenic regions, whereas antisense lncRNAs accounted for 35%. There were fewer lncRNAs identified in our study than in other studies identifying tomato lncRNAs. Functional classification of 794 lncRNAs associated with tomato genes showed that many lncRNAs were associated with binding functions required for interactions with other molecules and localized in the cytosol and membrane. In addition, we identified 19 up-regulated and 11 down-regulated tomato lncRNAs by comparing TYLCV infected plants to non-infected plants using previously published data. Based on these results, the lncRNAs identified in this study provide important resources for characterization of tomato lncRNAs in response to TYLCV infection.
bibliographic citation: Zhou et al. (2019) Genome-wide identification of long non-coding RNAs in tomato plants irradiated by neutrons followed by infection with Tomato yellow leaf curl virus. PeerJ 7:e6286 https://doi.org/10.7717/peerj.6286
date submitted: 2018-08-22
date accepted: 2018-12-14
issued: 2019-01-28
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Zhou
  given name: Yujie
author list: Agent
  family name: Cho
  given name: Won Kyong
author list: Agent
  family name: Byun
  given name: Hee-Seong
author list: Agent
  family name: Chavan
  given name: Vivek
author list: Agent
  family name: Kil
  given name: Eui-Joon
author list: Agent
  family name: Lee
  given name: Sukchan
author list: Agent
  family name: Hong
  given name: Seung-Woo
doi: 10.7717/peerj.6286
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-01-28
copyright: ©2019 Zhou et al.
attribution name: Zhou et al.

Gastric Helicobacter pylori infection perturbs human oral microbiota
type: item
type: AcademicArticle
description: Background We investigated the effects of gastric Helicobacter pylori infection on the daytime and overnight human oral microbiota. Methods Twenty four volunteers were recruited. Ten tested positive for H. pylori infection by the Carbon-14 Urea Breath Test, and the rest were negative. Two oral swabs were collected: one immediately after waking up in the morning and before brushing teeth, and another in the evening before teeth-brushing. DNA extract acquired from each swab was subjected to Illumina sequencing of 16S rRNA gene amplicons. The microbial abundance and composition were analysed in relation to H. pylori infection status. Results Helicobacter pylori-positive individuals had significant changes in the alpha and beta diversities in the daytime samples in comparison to those who were H. pylori negative. To identify which taxa could be significantly affected within the cohorts in the daytime, we employed the LEfSe method. When compared against UBT-negative samples, significantly higher abundances were detected in both Pseudomonas and Roseomonas, while Fusobacterium, Solobacterium, Haemophilus and Streptococcus were significantly decreased in the UBT-positive samples. Discussion Our data demonstrated that H. pylori infection affects the human daytime oral microbiota. The hitherto undocumented changes of several bacterial genera due to H. pylori infection require more studies to examine their potential health effects on affected individuals.
format: application/pdf
format: text/html
creator: Eng-Guan Chua
creator: Ju-Yee Chong
creator: Binit Lamichhane
creator: K. Mary Webberley
creator: Barry J. Marshall
creator: Michael J. Wise
creator: Chin-Yen Tay
subject: Biodiversity
subject: Bioinformatics
subject: Microbiology
description: doi:10.7717/peerj.6336
publisher: PeerJ Inc.
rights: © 2019 Chua et al.
abstract: Background We investigated the effects of gastric Helicobacter pylori infection on the daytime and overnight human oral microbiota. Methods Twenty four volunteers were recruited. Ten tested positive for H. pylori infection by the Carbon-14 Urea Breath Test, and the rest were negative. Two oral swabs were collected: one immediately after waking up in the morning and before brushing teeth, and another in the evening before teeth-brushing. DNA extract acquired from each swab was subjected to Illumina sequencing of 16S rRNA gene amplicons. The microbial abundance and composition were analysed in relation to H. pylori infection status. Results Helicobacter pylori-positive individuals had significant changes in the alpha and beta diversities in the daytime samples in comparison to those who were H. pylori negative. To identify which taxa could be significantly affected within the cohorts in the daytime, we employed the LEfSe method. When compared against UBT-negative samples, significantly higher abundances were detected in both Pseudomonas and Roseomonas, while Fusobacterium, Solobacterium, Haemophilus and Streptococcus were significantly decreased in the UBT-positive samples. Discussion Our data demonstrated that H. pylori infection affects the human daytime oral microbiota. The hitherto undocumented changes of several bacterial genera due to H. pylori infection require more studies to examine their potential health effects on affected individuals.
bibliographic citation: Chua et al. (2019) Gastric Helicobacter pylori infection perturbs human oral microbiota. PeerJ 7:e6336 https://doi.org/10.7717/peerj.6336
date submitted: 2018-09-18
date accepted: 2018-12-22
issued: 2019-01-28
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Chua
  given name: Eng-Guan
author list: Agent
  family name: Chong
  given name: Ju-Yee
author list: Agent
  family name: Lamichhane
  given name: Binit
author list: Agent
  family name: Webberley
  given name: K. Mary
author list: Agent
  family name: Marshall
  given name: Barry J.
author list: Agent
  family name: Wise
  given name: Michael J.
author list: Agent
  family name: Tay
  given name: Chin-Yen
doi: 10.7717/peerj.6336
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-01-28
copyright: ©2019 Chua et al.
attribution name: Chua et al.

Optimizing influenza vaccine policies for controlling 2009-like pandemics and regular outbreaks
type: item
type: AcademicArticle
description: Background This study examined the effectiveness of various vaccine policies against influenza. The transmission rate was calculated by use of the time-series influenza-like illness case during the year of 2009 and recent epidemics in Taiwan. Methods We developed a stochastic compartmental model to analyze the transmission of influenza, where the population was stratified by location and age group, and the vaccine distribution was considered using the current policy. The simulation study compared the previous vaccine policy and a new policy with expanded coverage and various lengths of the vaccination campaign. The sensitivity analysis investigated different levels of vaccine efficacy to confirm the robustness of the recommended policies. Results Doubling vaccine coverage can decrease the number of infections effectively in the regular epidemic scenario. However, a peak of infections occurs if the duration of implementing vaccination is too long. In the 2009-like pandemic scenario, both increasing vaccine doses and reducing the program’s duration can mitigate infections, although the early outbreak restricts the effectiveness of vaccination programs. Conclusions The finding indicates that only increasing vaccine coverage can reduce influenza infections. To avoid the peak of infections, it is also necessary to execute the vaccination activity immediately. Vaccine efficacy significantly impacts the vaccination policy’s performance. When vaccine efficacy is low, neither increasing vaccination doses nor reducing vaccination timeframe prevents infections. Therefore, the variation in vaccine efficacy should be taken into account when making immunization policies against influenza.
format: application/pdf
format: text/html
creator: Sheng-I Chen
creator: Chia-Yuan Wu
creator: Yu-Hsuan Wu
creator: Min-Wei Hsieh
subject: Epidemiology
subject: Public Health
subject: Data Science
description: doi:10.7717/peerj.6340
publisher: PeerJ Inc.
rights: © 2019 Chen et al.
abstract: Background This study examined the effectiveness of various vaccine policies against influenza. The transmission rate was calculated by use of the time-series influenza-like illness case during the year of 2009 and recent epidemics in Taiwan. Methods We developed a stochastic compartmental model to analyze the transmission of influenza, where the population was stratified by location and age group, and the vaccine distribution was considered using the current policy. The simulation study compared the previous vaccine policy and a new policy with expanded coverage and various lengths of the vaccination campaign. The sensitivity analysis investigated different levels of vaccine efficacy to confirm the robustness of the recommended policies. Results Doubling vaccine coverage can decrease the number of infections effectively in the regular epidemic scenario. However, a peak of infections occurs if the duration of implementing vaccination is too long. In the 2009-like pandemic scenario, both increasing vaccine doses and reducing the program’s duration can mitigate infections, although the early outbreak restricts the effectiveness of vaccination programs. Conclusions The finding indicates that only increasing vaccine coverage can reduce influenza infections. To avoid the peak of infections, it is also necessary to execute the vaccination activity immediately. Vaccine efficacy significantly impacts the vaccination policy’s performance. When vaccine efficacy is low, neither increasing vaccination doses nor reducing vaccination timeframe prevents infections. Therefore, the variation in vaccine efficacy should be taken into account when making immunization policies against influenza.
bibliographic citation: Chen et al. (2019) Optimizing influenza vaccine policies for controlling 2009-like pandemics and regular outbreaks. PeerJ 7:e6340 https://doi.org/10.7717/peerj.6340
date submitted: 2018-08-24
date accepted: 2018-12-22
issued: 2019-01-28
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Chen
  given name: Sheng-I
author list: Agent
  family name: Wu
  given name: Chia-Yuan
author list: Agent
  family name: Wu
  given name: Yu-Hsuan
author list: Agent
  family name: Hsieh
  given name: Min-Wei
doi: 10.7717/peerj.6340
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-01-28
copyright: ©2019 Chen et al.
attribution name: Chen et al.

A scalable discrete-time survival model for neural networks
type: item
type: AcademicArticle
description: There is currently great interest in applying neural networks to prediction tasks in medicine. It is important for predictive models to be able to use survival data, where each patient has a known follow-up time and event/censoring indicator. This avoids information loss when training the model and enables generation of predicted survival curves. In this paper, we describe a discrete-time survival model that is designed to be used with neural networks, which we refer to as Nnet-survival. The model is trained with the maximum likelihood method using mini-batch stochastic gradient descent (SGD). The use of SGD enables rapid convergence and application to large datasets that do not fit in memory. The model is flexible, so that the baseline hazard rate and the effect of the input data on hazard probability can vary with follow-up time. It has been implemented in the Keras deep learning framework, and source code for the model and several examples is available online. We demonstrate the performance of the model on both simulated and real data and compare it to existing models Cox-nnet and Deepsurv.
format: application/pdf
format: text/html
creator: Michael F. Gensheimer
creator: Balasubramanian Narasimhan
subject: Data Mining and Machine Learning
subject: Data Science
description: doi:10.7717/peerj.6257
publisher: PeerJ Inc.
rights: © 2019 Gensheimer and Narasimhan
abstract: There is currently great interest in applying neural networks to prediction tasks in medicine. It is important for predictive models to be able to use survival data, where each patient has a known follow-up time and event/censoring indicator. This avoids information loss when training the model and enables generation of predicted survival curves. In this paper, we describe a discrete-time survival model that is designed to be used with neural networks, which we refer to as Nnet-survival. The model is trained with the maximum likelihood method using mini-batch stochastic gradient descent (SGD). The use of SGD enables rapid convergence and application to large datasets that do not fit in memory. The model is flexible, so that the baseline hazard rate and the effect of the input data on hazard probability can vary with follow-up time. It has been implemented in the Keras deep learning framework, and source code for the model and several examples is available online. We demonstrate the performance of the model on both simulated and real data and compare it to existing models Cox-nnet and Deepsurv.
bibliographic citation: Gensheimer et al. (2019) A scalable discrete-time survival model for neural networks. PeerJ 7:e6257 https://doi.org/10.7717/peerj.6257
date submitted: 2018-05-14
date accepted: 2018-12-10
issued: 2019-01-25
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Gensheimer
  given name: Michael F.
author list: Agent
  family name: Narasimhan
  given name: Balasubramanian
doi: 10.7717/peerj.6257
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-01-25
copyright: ©2019 Gensheimer and Narasimhan
attribution name: Gensheimer and Narasimhan

Diatom ecological response to deposition of the 833-850 CE White River Ash (east lobe) ashfall in a small subarctic Canadian lake
type: item
type: AcademicArticle
description: A <5 mm thick volcanic ashfall layer associated with the White River Ash (east lobe [WRAe]) originating from the eruption of Mount Churchill, Alaska (833-850 CE; 1,117–1,100 cal BP) was observed in two freeze cores obtained from Pocket Lake (62.5090°N, −114.3719°W), a small subarctic lake located within the city limits of Yellowknife, Northwest Territories, Canada. Here we analyze changes in diatom assemblages to assess impact of tephra deposition on the aquatic biota of a subarctic lake. In a well-dated core constrained by 8 radiocarbon dates, diatom counts were carried out at 1-mm intervals through an interval spanning 1 cm above and below the tephra layer with each 1 mm sub-sample represented about 2 years of deposition. Non-metric Multidimensional Scaling (NMDS) and Stratigraphically Constrained Incremental Sum of Squares (CONISS) analyses were carried out and three distinct diatom assemblages were identified throughout the interval. The lowermost “Pre-WRAe Assemblage (Pre-WRAeA)” was indicative of slightly acidic and eutrophic lacustrine conditions. Winter deposition of the tephra layer drove a subsequent diatom flora shift to the “WRAe Assemblage (WRAeA)” the following spring. The WRAeA contained elevated abundances of taxa associated with oligotrophic, nutrient depleted and slightly more alkaline lake waters. These changes were only apparent in samples within the WRAe containing interval indicating that they were short lived and only sustained for a single year of deposition. Immediately above the WRAe horizon, a third, “Post-WRAe Assemblage (Post-WRAeA)” was observed. This assemblage was initially similar to that of the Pre-WRAeA but gradually became more distinct upwards, likely due to climatic patterns independent of the WRAe event. These results suggest that lacustrine environments are sensitive to perturbations such as deposition of ash fall, but that ecological communities in subarctic systems can also have high resilience and can recover rapidly. If su…
format: application/pdf
format: text/html
creator: Scott J. Hutchinson
creator: Paul B. Hamilton
creator: R. Timothy Patterson
creator: Jennifer M. Galloway
creator: Nawaf A. Nasser
creator: Christopher Spence
creator: Hendrik Falck
subject: Ecology
subject: Freshwater Biology
subject: Environmental Impacts
description: doi:10.7717/peerj.6269
publisher: PeerJ Inc.
rights: © 2019 Hutchinson et al.
abstract: A <5 mm thick volcanic ashfall layer associated with the White River Ash (east lobe [WRAe]) originating from the eruption of Mount Churchill, Alaska (833-850 CE; 1,117–1,100 cal BP) was observed in two freeze cores obtained from Pocket Lake (62.5090°N, −114.3719°W), a small subarctic lake located within the city limits of Yellowknife, Northwest Territories, Canada. Here we analyze changes in diatom assemblages to assess impact of tephra deposition on the aquatic biota of a subarctic lake. In a well-dated core constrained by 8 radiocarbon dates, diatom counts were carried out at 1-mm intervals through an interval spanning 1 cm above and below the tephra layer with each 1 mm sub-sample represented about 2 years of deposition. Non-metric Multidimensional Scaling (NMDS) and Stratigraphically Constrained Incremental Sum of Squares (CONISS) analyses were carried out and three distinct diatom assemblages were identified throughout the interval. The lowermost “Pre-WRAe Assemblage (Pre-WRAeA)” was indicative of slightly acidic and eutrophic lacustrine conditions. Winter deposition of the tephra layer drove a subsequent diatom flora shift to the “WRAe Assemblage (WRAeA)” the following spring. The WRAeA contained elevated abundances of taxa associated with oligotrophic, nutrient depleted and slightly more alkaline lake waters. These changes were only apparent in samples within the WRAe containing interval indicating that they were short lived and only sustained for a single year of deposition. Immediately above the WRAe horizon, a third, “Post-WRAe Assemblage (Post-WRAeA)” was observed. This assemblage was initially similar to that of the Pre-WRAeA but gradually became more distinct upwards, likely due to climatic patterns independent of the WRAe event. These results suggest that lacustrine environments are sensitive to perturbations such as deposition of ash fall, but that ecological communities in subarctic systems can also have high resilience and can recover rapidly. If su…
bibliographic citation: Hutchinson et al. (2019) Diatom ecological response to deposition of the 833-850 CE White River Ash (east lobe) ashfall in a small subarctic Canadian lake. PeerJ 7:e6269 https://doi.org/10.7717/peerj.6269
date submitted: 2018-02-10
date accepted: 2018-12-07
issued: 2019-01-25
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Hutchinson
  given name: Scott J.
author list: Agent
  family name: Hamilton
  given name: Paul B.
author list: Agent
  family name: Patterson
  given name: R. Timothy
author list: Agent
  family name: Galloway
  given name: Jennifer M.
author list: Agent
  family name: Nasser
  given name: Nawaf A.
author list: Agent
  family name: Spence
  given name: Christopher
author list: Agent
  family name: Falck
  given name: Hendrik
doi: 10.7717/peerj.6269
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-01-25
copyright: ©2019 Hutchinson et al.
attribution name: Hutchinson et al.

Convergent origin of the narrowly lanceolate leaf in the genus Aster—with special reference to an unexpected discovery of a new Aster species from East China
type: item
type: AcademicArticle
description: Narrowly lanceolate leaves occur frequently in the genus Aster. It was often employed as a distinguishing character in the taxonomy of this genus. The origin of this particular leaf shape, however, has never been investigated using comparative methods. In this study, we reconstructed a comprehensive phylogeny that includes most species of Aster with narrowly lanceolate leaf. We then gathered data on riparian habitats and the presence or absence of narrowly lanceolate leaves, and investigated the evolutionary association between them in a phylogenetic context. Our analysis indicated that the species with narrowly lanceolate leaves are nested in unrelated lineages of the genus Aster, implying that they originated independently several times. Using Pagel’s comparative method of discrete data, we demonstrated a significant correlation between riparian habitats and narrowly lanceolate leaves. We further inferred the sequence of transition of the two characters. This analysis indicated that the sequence of evolution of riparian habitat and narrowly lanceolate leaf form was usually uncertain, but some positive results showed that the occurrence of riparian habitats may not precede the evolution of narrowly lanceolate leaf form. This study provided new insights into the adaptive evolution in a mega-diverse family. In addition, Aster tonglingensis, an unexpected new species with narrowly lanceolate leaves, was discovered and established based on the evidence from morphology, micromorphology and molecular phylogeny.
format: application/pdf
format: text/html
creator: Guo-Jin Zhang
creator: Hai-Hua Hu
creator: Tian-Gang Gao
creator: Michael G. Gilbert
creator: Xiao-Feng Jin
subject: Biodiversity
subject: Evolutionary Studies
subject: Plant Science
subject: Taxonomy
description: doi:10.7717/peerj.6288
publisher: PeerJ Inc.
rights: © 2019 Zhang et al.
abstract: Narrowly lanceolate leaves occur frequently in the genus Aster. It was often employed as a distinguishing character in the taxonomy of this genus. The origin of this particular leaf shape, however, has never been investigated using comparative methods. In this study, we reconstructed a comprehensive phylogeny that includes most species of Aster with narrowly lanceolate leaf. We then gathered data on riparian habitats and the presence or absence of narrowly lanceolate leaves, and investigated the evolutionary association between them in a phylogenetic context. Our analysis indicated that the species with narrowly lanceolate leaves are nested in unrelated lineages of the genus Aster, implying that they originated independently several times. Using Pagel’s comparative method of discrete data, we demonstrated a significant correlation between riparian habitats and narrowly lanceolate leaves. We further inferred the sequence of transition of the two characters. This analysis indicated that the sequence of evolution of riparian habitat and narrowly lanceolate leaf form was usually uncertain, but some positive results showed that the occurrence of riparian habitats may not precede the evolution of narrowly lanceolate leaf form. This study provided new insights into the adaptive evolution in a mega-diverse family. In addition, Aster tonglingensis, an unexpected new species with narrowly lanceolate leaves, was discovered and established based on the evidence from morphology, micromorphology and molecular phylogeny.
bibliographic citation: Zhang et al. (2019) Convergent origin of the narrowly lanceolate leaf in the genus Aster—with special reference to an unexpected discovery of a new Aster species from East China. PeerJ 7:e6288 https://doi.org/10.7717/peerj.6288
date submitted: 2018-10-10
date accepted: 2018-12-15
issued: 2019-01-25
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Zhang
  given name: Guo-Jin
author list: Agent
  family name: Hu
  given name: Hai-Hua
author list: Agent
  family name: Gao
  given name: Tian-Gang
author list: Agent
  family name: Gilbert
  given name: Michael G.
author list: Agent
  family name: Jin
  given name: Xiao-Feng
doi: 10.7717/peerj.6288
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-01-25
copyright: ©2019 Zhang et al.
attribution name: Zhang et al.

Isolation of wheat bran-colonizing and metabolizing species from the human fecal microbiota
type: item
type: AcademicArticle
description: Undigestible, insoluble food particles, such as wheat bran, are important dietary constituents that serve as a fermentation substrate for the human gut microbiota. The first step in wheat bran fermentation involves the poorly studied solubilization of fibers from the complex insoluble wheat bran structure. Attachment of bacteria has been suggested to promote the efficient hydrolysis of insoluble substrates, but the mechanisms and drivers of this microbial attachment and colonization, as well as subsequent fermentation remain to be elucidated. We have previously shown that an individually dependent subset of gut bacteria is able to colonize the wheat bran residue. Here, we isolated these bran-attached microorganisms, which can then be used to gain mechanistic insights in future pure culture experiments. Four healthy fecal donors were screened to account for inter-individual differences in gut microbiota composition. A combination of a direct plating and enrichment method resulted in the isolation of a phylogenetically diverse set of species, belonging to the Bacteroidetes, Firmicutes, Proteobacteria and Actinobacteria phyla. A comparison with 16S rRNA gene sequences that were found enriched on wheat bran particles in previous studies, however, showed that the isolates do not yet cover the entire diversity of wheat-bran colonizing species, comprising among others a broad range of Prevotella, Bacteroides and Clostridium cluster XIVa species. We, therefore, suggest several modifications to the experiment set-up to further expand the array of isolated species.
format: application/pdf
format: text/html
creator: Kim De Paepe
creator: Joran Verspreet
creator: Mohammad Naser Rezaei
creator: Silvia Hidalgo Martinez
creator: Filip Meysman
creator: Davy Van de Walle
creator: Koen Dewettinck
creator: Jeroen Raes
creator: Christophe Courtin
creator: Tom Van de Wiele
subject: Microbiology
subject: Molecular Biology
description: doi:10.7717/peerj.6293
publisher: PeerJ Inc.
rights: © 2019 De Paepe et al.
abstract: Undigestible, insoluble food particles, such as wheat bran, are important dietary constituents that serve as a fermentation substrate for the human gut microbiota. The first step in wheat bran fermentation involves the poorly studied solubilization of fibers from the complex insoluble wheat bran structure. Attachment of bacteria has been suggested to promote the efficient hydrolysis of insoluble substrates, but the mechanisms and drivers of this microbial attachment and colonization, as well as subsequent fermentation remain to be elucidated. We have previously shown that an individually dependent subset of gut bacteria is able to colonize the wheat bran residue. Here, we isolated these bran-attached microorganisms, which can then be used to gain mechanistic insights in future pure culture experiments. Four healthy fecal donors were screened to account for inter-individual differences in gut microbiota composition. A combination of a direct plating and enrichment method resulted in the isolation of a phylogenetically diverse set of species, belonging to the Bacteroidetes, Firmicutes, Proteobacteria and Actinobacteria phyla. A comparison with 16S rRNA gene sequences that were found enriched on wheat bran particles in previous studies, however, showed that the isolates do not yet cover the entire diversity of wheat-bran colonizing species, comprising among others a broad range of Prevotella, Bacteroides and Clostridium cluster XIVa species. We, therefore, suggest several modifications to the experiment set-up to further expand the array of isolated species.
bibliographic citation: De Paepe et al. (2019) Isolation of wheat bran-colonizing and metabolizing species from the human fecal microbiota. PeerJ 7:e6293 https://doi.org/10.7717/peerj.6293
date submitted: 2018-10-23
date accepted: 2018-12-17
issued: 2019-01-25
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: De Paepe
  given name: Kim
author list: Agent
  family name: Verspreet
  given name: Joran
author list: Agent
  family name: Rezaei
  given name: Mohammad Naser
author list: Agent
  family name: Hidalgo Martinez
  given name: Silvia
author list: Agent
  family name: Meysman
  given name: Filip
author list: Agent
  family name: Van de Walle
  given name: Davy
author list: Agent
  family name: Dewettinck
  given name: Koen
author list: Agent
  family name: Raes
  given name: Jeroen
author list: Agent
  family name: Courtin
  given name: Christophe
author list: Agent
  family name: Van de Wiele
  given name: Tom
doi: 10.7717/peerj.6293
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-01-25
copyright: ©2019 De Paepe et al.
attribution name: De Paepe et al.

Prognostic values of GMPS, PR, CD40, and p21 in ovarian cancer
type: item
type: AcademicArticle
description: Early detection and prediction of prognosis and treatment responses are all the keys in improving survival of ovarian cancer patients. This study profiled an ovarian cancer progression model to identify prognostic biomarkers for ovarian cancer patients. Mouse ovarian surface epithelial cells (MOSECs) can undergo spontaneous malignant transformation in vitro cell culture. These were used as a model of ovarian cancer progression for alterations in gene expression and signaling detected using the Illumina HiSeq2000 Next-Generation Sequencing platform and bioinformatical analyses. The differential expression of four selected genes was identified using the gene expression profiling interaction analysis (http://gepia.cancer-pku.cn/) and then associated with survival in ovarian cancer patients using the Cancer Genome Atlas dataset and the online Kaplan–Meier Plotter (http://www.kmplot.com) data. The data showed 263 aberrantly expressed genes, including 182 up-regulated and 81 down-regulated genes between the early and late stages of tumor progression in MOSECs. The bioinformatic data revealed four genes (i.e., guanosine 5′-monophosphate synthase (GMPS), progesterone receptor (PR), CD40, and p21 (cyclin-dependent kinase inhibitor 1A)) to play an important role in ovarian cancer progression. Furthermore, the Cancer Genome Atlas dataset validated the differential expression of these four genes, which were associated with prognosis in ovarian cancer patients. In conclusion, this study profiled differentially expressed genes using the ovarian cancer progression model and identified four (i.e., GMPS, PR, CD40, and p21) as prognostic markers for ovarian cancer patients. Future studies of prospective patients could further verify the clinical usefulness of this four-gene signature.
format: application/pdf
format: text/html
creator: Ping Wang
creator: Zengli Zhang
creator: Yujie Ma
creator: Jun Lu
creator: Hu Zhao
creator: Shuiliang Wang
creator: Jianming Tan
creator: Bingyan Li
subject: Bioinformatics
subject: Cell Biology
subject: Oncology
description: doi:10.7717/peerj.6301
publisher: PeerJ Inc.
rights: © 2019 Wang et al.
abstract: Early detection and prediction of prognosis and treatment responses are all the keys in improving survival of ovarian cancer patients. This study profiled an ovarian cancer progression model to identify prognostic biomarkers for ovarian cancer patients. Mouse ovarian surface epithelial cells (MOSECs) can undergo spontaneous malignant transformation in vitro cell culture. These were used as a model of ovarian cancer progression for alterations in gene expression and signaling detected using the Illumina HiSeq2000 Next-Generation Sequencing platform and bioinformatical analyses. The differential expression of four selected genes was identified using the gene expression profiling interaction analysis (http://gepia.cancer-pku.cn/) and then associated with survival in ovarian cancer patients using the Cancer Genome Atlas dataset and the online Kaplan–Meier Plotter (http://www.kmplot.com) data. The data showed 263 aberrantly expressed genes, including 182 up-regulated and 81 down-regulated genes between the early and late stages of tumor progression in MOSECs. The bioinformatic data revealed four genes (i.e., guanosine 5′-monophosphate synthase (GMPS), progesterone receptor (PR), CD40, and p21 (cyclin-dependent kinase inhibitor 1A)) to play an important role in ovarian cancer progression. Furthermore, the Cancer Genome Atlas dataset validated the differential expression of these four genes, which were associated with prognosis in ovarian cancer patients. In conclusion, this study profiled differentially expressed genes using the ovarian cancer progression model and identified four (i.e., GMPS, PR, CD40, and p21) as prognostic markers for ovarian cancer patients. Future studies of prospective patients could further verify the clinical usefulness of this four-gene signature.
bibliographic citation: Wang et al. (2019) Prognostic values of GMPS, PR, CD40, and p21 in ovarian cancer. PeerJ 7:e6301 https://doi.org/10.7717/peerj.6301
date submitted: 2018-08-15
date accepted: 2018-12-14
issued: 2019-01-25
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Wang
  given name: Ping
author list: Agent
  family name: Zhang
  given name: Zengli
author list: Agent
  family name: Ma
  given name: Yujie
author list: Agent
  family name: Lu
  given name: Jun
author list: Agent
  family name: Zhao
  given name: Hu
author list: Agent
  family name: Wang
  given name: Shuiliang
author list: Agent
  family name: Tan
  given name: Jianming
author list: Agent
  family name: Li
  given name: Bingyan
doi: 10.7717/peerj.6301
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-01-25
copyright: ©2019 Wang et al.
attribution name: Wang et al.

Impact assessment of high soil CO2 on plant growth and soil environment: a greenhouse study
type: item
type: AcademicArticle
description: To ensure the safety of carbon capture and storage (CCS) technology, insight into the potential impacts of CO2 leakage on the ecosystem is necessary. We conducted a greenhouse experiment to investigate the effects of high soil CO2 on plant growth and the soil environment. Treatments comprised 99.99% CO2 injection (CG), 99.99% N2injection (NG), and no injection (BG). NG treatment was employed to differentiate the effects of O2 depletion from those of CO2 enrichment. Soil CO2 and O2 concentrations were maintained at an average of 53% and 11%, respectively, under CG treatment. We verified that high soil CO2 had negative effects on root water absorption, chlorophyll, starch content and total biomass. Soil microbial acid phosphatase activity was affected by CG treatment. These negative effects were attributed to high soil CO2 instead of low O2 or low pH. Our results indicate that high soil CO2 affected the root system, which in turn triggered further changes in aboveground plant tissues and rhizospheric soil water conditions. A conceptual diagram of CO2 toxicity to plants and soil is suggested to act as a useful guideline for impact assessment of CCS technology.
format: application/pdf
format: text/html
creator: Wenmei He
creator: Gayoung Yoo
creator: Mohammad Moonis
creator: Youjin Kim
creator: Xuanlin Chen
subject: Biochemistry
subject: Ecosystem Science
subject: Plant Science
subject: Soil Science
subject: Environmental Impacts
description: doi:10.7717/peerj.6311
publisher: PeerJ Inc.
rights: © 2019 He et al.
abstract: To ensure the safety of carbon capture and storage (CCS) technology, insight into the potential impacts of CO2 leakage on the ecosystem is necessary. We conducted a greenhouse experiment to investigate the effects of high soil CO2 on plant growth and the soil environment. Treatments comprised 99.99% CO2 injection (CG), 99.99% N2injection (NG), and no injection (BG). NG treatment was employed to differentiate the effects of O2 depletion from those of CO2 enrichment. Soil CO2 and O2 concentrations were maintained at an average of 53% and 11%, respectively, under CG treatment. We verified that high soil CO2 had negative effects on root water absorption, chlorophyll, starch content and total biomass. Soil microbial acid phosphatase activity was affected by CG treatment. These negative effects were attributed to high soil CO2 instead of low O2 or low pH. Our results indicate that high soil CO2 affected the root system, which in turn triggered further changes in aboveground plant tissues and rhizospheric soil water conditions. A conceptual diagram of CO2 toxicity to plants and soil is suggested to act as a useful guideline for impact assessment of CCS technology.
bibliographic citation: He et al. (2019) Impact assessment of high soil CO2 on plant growth and soil environment: a greenhouse study. PeerJ 7:e6311 https://doi.org/10.7717/peerj.6311
date submitted: 2018-10-11
date accepted: 2018-12-19
issued: 2019-01-25
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: He
  given name: Wenmei
author list: Agent
  family name: Yoo
  given name: Gayoung
author list: Agent
  family name: Moonis
  given name: Mohammad
author list: Agent
  family name: Kim
  given name: Youjin
author list: Agent
  family name: Chen
  given name: Xuanlin
doi: 10.7717/peerj.6311
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-01-25
copyright: ©2019 He et al.
attribution name: He et al.

Nonconventional opponents: a review of malaria and leishmaniasis among United States Armed Forces
type: item
type: AcademicArticle
description: As the United States military engage with different countries and cultures throughout the world, personnel become exposed to new biospheres as well. There are many infectious pathogens that are not endemic to the US, but two of particular importance are Plasmodium and Leishmania, which respectively cause malaria and leishmaniasis. These parasites are both known to cause significant disease burden in their endemic locales, and thus pose a threat to military travelers. This review introduces readers to basic life cycle and disease mechanisms for each. Local and military epidemiology are described, as are the specific actions taken by the US military for prevention and treatment purposes. Complications of such measures with regard to human health are also discussed, including possible chemical toxicities. Additionally, poor recognition of these diseases upon an individual’s return leading to complications and treatment delays in the United States are examined. Information about canine leishmaniasis, poorly studied relative to its human manifestation, but of importance due to the utilization of dogs in military endeavors is presented. Future implications for the American healthcare system regarding malaria and leishmaniasis are also presented.
format: application/pdf
format: text/html
creator: Kaylin J. Beiter
creator: Zachariah J. Wentlent
creator: Adrian R. Hamouda
creator: Bolaji N. Thomas
subject: Parasitology
subject: Epidemiology
subject: Global Health
subject: Public Health
description: doi:10.7717/peerj.6313
publisher: PeerJ Inc.
rights: © 2019 Beiter et al.
abstract: As the United States military engage with different countries and cultures throughout the world, personnel become exposed to new biospheres as well. There are many infectious pathogens that are not endemic to the US, but two of particular importance are Plasmodium and Leishmania, which respectively cause malaria and leishmaniasis. These parasites are both known to cause significant disease burden in their endemic locales, and thus pose a threat to military travelers. This review introduces readers to basic life cycle and disease mechanisms for each. Local and military epidemiology are described, as are the specific actions taken by the US military for prevention and treatment purposes. Complications of such measures with regard to human health are also discussed, including possible chemical toxicities. Additionally, poor recognition of these diseases upon an individual’s return leading to complications and treatment delays in the United States are examined. Information about canine leishmaniasis, poorly studied relative to its human manifestation, but of importance due to the utilization of dogs in military endeavors is presented. Future implications for the American healthcare system regarding malaria and leishmaniasis are also presented.
bibliographic citation: Beiter et al. (2019) Nonconventional opponents: a review of malaria and leishmaniasis among United States Armed Forces. PeerJ 7:e6313 https://doi.org/10.7717/peerj.6313
date submitted: 2018-09-10
date accepted: 2018-12-19
issued: 2019-01-25
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Beiter
  given name: Kaylin J.
author list: Agent
  family name: Wentlent
  given name: Zachariah J.
author list: Agent
  family name: Hamouda
  given name: Adrian R.
author list: Agent
  family name: Thomas
  given name: Bolaji N.
doi: 10.7717/peerj.6313
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-01-25
copyright: ©2019 Beiter et al.
attribution name: Beiter et al.

Increased tooth brushing frequency is associated with reduced gingival pocket bacterial diversity in patients with intracranial aneurysms
type: item
type: AcademicArticle
description: Objectives The objective of this study was to investigate the association of tooth brushing frequency and bacterial communities of gingival crevicular fluid in patients subjected to preoperative dental examination prior to operative treatment for unruptured intracranial aneurysms. Methods Gingival crevicular fluid samples were taken from their deepest gingival pocket from a series of hospitalized neurosurgical patients undergoing preoperative dental screening (n = 60). The patients were asked whether they brushed their teeth two times a day, once a day, or less than every day. Total bacterial DNA was isolated and the V3–V4 region of the 16S rRNA gene was amplificated. Sequencing was performed with Illumina’s 16S metagenomic sequencing library preparation protocol and data were analyzed with QIIME (1.9.1) and R statistical software (3.3.2). Results Bacterial diversity (Chao1 index) in the crevicular fluid reduced along with reported tooth brushing frequency (p = 0.0002; R2 = 34%; p (adjusted with age and sex) = 0.09; R2 = 11%) showing that patients who reported brushing their teeth twice a day had the lowest bacterial diversity. According to the differential abundant analysis between the tooth brushing groups, tooth brushing associated with two phyla of fusobacteria [p = 0.0001; p = 0.0007], and one bacteroidetes (p = 0.004) by reducing their amounts. Conclusions Tooth brushing may reduce the gingival bacterial diversity and the abundance of periodontal bacteria maintaining oral health and preventing periodontitis, and thus it is highly recommended for neurosurgical patients.
format: application/pdf
format: text/html
creator: Mikko J. Pyysalo
creator: Pashupati P. Mishra
creator: Kati Sundström
creator: Terho Lehtimäki
creator: Pekka J. Karhunen
creator: Tanja Pessi
subject: Bioinformatics
subject: Microbiology
subject: Dentistry
description: doi:10.7717/peerj.6316
publisher: PeerJ Inc.
rights: © 2019 Pyysalo et al.
abstract: Objectives The objective of this study was to investigate the association of tooth brushing frequency and bacterial communities of gingival crevicular fluid in patients subjected to preoperative dental examination prior to operative treatment for unruptured intracranial aneurysms. Methods Gingival crevicular fluid samples were taken from their deepest gingival pocket from a series of hospitalized neurosurgical patients undergoing preoperative dental screening (n = 60). The patients were asked whether they brushed their teeth two times a day, once a day, or less than every day. Total bacterial DNA was isolated and the V3–V4 region of the 16S rRNA gene was amplificated. Sequencing was performed with Illumina’s 16S metagenomic sequencing library preparation protocol and data were analyzed with QIIME (1.9.1) and R statistical software (3.3.2). Results Bacterial diversity (Chao1 index) in the crevicular fluid reduced along with reported tooth brushing frequency (p = 0.0002; R2 = 34%; p (adjusted with age and sex) = 0.09; R2 = 11%) showing that patients who reported brushing their teeth twice a day had the lowest bacterial diversity. According to the differential abundant analysis between the tooth brushing groups, tooth brushing associated with two phyla of fusobacteria [p = 0.0001; p = 0.0007], and one bacteroidetes (p = 0.004) by reducing their amounts. Conclusions Tooth brushing may reduce the gingival bacterial diversity and the abundance of periodontal bacteria maintaining oral health and preventing periodontitis, and thus it is highly recommended for neurosurgical patients.
bibliographic citation: Pyysalo et al. (2019) Increased tooth brushing frequency is associated with reduced gingival pocket bacterial diversity in patients with intracranial aneurysms. PeerJ 7:e6316 https://doi.org/10.7717/peerj.6316
date submitted: 2018-06-07
date accepted: 2018-12-19
issued: 2019-01-25
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Pyysalo
  given name: Mikko J.
author list: Agent
  family name: Mishra
  given name: Pashupati P.
author list: Agent
  family name: Sundström
  given name: Kati
author list: Agent
  family name: Lehtimäki
  given name: Terho
author list: Agent
  family name: Karhunen
  given name: Pekka J.
author list: Agent
  family name: Pessi
  given name: Tanja
doi: 10.7717/peerj.6316
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-01-25
copyright: ©2019 Pyysalo et al.
attribution name: Pyysalo et al.

The complete chloroplast genomes of three Betulaceae species: implications for molecular phylogeny and historical biogeography
type: item
type: AcademicArticle
description: Background Previous phylogenetic conclusions on the family Betulaceae were based on either morphological characters or traditional single loci, which may indicate some limitations. The chloroplast genome contains rich polymorphism information, which is very suitable for phylogenetic studies. Thus, we sequenced the chloroplast genome sequences of three Betulaceae species and performed multiple analyses to investigate the genome variation, resolve the phylogenetic relationships, and clarify the divergence history. Methods Chloroplast genomes were sequenced using the high-throughput sequencing. A comparative genomic analysis was conducted to examine the global genome variation and screen the hotspots. Three chloroplast partitions were used to reconstruct the phylogenetic relationships using Maximum Likelihood and Bayesian Inference approaches. Then, molecular dating and biogeographic inferences were conducted based on the whole chloroplast genome data. Results Betulaceae chloroplast genomes consisted of a small single-copy region and a large single copy region, and two copies of inverted repeat regions. Nine hotspots can be used as potential DNA barcodes for species delimitation. Phylogenies strongly supported the division of Betulaceae into two subfamilies: Coryloideae and Betuloideae. The phylogenetic position of Ostryopsis davidiana was controversial among different datasets. The divergence time between subfamily Coryloideae and Betuloideae was about 70.49 Mya, and all six extant genera were inferred to have diverged fully by the middle Oligocene. Betulaceae ancestors were probably originated from the ancient Laurasia. Discussions This research elucidates the potential of chloroplast genome sequences in the application of developing molecular markers, studying evolutionary relationships and historical dynamic of Betulaceae.It also reveals the advantages of using chloroplast genome data to illuminate those phylogenies that have not been well solved yet by traditional…
format: application/pdf
format: text/html
creator: Zhen Yang
creator: Guixi Wang
creator: Qinghua Ma
creator: Wenxu Ma
creator: Lisong Liang
creator: Tiantian Zhao
subject: Evolutionary Studies
subject: Genomics
subject: Taxonomy
subject: Forestry
description: doi:10.7717/peerj.6320
publisher: PeerJ Inc.
rights: © 2019 Yang et al.
abstract: Background Previous phylogenetic conclusions on the family Betulaceae were based on either morphological characters or traditional single loci, which may indicate some limitations. The chloroplast genome contains rich polymorphism information, which is very suitable for phylogenetic studies. Thus, we sequenced the chloroplast genome sequences of three Betulaceae species and performed multiple analyses to investigate the genome variation, resolve the phylogenetic relationships, and clarify the divergence history. Methods Chloroplast genomes were sequenced using the high-throughput sequencing. A comparative genomic analysis was conducted to examine the global genome variation and screen the hotspots. Three chloroplast partitions were used to reconstruct the phylogenetic relationships using Maximum Likelihood and Bayesian Inference approaches. Then, molecular dating and biogeographic inferences were conducted based on the whole chloroplast genome data. Results Betulaceae chloroplast genomes consisted of a small single-copy region and a large single copy region, and two copies of inverted repeat regions. Nine hotspots can be used as potential DNA barcodes for species delimitation. Phylogenies strongly supported the division of Betulaceae into two subfamilies: Coryloideae and Betuloideae. The phylogenetic position of Ostryopsis davidiana was controversial among different datasets. The divergence time between subfamily Coryloideae and Betuloideae was about 70.49 Mya, and all six extant genera were inferred to have diverged fully by the middle Oligocene. Betulaceae ancestors were probably originated from the ancient Laurasia. Discussions This research elucidates the potential of chloroplast genome sequences in the application of developing molecular markers, studying evolutionary relationships and historical dynamic of Betulaceae.It also reveals the advantages of using chloroplast genome data to illuminate those phylogenies that have not been well solved yet by traditional…
bibliographic citation: Yang et al. (2019) The complete chloroplast genomes of three Betulaceae species: implications for molecular phylogeny and historical biogeography. PeerJ 7:e6320 https://doi.org/10.7717/peerj.6320
date submitted: 2018-10-16
date accepted: 2018-12-20
issued: 2019-01-25
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Yang
  given name: Zhen
author list: Agent
  family name: Wang
  given name: Guixi
author list: Agent
  family name: Ma
  given name: Qinghua
author list: Agent
  family name: Ma
  given name: Wenxu
author list: Agent
  family name: Liang
  given name: Lisong
author list: Agent
  family name: Zhao
  given name: Tiantian
doi: 10.7717/peerj.6320
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-01-25
copyright: ©2019 Yang et al.
attribution name: Yang et al.

New material of the ‘microsaur’ Llistrofus from the cave deposits of Richards Spur, Oklahoma and the paleoecology of the Hapsidopareiidae
type: item
type: AcademicArticle
description: The Hapsidopareiidae is a group of “microsaurs” characterized by a substantial reduction of several elements in the cheek region that results in a prominent, enlarged temporal emargination. The clade comprises two markedly similar taxa from the early Permian of Oklahoma, Hapsidopareion lepton and Llistrofus pricei, which have been suggested to be synonymous by past workers. Llistrofus was previously known solely from the holotype found near Richards Spur, which consists of a dorsoventrally compressed skull in which the internal structures are difficult to characterize. Here, we present data from two new specimens of Llistrofus. This includes data collected through the use of neutron tomography, which revealed important new details of the palate and the neurocranium. Important questions within “Microsauria” related to the evolutionary transformations that likely occurred as part of the acquisition of the highly modified recumbirostran morphology for a fossorial ecology justify detailed reexamination of less well-studied taxa, such as Llistrofus. Although this study eliminates all but one of the previous features that differentiated Llistrofus and Hapsidopareion, the new data and redescription identify new features that justify the maintained separation of the two hapsidopareiids. Llistrofus possesses some of the adaptations for a fossorial lifestyle that have been identified in recumbirostrans but with a lesser degree of modification (e.g., reduced neurocranial ossification and mandibular modification). Incorporating the new data for Llistrofus into an existing phylogenetic matrix maintains the Hapsidopareiidae’s (Llistrofus + Hapsidopareion) position as the sister group to Recumbirostra. Given its phylogenetic position, we contextualize Llistrofus within the broader “microsaur” framework. Specifically, we propose that Llistrofus may have been fossorial but was probably incapable of active burrowing in the fashion of recumbirostrans, which had more consolidated and r…
format: application/pdf
format: text/html
creator: Bryan M. Gee
creator: Joseph J. Bevitt
creator: Ulf Garbe
creator: Robert R. Reisz
subject: Evolutionary Studies
subject: Paleontology
subject: Taxonomy
description: doi:10.7717/peerj.6327
publisher: PeerJ Inc.
rights: © 2019 Gee et al.
abstract: The Hapsidopareiidae is a group of “microsaurs” characterized by a substantial reduction of several elements in the cheek region that results in a prominent, enlarged temporal emargination. The clade comprises two markedly similar taxa from the early Permian of Oklahoma, Hapsidopareion lepton and Llistrofus pricei, which have been suggested to be synonymous by past workers. Llistrofus was previously known solely from the holotype found near Richards Spur, which consists of a dorsoventrally compressed skull in which the internal structures are difficult to characterize. Here, we present data from two new specimens of Llistrofus. This includes data collected through the use of neutron tomography, which revealed important new details of the palate and the neurocranium. Important questions within “Microsauria” related to the evolutionary transformations that likely occurred as part of the acquisition of the highly modified recumbirostran morphology for a fossorial ecology justify detailed reexamination of less well-studied taxa, such as Llistrofus. Although this study eliminates all but one of the previous features that differentiated Llistrofus and Hapsidopareion, the new data and redescription identify new features that justify the maintained separation of the two hapsidopareiids. Llistrofus possesses some of the adaptations for a fossorial lifestyle that have been identified in recumbirostrans but with a lesser degree of modification (e.g., reduced neurocranial ossification and mandibular modification). Incorporating the new data for Llistrofus into an existing phylogenetic matrix maintains the Hapsidopareiidae’s (Llistrofus + Hapsidopareion) position as the sister group to Recumbirostra. Given its phylogenetic position, we contextualize Llistrofus within the broader “microsaur” framework. Specifically, we propose that Llistrofus may have been fossorial but was probably incapable of active burrowing in the fashion of recumbirostrans, which had more consolidated and r…
bibliographic citation: Gee et al. (2019) New material of the ‘microsaur’ Llistrofus from the cave deposits of Richards Spur, Oklahoma and the paleoecology of the Hapsidopareiidae. PeerJ 7:e6327 https://doi.org/10.7717/peerj.6327
date submitted: 2018-09-24
date accepted: 2018-12-17
issued: 2019-01-25
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Gee
  given name: Bryan M.
author list: Agent
  family name: Bevitt
  given name: Joseph J.
author list: Agent
  family name: Garbe
  given name: Ulf
author list: Agent
  family name: Reisz
  given name: Robert R.
doi: 10.7717/peerj.6327
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-01-25
copyright: © 2019 Gee et al.
attribution name: Gee et al.

The dynamics of grooming interactions: maintenance of partner choice and the consequences of demographic variation for female mandrills
type: item
type: AcademicArticle
description: A large body of evidence suggests that female Old World monkeys maintain selective long-term grooming interactions with fitness benefits. The last two decades have produced evidence that the regulation of social interactions among primates can be, in part, explained by the Biological Markets theory, with grooming behaviour as the focus of these studies. Grooming facilitates bonding between individuals, constituting an essential part of the regulation of social relationships among female cercopithecids. In contrast to the well-studied baboons (Papio spp), knowledge about the nature of grooming interactions and their regulation is generally lacking for the large, terrestrial species of mandrills (Mandrillus sphinx). We used a combination of social network analysis tools and well-established methods for assessing partner diversity and reciprocity to characterise grooming networks, partner choice and patterns of trade (be groomed, give grooming) among females in a captive group of mandrills, both within and across two separate observation periods. Our results suggest that, even though the relatively stable conditions of captivity allowed the studied females to maintain selective grooming interactions across time, small scale demographic changes affected the grooming dynamics of the group in accordance with the expectations of the Biological Markets theory. In particular, the maturation and consequent integration of a high ranking female into the group’s grooming network from one period to the next resulted in a more pronounced effect of rank on the regulation of grooming interactions. In addition, the influence of the maturation of a dependent infant on the grooming interactions of his mother were evident between periods. Our results also demonstrate that grooming networks are dynamic and that high ranking individuals are not necessarily the most central in grooming networks. Finally, we discuss the potential of social network analysis to identify cases of social exclus…
format: application/pdf
format: text/html
creator: André S. Pereira
creator: Inês D. Rebelo
creator: Catarina Casanova
creator: Phyllis C. Lee
creator: Vasilis Louca
subject: Animal Behavior
subject: Anthropology
subject: Zoology
description: doi:10.7717/peerj.6332
publisher: PeerJ Inc.
rights: © 2019 Pereira et al.
abstract: A large body of evidence suggests that female Old World monkeys maintain selective long-term grooming interactions with fitness benefits. The last two decades have produced evidence that the regulation of social interactions among primates can be, in part, explained by the Biological Markets theory, with grooming behaviour as the focus of these studies. Grooming facilitates bonding between individuals, constituting an essential part of the regulation of social relationships among female cercopithecids. In contrast to the well-studied baboons (Papio spp), knowledge about the nature of grooming interactions and their regulation is generally lacking for the large, terrestrial species of mandrills (Mandrillus sphinx). We used a combination of social network analysis tools and well-established methods for assessing partner diversity and reciprocity to characterise grooming networks, partner choice and patterns of trade (be groomed, give grooming) among females in a captive group of mandrills, both within and across two separate observation periods. Our results suggest that, even though the relatively stable conditions of captivity allowed the studied females to maintain selective grooming interactions across time, small scale demographic changes affected the grooming dynamics of the group in accordance with the expectations of the Biological Markets theory. In particular, the maturation and consequent integration of a high ranking female into the group’s grooming network from one period to the next resulted in a more pronounced effect of rank on the regulation of grooming interactions. In addition, the influence of the maturation of a dependent infant on the grooming interactions of his mother were evident between periods. Our results also demonstrate that grooming networks are dynamic and that high ranking individuals are not necessarily the most central in grooming networks. Finally, we discuss the potential of social network analysis to identify cases of social exclus…
bibliographic citation: Pereira et al. (2019) The dynamics of grooming interactions: maintenance of partner choice and the consequences of demographic variation for female mandrills. PeerJ 7:e6332 https://doi.org/10.7717/peerj.6332
date submitted: 2018-07-20
date accepted: 2018-12-20
issued: 2019-01-25
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Pereira
  given name: André S.
author list: Agent
  family name: Rebelo
  given name: Inês D.
author list: Agent
  family name: Casanova
  given name: Catarina
author list: Agent
  family name: Lee
  given name: Phyllis C.
author list: Agent
  family name: Louca
  given name: Vasilis
doi: 10.7717/peerj.6332
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-01-25
copyright: ©2019 Pereira et al.
attribution name: Pereira et al.

Food-burying behavior in red imported fire ants (Hymenoptera: Formicidae)
type: item
type: AcademicArticle
description: The food-burying behavior has been reported in many mammals and birds, but was rarely observed in invertebrates. The red imported fire ants, Solenopsis invicta Buren, is an invasive pest in many areas of the world that usually performing food-burying during the foraging processes. However, the impacted factors and measureable patterns of this behavior is largely unknown. In the present study, food-burying vs food-transport behaviors of Solenopsis invicta were observed under laboratory and field conditions. When starved (no food was provided for 37 days) in the laboratory, food (sausage) was consumed by large numbers of ants, and few burying behaviors were observed. However, when food was provided until satiation of the colonies, food-transport was suppressed and significantly more soil particles were relocated on the food and graph paper square (where the food was placed) when compared with these colonies exposed to starved conditions. Videotapes showed that soil particles (1.47 ± 0.09 mm2) were preferentially placed adjacent to (in contact with) the food items at the beginning; and after the edges were covered, ants transported significantly smaller soil particles (1.13 ± 0.06 mm2) to cover the food. Meanwhile, larger particles (1.96 ± 0.08 mm2) were pulled/dragged around (but not in contact with) the food. Interestingly, only a small number of ants, mainly the small workers, were involved in food-burying, and the ants tended to repeatedly transport soil particles. A total of 12 patterns of particle transport were identified, and soil particles were most frequently picked from the foraging arena and subsequently placed adjacent to the food. In the field, almost all released food was actively transported by Solenopsis invicta workers, and no burying behavior was observed. Our results show that the food-burying behavior of Solenopsis invicta may be associated with the suppressed foraging activity, and the burying task may be carried out by certain groups of workers.
format: application/pdf
format: text/html
creator: Wenquan Qin
creator: Xuan Chen
creator: Linda M. Hooper-Bùi
creator: Jiacheng Cai
creator: Lei Wang
creator: Zhaohui Sun
creator: Xiujun Wen
creator: Cai Wang
subject: Agricultural Science
subject: Animal Behavior
subject: Entomology
description: doi:10.7717/peerj.6349
publisher: PeerJ Inc.
rights: © 2019 Qin et al.
abstract: The food-burying behavior has been reported in many mammals and birds, but was rarely observed in invertebrates. The red imported fire ants, Solenopsis invicta Buren, is an invasive pest in many areas of the world that usually performing food-burying during the foraging processes. However, the impacted factors and measureable patterns of this behavior is largely unknown. In the present study, food-burying vs food-transport behaviors of Solenopsis invicta were observed under laboratory and field conditions. When starved (no food was provided for 37 days) in the laboratory, food (sausage) was consumed by large numbers of ants, and few burying behaviors were observed. However, when food was provided until satiation of the colonies, food-transport was suppressed and significantly more soil particles were relocated on the food and graph paper square (where the food was placed) when compared with these colonies exposed to starved conditions. Videotapes showed that soil particles (1.47 ± 0.09 mm2) were preferentially placed adjacent to (in contact with) the food items at the beginning; and after the edges were covered, ants transported significantly smaller soil particles (1.13 ± 0.06 mm2) to cover the food. Meanwhile, larger particles (1.96 ± 0.08 mm2) were pulled/dragged around (but not in contact with) the food. Interestingly, only a small number of ants, mainly the small workers, were involved in food-burying, and the ants tended to repeatedly transport soil particles. A total of 12 patterns of particle transport were identified, and soil particles were most frequently picked from the foraging arena and subsequently placed adjacent to the food. In the field, almost all released food was actively transported by Solenopsis invicta workers, and no burying behavior was observed. Our results show that the food-burying behavior of Solenopsis invicta may be associated with the suppressed foraging activity, and the burying task may be carried out by certain groups of workers.
bibliographic citation: Qin et al. (2019) Food-burying behavior in red imported fire ants (Hymenoptera: Formicidae). PeerJ 7:e6349 https://doi.org/10.7717/peerj.6349
date submitted: 2018-10-08
date accepted: 2018-12-27
issued: 2019-01-25
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Qin
  given name: Wenquan
author list: Agent
  family name: Chen
  given name: Xuan
author list: Agent
  family name: Hooper-Bùi
  given name: Linda M.
author list: Agent
  family name: Cai
  given name: Jiacheng
author list: Agent
  family name: Wang
  given name: Lei
author list: Agent
  family name: Sun
  given name: Zhaohui
author list: Agent
  family name: Wen
  given name: Xiujun
author list: Agent
  family name: Wang
  given name: Cai
doi: 10.7717/peerj.6349
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-01-25
copyright: © 2019 Qin et al.
attribution name: Qin et al.

Effects of Salmonella enterica serovar Enteritidis infection on egg production and the immune response of the laying duck Anas platyrhynchos
type: item
type: AcademicArticle
description: Persistent colonization of the avian reproductive tract by Salmonella enterica serovar Enteritidis (SE) negatively affects egg production and contaminates the egg. The immune function of the ovary and oviduct is essential for protection from infection and for the production of wholesome eggs. However, the immune response of laying ducks during SE infection is not well-understood. In this study, ducks (Anas platyrhynchos) were infected with SE and were systematically monitored for fecal shedding during a 13-week period. We also assessed bacterial distribution in the reproductive tract and classified infected ducks as resistant or susceptible based on the presence of tissue lesions and on SE isolation from fecal samples. We found that infected animals had persistent, but intermittent, bacterial shedding that resulted in the induction of carrier ducks. Laying rate and egg quality were also decreased after SE infection (P < 0.05). SE readily colonized the stroma, small follicle, isthmus, and vagina in the reproductive tracts of susceptible ducks. Immunoglobulin (IgA, IgG, IgM) levels were higher in susceptible ducks compared with resistant birds (P < 0.05); T-lymphocyte subpopulations (CD3+, CD4+, CD8+) displayed the opposite trend. qRT-PCR analysis was used to examine expression profiles of immune response genes in the reproductive tract of infected ducks. The analysis revealed that immune genes, including toll-like receptors (TLR2, TLR4-5, TLR15, TLR21), NOD-like receptors (NOD1, NLRX1, NLRP12), avian β-defensins (AvβD4-5, AvβD7, AvβD12), cytokines (IL-6, IL-1β, IFN-γ), and MyD88 were markedly upregulated in the reproductive tracts of SE-infected ducks (all P < 0.05); TLR3, TLR7, NLRC3, NLRC5, and TNF-α were significantly downregulated. These results revealed that SE infection promoted lower egg production and quality, and altered the expression of TLRs, NLRs, AvβDs, and cytokine family genes. These findings provide a basis for further investigation of the physiologic…
format: application/pdf
format: text/html
creator: Yu Zhang
creator: Yang Chen
creator: Tiantian Gu
creator: Qi Xu
creator: Guoqiang Zhu
creator: Guohong Chen
subject: Agricultural Science
subject: Microbiology
subject: Veterinary Medicine
subject: Immunology
description: doi:10.7717/peerj.6359
publisher: PeerJ Inc.
rights: © 2019 Zhang et al.
abstract: Persistent colonization of the avian reproductive tract by Salmonella enterica serovar Enteritidis (SE) negatively affects egg production and contaminates the egg. The immune function of the ovary and oviduct is essential for protection from infection and for the production of wholesome eggs. However, the immune response of laying ducks during SE infection is not well-understood. In this study, ducks (Anas platyrhynchos) were infected with SE and were systematically monitored for fecal shedding during a 13-week period. We also assessed bacterial distribution in the reproductive tract and classified infected ducks as resistant or susceptible based on the presence of tissue lesions and on SE isolation from fecal samples. We found that infected animals had persistent, but intermittent, bacterial shedding that resulted in the induction of carrier ducks. Laying rate and egg quality were also decreased after SE infection (P < 0.05). SE readily colonized the stroma, small follicle, isthmus, and vagina in the reproductive tracts of susceptible ducks. Immunoglobulin (IgA, IgG, IgM) levels were higher in susceptible ducks compared with resistant birds (P < 0.05); T-lymphocyte subpopulations (CD3+, CD4+, CD8+) displayed the opposite trend. qRT-PCR analysis was used to examine expression profiles of immune response genes in the reproductive tract of infected ducks. The analysis revealed that immune genes, including toll-like receptors (TLR2, TLR4-5, TLR15, TLR21), NOD-like receptors (NOD1, NLRX1, NLRP12), avian β-defensins (AvβD4-5, AvβD7, AvβD12), cytokines (IL-6, IL-1β, IFN-γ), and MyD88 were markedly upregulated in the reproductive tracts of SE-infected ducks (all P < 0.05); TLR3, TLR7, NLRC3, NLRC5, and TNF-α were significantly downregulated. These results revealed that SE infection promoted lower egg production and quality, and altered the expression of TLRs, NLRs, AvβDs, and cytokine family genes. These findings provide a basis for further investigation of the physiologic…
bibliographic citation: Zhang et al. (2019) Effects of Salmonella enterica serovar Enteritidis infection on egg production and the immune response of the laying duck Anas platyrhynchos. PeerJ 7:e6359 https://doi.org/10.7717/peerj.6359
date submitted: 2018-08-06
date accepted: 2018-12-27
issued: 2019-01-25
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Zhang
  given name: Yu
author list: Agent
  family name: Chen
  given name: Yang
author list: Agent
  family name: Gu
  given name: Tiantian
author list: Agent
  family name: Xu
  given name: Qi
author list: Agent
  family name: Zhu
  given name: Guoqiang
author list: Agent
  family name: Chen
  given name: Guohong
doi: 10.7717/peerj.6359
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-01-25
copyright: ©2019 Zhang et al.
attribution name: Zhang et al.

Sleeping mattress determinants and evaluation: a biomechanical review and critique
type: item
type: AcademicArticle
description: Background Sleeping mattress parameters significantly influence sleeping comfort and health, as reflected by the extensive investigations of sleeping support biomechanics to prevent sleep-related musculoskeletal problems. Methodology Herein, we review the current trends, research methodologies, and determinants of mattress biomechanics research, summarizing evidence published since 2008. In particular, we scrutinize 18 articles dealing with the development of new designs, recommendation criteria, instruments/methods of spine alignment evaluation, and comparative evaluation of different designs. Results The review demonstrated that mattress designs have strived for customization, regional features, and real-time active control to adapt to the biomechanical features of different body builds and postures. However, the suggested threshold or target values for desirable spine alignment and body pressure distribution during sleep cannot yet be justified in view of the lack of sufficient evidence. Conclusions It is necessary to formulate standard objectives and protocols for carrying out mattress evaluation.
format: application/pdf
format: text/html
creator: Duo Wai-Chi Wong
creator: Yan Wang
creator: Jin Lin
creator: Qitao Tan
creator: Tony Lin-Wei Chen
creator: Ming Zhang
subject: Kinesiology
subject: Orthopedics
subject: Science and Medical Education
description: doi:10.7717/peerj.6364
publisher: PeerJ Inc.
rights: © 2019 Wong et al.
abstract: Background Sleeping mattress parameters significantly influence sleeping comfort and health, as reflected by the extensive investigations of sleeping support biomechanics to prevent sleep-related musculoskeletal problems. Methodology Herein, we review the current trends, research methodologies, and determinants of mattress biomechanics research, summarizing evidence published since 2008. In particular, we scrutinize 18 articles dealing with the development of new designs, recommendation criteria, instruments/methods of spine alignment evaluation, and comparative evaluation of different designs. Results The review demonstrated that mattress designs have strived for customization, regional features, and real-time active control to adapt to the biomechanical features of different body builds and postures. However, the suggested threshold or target values for desirable spine alignment and body pressure distribution during sleep cannot yet be justified in view of the lack of sufficient evidence. Conclusions It is necessary to formulate standard objectives and protocols for carrying out mattress evaluation.
bibliographic citation: Wong et al. (2019) Sleeping mattress determinants and evaluation: a biomechanical review and critique. PeerJ 7:e6364 https://doi.org/10.7717/peerj.6364
date submitted: 2018-10-11
date accepted: 2018-12-30
issued: 2019-01-25
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Wong
  given name: Duo Wai-Chi
author list: Agent
  family name: Wang
  given name: Yan
author list: Agent
  family name: Lin
  given name: Jin
author list: Agent
  family name: Tan
  given name: Qitao
author list: Agent
  family name: Chen
  given name: Tony Lin-Wei
author list: Agent
  family name: Zhang
  given name: Ming
doi: 10.7717/peerj.6364
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-01-25
copyright: © 2019 Wong et al.
attribution name: Wong et al.

Effects of different training modalities on phosphate homeostasis and local vitamin D metabolism in rat bone
type: item
type: AcademicArticle
description: Objectives Mechanical loading may be an important factor in the regulation of bone derived hormones involved in phosphate homeostasis. This study investigated the effects of peak power and endurance training on expression levels of fibroblast growth factor 23 (FGF23) and 1α-hydroxylase (CYP27b1) in bone. Methods Thirty-eight rats were assigned to six weeks of training in four groups: peak power (PT), endurance (ET), PT followed by ET (PET) or no training (control). In cortical bone, FGF23 was quantified using immunohistochemistry. mRNA expression levels of proteins involved in phosphate and vitamin D homeostasis were quantified in cortical bone and kidney. C-terminal FGF23, 25-hydroxyvitamin D3, parathyroid hormone (PTH), calcium and phosphate concentrations were measured in plasma or serum. Results Neither FGF23 mRNA and protein expression levels in cortical bone nor FGF23 plasma concentrations differed between the groups. In cortical bone, mRNA expression levels of sclerostin (SOST), dental matrix protein 1 (DMP1), phosphate-regulating gene with homologies to endopeptidases on the X chromosome (PHEX) and matrix extracellular phosphoglycoprotein (MEPE) were lower after PT compared to ET and PET. Expression levels of CYP27b1 and vitamin D receptor (VDR) in tibial bone were decreased after PT compared to ET. In kidney, no differences between groups were observed for mRNA expression levels of CYP27b1, 24-hydroxylase (CYP24), VDR, NaPi-IIa cotransporter (NPT2a) and NaPi-IIc cotransporter (NPT2c). Serum PTH concentrations were higher after PT compared to controls. Conclusion After six weeks, none of the training modalities induced changes in FGF23 expression levels. However, PT might have caused changes in local phosphate regulation within bone compared to ET and PET. CYP27b1 and VDR expression in bone was reduced after PT compared to ET, suggesting high intensity peak power training in this rat model is associated with decreased vitamin D signalling in bone.
format: application/pdf
format: text/html
creator: Joost Buskermolen
creator: Karen van der Meijden
creator: Regula Furrer
creator: Dirk-Jan Mons
creator: Huib W. van Essen
creator: Annemieke C. Heijboer
creator: Paul Lips
creator: Richard T. Jaspers
creator: Nathalie Bravenboer
subject: Anatomy and Physiology
subject: Diabetes and Endocrinology
subject: Internal Medicine
subject: Kinesiology
description: doi:10.7717/peerj.6184
publisher: PeerJ Inc.
rights: © 2019 Buskermolen et al.
abstract: Objectives Mechanical loading may be an important factor in the regulation of bone derived hormones involved in phosphate homeostasis. This study investigated the effects of peak power and endurance training on expression levels of fibroblast growth factor 23 (FGF23) and 1α-hydroxylase (CYP27b1) in bone. Methods Thirty-eight rats were assigned to six weeks of training in four groups: peak power (PT), endurance (ET), PT followed by ET (PET) or no training (control). In cortical bone, FGF23 was quantified using immunohistochemistry. mRNA expression levels of proteins involved in phosphate and vitamin D homeostasis were quantified in cortical bone and kidney. C-terminal FGF23, 25-hydroxyvitamin D3, parathyroid hormone (PTH), calcium and phosphate concentrations were measured in plasma or serum. Results Neither FGF23 mRNA and protein expression levels in cortical bone nor FGF23 plasma concentrations differed between the groups. In cortical bone, mRNA expression levels of sclerostin (SOST), dental matrix protein 1 (DMP1), phosphate-regulating gene with homologies to endopeptidases on the X chromosome (PHEX) and matrix extracellular phosphoglycoprotein (MEPE) were lower after PT compared to ET and PET. Expression levels of CYP27b1 and vitamin D receptor (VDR) in tibial bone were decreased after PT compared to ET. In kidney, no differences between groups were observed for mRNA expression levels of CYP27b1, 24-hydroxylase (CYP24), VDR, NaPi-IIa cotransporter (NPT2a) and NaPi-IIc cotransporter (NPT2c). Serum PTH concentrations were higher after PT compared to controls. Conclusion After six weeks, none of the training modalities induced changes in FGF23 expression levels. However, PT might have caused changes in local phosphate regulation within bone compared to ET and PET. CYP27b1 and VDR expression in bone was reduced after PT compared to ET, suggesting high intensity peak power training in this rat model is associated with decreased vitamin D signalling in bone.
bibliographic citation: Buskermolen et al. (2019) Effects of different training modalities on phosphate homeostasis and local vitamin D metabolism in rat bone. PeerJ 7:e6184 https://doi.org/10.7717/peerj.6184
date submitted: 2018-05-23
date accepted: 2018-11-29
issued: 2019-01-24
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Buskermolen
  given name: Joost
author list: Agent
  family name: van der Meijden
  given name: Karen
author list: Agent
  family name: Furrer
  given name: Regula
author list: Agent
  family name: Mons
  given name: Dirk-Jan
author list: Agent
  family name: van Essen
  given name: Huib W.
author list: Agent
  family name: Heijboer
  given name: Annemieke C.
author list: Agent
  family name: Lips
  given name: Paul
author list: Agent
  family name: Jaspers
  given name: Richard T.
author list: Agent
  family name: Bravenboer
  given name: Nathalie
doi: 10.7717/peerj.6184
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-01-24
copyright: ©2019 Buskermolen et al.
attribution name: Buskermolen et al.

GPs’ motivation for teaching medical students in a rural area—development of the Motivation for Medical Education Questionnaire (MoME-Q)
type: item
type: AcademicArticle
description: Background The establishment of a medical education program in the rural area of Siegen is planned to be the first step against a shortage of physicians in this region. General practitioners (GPs) will be extensively involved in this program as Family Medicine (Allgemeinmedizin) will become a core subject in the curriculum nationwide. Based on this situation we aim to figure out GPs motivation to participate in medical education. For this purpose, we had to construct and test a new questionnaire. Methods A survey was conducted among general practitioners (GPs) in the region of Siegen-Wittgenstein regarding their motivation to participate in medical education. For this purpose, the Motivation for Medical Education Questionnaire (MoME-Q), a 24-item questionnaire, was developed. Structural characteristics of GPs, the Maslach Burnout Inventory (MBI) and the Work Satisfaction Questionnaire (WSQ) were used for validation purposes. Results A representative number of GPs took part in the study (53.8%). Although the majority had no connection to a university (86%), 83% can imagine participating in the education of medical students. The items of the MoME-Q load on two factors (commitment and personal benefit). The confirmatory factor analysis shows a good model fit. Subscales of the MoME-Q were able to differentiate between physicians with and without authorization to train GP residents, between practices with and without a specialized practice nurse, and between physicians with and without previous experience in medical education. The MoME-Q subscale “commitment” correlated significantly with all three subscales of the MBI. Correlations were in the medium range around |.30|. Conclusion The MoME-Q seems to be an appropriate tool to assess motivation to participate in medical education of GPs. In our sample, a large number of GPs was motivated to participate in the education of medical students. Future studies with larger number of GPs should be carried out to validate and con…
format: application/pdf
format: text/html
creator: Charles Christian Adarkwah
creator: Annette Schwaffertz
creator: Joachim Labenz
creator: Annette Becker
creator: Oliver Hirsch
subject: Public Health
subject: Science and Medical Education
description: doi:10.7717/peerj.6235
publisher: PeerJ Inc.
rights: © 2019 Adarkwah et al.
abstract: Background The establishment of a medical education program in the rural area of Siegen is planned to be the first step against a shortage of physicians in this region. General practitioners (GPs) will be extensively involved in this program as Family Medicine (Allgemeinmedizin) will become a core subject in the curriculum nationwide. Based on this situation we aim to figure out GPs motivation to participate in medical education. For this purpose, we had to construct and test a new questionnaire. Methods A survey was conducted among general practitioners (GPs) in the region of Siegen-Wittgenstein regarding their motivation to participate in medical education. For this purpose, the Motivation for Medical Education Questionnaire (MoME-Q), a 24-item questionnaire, was developed. Structural characteristics of GPs, the Maslach Burnout Inventory (MBI) and the Work Satisfaction Questionnaire (WSQ) were used for validation purposes. Results A representative number of GPs took part in the study (53.8%). Although the majority had no connection to a university (86%), 83% can imagine participating in the education of medical students. The items of the MoME-Q load on two factors (commitment and personal benefit). The confirmatory factor analysis shows a good model fit. Subscales of the MoME-Q were able to differentiate between physicians with and without authorization to train GP residents, between practices with and without a specialized practice nurse, and between physicians with and without previous experience in medical education. The MoME-Q subscale “commitment” correlated significantly with all three subscales of the MBI. Correlations were in the medium range around |.30|. Conclusion The MoME-Q seems to be an appropriate tool to assess motivation to participate in medical education of GPs. In our sample, a large number of GPs was motivated to participate in the education of medical students. Future studies with larger number of GPs should be carried out to validate and con…
bibliographic citation: Adarkwah et al. (2019) GPs’ motivation for teaching medical students in a rural area—development of the Motivation for Medical Education Questionnaire (MoME-Q). PeerJ 7:e6235 https://doi.org/10.7717/peerj.6235
date submitted: 2018-09-27
date accepted: 2018-12-07
issued: 2019-01-24
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Adarkwah
  given name: Charles Christian
author list: Agent
  family name: Schwaffertz
  given name: Annette
author list: Agent
  family name: Labenz
  given name: Joachim
author list: Agent
  family name: Becker
  given name: Annette
author list: Agent
  family name: Hirsch
  given name: Oliver
doi: 10.7717/peerj.6235
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-01-24
copyright: ©2019 Adarkwah et al.
attribution name: Adarkwah et al.

Intraspecific divergences and phylogeography of Panzerina lanata (Lamiaceae) in northwest China
type: item
type: AcademicArticle
description: Climatic fluctuations during the Quaternary significantly affect many species in their intraspecific divergence and population structure across northwest China. In order to investigate the impact of climate change on herbaceous plants, we studied Panzerina lanata (Lamiaceae), a widely distributed species. Sequences of two chloroplast DNA (cpDNA) intergenic spacers (trnH-psbA and rpoB-trnC) and a nuclear ribosomal region (nrDNA, ITS) were generated from 27 populations of Panzerina lanata and resulted in the identification of seven chloroplast haplotypes and thirty-two nuclear haplotypes. We applied AMOVA, neutrality test and mismatch distribution analysis to estimate genetic differentiation and demographic characteristics. The divergence times of the seven cpDNA haplotypes were estimated using BEAST. Our results revealed high levels of genetic diversity (cpDNA: Hcp = 0.6691, HT = 0.673; nrDNA: Hnr = 0.5668, HT = 0.577). High level of genetic differentiation (GST = 0.950) among populations was observed in the cpDNA sequences, while the genetic differentiation values (GST = 0.348) were low in nuclear sequences. AMOVA results revealed major genetic variation among the three groups: northern, central, and eastern group. However, the genetic differentiation in ITS data was not found. The species distribution modeling and demographic analysis indicated that P. lanata had not experienced recent range expansion. The occurrence of divergence between seven cpDNA haplotypes, probably during Pleistocene, coincides with aridification and expansion of the desert across northwest China that resulted in species diversification and habitat fragmentation. In addition, we discovered that the deserts and the Helan Mountains acted as effective geographic barriers that promoting the intraspecific diversity of P. lanata.
format: application/pdf
format: text/html
creator: Yanfen Zhao
creator: Hongxiang Zhang
creator: Borong Pan
creator: Mingli Zhang
subject: Biodiversity
subject: Biogeography
subject: Plant Science
description: doi:10.7717/peerj.6264
publisher: PeerJ Inc.
rights: © 2019 Zhao et al.
abstract: Climatic fluctuations during the Quaternary significantly affect many species in their intraspecific divergence and population structure across northwest China. In order to investigate the impact of climate change on herbaceous plants, we studied Panzerina lanata (Lamiaceae), a widely distributed species. Sequences of two chloroplast DNA (cpDNA) intergenic spacers (trnH-psbA and rpoB-trnC) and a nuclear ribosomal region (nrDNA, ITS) were generated from 27 populations of Panzerina lanata and resulted in the identification of seven chloroplast haplotypes and thirty-two nuclear haplotypes. We applied AMOVA, neutrality test and mismatch distribution analysis to estimate genetic differentiation and demographic characteristics. The divergence times of the seven cpDNA haplotypes were estimated using BEAST. Our results revealed high levels of genetic diversity (cpDNA: Hcp = 0.6691, HT = 0.673; nrDNA: Hnr = 0.5668, HT = 0.577). High level of genetic differentiation (GST = 0.950) among populations was observed in the cpDNA sequences, while the genetic differentiation values (GST = 0.348) were low in nuclear sequences. AMOVA results revealed major genetic variation among the three groups: northern, central, and eastern group. However, the genetic differentiation in ITS data was not found. The species distribution modeling and demographic analysis indicated that P. lanata had not experienced recent range expansion. The occurrence of divergence between seven cpDNA haplotypes, probably during Pleistocene, coincides with aridification and expansion of the desert across northwest China that resulted in species diversification and habitat fragmentation. In addition, we discovered that the deserts and the Helan Mountains acted as effective geographic barriers that promoting the intraspecific diversity of P. lanata.
bibliographic citation: Zhao et al. (2019) Intraspecific divergences and phylogeography of Panzerina lanata (Lamiaceae) in northwest China. PeerJ 7:e6264 https://doi.org/10.7717/peerj.6264
date submitted: 2018-04-04
date accepted: 2018-12-11
issued: 2019-01-24
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Zhao
  given name: Yanfen
author list: Agent
  family name: Zhang
  given name: Hongxiang
author list: Agent
  family name: Pan
  given name: Borong
author list: Agent
  family name: Zhang
  given name: Mingli
doi: 10.7717/peerj.6264
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-01-24
copyright: ©2019 Zhao et al.
attribution name: Zhao et al.

Association of TIMP4 gene variants with steroid-induced osteonecrosis of the femoral head in the population of northern China
type: item
type: AcademicArticle
description: Background In clinical treatment, the use of steroid hormones is an important etiological factor of non-traumatic osteonecrosis of the femoral head (ONFH) risk. As an endogenous inhibitor of matrix metalloproteinases (MMPs) in the extracellular matrix, the expression of tissue inhibitors of metalloprotease-4 (TIMP4) plays an essential role in cartilage and bone tissue damage and remodeling, vasculitis formation, intravascular thrombosis, and lipid metabolism. Methods This study aimed to detect the association between TIMP4 polymorphism and steroid-induced ONFH. We genotyped seven single-nucleotide polymorphisms (SNPs) in TIMP4 genes and analyzed the association with steroid-induced ONFH from 286 steroid-induced ONFH patients and 309 normal individuals. Results We performed allelic model analysis and found that the minor alleles of five SNPs (rs99365, rs308952, rs3817004, rs2279750, and rs3755724) were associated with decreased steroid-induced ONFH (p = 0.02, p = 0.03, p = 0.04, p = 0.01, p = 0.04, respectively). rs2279750 showed a significant association with decreased risk of steroid-induced ONFH in the Dominant and Log-additive models (p = 0.042, p = 0.028, respectively), and rs9935, rs30892, and rs3817004 were associated with decreased risk in the Log-additive model (p = 0.038, p = 0.044, p = 0.042, respectively). In further stratification analysis, TIMP4 gene variants showed a significant association with steroid-induced ONFH in gender under the genotypes. Haplotype analysis also revealed that “TCAGAC” and “CCGGAA” sequences have protective effect on steroid-induced ONFH. Conclusion Our results indicate that five TIMP4 SNPs (rs99365, rs308952, rs3817004 rs2279750, and rs3755724) are significantly associated with decreased risk of steroid-induced ONFH in the population of northern China.
format: application/pdf
format: text/html
creator: Jiaqi Wang
creator: Feimeng An
creator: Yuju Cao
creator: Hongyan Gao
creator: Mingqi Sun
creator: Chao Ma
creator: Hao Wu
creator: Baoxin Zhang
creator: Wanlin Liu
creator: Jianzhong Wang
subject: Genomics
subject: Orthopedics
subject: Surgery and Surgical Specialties
description: doi:10.7717/peerj.6270
publisher: PeerJ Inc.
rights: © 2019 Wang et al.
abstract: Background In clinical treatment, the use of steroid hormones is an important etiological factor of non-traumatic osteonecrosis of the femoral head (ONFH) risk. As an endogenous inhibitor of matrix metalloproteinases (MMPs) in the extracellular matrix, the expression of tissue inhibitors of metalloprotease-4 (TIMP4) plays an essential role in cartilage and bone tissue damage and remodeling, vasculitis formation, intravascular thrombosis, and lipid metabolism. Methods This study aimed to detect the association between TIMP4 polymorphism and steroid-induced ONFH. We genotyped seven single-nucleotide polymorphisms (SNPs) in TIMP4 genes and analyzed the association with steroid-induced ONFH from 286 steroid-induced ONFH patients and 309 normal individuals. Results We performed allelic model analysis and found that the minor alleles of five SNPs (rs99365, rs308952, rs3817004, rs2279750, and rs3755724) were associated with decreased steroid-induced ONFH (p = 0.02, p = 0.03, p = 0.04, p = 0.01, p = 0.04, respectively). rs2279750 showed a significant association with decreased risk of steroid-induced ONFH in the Dominant and Log-additive models (p = 0.042, p = 0.028, respectively), and rs9935, rs30892, and rs3817004 were associated with decreased risk in the Log-additive model (p = 0.038, p = 0.044, p = 0.042, respectively). In further stratification analysis, TIMP4 gene variants showed a significant association with steroid-induced ONFH in gender under the genotypes. Haplotype analysis also revealed that “TCAGAC” and “CCGGAA” sequences have protective effect on steroid-induced ONFH. Conclusion Our results indicate that five TIMP4 SNPs (rs99365, rs308952, rs3817004 rs2279750, and rs3755724) are significantly associated with decreased risk of steroid-induced ONFH in the population of northern China.
bibliographic citation: Wang et al. (2019) Association of TIMP4 gene variants with steroid-induced osteonecrosis of the femoral head in the population of northern China. PeerJ 7:e6270 https://doi.org/10.7717/peerj.6270
date submitted: 2018-09-26
date accepted: 2018-12-09
issued: 2019-01-24
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Wang
  given name: Jiaqi
author list: Agent
  family name: An
  given name: Feimeng
author list: Agent
  family name: Cao
  given name: Yuju
author list: Agent
  family name: Gao
  given name: Hongyan
author list: Agent
  family name: Sun
  given name: Mingqi
author list: Agent
  family name: Ma
  given name: Chao
author list: Agent
  family name: Wu
  given name: Hao
author list: Agent
  family name: Zhang
  given name: Baoxin
author list: Agent
  family name: Liu
  given name: Wanlin
author list: Agent
  family name: Wang
  given name: Jianzhong
doi: 10.7717/peerj.6270
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-01-24
copyright: ©2019 Wang et al.
attribution name: Wang et al.

Accessible molecular phylogenomics at no cost: obtaining 14 new mitogenomes for the ant subfamily Pseudomyrmecinae from public data
type: item
type: AcademicArticle
description: The advent of Next Generation Sequencing has reduced sequencing costs and increased genomic projects from a huge amount of organismal taxa, generating an unprecedented amount of genomic datasets publicly available. Often, only a tiny fraction of outstanding relevance of the genomic data produced by researchers is used in their works. This fact allows the data generated to be recycled in further projects worldwide. The assembly of complete mitogenomes is frequently overlooked though it is useful to understand evolutionary relationships among taxa, especially those presenting poor mtDNA sampling at the level of genera and families. This is exactly the case for ants (Hymenoptera:Formicidae) and more specifically for the subfamily Pseudomyrmecinae, a group of arboreal ants with several cases of convergent coevolution without any complete mitochondrial sequence available. In this work, we assembled, annotated and performed comparative genomics analyses of 14 new complete mitochondria from Pseudomyrmecinae species relying solely on public datasets available from the Sequence Read Archive (SRA). We used all complete mitogenomes available for ants to study the gene order conservation and also to generate two phylogenetic trees using both (i) concatenated set of 13 mitochondrial genes and (ii) the whole mitochondrial sequences. Even though the tree topologies diverged subtly from each other (and from previous studies), our results confirm several known relationships and generate new evidences for sister clade classification inside Pseudomyrmecinae clade. We also performed a synteny analysis for Formicidae and identified possible sites in which nucleotidic insertions happened in mitogenomes of pseudomyrmecine ants. Using a data mining/bioinformatics approach, the current work increased the number of complete mitochondrial genomes available for ants from 15 to 29, demonstrating the unique potential of public databases for mitogenomics studies. The wide applications of mitogeno…
format: application/pdf
format: text/html
creator: Gabriel A. Vieira
creator: Francisco Prosdocimi
subject: Biodiversity
subject: Bioinformatics
subject: Entomology
subject: Evolutionary Studies
subject: Genomics
description: doi:10.7717/peerj.6271
publisher: PeerJ Inc.
rights: © 2019 Vieira et al.
abstract: The advent of Next Generation Sequencing has reduced sequencing costs and increased genomic projects from a huge amount of organismal taxa, generating an unprecedented amount of genomic datasets publicly available. Often, only a tiny fraction of outstanding relevance of the genomic data produced by researchers is used in their works. This fact allows the data generated to be recycled in further projects worldwide. The assembly of complete mitogenomes is frequently overlooked though it is useful to understand evolutionary relationships among taxa, especially those presenting poor mtDNA sampling at the level of genera and families. This is exactly the case for ants (Hymenoptera:Formicidae) and more specifically for the subfamily Pseudomyrmecinae, a group of arboreal ants with several cases of convergent coevolution without any complete mitochondrial sequence available. In this work, we assembled, annotated and performed comparative genomics analyses of 14 new complete mitochondria from Pseudomyrmecinae species relying solely on public datasets available from the Sequence Read Archive (SRA). We used all complete mitogenomes available for ants to study the gene order conservation and also to generate two phylogenetic trees using both (i) concatenated set of 13 mitochondrial genes and (ii) the whole mitochondrial sequences. Even though the tree topologies diverged subtly from each other (and from previous studies), our results confirm several known relationships and generate new evidences for sister clade classification inside Pseudomyrmecinae clade. We also performed a synteny analysis for Formicidae and identified possible sites in which nucleotidic insertions happened in mitogenomes of pseudomyrmecine ants. Using a data mining/bioinformatics approach, the current work increased the number of complete mitochondrial genomes available for ants from 15 to 29, demonstrating the unique potential of public databases for mitogenomics studies. The wide applications of mitogeno…
bibliographic citation: Vieira et al. (2019) Accessible molecular phylogenomics at no cost: obtaining 14 new mitogenomes for the ant subfamily Pseudomyrmecinae from public data. PeerJ 7:e6271 https://doi.org/10.7717/peerj.6271
date submitted: 2018-11-07
date accepted: 2018-12-10
issued: 2019-01-24
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Vieira
  given name: Gabriel A.
author list: Agent
  family name: Prosdocimi
  given name: Francisco
doi: 10.7717/peerj.6271
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-01-24
copyright: ©2019 Vieira and Prosdocimi
attribution name: Vieira et al.

Prioritizing bona fide bacterial small RNAs with machine learning classifiers
type: item
type: AcademicArticle
description: Bacterial small (sRNAs) are involved in the control of several cellular processes. Hundreds of putative sRNAs have been identified in many bacterial species through RNA sequencing. The existence of putative sRNAs is usually validated by Northern blot analysis. However, the large amount of novel putative sRNAs reported in the literature makes it impractical to validate each of them in the wet lab. In this work, we applied five machine learning approaches to construct twenty models to discriminate bona fide sRNAs from random genomic sequences in five bacterial species. Sequences were represented using seven features including free energy of their predicted secondary structure, their distances to the closest predicted promoter site and Rho-independent terminator, and their distance to the closest open reading frames (ORFs). To automatically calculate these features, we developed an sRNA Characterization Pipeline (sRNACharP). All seven features used in the classification task contributed positively to the performance of the predictive models. The best performing model obtained a median precision of 100% at 10% recall and of 64% at 40% recall across all five bacterial species, and it outperformed previous published approaches on two benchmark datasets in terms of precision and recall. Our results indicate that even though there is limited sRNA sequence conservation across different bacterial species, there are intrinsic features in the genomic context of sRNAs that are conserved across taxa. We show that these features are utilized by machine learning approaches to learn a species-independent model to prioritize bona fide bacterial sRNAs.
format: application/pdf
format: text/html
creator: Erik J.J. Eppenhof
creator: Lourdes Peña-Castillo
subject: Bioinformatics
subject: Microbiology
subject: Data Mining and Machine Learning
description: doi:10.7717/peerj.6304
publisher: PeerJ Inc.
rights: © 2019 Eppenhof and Peña-Castillo
abstract: Bacterial small (sRNAs) are involved in the control of several cellular processes. Hundreds of putative sRNAs have been identified in many bacterial species through RNA sequencing. The existence of putative sRNAs is usually validated by Northern blot analysis. However, the large amount of novel putative sRNAs reported in the literature makes it impractical to validate each of them in the wet lab. In this work, we applied five machine learning approaches to construct twenty models to discriminate bona fide sRNAs from random genomic sequences in five bacterial species. Sequences were represented using seven features including free energy of their predicted secondary structure, their distances to the closest predicted promoter site and Rho-independent terminator, and their distance to the closest open reading frames (ORFs). To automatically calculate these features, we developed an sRNA Characterization Pipeline (sRNACharP). All seven features used in the classification task contributed positively to the performance of the predictive models. The best performing model obtained a median precision of 100% at 10% recall and of 64% at 40% recall across all five bacterial species, and it outperformed previous published approaches on two benchmark datasets in terms of precision and recall. Our results indicate that even though there is limited sRNA sequence conservation across different bacterial species, there are intrinsic features in the genomic context of sRNAs that are conserved across taxa. We show that these features are utilized by machine learning approaches to learn a species-independent model to prioritize bona fide bacterial sRNAs.
bibliographic citation: Eppenhof et al. (2019) Prioritizing bona fide bacterial small RNAs with machine learning classifiers. PeerJ 7:e6304 https://doi.org/10.7717/peerj.6304
date submitted: 2018-05-31
date accepted: 2018-12-16
issued: 2019-01-24
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Eppenhof
  given name: Erik J.J.
author list: Agent
  family name: Peña-Castillo
  given name: Lourdes
doi: 10.7717/peerj.6304
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-01-24
copyright: ©2019 Eppenhof and Peña-Castillo
attribution name: Eppenhof and Peña-Castillo

Dietary analysis of an uncharacteristic population of the Mountain Pygmy-possum (Burramys parvus) in the Kosciuszko National Park, New South Wales, Australia
type: item
type: AcademicArticle
description: Background The Mountain Pygmy-possum (Burramys parvus) is a critically endangered marsupial, endemic to alpine regions of southern Australia. We investigated the diet of a recently discovered population of the possum in northern Kosciuszko National Park, NSW, Australia. This new population occurs at elevations well below the once-presumed lower elevation limit of 1,600 m. Goals and Methods Faecal material was analysed to determine if dietary composition differed between individuals in the newly discovered northern population and those in the higher elevation southern population, and to examine how diet was influenced by rainfall in the southern population and seasonal changes in resource availability in the northern population. Results and Discussion The diet of B. parvus in the northern population comprised of arthropods, fruits and seeds. Results indicate the diet of both populations shares most of the same invertebrate orders and plant species. However, in the absence of preferred food types available to the southern population, individuals of the northern population opportunistically consumed different species that were similar to those preferred by individuals in higher altitude populations. Differing rainfall amounts had a significant effect on diet, with years of below average rainfall having a greater percentage composition and diversity of invertebrates. Seasonal variation was also recorded, with the northern population increasing the diversity of invertebrates in their diet during the Autumn months when Bogong Moths (Agrotis infusa) were absent from those sites, raising questions about the possum’s dependence on the species Conclusions Measurable effects of rainfall amount and seasonal variation on the dietary composition suggest that predicted climatic variability will have a significant impact on its diet, potentially impacting its future survival. Findings suggest that it is likely that B. parvus is not restricted by dietary requirements to its current …
format: application/pdf
format: text/html
creator: Tahneal Hawke
creator: Hayley Bates
creator: Suzanne Hand
creator: Michael Archer
creator: Linda Broome
subject: Biodiversity
subject: Conservation Biology
subject: Ecology
subject: Zoology
description: doi:10.7717/peerj.6307
publisher: PeerJ Inc.
rights: © 2019 Hawke et al.
abstract: Background The Mountain Pygmy-possum (Burramys parvus) is a critically endangered marsupial, endemic to alpine regions of southern Australia. We investigated the diet of a recently discovered population of the possum in northern Kosciuszko National Park, NSW, Australia. This new population occurs at elevations well below the once-presumed lower elevation limit of 1,600 m. Goals and Methods Faecal material was analysed to determine if dietary composition differed between individuals in the newly discovered northern population and those in the higher elevation southern population, and to examine how diet was influenced by rainfall in the southern population and seasonal changes in resource availability in the northern population. Results and Discussion The diet of B. parvus in the northern population comprised of arthropods, fruits and seeds. Results indicate the diet of both populations shares most of the same invertebrate orders and plant species. However, in the absence of preferred food types available to the southern population, individuals of the northern population opportunistically consumed different species that were similar to those preferred by individuals in higher altitude populations. Differing rainfall amounts had a significant effect on diet, with years of below average rainfall having a greater percentage composition and diversity of invertebrates. Seasonal variation was also recorded, with the northern population increasing the diversity of invertebrates in their diet during the Autumn months when Bogong Moths (Agrotis infusa) were absent from those sites, raising questions about the possum’s dependence on the species Conclusions Measurable effects of rainfall amount and seasonal variation on the dietary composition suggest that predicted climatic variability will have a significant impact on its diet, potentially impacting its future survival. Findings suggest that it is likely that B. parvus is not restricted by dietary requirements to its current …
bibliographic citation: Hawke et al. (2019) Dietary analysis of an uncharacteristic population of the Mountain Pygmy-possum (Burramys parvus) in the Kosciuszko National Park, New South Wales, Australia. PeerJ 7:e6307 https://doi.org/10.7717/peerj.6307
date submitted: 2018-07-17
date accepted: 2018-12-18
issued: 2019-01-24
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Hawke
  given name: Tahneal
author list: Agent
  family name: Bates
  given name: Hayley
author list: Agent
  family name: Hand
  given name: Suzanne
author list: Agent
  family name: Archer
  given name: Michael
author list: Agent
  family name: Broome
  given name: Linda
doi: 10.7717/peerj.6307
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-01-24
copyright: ©2019 Hawke et al.
attribution name: Hawke et al.

A turiasaurian sauropod dinosaur from the Early Cretaceous Wealden Supergroup of the United Kingdom
type: item
type: AcademicArticle
description: The Jurassic/Cretaceous (J/K) boundary, 145 million years ago, has long been recognised as an extinction event or faunal turnover for sauropod dinosaurs, with many ‘basal’ lineages disappearing. However, recently, a number of ‘extinct’ groups have been recognised in the Early Cretaceous, including diplodocids in Gondwana, and non-titanosauriform macronarians in Laurasia. Turiasauria, a clade of non-neosauropod eusauropods, was originally thought to have been restricted to the Late Jurassic of western Europe. However, its distribution has recently been extended to the Late Jurassic of Tanzania (Tendaguria tanzaniensis), as well as to the Early Cretaceous of the USA (Mierasaurus bobyoungi and Moabosaurus utahensis), demonstrating the survival of another ‘basal’ clade across the J/K boundary. Teeth from the Middle Jurassic–Early Cretaceous of western Europe and North Africa have also tentatively been attributed to turiasaurs, whilst recent phylogenetic analyses recovered Late Jurassic taxa from Argentina and China as further members of Turiasauria. Here, an anterior dorsal centrum and neural arch (both NHMUK 1871) from the Early Cretaceous Wealden Supergroup of the UK are described for the first time. NHMUK 1871 shares several synapomorphies with Turiasauria, especially the turiasaurs Moabosaurus and Tendaguria, including: (1) a strongly dorsoventrally compressed centrum; (2) the retention of prominent epipophyses; and (3) an extremely low, non-bifid neural spine. NHMUK 1871 therefore represents the first postcranial evidence for Turiasauria from European deposits of Early Cretaceous age. Although turiasaurs show clear heterodont dentition, only broad, characteristically ‘heart’-shaped teeth can currently be attributed to Turiasauria with confidence. As such, several putative turiasaur occurrences based on isolated teeth from Europe, as well as the Middle Jurassic and Early Cretaceous of Africa, cannot be confidently referred to Turiasauria. Unequivocal evidence for tu…
format: application/pdf
format: text/html
creator: Philip D. Mannion
subject: Evolutionary Studies
subject: Paleontology
description: doi:10.7717/peerj.6348
publisher: PeerJ Inc.
rights: © 2019 Mannion
abstract: The Jurassic/Cretaceous (J/K) boundary, 145 million years ago, has long been recognised as an extinction event or faunal turnover for sauropod dinosaurs, with many ‘basal’ lineages disappearing. However, recently, a number of ‘extinct’ groups have been recognised in the Early Cretaceous, including diplodocids in Gondwana, and non-titanosauriform macronarians in Laurasia. Turiasauria, a clade of non-neosauropod eusauropods, was originally thought to have been restricted to the Late Jurassic of western Europe. However, its distribution has recently been extended to the Late Jurassic of Tanzania (Tendaguria tanzaniensis), as well as to the Early Cretaceous of the USA (Mierasaurus bobyoungi and Moabosaurus utahensis), demonstrating the survival of another ‘basal’ clade across the J/K boundary. Teeth from the Middle Jurassic–Early Cretaceous of western Europe and North Africa have also tentatively been attributed to turiasaurs, whilst recent phylogenetic analyses recovered Late Jurassic taxa from Argentina and China as further members of Turiasauria. Here, an anterior dorsal centrum and neural arch (both NHMUK 1871) from the Early Cretaceous Wealden Supergroup of the UK are described for the first time. NHMUK 1871 shares several synapomorphies with Turiasauria, especially the turiasaurs Moabosaurus and Tendaguria, including: (1) a strongly dorsoventrally compressed centrum; (2) the retention of prominent epipophyses; and (3) an extremely low, non-bifid neural spine. NHMUK 1871 therefore represents the first postcranial evidence for Turiasauria from European deposits of Early Cretaceous age. Although turiasaurs show clear heterodont dentition, only broad, characteristically ‘heart’-shaped teeth can currently be attributed to Turiasauria with confidence. As such, several putative turiasaur occurrences based on isolated teeth from Europe, as well as the Middle Jurassic and Early Cretaceous of Africa, cannot be confidently referred to Turiasauria. Unequivocal evidence for tu…
bibliographic citation: Mannion (2019) A turiasaurian sauropod dinosaur from the Early Cretaceous Wealden Supergroup of the United Kingdom. PeerJ 7:e6348 https://doi.org/10.7717/peerj.6348
date submitted: 2018-10-08
date accepted: 2018-12-27
issued: 2019-01-24
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Mannion
  given name: Philip D.
doi: 10.7717/peerj.6348
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-01-24
copyright: © 2019 Mannion
attribution name: Mannion

Transcriptome profiling reveals the role of ZBTB38 knock-down in human neuroblastoma
type: item
type: AcademicArticle
description: ZBTB38 belongs to the zinc finger protein family and contains the typical BTB domains. As a transcription factor, ZBTB38 is involved in cell regulation, proliferation and apoptosis, whereas, functional deficiency of ZBTB38 induces the human neuroblastoma (NB) cell death potentially. To have some insight into the role of ZBTB38 in NB development, high throughput RNA sequencing was performed using the human NB cell line SH-SY5Y with the deletion of ZBTB38. In the present study, 2,438 differentially expressed genes (DEGs) in ZBTB38−/− SH-SY5Y cells were obtained, 83.5% of which was down-regulated. Functional annotation of the DEGs in the Kyoto Encyclopedia of Genes and Genomes database revealed that most of the identified genes were enriched in the neurotrophin TRK receptor signaling pathway, including PI3K/Akt and MAPK signaling pathway. we also observed that ZBTB38 affects expression of CDK4/6, Cyclin E, MDM2, ATM, ATR, PTEN, Gadd45, and PIGs in the p53 signaling pathway. In addition, ZBTB38 knockdown significantly suppresses the expression of autophagy-related key genes including PIK3C2A and RB1CC1. The present meeting provides evidence to molecular mechanism of ZBTB38 modulating NB development and targeted anti-tumor therapies.
format: application/pdf
format: text/html
creator: Jie Chen
creator: Chaofeng Xing
creator: Li Yan
creator: Yabing Wang
creator: Haosen Wang
creator: Zongmeng Zhang
creator: Daolun Yu
creator: Jie Li
creator: Honglin Li
creator: Jun Li
creator: Yafei Cai
subject: Bioinformatics
subject: Cell Biology
subject: Genomics
subject: Nephrology
subject: Oncology
description: doi:10.7717/peerj.6352
publisher: PeerJ Inc.
rights: © 2019 Chen et al.
abstract: ZBTB38 belongs to the zinc finger protein family and contains the typical BTB domains. As a transcription factor, ZBTB38 is involved in cell regulation, proliferation and apoptosis, whereas, functional deficiency of ZBTB38 induces the human neuroblastoma (NB) cell death potentially. To have some insight into the role of ZBTB38 in NB development, high throughput RNA sequencing was performed using the human NB cell line SH-SY5Y with the deletion of ZBTB38. In the present study, 2,438 differentially expressed genes (DEGs) in ZBTB38−/− SH-SY5Y cells were obtained, 83.5% of which was down-regulated. Functional annotation of the DEGs in the Kyoto Encyclopedia of Genes and Genomes database revealed that most of the identified genes were enriched in the neurotrophin TRK receptor signaling pathway, including PI3K/Akt and MAPK signaling pathway. we also observed that ZBTB38 affects expression of CDK4/6, Cyclin E, MDM2, ATM, ATR, PTEN, Gadd45, and PIGs in the p53 signaling pathway. In addition, ZBTB38 knockdown significantly suppresses the expression of autophagy-related key genes including PIK3C2A and RB1CC1. The present meeting provides evidence to molecular mechanism of ZBTB38 modulating NB development and targeted anti-tumor therapies.
bibliographic citation: Chen et al. (2019) Transcriptome profiling reveals the role of ZBTB38 knock-down in human neuroblastoma. PeerJ 7:e6352 https://doi.org/10.7717/peerj.6352
date submitted: 2018-09-25
date accepted: 2018-12-27
issued: 2019-01-24
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Chen
  given name: Jie
author list: Agent
  family name: Xing
  given name: Chaofeng
author list: Agent
  family name: Yan
  given name: Li
author list: Agent
  family name: Wang
  given name: Yabing
author list: Agent
  family name: Wang
  given name: Haosen
author list: Agent
  family name: Zhang
  given name: Zongmeng
author list: Agent
  family name: Yu
  given name: Daolun
author list: Agent
  family name: Li
  given name: Jie
author list: Agent
  family name: Li
  given name: Honglin
author list: Agent
  family name: Li
  given name: Jun
author list: Agent
  family name: Cai
  given name: Yafei
doi: 10.7717/peerj.6352
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-01-24
copyright: © 2019 Chen et al.
attribution name: Chen et al.

Genome-wide characterization and expression analyses of the MYB superfamily genes during developmental stages in Chinese jujube
type: item
type: AcademicArticle
description: The MYB transcription factor (TF) superfamily, one of the largest gene superfamilies, regulates a variety of physiological processes in plants. Although many MYB superfamily genes have been identified in plants, the MYB TFs in Chinese jujube (Ziziphus jujuba Mill.) have not been fully identified and characterized. Additionally, the functions of these genes remain unclear. In total, we identified 171 MYB superfamily genes in jujube and divided them into five subfamilies containing 99 genes of the R2R3-MYB subfamily, 58 genes of the MYB-related subfamily, four genes of the R1R2R3-MYB subfamily, one gene of the 4R-MYB subfamily, and nine genes of the atypical MYB subfamily. The 99 R2R3-MYB genes of jujube were divided into 35 groups, C1–C35, and the 58 MYB-related genes were divided into the following groups: the R-R-type, CCA1-like, I-box-binding-like, TBP-like, CPC-like, and Chinese jujube-specific groups. ZjMYB genes in jujube were well supported by additional highly conserved motifs and exon/intron structures. Most R1 repeats of MYB-related proteins comprised the R2 repeat and had highly conserved EED and EEE residue groups in jujube. Three tandem duplicated gene pairs were found on 12 chromosomes in jujube. According to an expression analysis of 126 ZjMYB genes, MYB-related genes played important roles in jujube development and fruit-related biological processes. The total flavonoid content of jujube fruit decreased as ripening progressed. A total of 93 expressed genes were identified in the RNA-sequencing data from jujube fruit, and 56 ZjMYB members presented significant correlations with total flavonoid contents by correlation analysis. Five pairs of paralogous MYB genes within jujube were composed of nine jujube MYB genes. A total of 14 ZjMYB genes had the same homology to the MYB genes of Arabidopsis and peach, indicating that these 14 MYB genes and their orthologs probably existed before the ancestral divergence of the MYB superfamily. We used a synteny analy…
format: application/pdf
format: text/html
creator: Ji Qing
creator: Wang Dawei
creator: Zhou Jun
creator: Xu Yulan
creator: Shen Bingqi
creator: Zhou Fan
subject: Bioinformatics
subject: Genomics
subject: Molecular Biology
subject: Plant Science
description: doi:10.7717/peerj.6353
publisher: PeerJ Inc.
rights: © 2019 Qing et al.
abstract: The MYB transcription factor (TF) superfamily, one of the largest gene superfamilies, regulates a variety of physiological processes in plants. Although many MYB superfamily genes have been identified in plants, the MYB TFs in Chinese jujube (Ziziphus jujuba Mill.) have not been fully identified and characterized. Additionally, the functions of these genes remain unclear. In total, we identified 171 MYB superfamily genes in jujube and divided them into five subfamilies containing 99 genes of the R2R3-MYB subfamily, 58 genes of the MYB-related subfamily, four genes of the R1R2R3-MYB subfamily, one gene of the 4R-MYB subfamily, and nine genes of the atypical MYB subfamily. The 99 R2R3-MYB genes of jujube were divided into 35 groups, C1–C35, and the 58 MYB-related genes were divided into the following groups: the R-R-type, CCA1-like, I-box-binding-like, TBP-like, CPC-like, and Chinese jujube-specific groups. ZjMYB genes in jujube were well supported by additional highly conserved motifs and exon/intron structures. Most R1 repeats of MYB-related proteins comprised the R2 repeat and had highly conserved EED and EEE residue groups in jujube. Three tandem duplicated gene pairs were found on 12 chromosomes in jujube. According to an expression analysis of 126 ZjMYB genes, MYB-related genes played important roles in jujube development and fruit-related biological processes. The total flavonoid content of jujube fruit decreased as ripening progressed. A total of 93 expressed genes were identified in the RNA-sequencing data from jujube fruit, and 56 ZjMYB members presented significant correlations with total flavonoid contents by correlation analysis. Five pairs of paralogous MYB genes within jujube were composed of nine jujube MYB genes. A total of 14 ZjMYB genes had the same homology to the MYB genes of Arabidopsis and peach, indicating that these 14 MYB genes and their orthologs probably existed before the ancestral divergence of the MYB superfamily. We used a synteny analy…
bibliographic citation: Qing et al. (2019) Genome-wide characterization and expression analyses of the MYB superfamily genes during developmental stages in Chinese jujube. PeerJ 7:e6353 https://doi.org/10.7717/peerj.6353
date submitted: 2018-10-16
date accepted: 2018-12-27
issued: 2019-01-24
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Qing
  given name: Ji
author list: Agent
  family name: Dawei
  given name: Wang
author list: Agent
  family name: Jun
  given name: Zhou
author list: Agent
  family name: Yulan
  given name: Xu
author list: Agent
  family name: Bingqi
  given name: Shen
author list: Agent
  family name: Fan
  given name: Zhou
doi: 10.7717/peerj.6353
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-01-24
copyright: © 2019 Qing et al.
attribution name: Qing et al.

Exploring wearable sensors as an alternative to marker-based motion capture in the pitching delivery
type: item
type: AcademicArticle
description: Background Improvements in data processing, increased understanding of the biomechanical background behind kinetics and kinematics, and technological advancements in inertial measurement unit (IMU) sensors have enabled high precision in the measurement of joint angles and acceleration on human subjects. This has resulted in new devices that reportedly measure joint angles, arm speed, and stresses to the pitching arms of baseball players. This study seeks to validate one such sensor, the MotusBASEBALL unit, with a marker-based motion capture laboratory. Hypothesis We hypothesize that the joint angle measurements (“arm slot” and “shoulder rotation”) of the MotusBASEBALL device will hold a statistically significant level of reliability and accuracy, but that the “arm speed” and “stress” metrics will not be accurate due to limitations in IMU technology. Methods A total of 10 healthy subjects threw five to seven fastballs followed by five to seven breaking pitches (slider or curveball) in the motion capture lab. Subjects wore retroreflective markers and the MotusBASEBALL sensor simultaneously. Results It was found that the arm slot (R = 0.975, P < 0.001), shoulder rotation (R = 0.749, P < 0.001), and stress (R = 0.667, P = 0.001 when compared to elbow torque; R = 0.653, P = 0.002 when compared to shoulder torque) measurements were all significantly correlated with the results from the motion capture lab. Arm speed showed significant correlations to shoulder internal rotation speed (R = 0.668, P = 0.001) and shoulder velocity magnitude (R = 0.659, P = 0.002). For the entire sample, arm slot and shoulder rotation measurements were on a similar scale, or within 5–15% in absolute value, of magnitude to measurements from the motion capture test, averaging eight degrees less (12.9% relative differences) and nine degrees (5.4%) less, respectively. Arm speed had a much larger difference, averaging 3,745 deg/s (80.2%) lower than shoulder internal rotation velocity, and 3,891 deg/…
format: application/pdf
format: text/html
creator: Kyle J. Boddy
creator: Joseph A. Marsh
creator: Alex Caravan
creator: Kyle E. Lindley
creator: John O. Scheffey
creator: Michael E. O’Connell
subject: Anatomy and Physiology
subject: Kinesiology
description: doi:10.7717/peerj.6365
publisher: PeerJ Inc.
rights: © 2019 Boddy et al.
abstract: Background Improvements in data processing, increased understanding of the biomechanical background behind kinetics and kinematics, and technological advancements in inertial measurement unit (IMU) sensors have enabled high precision in the measurement of joint angles and acceleration on human subjects. This has resulted in new devices that reportedly measure joint angles, arm speed, and stresses to the pitching arms of baseball players. This study seeks to validate one such sensor, the MotusBASEBALL unit, with a marker-based motion capture laboratory. Hypothesis We hypothesize that the joint angle measurements (“arm slot” and “shoulder rotation”) of the MotusBASEBALL device will hold a statistically significant level of reliability and accuracy, but that the “arm speed” and “stress” metrics will not be accurate due to limitations in IMU technology. Methods A total of 10 healthy subjects threw five to seven fastballs followed by five to seven breaking pitches (slider or curveball) in the motion capture lab. Subjects wore retroreflective markers and the MotusBASEBALL sensor simultaneously. Results It was found that the arm slot (R = 0.975, P < 0.001), shoulder rotation (R = 0.749, P < 0.001), and stress (R = 0.667, P = 0.001 when compared to elbow torque; R = 0.653, P = 0.002 when compared to shoulder torque) measurements were all significantly correlated with the results from the motion capture lab. Arm speed showed significant correlations to shoulder internal rotation speed (R = 0.668, P = 0.001) and shoulder velocity magnitude (R = 0.659, P = 0.002). For the entire sample, arm slot and shoulder rotation measurements were on a similar scale, or within 5–15% in absolute value, of magnitude to measurements from the motion capture test, averaging eight degrees less (12.9% relative differences) and nine degrees (5.4%) less, respectively. Arm speed had a much larger difference, averaging 3,745 deg/s (80.2%) lower than shoulder internal rotation velocity, and 3,891 deg/…
bibliographic citation: Boddy et al. (2019) Exploring wearable sensors as an alternative to marker-based motion capture in the pitching delivery. PeerJ 7:e6365 https://doi.org/10.7717/peerj.6365
date submitted: 2018-07-10
date accepted: 2018-12-30
issued: 2019-01-24
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Boddy
  given name: Kyle J.
author list: Agent
  family name: Marsh
  given name: Joseph A.
author list: Agent
  family name: Caravan
  given name: Alex
author list: Agent
  family name: Lindley
  given name: Kyle E.
author list: Agent
  family name: Scheffey
  given name: John O.
author list: Agent
  family name: O’Connell
  given name: Michael E.
doi: 10.7717/peerj.6365
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-01-24
copyright: © 2019 Boddy et al.
attribution name: Boddy et al.

Reproductive pattern and population dynamics of commercial red swamp crayfish (Procambarus clarkii) from China: implications for sustainable aquaculture management
type: item
type: AcademicArticle
description: Background The red swamp crayfish, Procambarus clarkii (Girard, 1852), is one of the most promising freshwater species for aquaculture in China. Understanding its reproductive pattern and population dynamics is crucial for sustainable management, but there is currently a lack of fundamental knowledge of commercial P. clarkii populations. Therefore, the purpose of this study was to investigate the reproductive pattern and population dynamics of commercial P. clarkii throughout the yearly cycle. Methods A total of 2,051 crayfish (1,012 females and 1,039 males) were collected from March 2016 to February 2017 in the area of Selection and Reproduction Center of Crayfish. The reproductive pattern was evaluated by the gonadosomatic index (GSI), hepatosomatic index (HSI), ovarian development and fecundity. Growth, mortality rates and exploitation rate were estimated by electronic length frequency analysis by R package “TropFishR” based on data of cephalothorax length (CTL). Results Our results demonstrated that spawning activities of P. clarkii took place from September to November, with a mean fecundity of 429 ± 9 eggs per female. There were two recruitments yearly, a major one from October to November and a minor one from March to May. With respect to population growth, five growth cohorts were identified for both females and males. Crayfish grew faster but attained smaller asymptotic maximum CTL as indicated by higher growth coefficient (K), growth parameter index (Ø′) and lower asymptotic CTL (Linf). The estimates of total mortality rate (Z), natural mortality rate (M) and fishing mortality rate (F) were 1.93, 1.02, 0.91 year−1 for females and 2.32, 0.93, 1.39 year−1 for males, which showed that the mortality of male crayfish was mainly caused by fishing. The estimates of exploitation rate (E) indicated that male crayfish were overexploited, with the values of 0.47 and 0.60 year−1 for females and males, respectively. Discussion P. clarkii spawned from September to Novem…
format: application/pdf
format: text/html
creator: Shiyu Jin
creator: Lisa Jacquin
creator: Mantang Xiong
creator: Ruojing Li
creator: Sovan Lek
creator: Wei Li
creator: Tanglin Zhang
subject: Aquaculture, Fisheries and Fish Science
subject: Ecology
subject: Zoology
subject: Freshwater Biology
description: doi:10.7717/peerj.6214
publisher: PeerJ Inc.
rights: © 2019 Jin et al.
abstract: Background The red swamp crayfish, Procambarus clarkii (Girard, 1852), is one of the most promising freshwater species for aquaculture in China. Understanding its reproductive pattern and population dynamics is crucial for sustainable management, but there is currently a lack of fundamental knowledge of commercial P. clarkii populations. Therefore, the purpose of this study was to investigate the reproductive pattern and population dynamics of commercial P. clarkii throughout the yearly cycle. Methods A total of 2,051 crayfish (1,012 females and 1,039 males) were collected from March 2016 to February 2017 in the area of Selection and Reproduction Center of Crayfish. The reproductive pattern was evaluated by the gonadosomatic index (GSI), hepatosomatic index (HSI), ovarian development and fecundity. Growth, mortality rates and exploitation rate were estimated by electronic length frequency analysis by R package “TropFishR” based on data of cephalothorax length (CTL). Results Our results demonstrated that spawning activities of P. clarkii took place from September to November, with a mean fecundity of 429 ± 9 eggs per female. There were two recruitments yearly, a major one from October to November and a minor one from March to May. With respect to population growth, five growth cohorts were identified for both females and males. Crayfish grew faster but attained smaller asymptotic maximum CTL as indicated by higher growth coefficient (K), growth parameter index (Ø′) and lower asymptotic CTL (Linf). The estimates of total mortality rate (Z), natural mortality rate (M) and fishing mortality rate (F) were 1.93, 1.02, 0.91 year−1 for females and 2.32, 0.93, 1.39 year−1 for males, which showed that the mortality of male crayfish was mainly caused by fishing. The estimates of exploitation rate (E) indicated that male crayfish were overexploited, with the values of 0.47 and 0.60 year−1 for females and males, respectively. Discussion P. clarkii spawned from September to Novem…
bibliographic citation: Jin et al. (2019) Reproductive pattern and population dynamics of commercial red swamp crayfish (Procambarus clarkii) from China: implications for sustainable aquaculture management. PeerJ 7:e6214 https://doi.org/10.7717/peerj.6214
date submitted: 2018-09-21
date accepted: 2018-12-04
issued: 2019-01-23
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Jin
  given name: Shiyu
author list: Agent
  family name: Jacquin
  given name: Lisa
author list: Agent
  family name: Xiong
  given name: Mantang
author list: Agent
  family name: Li
  given name: Ruojing
author list: Agent
  family name: Lek
  given name: Sovan
author list: Agent
  family name: Li
  given name: Wei
author list: Agent
  family name: Zhang
  given name: Tanglin
doi: 10.7717/peerj.6214
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-01-23
copyright: ©2019 Jin et al.
attribution name: Jin et al.

Temporal whole field sawtooth flicker without a spatial component elicits a myopic shift following optical defocus irrespective of waveform direction in chicks
type: item
type: AcademicArticle
description: Purpose Myopia (short-sightedness) is the commonest visual disorder and greatest risk factor for sight threatening secondary pathologies. Myopia and hyperopia can be induced in animal models by rearing with optical lens defocus of opposite sign. The degree of refractive compensation to lens-induced defocus in chicks has been shown to be modified by directionally drifting sawtooth spatio-temporal luminance diamond plaids, with Fast-ON sawtooth spatio-temporal luminance profiles inhibiting the myopic shift in response to negative lenses, and Fast-OFF profiles inhibiting the hyperopic shift in response to positive lenses. What is unknown is whether similar sign-of-defocus dependent results produced by spatio-temporal modulation of sawtooth patterns could be achieved by rearing chicks under whole field low temporal frequency sawtooth luminance profiles at 1 or 4 Hz without a spatial component, or whether such stimuli would indiscriminately elicit a myopic shift such as that previously shown with symmetrical (or near-symmetrical) low frequency flicker across a range of species. Methods Hatchling chicks (n = 166) were reared from days five to nine under one of three defocus conditions (No Lens, +10D lens, or −10D lens) and five light conditions (No Flicker, 1 Hz Fast-ON/Slow-OFF sawtooth flicker, 4 Hz Fast-ON/Slow-OFF sawtooth flicker, 1 Hz Fast-OFF/Slow-ON sawtooth flicker, or 4Hz Fast-OFF/Slow-ON sawtooth flicker). The sawtooth flicker was produced by light emitting diodes (white LEDs, 1.2 –183 Lux), and had no measurable dark phase. Biometrics (refraction and ocular axial dimensions) were measured on day nine. Results Both 1 Hz and 4 Hz Fast-ON and Fast-OFF sawtooth flicker induced an increase in vitreous chamber depth that was greater in the presence of negative compared to positive lens defocus. Both sawtooth profiles at both temporal frequencies inhibited the hyperopic shift in response to +10D lenses, whilst full myopic compensation (or over-compensation) in respon…
format: application/pdf
format: text/html
creator: Melanie J. Murphy
creator: Nina Riddell
creator: David P. Crewther
creator: David Simpson
creator: Sheila G. Crewther
subject: Neuroscience
subject: Ophthalmology
description: doi:10.7717/peerj.6277
publisher: PeerJ Inc.
rights: © 2019 Murphy et al.
abstract: Purpose Myopia (short-sightedness) is the commonest visual disorder and greatest risk factor for sight threatening secondary pathologies. Myopia and hyperopia can be induced in animal models by rearing with optical lens defocus of opposite sign. The degree of refractive compensation to lens-induced defocus in chicks has been shown to be modified by directionally drifting sawtooth spatio-temporal luminance diamond plaids, with Fast-ON sawtooth spatio-temporal luminance profiles inhibiting the myopic shift in response to negative lenses, and Fast-OFF profiles inhibiting the hyperopic shift in response to positive lenses. What is unknown is whether similar sign-of-defocus dependent results produced by spatio-temporal modulation of sawtooth patterns could be achieved by rearing chicks under whole field low temporal frequency sawtooth luminance profiles at 1 or 4 Hz without a spatial component, or whether such stimuli would indiscriminately elicit a myopic shift such as that previously shown with symmetrical (or near-symmetrical) low frequency flicker across a range of species. Methods Hatchling chicks (n = 166) were reared from days five to nine under one of three defocus conditions (No Lens, +10D lens, or −10D lens) and five light conditions (No Flicker, 1 Hz Fast-ON/Slow-OFF sawtooth flicker, 4 Hz Fast-ON/Slow-OFF sawtooth flicker, 1 Hz Fast-OFF/Slow-ON sawtooth flicker, or 4Hz Fast-OFF/Slow-ON sawtooth flicker). The sawtooth flicker was produced by light emitting diodes (white LEDs, 1.2 –183 Lux), and had no measurable dark phase. Biometrics (refraction and ocular axial dimensions) were measured on day nine. Results Both 1 Hz and 4 Hz Fast-ON and Fast-OFF sawtooth flicker induced an increase in vitreous chamber depth that was greater in the presence of negative compared to positive lens defocus. Both sawtooth profiles at both temporal frequencies inhibited the hyperopic shift in response to +10D lenses, whilst full myopic compensation (or over-compensation) in respon…
bibliographic citation: Murphy et al. (2019) Temporal whole field sawtooth flicker without a spatial component elicits a myopic shift following optical defocus irrespective of waveform direction in chicks. PeerJ 7:e6277 https://doi.org/10.7717/peerj.6277
date submitted: 2018-03-12
date accepted: 2018-12-11
issued: 2019-01-23
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Murphy
  given name: Melanie J.
author list: Agent
  family name: Riddell
  given name: Nina
author list: Agent
  family name: Crewther
  given name: David P.
author list: Agent
  family name: Simpson
  given name: David
author list: Agent
  family name: Crewther
  given name: Sheila G.
doi: 10.7717/peerj.6277
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-01-23
copyright: ©2019 Murphy et al.
attribution name: Murphy et al.

The use of one-stage meta-analytic method based on individual participant data for binary adverse events under the rule of three: a simulation study
type: item
type: AcademicArticle
description: Objective In evidence synthesis practice, dealing with binary rare adverse events (AEs) is a challenging problem. The pooled estimates for rare AEs through traditional inverse variance (IV), Mantel-Haenszel (MH), and Yusuf-Peto (Peto) methods are suboptimal, as the biases tend to be large. We proposed the “one-stage” approach based on multilevel variance component logistic regression (MVCL) to handle this problem. Methods We used simulations to generate trials of individual participant data (IPD) with a series of predefined parameters. We compared the performance of the MVCL “one-stage” approach and the five classical methods (fixed/random effect IV, fixed/random effect MH, and Peto) for rare binary AEs under different scenarios, which included different sample size setting rules, effect sizes, between-study heterogeneity, and numbers of studies in each meta-analysis. The percentage bias, mean square error (MSE), coverage probability, and average width of the 95% confidence intervals were used as performance indicators. Results We set 52 scenarios and each scenario was simulated 1,000 times. Under the rule of three (a sample size setting rule to ensure a 95% chance of detecting at least one AE case), the MVCL “one-stage” IPD method had the lowest percentage bias in most of the situations and the bias remained at a very low level (<10%), when compared to IV, MH, and Peto methods. In addition, the MVCL “one-stage” IPD method generally had the lowest MSE and the narrowest average width of 95% confidence intervals. However, it did not show better coverage probability over the other five methods. Conclusions The MVCL “one-stage” IPD meta-analysis is a useful method to handle binary rare events and superior compared to traditional methods under the rule of three. Further meta-analyses may take account of the “one-stage” IPD method for pooling rare event data.
format: application/pdf
format: text/html
creator: Liang-Liang Cheng
creator: Ke Ju
creator: Rui-Lie Cai
creator: Chang Xu
subject: Clinical Trials
subject: Epidemiology
subject: Evidence Based Medicine
subject: Statistics
description: doi:10.7717/peerj.6295
publisher: PeerJ Inc.
rights: © 2019 Cheng et al.
abstract: Objective In evidence synthesis practice, dealing with binary rare adverse events (AEs) is a challenging problem. The pooled estimates for rare AEs through traditional inverse variance (IV), Mantel-Haenszel (MH), and Yusuf-Peto (Peto) methods are suboptimal, as the biases tend to be large. We proposed the “one-stage” approach based on multilevel variance component logistic regression (MVCL) to handle this problem. Methods We used simulations to generate trials of individual participant data (IPD) with a series of predefined parameters. We compared the performance of the MVCL “one-stage” approach and the five classical methods (fixed/random effect IV, fixed/random effect MH, and Peto) for rare binary AEs under different scenarios, which included different sample size setting rules, effect sizes, between-study heterogeneity, and numbers of studies in each meta-analysis. The percentage bias, mean square error (MSE), coverage probability, and average width of the 95% confidence intervals were used as performance indicators. Results We set 52 scenarios and each scenario was simulated 1,000 times. Under the rule of three (a sample size setting rule to ensure a 95% chance of detecting at least one AE case), the MVCL “one-stage” IPD method had the lowest percentage bias in most of the situations and the bias remained at a very low level (<10%), when compared to IV, MH, and Peto methods. In addition, the MVCL “one-stage” IPD method generally had the lowest MSE and the narrowest average width of 95% confidence intervals. However, it did not show better coverage probability over the other five methods. Conclusions The MVCL “one-stage” IPD meta-analysis is a useful method to handle binary rare events and superior compared to traditional methods under the rule of three. Further meta-analyses may take account of the “one-stage” IPD method for pooling rare event data.
bibliographic citation: Cheng et al. (2019) The use of one-stage meta-analytic method based on individual participant data for binary adverse events under the rule of three: a simulation study. PeerJ 7:e6295 https://doi.org/10.7717/peerj.6295
date submitted: 2018-07-02
date accepted: 2018-12-15
issued: 2019-01-23
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Cheng
  given name: Liang-Liang
author list: Agent
  family name: Ju
  given name: Ke
author list: Agent
  family name: Cai
  given name: Rui-Lie
author list: Agent
  family name: Xu
  given name: Chang
doi: 10.7717/peerj.6295
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-01-23
copyright: © 2019 Cheng et al.
attribution name: Cheng et al.

GenoDup Pipeline: a tool to detect genome duplication using the dS-based method
type: item
type: AcademicArticle
description: Understanding whole genome duplication (WGD), or polyploidy, is fundamental to investigating the origin and diversification of organisms in evolutionary biology. The wealth of genomic data generated by next generation sequencing (NGS) has resulted in an urgent need for handy and accurate tools to detect WGD. Here, I present a useful and user-friendly pipeline called GenoDup for inferring WGD using the dS-based method. I have successfully applied GenoDup to identify WGD in empirical data from both plants and animals. The GenoDup Pipeline provides a reliable and useful tool to infer WGD from NGS data.
format: application/pdf
format: text/html
creator: Yafei Mao
subject: Bioinformatics
subject: Evolutionary Studies
subject: Genomics
description: doi:10.7717/peerj.6303
publisher: PeerJ Inc.
rights: © 2019 Mao
abstract: Understanding whole genome duplication (WGD), or polyploidy, is fundamental to investigating the origin and diversification of organisms in evolutionary biology. The wealth of genomic data generated by next generation sequencing (NGS) has resulted in an urgent need for handy and accurate tools to detect WGD. Here, I present a useful and user-friendly pipeline called GenoDup for inferring WGD using the dS-based method. I have successfully applied GenoDup to identify WGD in empirical data from both plants and animals. The GenoDup Pipeline provides a reliable and useful tool to infer WGD from NGS data.
bibliographic citation: Mao (2019) GenoDup Pipeline: a tool to detect genome duplication using the dS-based method. PeerJ 7:e6303 https://doi.org/10.7717/peerj.6303
date submitted: 2018-10-05
date accepted: 2018-12-16
issued: 2019-01-23
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Mao
  given name: Yafei
doi: 10.7717/peerj.6303
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-01-23
copyright: ©2019 Mao
attribution name: Mao

P-curve accurately rejects evidence for homeopathic ultramolecular dilutions
type: item
type: AcademicArticle
description: Background P-curve has been proposed as a statistical test of evidential value. The distributions of sets of statistically significant p-values are tested for skewness. P-curves of true effects are right-skewed, with greater density at lower p-values than higher p-values. Analyses of null effects result in a flat or left-skewed distribution. The accuracy of p-curve has not been tested using published research analyses of a null effect. We examined whether p-curve accurately rejects a set of significant p-values obtained for a nonexistent effect. Methods Homeopathic ultramolecular dilutions are medicinal preparations with active substances diluted beyond Avogadro’s number. Such dilute mixtures are unlikely to contain a single molecule of an active substance. We tested whether p-curve accurately rejects the evidential value of significant results obtained in placebo-controlled clinical trials of homeopathic ultramolecular dilutions. Results P-curve accurately rejected the evidential value of significant results obtained in placebo-controlled clinical trials of ultramolecular dilutions. Robustness testing using alternate p-values yielded similar results. Conclusion Our results suggest that p-curve can accurately detect when sets of statistically significant results lack evidential value.
format: application/pdf
format: text/html
creator: Samuel Reisman
creator: Mostafa Balboul
creator: Tashzna Jones
subject: Science Policy
subject: Statistics
description: doi:10.7717/peerj.6318
publisher: PeerJ Inc.
rights: © 2019 Reisman et al.
abstract: Background P-curve has been proposed as a statistical test of evidential value. The distributions of sets of statistically significant p-values are tested for skewness. P-curves of true effects are right-skewed, with greater density at lower p-values than higher p-values. Analyses of null effects result in a flat or left-skewed distribution. The accuracy of p-curve has not been tested using published research analyses of a null effect. We examined whether p-curve accurately rejects a set of significant p-values obtained for a nonexistent effect. Methods Homeopathic ultramolecular dilutions are medicinal preparations with active substances diluted beyond Avogadro’s number. Such dilute mixtures are unlikely to contain a single molecule of an active substance. We tested whether p-curve accurately rejects the evidential value of significant results obtained in placebo-controlled clinical trials of homeopathic ultramolecular dilutions. Results P-curve accurately rejected the evidential value of significant results obtained in placebo-controlled clinical trials of ultramolecular dilutions. Robustness testing using alternate p-values yielded similar results. Conclusion Our results suggest that p-curve can accurately detect when sets of statistically significant results lack evidential value.
bibliographic citation: Reisman et al. (2019) P-curve accurately rejects evidence for homeopathic ultramolecular dilutions. PeerJ 7:e6318 https://doi.org/10.7717/peerj.6318
date submitted: 2018-10-12
date accepted: 2018-12-16
issued: 2019-01-23
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Reisman
  given name: Samuel
author list: Agent
  family name: Balboul
  given name: Mostafa
author list: Agent
  family name: Jones
  given name: Tashzna
doi: 10.7717/peerj.6318
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-01-23
copyright: ©2019 Reisman et al.
attribution name: Reisman et al.

Comparison of automatic airway analysis function of Invivo5 and Romexis software
type: item
type: AcademicArticle
description: Background Visualization and calculation of the airway dimensions are important because an increase of airway resistance may lead to life-threatening emergencies. The visualization and calculation of the airway are possible using radiography technique with their advance software. The aim of this study was to compare and to test the reliability of the measurement of the upper airway volume and minimum area using airway analysis function in two software. Methods The sample consisted of 11 cone-beam computed tomography (CBCT) scans data, evaluated using the Invivo5 (Anatomage) and Romexis (version 3.8.2.R, Planmeca) software which afford image reconstruction, and airway analysis. The measurements were done twice with one week gap between the two measurements. The measurement obtained was analyzed with t-tests and intraclass correlation coefficient (ICC), with confidence intervals (CI) was set at 95%. Results From the analysis, the mean reading of volume and minimum area is not significantly different between Invivo5 and Romexis. Excellent intrarater reliability values were found for the both measurement on both software, with ICC values ranging from 0.940 to 0.998. Discussion The results suggested that both software can be used in further studies to investigate upper airway, thereby contributing to the diagnosis of upper airway obstructions.
format: application/pdf
format: text/html
creator: Noorshaida Kamaruddin
creator: Firdaus Daud
creator: Asilah Yusof
creator: Mohd Ezane Aziz
creator: Zainul A. Rajion
subject: Dentistry
subject: Radiology and Medical Imaging
description: doi:10.7717/peerj.6319
publisher: PeerJ Inc.
rights: © 2019 Kamaruddin et al.
abstract: Background Visualization and calculation of the airway dimensions are important because an increase of airway resistance may lead to life-threatening emergencies. The visualization and calculation of the airway are possible using radiography technique with their advance software. The aim of this study was to compare and to test the reliability of the measurement of the upper airway volume and minimum area using airway analysis function in two software. Methods The sample consisted of 11 cone-beam computed tomography (CBCT) scans data, evaluated using the Invivo5 (Anatomage) and Romexis (version 3.8.2.R, Planmeca) software which afford image reconstruction, and airway analysis. The measurements were done twice with one week gap between the two measurements. The measurement obtained was analyzed with t-tests and intraclass correlation coefficient (ICC), with confidence intervals (CI) was set at 95%. Results From the analysis, the mean reading of volume and minimum area is not significantly different between Invivo5 and Romexis. Excellent intrarater reliability values were found for the both measurement on both software, with ICC values ranging from 0.940 to 0.998. Discussion The results suggested that both software can be used in further studies to investigate upper airway, thereby contributing to the diagnosis of upper airway obstructions.
bibliographic citation: Kamaruddin et al. (2019) Comparison of automatic airway analysis function of Invivo5 and Romexis software. PeerJ 7:e6319 https://doi.org/10.7717/peerj.6319
date submitted: 2018-03-05
date accepted: 2018-12-17
issued: 2019-01-23
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Kamaruddin
  given name: Noorshaida
author list: Agent
  family name: Daud
  given name: Firdaus
author list: Agent
  family name: Yusof
  given name: Asilah
author list: Agent
  family name: Aziz
  given name: Mohd Ezane
author list: Agent
  family name: Rajion
  given name: Zainul A.
doi: 10.7717/peerj.6319
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-01-23
copyright: ©2019 Kamaruddin et al.
attribution name: Kamaruddin et al.

The sensitivity and specificity of methylene blue spray to identify the parathyroid gland during thyroidectomy
type: item
type: AcademicArticle
description: Background Hypocalcemia is a common complication of thyroidectomy resulting from an injury to the parathyroid gland. Methylene blue, which is a medication and dye that has been used for more than a century, is safe and readily available. The previous study has found that methylene blue spray on the surgical field is absorbed by the parathyroid gland faster than in the perithyroidal area. This study was aimed to evaluate the diagnostic value of methylene blue spray to identify the parathyroid gland during thyroid lobectomy. Methods Patients who underwent thyroid lobectomy were recruited. After the recurrent laryngeal nerve was identified, methylene blue was sprayed onto the thyroid bed. After 5 min, the thyroid bed was inspected for areas in which the blue color had been rapidly absorbed. Biopsies were conducted for histopathology at both the stained area and the area in which the color had faded. The sensitivity, specificity, positive predictive value (PPV), and negative predictive value (NPV) were calculated. Results A total of 47 patients participated in this study. The sensitivity of methylene blue spray to identify the parathyroid gland during thyroid lobectomy was 92.31% (95% CI [63.97–99.81]) and specificity was 56.79% (95% CI [45.31–67.76]). The PPV was 25.53% (95% CI [20.34–31.53]) and NPV was 97.87% (95% CI [87.39–99.67]). There were no patients with post-operative hypocalcemia, allergic reactions to the methylene blue, or methylene blue toxicity. Conclusion The methylene blue spray could serve as a screening tool for identification of the parathyroid gland.
format: application/pdf
format: text/html
creator: Patorn Piromchai
creator: Thipphailin Juengtrakool
creator: Supawan Laohasiriwong
creator: Pornthep Kasemsiri
creator: Piti Ungarereevittaya
subject: Clinical Trials
subject: Epidemiology
subject: Otorhinolaryngology
subject: Surgery and Surgical Specialties
description: doi:10.7717/peerj.6376
publisher: PeerJ Inc.
rights: © 2019 Piromchai et al.
abstract: Background Hypocalcemia is a common complication of thyroidectomy resulting from an injury to the parathyroid gland. Methylene blue, which is a medication and dye that has been used for more than a century, is safe and readily available. The previous study has found that methylene blue spray on the surgical field is absorbed by the parathyroid gland faster than in the perithyroidal area. This study was aimed to evaluate the diagnostic value of methylene blue spray to identify the parathyroid gland during thyroid lobectomy. Methods Patients who underwent thyroid lobectomy were recruited. After the recurrent laryngeal nerve was identified, methylene blue was sprayed onto the thyroid bed. After 5 min, the thyroid bed was inspected for areas in which the blue color had been rapidly absorbed. Biopsies were conducted for histopathology at both the stained area and the area in which the color had faded. The sensitivity, specificity, positive predictive value (PPV), and negative predictive value (NPV) were calculated. Results A total of 47 patients participated in this study. The sensitivity of methylene blue spray to identify the parathyroid gland during thyroid lobectomy was 92.31% (95% CI [63.97–99.81]) and specificity was 56.79% (95% CI [45.31–67.76]). The PPV was 25.53% (95% CI [20.34–31.53]) and NPV was 97.87% (95% CI [87.39–99.67]). There were no patients with post-operative hypocalcemia, allergic reactions to the methylene blue, or methylene blue toxicity. Conclusion The methylene blue spray could serve as a screening tool for identification of the parathyroid gland.
bibliographic citation: Piromchai et al. (2019) The sensitivity and specificity of methylene blue spray to identify the parathyroid gland during thyroidectomy. PeerJ 7:e6376 https://doi.org/10.7717/peerj.6376
date submitted: 2018-10-29
date accepted: 2019-01-02
issued: 2019-01-23
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Piromchai
  given name: Patorn
author list: Agent
  family name: Juengtrakool
  given name: Thipphailin
author list: Agent
  family name: Laohasiriwong
  given name: Supawan
author list: Agent
  family name: Kasemsiri
  given name: Pornthep
author list: Agent
  family name: Ungarereevittaya
  given name: Piti
doi: 10.7717/peerj.6376
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-01-23
copyright: © 2019 Piromchai et al.
attribution name: Piromchai et al.

Shifting faunal baselines through the Quaternary revealed by cave fossils of eastern Australia
type: item
type: AcademicArticle
description: Fossils from caves in the Manning Karst Region, New South Wales, Australia have long been known, but until now have never been assessed for their palaeontological significance. Here, we report on late Quaternary faunal records from eight caves in the region. Extinct Pleistocene megafaunal taxa are recognised in two systems and include giant echidnas (Tachyglossidae gen. et sp. indet.), devils (Sarcophilus laniarius), koalas (Phascolarctos stirtoni), marsupial ‘lions’ (Thylacoleo carnifex), and kangaroos (Macropus giganteus titan). Some caves contain skeletal remains of introduced exotics such as sheep and dogs, but also provide a rich record of small-bodied native species including Eastern Bettongs (Bettongia gaimardi), Eastern Chestnut Mice (Pseudomys gracilicaudatus), and White-footed Rabbit Rats (Conilurus albipes). These endemics are either locally extirpated or have suffered total extinction in the historic period. Their skeletal and dental remains were recorded as unmineralised surface specimens in the caves, indicating that they are recent in age. Extant populations have never been recorded locally, thus, their probable loss from the region in historic times had gone unnoticed in the absence of palaeo-evidence. Our findings suggest that the supposed habitat tolerances of such species have been substantially underestimated. It is highly likely that modern populations have suffered niche contraction since the time of European colonisation of the continent. The local extirpations of several species of digging mammal has likely led to decreased functionality of the current ecosystem.
format: application/pdf
format: text/html
creator: Gilbert J. Price
creator: Julien Louys
creator: Garry K. Smith
creator: Jonathan Cramb
subject: Biodiversity
subject: Paleontology
subject: Zoology
description: doi:10.7717/peerj.6099
publisher: PeerJ Inc.
rights: © 2019 Price et al.
abstract: Fossils from caves in the Manning Karst Region, New South Wales, Australia have long been known, but until now have never been assessed for their palaeontological significance. Here, we report on late Quaternary faunal records from eight caves in the region. Extinct Pleistocene megafaunal taxa are recognised in two systems and include giant echidnas (Tachyglossidae gen. et sp. indet.), devils (Sarcophilus laniarius), koalas (Phascolarctos stirtoni), marsupial ‘lions’ (Thylacoleo carnifex), and kangaroos (Macropus giganteus titan). Some caves contain skeletal remains of introduced exotics such as sheep and dogs, but also provide a rich record of small-bodied native species including Eastern Bettongs (Bettongia gaimardi), Eastern Chestnut Mice (Pseudomys gracilicaudatus), and White-footed Rabbit Rats (Conilurus albipes). These endemics are either locally extirpated or have suffered total extinction in the historic period. Their skeletal and dental remains were recorded as unmineralised surface specimens in the caves, indicating that they are recent in age. Extant populations have never been recorded locally, thus, their probable loss from the region in historic times had gone unnoticed in the absence of palaeo-evidence. Our findings suggest that the supposed habitat tolerances of such species have been substantially underestimated. It is highly likely that modern populations have suffered niche contraction since the time of European colonisation of the continent. The local extirpations of several species of digging mammal has likely led to decreased functionality of the current ecosystem.
bibliographic citation: Price et al. (2019) Shifting faunal baselines through the Quaternary revealed by cave fossils of eastern Australia. PeerJ 6:e6099 https://doi.org/10.7717/peerj.6099
date submitted: 2018-07-02
date accepted: 2018-11-11
issued: 2019-01-22
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Price
  given name: Gilbert J.
author list: Agent
  family name: Louys
  given name: Julien
author list: Agent
  family name: Smith
  given name: Garry K.
author list: Agent
  family name: Cramb
  given name: Jonathan
doi: 10.7717/peerj.6099
volume: 6
issn: 2167-8359
publication name: PeerJ
publication date: 2019-01-22
copyright: © 2019 Price et al.
attribution name: Price et al.

Antimicrobial susceptibility and virulence genes of clinical and environmental isolates of Pseudomonas aeruginosa
type: item
type: AcademicArticle
description: Background Pseudomonas aeruginosa is ubiquitous, has intrinsic antibiotic resistance mechanisms, and is associated with serious hospital-associated infections. It has evolved from being a burn wound infection into a major nosocomial threat. In this study, we compared and correlated the antimicrobial resistance, virulence traits and clonal relatedness between clinical and fresh water environmental isolates of P. aeruginosa. Methods 219 P. aeruginosa isolates were studied: (a) 105 clinical isolates from 1977 to 1985 (n = 52) and 2015 (n = 53), and (b) 114 environmental isolates from different fresh water sources. All isolates were subjected to ERIC-PCR typing, antimicrobial susceptibility testing and virulence factor genes screening. Results Clinical and environmental isolates of P. aeruginosa were genetically heterogenous, with only four clinical isolates showing 100% identical ERIC-PCR patterns to seven environmental isolates. Most of the clinical and environmental isolates were sensitive to almost all of the antipseudomonal drugs, except for ticarcillin/clavulanic acid. Increased resistant isolates was seen in 2015 compared to that of the archived isolates; four MDR strains were detected and all were retrieved in 2015. All clinical isolates retrieved from 1977 to 1985 were susceptible to ceftazidime and ciprofloxacin; but in comparison, the clinical isolates recovered in 2015 exhibited 9.4% resistance to ceftazidime and 5.7% to ciprofloxacin; a rise in resistance to imipenem (3.8% to 7.5%), piperacillin (9.6% to 11.3%) and amikacin (1.9% to 5.7%) and a slight drop in resistance rates to piperacillin/tazobactam (7.7% to 7.5%), ticarcillin/clavulanic acid (19.2% to 18.9%), meropenem (15.4% to 7.5%), doripenem (11.5% to 7.5%), gentamicin (7.7% to 7.5%) and netilmicin (7.7% to 7.5%). Environmental isolates were resistant to piperacillin/tazobactam (1.8%), ciprofloxacin (1.8%), piperacillin (4.4%) and carbapenems (doripenem 11.4%, meropenem 8.8% and imipenem 2.6%). Both…
format: application/pdf
format: text/html
creator: Siew Mun Liew
creator: Ganeswrei Rajasekaram
creator: SD Ampalam Puthucheary
creator: Kek Heng Chua
subject: Microbiology
description: doi:10.7717/peerj.6217
publisher: PeerJ Inc.
rights: © 2019 Liew et al.
abstract: Background Pseudomonas aeruginosa is ubiquitous, has intrinsic antibiotic resistance mechanisms, and is associated with serious hospital-associated infections. It has evolved from being a burn wound infection into a major nosocomial threat. In this study, we compared and correlated the antimicrobial resistance, virulence traits and clonal relatedness between clinical and fresh water environmental isolates of P. aeruginosa. Methods 219 P. aeruginosa isolates were studied: (a) 105 clinical isolates from 1977 to 1985 (n = 52) and 2015 (n = 53), and (b) 114 environmental isolates from different fresh water sources. All isolates were subjected to ERIC-PCR typing, antimicrobial susceptibility testing and virulence factor genes screening. Results Clinical and environmental isolates of P. aeruginosa were genetically heterogenous, with only four clinical isolates showing 100% identical ERIC-PCR patterns to seven environmental isolates. Most of the clinical and environmental isolates were sensitive to almost all of the antipseudomonal drugs, except for ticarcillin/clavulanic acid. Increased resistant isolates was seen in 2015 compared to that of the archived isolates; four MDR strains were detected and all were retrieved in 2015. All clinical isolates retrieved from 1977 to 1985 were susceptible to ceftazidime and ciprofloxacin; but in comparison, the clinical isolates recovered in 2015 exhibited 9.4% resistance to ceftazidime and 5.7% to ciprofloxacin; a rise in resistance to imipenem (3.8% to 7.5%), piperacillin (9.6% to 11.3%) and amikacin (1.9% to 5.7%) and a slight drop in resistance rates to piperacillin/tazobactam (7.7% to 7.5%), ticarcillin/clavulanic acid (19.2% to 18.9%), meropenem (15.4% to 7.5%), doripenem (11.5% to 7.5%), gentamicin (7.7% to 7.5%) and netilmicin (7.7% to 7.5%). Environmental isolates were resistant to piperacillin/tazobactam (1.8%), ciprofloxacin (1.8%), piperacillin (4.4%) and carbapenems (doripenem 11.4%, meropenem 8.8% and imipenem 2.6%). Both…
bibliographic citation: Liew et al. (2019) Antimicrobial susceptibility and virulence genes of clinical and environmental isolates of Pseudomonas aeruginosa. PeerJ 7:e6217 https://doi.org/10.7717/peerj.6217
date submitted: 2018-03-01
date accepted: 2018-12-05
issued: 2019-01-22
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Liew
  given name: Siew Mun
author list: Agent
  family name: Rajasekaram
  given name: Ganeswrei
author list: Agent
  family name: Puthucheary
  given name: SD Ampalam
author list: Agent
  family name: Chua
  given name: Kek Heng
doi: 10.7717/peerj.6217
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-01-22
copyright: ©2019 Liew et al.
attribution name: Liew et al.

Genome-wide analysis of circular RNAs in goat skin fibroblast cells in response to Orf virus infection
type: item
type: AcademicArticle
description: Orf, caused by Orf virus (ORFV), is a globally distributed zoonotic disease responsible for serious economic losses in the agricultural sector. However, the mechanism underlying ORFV infection remains largely unknown. Circular RNAs (circRNAs), a novel type of endogenous non-coding RNAs, play important roles in various pathological processes but their involvement in ORFV infection and host response is unclear. In the current study, whole transcriptome sequencing and small RNA sequencing were performed in ORFV-infected goat skin fibroblast cells and uninfected cells. A total of 151 circRNAs, 341 messenger RNAs (mRNAs), and 56 microRNAs (miRNAs) were differently expressed following ORFV infection. Four circRNAs: circRNA1001, circRNA1684, circRNA3127 and circRNA7880 were validated by qRT-PCR and Sanger sequencing. Gene ontology (GO) analysis indicated that host genes of differently expressed circRNAs were significantly enriched in regulation of inflammatory response, epithelial structure maintenance, positive regulation of cell migration, positive regulation of ubiquitin-protein transferase activity, regulation of ion transmembrane transport, etc. The constructed circRNA-miRNA-mRNA network suggested that circRNAs may function as miRNA sponges indirectly regulating gene expression following ORFV infection. Our study presented the first comprehensive profiles of circRNAs in response to ORFV infection, thus providing new clues for the mechanisms of interactions between ORFV and the host.
format: application/pdf
format: text/html
creator: Feng Pang
creator: Mengmeng Zhang
creator: Xiaojian Yang
creator: Guohua Li
creator: Shu Zhu
creator: Xin Nie
creator: Ruiyong Cao
creator: Xiaohong Yang
creator: Zhenxing Zhang
creator: Haifeng Huang
creator: Baobao Li
creator: Chengqiang Wang
creator: Li Du
creator: Fengyang Wang
subject: Bioinformatics
subject: Molecular Biology
subject: Virology
description: doi:10.7717/peerj.6267
publisher: PeerJ Inc.
rights: © 2019 Pang et al.
abstract: Orf, caused by Orf virus (ORFV), is a globally distributed zoonotic disease responsible for serious economic losses in the agricultural sector. However, the mechanism underlying ORFV infection remains largely unknown. Circular RNAs (circRNAs), a novel type of endogenous non-coding RNAs, play important roles in various pathological processes but their involvement in ORFV infection and host response is unclear. In the current study, whole transcriptome sequencing and small RNA sequencing were performed in ORFV-infected goat skin fibroblast cells and uninfected cells. A total of 151 circRNAs, 341 messenger RNAs (mRNAs), and 56 microRNAs (miRNAs) were differently expressed following ORFV infection. Four circRNAs: circRNA1001, circRNA1684, circRNA3127 and circRNA7880 were validated by qRT-PCR and Sanger sequencing. Gene ontology (GO) analysis indicated that host genes of differently expressed circRNAs were significantly enriched in regulation of inflammatory response, epithelial structure maintenance, positive regulation of cell migration, positive regulation of ubiquitin-protein transferase activity, regulation of ion transmembrane transport, etc. The constructed circRNA-miRNA-mRNA network suggested that circRNAs may function as miRNA sponges indirectly regulating gene expression following ORFV infection. Our study presented the first comprehensive profiles of circRNAs in response to ORFV infection, thus providing new clues for the mechanisms of interactions between ORFV and the host.
bibliographic citation: Pang et al. (2019) Genome-wide analysis of circular RNAs in goat skin fibroblast cells in response to Orf virus infection. PeerJ 7:e6267 https://doi.org/10.7717/peerj.6267
date submitted: 2018-08-27
date accepted: 2018-12-11
issued: 2019-01-22
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Pang
  given name: Feng
author list: Agent
  family name: Zhang
  given name: Mengmeng
author list: Agent
  family name: Yang
  given name: Xiaojian
author list: Agent
  family name: Li
  given name: Guohua
author list: Agent
  family name: Zhu
  given name: Shu
author list: Agent
  family name: Nie
  given name: Xin
author list: Agent
  family name: Cao
  given name: Ruiyong
author list: Agent
  family name: Yang
  given name: Xiaohong
author list: Agent
  family name: Zhang
  given name: Zhenxing
author list: Agent
  family name: Huang
  given name: Haifeng
author list: Agent
  family name: Li
  given name: Baobao
author list: Agent
  family name: Wang
  given name: Chengqiang
author list: Agent
  family name: Du
  given name: Li
author list: Agent
  family name: Wang
  given name: Fengyang
doi: 10.7717/peerj.6267
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-01-22
copyright: ©2019 Pang et al.
attribution name: Pang et al.

Effects of dredging on the vegetation in a small lowland river
type: item
type: AcademicArticle
description: Background Conventional river engineering operations have a substantial influence on the fluvial ecosystem. Regulation and channelization generally reduce the physical heterogeneity of river beds and banks and the heterogeneity of habitats. They determine the character, diversity and species richness of plant communities. The effect of river regulation on vegetation has been repeatedly investigated, but few studies have been conducted within reaches of previously regulated rivers. The aim of this work is to expand and current knowledge about the impact of dredging on the vegetation of a regulated section of a lowland river. Materials & Methods The study included pre-dredging (1 year before) and post-dredging surveys (results 1 and 2 years after dredging). The vegetation was analysed in terms of species composition, origin of species, life forms, distribution of Grime’s life strategies, and selected ecological factors. The Shannon–Wiener biodiversity index (H) and evenness were also analysed in each year of the study. The impact of dredging on the vascular flora was assessed by ‘before-after-control-impact’ (BACI) analysis. Results The number of species and biodiversity as measured by the Shannon–Wiener index (H) increased in the analysed section of the river valley. However, enrichment of the flora was observed only on the floodplain, on the surface of the deposited dredging material, while the number of species in the river channel decreased, as dredging of the river bed and levelling of the banks had markedly reduced habitat diversity. Although species richness in the second year after the dredging approached the values recorded before the intervention, the absence of particularly species or phytocenoses associated with shallow river banks and sandbars was still observed. The change in habitat conditions and the destruction of the vegetation cover during the dredging enabled penetration by numerous previously unrecorded alien species of plants and apophytes. There…
format: application/pdf
format: text/html
creator: Edyta Stępień
creator: Andrzej Zawal
creator: Paweł Buczyński
creator: Edyta Buczyńska
creator: Magdalena Szenejko
subject: Biodiversity
subject: Conservation Biology
subject: Ecology
subject: Plant Science
subject: Environmental Impacts
description: doi:10.7717/peerj.6282
publisher: PeerJ Inc.
rights: © 2019 Stępień et al.
abstract: Background Conventional river engineering operations have a substantial influence on the fluvial ecosystem. Regulation and channelization generally reduce the physical heterogeneity of river beds and banks and the heterogeneity of habitats. They determine the character, diversity and species richness of plant communities. The effect of river regulation on vegetation has been repeatedly investigated, but few studies have been conducted within reaches of previously regulated rivers. The aim of this work is to expand and current knowledge about the impact of dredging on the vegetation of a regulated section of a lowland river. Materials & Methods The study included pre-dredging (1 year before) and post-dredging surveys (results 1 and 2 years after dredging). The vegetation was analysed in terms of species composition, origin of species, life forms, distribution of Grime’s life strategies, and selected ecological factors. The Shannon–Wiener biodiversity index (H) and evenness were also analysed in each year of the study. The impact of dredging on the vascular flora was assessed by ‘before-after-control-impact’ (BACI) analysis. Results The number of species and biodiversity as measured by the Shannon–Wiener index (H) increased in the analysed section of the river valley. However, enrichment of the flora was observed only on the floodplain, on the surface of the deposited dredging material, while the number of species in the river channel decreased, as dredging of the river bed and levelling of the banks had markedly reduced habitat diversity. Although species richness in the second year after the dredging approached the values recorded before the intervention, the absence of particularly species or phytocenoses associated with shallow river banks and sandbars was still observed. The change in habitat conditions and the destruction of the vegetation cover during the dredging enabled penetration by numerous previously unrecorded alien species of plants and apophytes. There…
bibliographic citation: Stępień et al. (2019) Effects of dredging on the vegetation in a small lowland river. PeerJ 7:e6282 https://doi.org/10.7717/peerj.6282
date submitted: 2018-06-04
date accepted: 2018-12-13
issued: 2019-01-22
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Stępień
  given name: Edyta
author list: Agent
  family name: Zawal
  given name: Andrzej
author list: Agent
  family name: Buczyński
  given name: Paweł
author list: Agent
  family name: Buczyńska
  given name: Edyta
author list: Agent
  family name: Szenejko
  given name: Magdalena
doi: 10.7717/peerj.6282
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-01-22
copyright: ©2019 Stępień et al.
attribution name: Stępień et al.

Use of open mobile mapping tool to assess human mobility traceability in rural offline populations with contrasting malaria dynamics
type: item
type: AcademicArticle
description: Infectious disease dynamics are affected by human mobility more powerfully than previously thought, and thus reliable traceability data are essential. In rural riverine settings, lack of infrastructure and dense tree coverage deter the implementation of cutting-edge technology to collect human mobility data. To overcome this challenge, this study proposed the use of a novel open mobile mapping tool, GeoODK. This study consists of a purposive sampling of 33 participants in six villages with contrasting patterns of malaria transmission that demonstrates a feasible approach to map human mobility. The self-reported traceability data allowed the construction of the first human mobility framework in rural riverine villages in the Peruvian Amazon. The mobility spectrum in these areas resulted in travel profiles ranging from 2 hours to 19 days; and distances between 10 to 167 km. Most Importantly, occupational-related mobility profiles with the highest displacements (in terms of time and distance) were observed in commercial, logging, and hunting activities. These data are consistent with malaria transmission studies in the area that show villages in watersheds with higher human movement are concurrently those with greater malaria risk. The approach we describe represents a potential tool to gather critical information that can facilitate malaria control activities.
format: application/pdf
format: text/html
creator: Gabriel Carrasco-Escobar
creator: Marcia C. Castro
creator: Jose Luis Barboza
creator: Jorge Ruiz-Cabrejos
creator: Alejandro Llanos-Cuentas
creator: Joseph M. Vinetz
creator: Dionicia Gamboa
subject: Infectious Diseases
subject: Spatial and Geographic Information Science
description: doi:10.7717/peerj.6298
publisher: PeerJ Inc.
rights: © 2019 Carrasco-Escobar et al.
abstract: Infectious disease dynamics are affected by human mobility more powerfully than previously thought, and thus reliable traceability data are essential. In rural riverine settings, lack of infrastructure and dense tree coverage deter the implementation of cutting-edge technology to collect human mobility data. To overcome this challenge, this study proposed the use of a novel open mobile mapping tool, GeoODK. This study consists of a purposive sampling of 33 participants in six villages with contrasting patterns of malaria transmission that demonstrates a feasible approach to map human mobility. The self-reported traceability data allowed the construction of the first human mobility framework in rural riverine villages in the Peruvian Amazon. The mobility spectrum in these areas resulted in travel profiles ranging from 2 hours to 19 days; and distances between 10 to 167 km. Most Importantly, occupational-related mobility profiles with the highest displacements (in terms of time and distance) were observed in commercial, logging, and hunting activities. These data are consistent with malaria transmission studies in the area that show villages in watersheds with higher human movement are concurrently those with greater malaria risk. The approach we describe represents a potential tool to gather critical information that can facilitate malaria control activities.
bibliographic citation: Carrasco-Escobar et al. (2019) Use of open mobile mapping tool to assess human mobility traceability in rural offline populations with contrasting malaria dynamics. PeerJ 7:e6298 https://doi.org/10.7717/peerj.6298
date submitted: 2018-10-23
date accepted: 2018-12-18
issued: 2019-01-22
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Carrasco-Escobar
  given name: Gabriel
author list: Agent
  family name: Castro
  given name: Marcia C.
author list: Agent
  family name: Barboza
  given name: Jose Luis
author list: Agent
  family name: Ruiz-Cabrejos
  given name: Jorge
author list: Agent
  family name: Llanos-Cuentas
  given name: Alejandro
author list: Agent
  family name: Vinetz
  given name: Joseph M.
author list: Agent
  family name: Gamboa
  given name: Dionicia
doi: 10.7717/peerj.6298
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-01-22
copyright: ©2019 Carrasco-Escobar et al.
attribution name: Carrasco-Escobar et al.

Quantitatively estimating main soil water-soluble salt ions content based on Visible-near infrared wavelength selected using GC, SR and VIP
type: item
type: AcademicArticle
description: Soil salinization is the primary obstacle to the sustainable development of agriculture and eco-environment in arid regions. The accurate inversion of the major water-soluble salt ions in the soil using visible-near infrared (VIS-NIR) spectroscopy technique can enhance the effectiveness of saline soil management. However, the accuracy of spectral models of soil salt ions turns out to be affected by high dimensionality and noise information of spectral data. This study aims to improve the model accuracy by optimizing the spectral models based on the exploration of the sensitive spectral intervals of different salt ions. To this end, 120 soil samples were collected from Shahaoqu Irrigation Area in Inner Mongolia, China. After determining the raw reflectance spectrum and content of salt ions in the lab, the spectral data were pre-treated by standard normal variable (SNV). Subsequently the sensitive spectral intervals of each ion were selected using methods of gray correlation (GC), stepwise regression (SR) and variable importance in projection (VIP). Finally, the performance of both models of partial least squares regression (PLSR) and support vector regression (SVR) was investigated on the basis of the sensitive spectral intervals. The results indicated that the model accuracy based on the sensitive spectral intervals selected using different analytical methods turned out to be different: VIP was the highest, SR came next and GC was the lowest. The optimal inversion models of different ions were different. In general, both PLSR and SVR had achieved satisfactory model accuracy, but PLSR outperformed SVR in the forecasting effects. Great difference existed among the optimal inversion accuracy of different ions: the predicative accuracy of Ca2+, Na+, Cl−, Mg2+ and SO42− was very high, that of CO32− was high and K+ was relatively lower, but HCO3− failed to have any predicative power. These findings provide a new approach for the optimization of the spectral model of water…
format: application/pdf
format: text/html
creator: Haifeng Wang
creator: Yinwen Chen
creator: Zhitao Zhang
creator: Haorui Chen
creator: Xianwen Li
creator: Mingxiu Wang
creator: Hongyang Chai
subject: Soil Science
subject: Data Mining and Machine Learning
subject: Natural Resource Management
subject: Environmental Impacts
subject: Spatial and Geographic Information Science
description: doi:10.7717/peerj.6310
publisher: PeerJ Inc.
rights: © 2019 Wang et al.
abstract: Soil salinization is the primary obstacle to the sustainable development of agriculture and eco-environment in arid regions. The accurate inversion of the major water-soluble salt ions in the soil using visible-near infrared (VIS-NIR) spectroscopy technique can enhance the effectiveness of saline soil management. However, the accuracy of spectral models of soil salt ions turns out to be affected by high dimensionality and noise information of spectral data. This study aims to improve the model accuracy by optimizing the spectral models based on the exploration of the sensitive spectral intervals of different salt ions. To this end, 120 soil samples were collected from Shahaoqu Irrigation Area in Inner Mongolia, China. After determining the raw reflectance spectrum and content of salt ions in the lab, the spectral data were pre-treated by standard normal variable (SNV). Subsequently the sensitive spectral intervals of each ion were selected using methods of gray correlation (GC), stepwise regression (SR) and variable importance in projection (VIP). Finally, the performance of both models of partial least squares regression (PLSR) and support vector regression (SVR) was investigated on the basis of the sensitive spectral intervals. The results indicated that the model accuracy based on the sensitive spectral intervals selected using different analytical methods turned out to be different: VIP was the highest, SR came next and GC was the lowest. The optimal inversion models of different ions were different. In general, both PLSR and SVR had achieved satisfactory model accuracy, but PLSR outperformed SVR in the forecasting effects. Great difference existed among the optimal inversion accuracy of different ions: the predicative accuracy of Ca2+, Na+, Cl−, Mg2+ and SO42− was very high, that of CO32− was high and K+ was relatively lower, but HCO3− failed to have any predicative power. These findings provide a new approach for the optimization of the spectral model of water…
bibliographic citation: Wang et al. (2019) Quantitatively estimating main soil water-soluble salt ions content based on Visible-near infrared wavelength selected using GC, SR and VIP. PeerJ 7:e6310 https://doi.org/10.7717/peerj.6310
date submitted: 2018-10-23
date accepted: 2018-12-19
issued: 2019-01-22
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Wang
  given name: Haifeng
author list: Agent
  family name: Chen
  given name: Yinwen
author list: Agent
  family name: Zhang
  given name: Zhitao
author list: Agent
  family name: Chen
  given name: Haorui
author list: Agent
  family name: Li
  given name: Xianwen
author list: Agent
  family name: Wang
  given name: Mingxiu
author list: Agent
  family name: Chai
  given name: Hongyang
doi: 10.7717/peerj.6310
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-01-22
copyright: ©2019 Wang et al.
attribution name: Wang et al.

Seasonal changes of commercial traits, proximate and fatty acid compositions of the scallop Flexopecten glaber from the Mediterranean Sea (Southern Italy)
type: item
type: AcademicArticle
description: This study provides information on biological (gonadosomatic index), commercial quality (condition index and meat yield) and biochemical aspects (proximate composition, fatty acids) of the soft tissues of Flexopecten glaber reared in suspended cages in the Ionian Sea. The results showed that condition index (CI) and meat yield (MY) peaked in December (60 and 30%, respectively) and in April, May and June (from 53 to 60% for CI and from 34 to 36% for MY). Gonadosomatic index showed three main peaks in winter, spring and summer months. Contents of protein 8.18–11.9 g/100 g), lipid (0,.78–1.18 g/100 g) and carbohydrate (1.19–3.30 g/100 g) varied significantly during the study period. Saturated fatty acids was the dominant group, except in December when polyunsaturated fatty acids showed the highest proportion (43% of total FAs). Fatty acids of the n3 group were dominant with docosahexaenoic and eicosapentaenoic acids. Highest n3/n6 ratios were recorded in spring-summer specimens, with values > of 5. The results showed a better nutritional quality of scallops in May, July and December.
format: application/pdf
format: text/html
creator: Ermelinda Prato
creator: Francesca Biandolino
creator: Isabella Parlapiano
creator: Loredana Papa
creator: Giuseppe Denti
creator: Giovanni Fanelli
subject: Aquaculture, Fisheries and Fish Science
subject: Biochemistry
subject: Food Science and Technology
subject: Marine Biology
subject: Nutrition
description: doi:10.7717/peerj.5810
publisher: PeerJ Inc.
rights: © 2019 Prato et al.
abstract: This study provides information on biological (gonadosomatic index), commercial quality (condition index and meat yield) and biochemical aspects (proximate composition, fatty acids) of the soft tissues of Flexopecten glaber reared in suspended cages in the Ionian Sea. The results showed that condition index (CI) and meat yield (MY) peaked in December (60 and 30%, respectively) and in April, May and June (from 53 to 60% for CI and from 34 to 36% for MY). Gonadosomatic index showed three main peaks in winter, spring and summer months. Contents of protein 8.18–11.9 g/100 g), lipid (0,.78–1.18 g/100 g) and carbohydrate (1.19–3.30 g/100 g) varied significantly during the study period. Saturated fatty acids was the dominant group, except in December when polyunsaturated fatty acids showed the highest proportion (43% of total FAs). Fatty acids of the n3 group were dominant with docosahexaenoic and eicosapentaenoic acids. Highest n3/n6 ratios were recorded in spring-summer specimens, with values > of 5. The results showed a better nutritional quality of scallops in May, July and December.
bibliographic citation: Prato et al. (2019) Seasonal changes of commercial traits, proximate and fatty acid compositions of the scallop Flexopecten glaber from the Mediterranean Sea (Southern Italy). PeerJ 7:e5810 https://doi.org/10.7717/peerj.5810
date submitted: 2018-07-03
date accepted: 2018-09-23
issued: 2019-01-21
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Prato
  given name: Ermelinda
author list: Agent
  family name: Biandolino
  given name: Francesca
author list: Agent
  family name: Parlapiano
  given name: Isabella
author list: Agent
  family name: Papa
  given name: Loredana
author list: Agent
  family name: Denti
  given name: Giuseppe
author list: Agent
  family name: Fanelli
  given name: Giovanni
doi: 10.7717/peerj.5810
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-01-21
copyright: ©2019 Prato et al.
attribution name: Prato et al.

Genetic variability in a Brazilian apple germplasm collection with low chilling requirements
type: item
type: AcademicArticle
description: The apple (Malus domestica Borkh) originally evolved to require temperatures below 7.2 °C for the induction of budding and flowering. In Brazil, breeders have overcome the climate barrier and developed the cultivars Anabela, Julieta, Carícia, and Eva, with low chilling requirements and good yield characteristics. These cultivars are grown in many warmer climate countries in South America, Africa, and the Middle East. The apple germplasm collection that originated these cultivars has several genotypes with pedigrees for a low chilling requirement. Knowledge of the variability and genetic relationships among these genotypes may be useful in the development of superior new cultivars. In this work, we first selected the best ISSR (inter-simple sequence repeat) primers for genetic studies in apple, and then we used the selected primers to evaluate the genetic variability of the apple germplasm collection at the Instituto Agronômico do Paraná. The evaluation of 42 ISSR primers in 10 apple genotypes allowed us to select the best nine primers based on the polymorphic information content (PIC) and resolving power (RP) indexes. The primer selection step was robust since the dendrogram obtained with the nine selected primers was the same as the one obtained using all 26 polymorphic primers. Primer selection using PIC and RP indexes allowed us to save about 60% of time and costs in the genetic variability study. The nine ISSR primers showed high levels of genetic variability in the 60 apple genotypes evaluated. The relevance of the primer selection step is discussed from the perspective of saving time and money in germplasm characterization. The high genetic variability and the genetic relationships among the genotypes are discussed from the perspective of the development of new apple cultivars, mainly aiming for a low chilling requirement that can better adapt to current climatic conditions or those that may arise with global warming.
format: application/pdf
format: text/html
creator: Livia Costa Mariano
creator: Felipe Liss Zchonski
creator: Clandio Medeiros da Silva
creator: Paulo Roberto Da-Silva
subject: Agricultural Science
subject: Biotechnology
subject: Genetics
subject: Plant Science
description: doi:10.7717/peerj.6265
publisher: PeerJ Inc.
rights: © 2019 Mariano et al.
abstract: The apple (Malus domestica Borkh) originally evolved to require temperatures below 7.2 °C for the induction of budding and flowering. In Brazil, breeders have overcome the climate barrier and developed the cultivars Anabela, Julieta, Carícia, and Eva, with low chilling requirements and good yield characteristics. These cultivars are grown in many warmer climate countries in South America, Africa, and the Middle East. The apple germplasm collection that originated these cultivars has several genotypes with pedigrees for a low chilling requirement. Knowledge of the variability and genetic relationships among these genotypes may be useful in the development of superior new cultivars. In this work, we first selected the best ISSR (inter-simple sequence repeat) primers for genetic studies in apple, and then we used the selected primers to evaluate the genetic variability of the apple germplasm collection at the Instituto Agronômico do Paraná. The evaluation of 42 ISSR primers in 10 apple genotypes allowed us to select the best nine primers based on the polymorphic information content (PIC) and resolving power (RP) indexes. The primer selection step was robust since the dendrogram obtained with the nine selected primers was the same as the one obtained using all 26 polymorphic primers. Primer selection using PIC and RP indexes allowed us to save about 60% of time and costs in the genetic variability study. The nine ISSR primers showed high levels of genetic variability in the 60 apple genotypes evaluated. The relevance of the primer selection step is discussed from the perspective of saving time and money in germplasm characterization. The high genetic variability and the genetic relationships among the genotypes are discussed from the perspective of the development of new apple cultivars, mainly aiming for a low chilling requirement that can better adapt to current climatic conditions or those that may arise with global warming.
bibliographic citation: Mariano et al. (2019) Genetic variability in a Brazilian apple germplasm collection with low chilling requirements. PeerJ 6:e6265 https://doi.org/10.7717/peerj.6265
date submitted: 2018-07-31
date accepted: 2018-12-11
issued: 2019-01-21
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Mariano
  given name: Livia Costa
author list: Agent
  family name: Zchonski
  given name: Felipe Liss
author list: Agent
  family name: da Silva
  given name: Clandio Medeiros
author list: Agent
  family name: Da-Silva
  given name: Paulo Roberto
doi: 10.7717/peerj.6265
volume: 6
issn: 2167-8359
publication name: PeerJ
publication date: 2019-01-21
copyright: ©2019 Mariano et al.
attribution name: Mariano et al.

Molecular mechanism of point mutation-induced Monopolar spindle 1 (Mps1/TTK) inhibitor resistance revealed by a comprehensive molecular modeling study
type: item
type: AcademicArticle
description: Background Monopolar spindle 1 (Mps1/TTK) is an apical dual-specificity protein kinase in the spindle assembly checkpoint (SAC) that guarantees accurate segregation of chromosomes during mitosis. High levels of Mps1 are found in various types of human malignancies, such as glioblastoma, osteosarcoma, hepatocellular carcinoma, and breast cancer. Several potent inhibitors of Mps1 exist, and exhibit promising activity in many cell cultures and xenograft models. However, resistance due to point mutations in the kinase domain of Mps1 limits the therapeutic effects of these inhibitors. Understanding the detailed resistance mechanism induced by Mps1 point mutations is therefore vital for the development of novel inhibitors against malignancies. Methods In this study, conventional molecular dynamics (MD) simulation and Gaussian accelerated MD (GaMD) simulation were performed to elucidate the resistance mechanisms of Cpd-5, a potent Mps1 inhibitor, induced by the four representative mutations I531M, I598F, C604Y, S611R. Results Our results from conventional MD simulation combined with structural analysis and free energy calculation indicated that the four mutations weaken the binding affinity of Cpd-5 and the major variations in structural were the conformational changes of the P-loop, A-loop and αC-helix. Energetic differences of per-residue between the WT system and the mutant systems indicated the mutations may allosterically regulate the conformational ensemble and the major variations were residues of Ile-663 and Gln-683, which located in the key loops of catalytic loop and A-loop, respectively. The large conformational and energetic differences were further supported by the GaMD simulations. Overall, these obtained molecular mechanisms will aid rational design of novel Mps1 inhibitors to combat inhibitor resistance.
format: application/pdf
format: text/html
creator: Yan Han
creator: Yungang Wu
creator: Yi Xu
creator: Wentao Guo
creator: Na Zhang
creator: Xiaoyi Wang
subject: Computational Biology
subject: Oncology
description: doi:10.7717/peerj.6299
publisher: PeerJ Inc.
rights: © 2019 Han et al.
abstract: Background Monopolar spindle 1 (Mps1/TTK) is an apical dual-specificity protein kinase in the spindle assembly checkpoint (SAC) that guarantees accurate segregation of chromosomes during mitosis. High levels of Mps1 are found in various types of human malignancies, such as glioblastoma, osteosarcoma, hepatocellular carcinoma, and breast cancer. Several potent inhibitors of Mps1 exist, and exhibit promising activity in many cell cultures and xenograft models. However, resistance due to point mutations in the kinase domain of Mps1 limits the therapeutic effects of these inhibitors. Understanding the detailed resistance mechanism induced by Mps1 point mutations is therefore vital for the development of novel inhibitors against malignancies. Methods In this study, conventional molecular dynamics (MD) simulation and Gaussian accelerated MD (GaMD) simulation were performed to elucidate the resistance mechanisms of Cpd-5, a potent Mps1 inhibitor, induced by the four representative mutations I531M, I598F, C604Y, S611R. Results Our results from conventional MD simulation combined with structural analysis and free energy calculation indicated that the four mutations weaken the binding affinity of Cpd-5 and the major variations in structural were the conformational changes of the P-loop, A-loop and αC-helix. Energetic differences of per-residue between the WT system and the mutant systems indicated the mutations may allosterically regulate the conformational ensemble and the major variations were residues of Ile-663 and Gln-683, which located in the key loops of catalytic loop and A-loop, respectively. The large conformational and energetic differences were further supported by the GaMD simulations. Overall, these obtained molecular mechanisms will aid rational design of novel Mps1 inhibitors to combat inhibitor resistance.
bibliographic citation: Han et al. (2019) Molecular mechanism of point mutation-induced Monopolar spindle 1 (Mps1/TTK) inhibitor resistance revealed by a comprehensive molecular modeling study. PeerJ 7:e6299 https://doi.org/10.7717/peerj.6299
date submitted: 2018-10-11
date accepted: 2018-12-18
issued: 2019-01-21
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Han
  given name: Yan
author list: Agent
  family name: Wu
  given name: Yungang
author list: Agent
  family name: Xu
  given name: Yi
author list: Agent
  family name: Guo
  given name: Wentao
author list: Agent
  family name: Zhang
  given name: Na
author list: Agent
  family name: Wang
  given name: Xiaoyi
doi: 10.7717/peerj.6299
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-01-21
copyright: ©2019 Han et al.
attribution name: Han et al.

Photosynthesis, yield and raw material quality of sugarcane injured by multiple pests
type: item
type: AcademicArticle
description: Understanding sugarcane (Saccharum spp.) response to multiple pest injury, sugarcane borer (Diatraea saccharalis) and spittlebug (Mahanarva fimbriolata), is essential to make better management decisions. Moreover, the consequences of both pests on the sugarcane raw material quality have not yet been studied. A field experiment was performed in São Paulo State, Brazil, where sugarcane plants were exposed to pests individually or in combination. Plots consisted of a 2-m long row of caged sugarcane plants. Photosynthesis was measured once every 3 months (seasonal measurement). Yield and sugar production were assessed. The measured photosynthesis rate was negatively affected by both borer and spittlebug infestations. Photosynthesis reduction was similar on plants infested by both pests as well as by spittlebug individual infestation. Plants under spittlebug infestation resulted in yield losses and represented 17.6% (individual infestation) and 15.5% (multiple infestations). The sucrose content and the sucrose yield per area were reduced when plants were infested by multiple pests or spittlebug.
format: application/pdf
format: text/html
creator: José A.S. Rossato Jr
creator: Leonardo L. Madaleno
creator: Márcia J.R. Mutton
creator: Leon G. Higley
creator: Odair A. Fernandes
subject: Agricultural Science
subject: Entomology
description: doi:10.7717/peerj.6166
publisher: PeerJ Inc.
rights: © 2019 Rossato Jr. et al.
abstract: Understanding sugarcane (Saccharum spp.) response to multiple pest injury, sugarcane borer (Diatraea saccharalis) and spittlebug (Mahanarva fimbriolata), is essential to make better management decisions. Moreover, the consequences of both pests on the sugarcane raw material quality have not yet been studied. A field experiment was performed in São Paulo State, Brazil, where sugarcane plants were exposed to pests individually or in combination. Plots consisted of a 2-m long row of caged sugarcane plants. Photosynthesis was measured once every 3 months (seasonal measurement). Yield and sugar production were assessed. The measured photosynthesis rate was negatively affected by both borer and spittlebug infestations. Photosynthesis reduction was similar on plants infested by both pests as well as by spittlebug individual infestation. Plants under spittlebug infestation resulted in yield losses and represented 17.6% (individual infestation) and 15.5% (multiple infestations). The sucrose content and the sucrose yield per area were reduced when plants were infested by multiple pests or spittlebug.
bibliographic citation: Rossato Jr et al. (2019) Photosynthesis, yield and raw material quality of sugarcane injured by multiple pests. PeerJ 7:e6166 https://doi.org/10.7717/peerj.6166
date submitted: 2014-03-20
date accepted: 2018-11-27
issued: 2019-01-18
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Rossato Jr
  given name: José A.S.
author list: Agent
  family name: Madaleno
  given name: Leonardo L.
author list: Agent
  family name: Mutton
  given name: Márcia J.R.
author list: Agent
  family name: Higley
  given name: Leon G.
author list: Agent
  family name: Fernandes
  given name: Odair A.
doi: 10.7717/peerj.6166
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-01-18
copyright: ©2019 Rossato Jr. et al.
attribution name: Rossato Jr. et al.

Potential surrogate plants for use in semi-field pesticide risk assessment with Megachile rotundata
type: item
type: AcademicArticle
description: Background Current regulatory pesticide risk assessments for bees are based primarily on the honey bee (Apis mellifera) and may not always be protective of solitary bees. To incorporate solitary bees into the risk assessment process, standardized methods to assess the hazard of pesticides under semi-field (Tier II) conditions will be needed. We conducted a series of experiments over 2 years to assess potential surrogate plants and adult release rates for use in semi-field experiments with the alfalfa leafcutting bee (ALB, Megachile rotundata). Methods We compared ALB foraging activity and reproduction on 12 m2 plots of flowering alfalfa (Medicago sativa) and buckwheat (Fagopyrum esculentum) at low (10♀/20♂) and high (20♀/40♂) adult release rates. The following year, we assessed the same endpoints on plots of purple tansy (Phacelia tanacetifolia) at a release rate of 10♀/15♂. Results Although ALB foraging activity was high on buckwheat plots, fewer adults were produced compared to alfalfa plots. On alfalfa, there were no differences in foraging activity, nesting, or reproduction between the low and high release rates. ALB readily foraged from purple tansy flowers, but females avoided purple tansy leaves for leaf cell construction. Discussion Our study suggests that buckwheat alone cannot support ALB during semi-field studies on small plots. For alfalfa, we recommend a maximum release rate of 10♀/20♂ in 12 m2 plots. Further study of higher ALB release rates on purple tansy is warranted. A mixed planting of purple tansy and a plant suitable for leaf piece collection (e.g., buckwheat) may provide favorable conditions for ALB activity and reproduction during semi-field testing.
format: application/pdf
format: text/html
creator: Andrew J. Frewin
creator: Angela E. Gradish
creator: Graham R. Ansell
creator: Cynthia D. Scott-Dupree
subject: Agricultural Science
subject: Entomology
subject: Toxicology
description: doi:10.7717/peerj.6278
publisher: PeerJ Inc.
rights: © 2019 Frewin et al.
abstract: Background Current regulatory pesticide risk assessments for bees are based primarily on the honey bee (Apis mellifera) and may not always be protective of solitary bees. To incorporate solitary bees into the risk assessment process, standardized methods to assess the hazard of pesticides under semi-field (Tier II) conditions will be needed. We conducted a series of experiments over 2 years to assess potential surrogate plants and adult release rates for use in semi-field experiments with the alfalfa leafcutting bee (ALB, Megachile rotundata). Methods We compared ALB foraging activity and reproduction on 12 m2 plots of flowering alfalfa (Medicago sativa) and buckwheat (Fagopyrum esculentum) at low (10♀/20♂) and high (20♀/40♂) adult release rates. The following year, we assessed the same endpoints on plots of purple tansy (Phacelia tanacetifolia) at a release rate of 10♀/15♂. Results Although ALB foraging activity was high on buckwheat plots, fewer adults were produced compared to alfalfa plots. On alfalfa, there were no differences in foraging activity, nesting, or reproduction between the low and high release rates. ALB readily foraged from purple tansy flowers, but females avoided purple tansy leaves for leaf cell construction. Discussion Our study suggests that buckwheat alone cannot support ALB during semi-field studies on small plots. For alfalfa, we recommend a maximum release rate of 10♀/20♂ in 12 m2 plots. Further study of higher ALB release rates on purple tansy is warranted. A mixed planting of purple tansy and a plant suitable for leaf piece collection (e.g., buckwheat) may provide favorable conditions for ALB activity and reproduction during semi-field testing.
bibliographic citation: Frewin et al. (2019) Potential surrogate plants for use in semi-field pesticide risk assessment with Megachile rotundata. PeerJ 6:e6278 https://doi.org/10.7717/peerj.6278
date submitted: 2018-06-06
date accepted: 2018-12-12
issued: 2019-01-18
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Frewin
  given name: Andrew J.
author list: Agent
  family name: Gradish
  given name: Angela E.
author list: Agent
  family name: Ansell
  given name: Graham R.
author list: Agent
  family name: Scott-Dupree
  given name: Cynthia D.
doi: 10.7717/peerj.6278
volume: 6
issn: 2167-8359
publication name: PeerJ
publication date: 2019-01-18
copyright: ©2019 Frewin et al.
attribution name: Frewin et al.

Review of the ant genus Meranoplus Smith, 1853 (Hymenoptera: Formicidae) in the Arabian Peninsula with description of a new species M. mosalahi sp. n. from Oman
type: item
type: AcademicArticle
description: The species of Meranoplus Smith, 1853 of the Arabian Peninsula are reviewed based on the worker caste. Two species are recognized, keyed, and illustrated by Scanning Electron Microscope images (SEM), Meranoplus mosalahi and M. pulcher, Sharaf, 2014. Meranoplus mosalahi sp. n. is described from the Dhofar Governorate, Oman based on the worker caste. The new species belongs to the M. magrettii-group and closely resembles M. pulcher Sharaf, 2014 from the Kingdom of Saudi Arabia (KSA), from which it can be distinguished by the bicolored body, the shallowly concave anterior clypeal margin, the absence of well-developed anterior clypeal teeth, the fewer irregular longitudinal cephalic rugae, and the feeble longitudinal rugae on posterior face of petiolar node.
format: application/pdf
format: text/html
creator: Mostafa R. Sharaf
creator: Abdulrahman S. Aldawood
subject: Biodiversity
subject: Entomology
subject: Taxonomy
subject: Zoology
description: doi:10.7717/peerj.6287
publisher: PeerJ Inc.
rights: © 2019 Sharaf and Aldawood
abstract: The species of Meranoplus Smith, 1853 of the Arabian Peninsula are reviewed based on the worker caste. Two species are recognized, keyed, and illustrated by Scanning Electron Microscope images (SEM), Meranoplus mosalahi and M. pulcher, Sharaf, 2014. Meranoplus mosalahi sp. n. is described from the Dhofar Governorate, Oman based on the worker caste. The new species belongs to the M. magrettii-group and closely resembles M. pulcher Sharaf, 2014 from the Kingdom of Saudi Arabia (KSA), from which it can be distinguished by the bicolored body, the shallowly concave anterior clypeal margin, the absence of well-developed anterior clypeal teeth, the fewer irregular longitudinal cephalic rugae, and the feeble longitudinal rugae on posterior face of petiolar node.
bibliographic citation: Sharaf et al. (2019) Review of the ant genus Meranoplus Smith, 1853 (Hymenoptera: Formicidae) in the Arabian Peninsula with description of a new species M. mosalahi sp. n. from Oman. PeerJ 7:e6287 https://doi.org/10.7717/peerj.6287
date submitted: 2018-11-11
date accepted: 2018-12-15
issued: 2019-01-18
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Sharaf
  given name: Mostafa R.
author list: Agent
  family name: Aldawood
  given name: Abdulrahman S.
doi: 10.7717/peerj.6287
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-01-18
copyright: ©2019 Sharaf and Aldawood
attribution name: Sharaf and Aldawood

Aetiology of livestock fetal mortality in Mazandaran province, Iran
type: item
type: AcademicArticle
description: In the farming industry, the productivity of livestock herds depends on the fertility efficiency of animals. The accurate diagnosis of a broad range of aetiological agents causing fetal death is often difficult. Our aim was to assess the prevalence rates of Toxoplasma gondii, Neospora caninum, and Brucella spp. infections in ruminant abortion using bacteriological culture and molecular techniques in Mazandaran Province, northern Iran. Samples were collected from 70 aborted sheep, goat, and cattle fetuses between September 2014 and December 2015. Necropsy was performed on all the received samples, and brain tissue and abomasal content were obtained from the aborted fetuses. Protozoan infections were detected by specific polymerase chain reaction (PCR) and bacterial agents using bacteriological examinations and PCR assay. Infectious pathogens were detected in 22 out of 70 (31.4%) examined fetuses. Moreover, T. gondii, N. caninum, and B. melitensis were verified in 13 (18.6%), four (5.7%), and two (2.85%) samples, respectively. Our results showed that infection with the mentioned pathogenic agents may lead to fetal mortality, which can be a major cause of economic loss. The listed pathogens could be considered important etiological agents of fetal loss in Mazandaran Province, for which appropriate control measures such as vaccination and biosecurity can be implemented to prevent infection and reduce reproductive loss in livestock farms.
format: application/pdf
format: text/html
creator: Afsaneh Amouei
creator: Mehdi Sharif
creator: Shahabeddin Sarvi
creator: Ramin Bagheri Nejad
creator: Sargis A. Aghayan
creator: Mohammad Bagher Hashemi-Soteh
creator: Azadeh Mizani
creator: Seyed Abdollah Hosseini
creator: Sara Gholami
creator: Alireza Sadeghi
creator: Mohammad Sarafrazi
creator: Ahmad Daryani
subject: Agricultural Science
subject: Microbiology
subject: Parasitology
subject: Veterinary Medicine
description: doi:10.7717/peerj.5920
publisher: PeerJ Inc.
rights: © 2019 Amouei et al.
abstract: In the farming industry, the productivity of livestock herds depends on the fertility efficiency of animals. The accurate diagnosis of a broad range of aetiological agents causing fetal death is often difficult. Our aim was to assess the prevalence rates of Toxoplasma gondii, Neospora caninum, and Brucella spp. infections in ruminant abortion using bacteriological culture and molecular techniques in Mazandaran Province, northern Iran. Samples were collected from 70 aborted sheep, goat, and cattle fetuses between September 2014 and December 2015. Necropsy was performed on all the received samples, and brain tissue and abomasal content were obtained from the aborted fetuses. Protozoan infections were detected by specific polymerase chain reaction (PCR) and bacterial agents using bacteriological examinations and PCR assay. Infectious pathogens were detected in 22 out of 70 (31.4%) examined fetuses. Moreover, T. gondii, N. caninum, and B. melitensis were verified in 13 (18.6%), four (5.7%), and two (2.85%) samples, respectively. Our results showed that infection with the mentioned pathogenic agents may lead to fetal mortality, which can be a major cause of economic loss. The listed pathogens could be considered important etiological agents of fetal loss in Mazandaran Province, for which appropriate control measures such as vaccination and biosecurity can be implemented to prevent infection and reduce reproductive loss in livestock farms.
bibliographic citation: Amouei et al. (2019) Aetiology of livestock fetal mortality in Mazandaran province, Iran. PeerJ 6:e5920 https://doi.org/10.7717/peerj.5920
date submitted: 2017-10-12
date accepted: 2018-10-03
issued: 2019-01-18
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Amouei
  given name: Afsaneh
author list: Agent
  family name: Sharif
  given name: Mehdi
author list: Agent
  family name: Sarvi
  given name: Shahabeddin
author list: Agent
  family name: Bagheri Nejad
  given name: Ramin
author list: Agent
  family name: Aghayan
  given name: Sargis A.
author list: Agent
  family name: Hashemi-Soteh
  given name: Mohammad Bagher
author list: Agent
  family name: Mizani
  given name: Azadeh
author list: Agent
  family name: Hosseini
  given name: Seyed Abdollah
author list: Agent
  family name: Gholami
  given name: Sara
author list: Agent
  family name: Sadeghi
  given name: Alireza
author list: Agent
  family name: Sarafrazi
  given name: Mohammad
author list: Agent
  family name: Daryani
  given name: Ahmad
doi: 10.7717/peerj.5920
volume: 6
issn: 2167-8359
publication name: PeerJ
publication date: 2019-01-18
copyright: ©2019 Amouei et al.
attribution name: Amouei et al.

A large cockroach from the mesosaur-bearing Konservat-Lagerstätte (Mangrullo Formation), Late Paleozoic of Uruguay
type: item
type: AcademicArticle
description: Barona arcuata, n.gen et n.sp., a left forewing of a relatively large cockroach of the Order Blattaria, is described from mesosaur-bearing lagoonal shales of the Mangrullo Formation (north-eastern Uruguay). While most of the insect remains recovered from the Mangrullo Formation come from sandy limestones, associated to scarce isolated mesosaur bones and pygocephalomorph crustaceans, the cockroach wing here described was found in the overlaying green to brownish, gray and dark black shales associated to intercalated bentonites and evaporitic gypsum crystals. Barona arcuata shares some features with typical Late Carboniferous taxa such as its general venation pattern and outline of the wing, four main and powerful veins arising close together from near the base of the wing, Sc simple forked, pectinate, reaching the costal border through a long fork, R and M bifurcating and terminating in the wing margin above and below the apex respectively, short and narrow CuA, and the presence of a broad interspace between CuP and AA. Cross venation seems to be absent or it was not preserved. Some characters might relate Barona arcuata to the Late Carboniferous-Early Permian Neothroblattinidae such as the presence of sigmoidal veins in the anal area, a condition not found in any of the remaining representatives of the Palaeozoic Blattaria. Intriguingly, the Uruguayan blattarian also presents a strong similarity with Qilianiblatta namurensis Zhang, Schneider & Hong, 2012 from the Westphalian of China, clearly a smaller taxon that is also difficult to relate to any of the preexistent families. The apparent plesiomorphic venation pattern of the new species which is reminiscent of that present in the oldest known blattarians, is in agreement with a Permo-Carboniferous (Gzhelian-Asselian) age for the Mangrullo Formation also supported by the presence of a macrofloral assemblage dominated by arborescent lepidondendrids and other lycopsids and the pygocephalid-like morphology of the pygoc…
format: application/pdf
format: text/html
creator: Viviana Calisto
creator: Graciela Piñeiro
subject: Paleontology
subject: Taxonomy
description: doi:10.7717/peerj.6289
publisher: PeerJ Inc.
rights: © 2019 Calisto et al.
abstract: Barona arcuata, n.gen et n.sp., a left forewing of a relatively large cockroach of the Order Blattaria, is described from mesosaur-bearing lagoonal shales of the Mangrullo Formation (north-eastern Uruguay). While most of the insect remains recovered from the Mangrullo Formation come from sandy limestones, associated to scarce isolated mesosaur bones and pygocephalomorph crustaceans, the cockroach wing here described was found in the overlaying green to brownish, gray and dark black shales associated to intercalated bentonites and evaporitic gypsum crystals. Barona arcuata shares some features with typical Late Carboniferous taxa such as its general venation pattern and outline of the wing, four main and powerful veins arising close together from near the base of the wing, Sc simple forked, pectinate, reaching the costal border through a long fork, R and M bifurcating and terminating in the wing margin above and below the apex respectively, short and narrow CuA, and the presence of a broad interspace between CuP and AA. Cross venation seems to be absent or it was not preserved. Some characters might relate Barona arcuata to the Late Carboniferous-Early Permian Neothroblattinidae such as the presence of sigmoidal veins in the anal area, a condition not found in any of the remaining representatives of the Palaeozoic Blattaria. Intriguingly, the Uruguayan blattarian also presents a strong similarity with Qilianiblatta namurensis Zhang, Schneider & Hong, 2012 from the Westphalian of China, clearly a smaller taxon that is also difficult to relate to any of the preexistent families. The apparent plesiomorphic venation pattern of the new species which is reminiscent of that present in the oldest known blattarians, is in agreement with a Permo-Carboniferous (Gzhelian-Asselian) age for the Mangrullo Formation also supported by the presence of a macrofloral assemblage dominated by arborescent lepidondendrids and other lycopsids and the pygocephalid-like morphology of the pygoc…
bibliographic citation: Calisto et al. (2019) A large cockroach from the mesosaur-bearing Konservat-Lagerstätte (Mangrullo Formation), Late Paleozoic of Uruguay. PeerJ 7:e6289 https://doi.org/10.7717/peerj.6289
date submitted: 2018-08-06
date accepted: 2018-12-16
issued: 2019-01-18
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Calisto
  given name: Viviana
author list: Agent
  family name: Piñeiro
  given name: Graciela
doi: 10.7717/peerj.6289
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-01-18
copyright: ©2019 Calisto and Piñeiro
attribution name: Calisto et al.

Phylogeography and population genetics of the endemic Malagasy bat, Macronycteris commersoni s.s. (Chiroptera: Hipposideridae)
type: item
type: AcademicArticle
description: Macronycteris commersoni (Hipposideridae), a bat species endemic to Madagascar, is widespread across the island and utilizes a range of habitat types including open woodland, degraded habitats, and forested areas from sea level to 1,325 m. Despite being widely distributed, there is evidence that M. commersoni exhibits morphological and bioacoustic variation across its geographical range. We investigated the fine-scale phylogeographic structure of populations in the western half of the island using extensive spatial sampling and sequence data from two mitochondrial DNA regions. Our results indicated several lineages within M. commersoni. Individuals collected from northern Madagascar formed a single monophyletic clade (clade C). A second clade (clade B) included individuals collected from the south-western portion of the island. This second clade displayed more phylogeographical partitioning with differences in mtDNA haplotypes frequency detected between populations collected in different bioclimatic regions. Lineage dispersal, genetic divergence, and timing of expansion events of M. commersoni were probably associated with Pleistocene climate fluctuations. Our data suggest that the northern and the central western regions of Madagascar may have acted as refugia for this species during periods of cooler and drier climate conditions associated with the Pleistocene.
format: application/pdf
format: text/html
creator: Andrinajoro R. Rakotoarivelo
creator: Steven M. Goodman
creator: M. Corrie Schoeman
creator: Sandi Willows-Munro
subject: Biogeography
subject: Evolutionary Studies
description: doi:10.7717/peerj.5866
publisher: PeerJ Inc.
rights: © 2019 Rakotoarivelo et al.
abstract: Macronycteris commersoni (Hipposideridae), a bat species endemic to Madagascar, is widespread across the island and utilizes a range of habitat types including open woodland, degraded habitats, and forested areas from sea level to 1,325 m. Despite being widely distributed, there is evidence that M. commersoni exhibits morphological and bioacoustic variation across its geographical range. We investigated the fine-scale phylogeographic structure of populations in the western half of the island using extensive spatial sampling and sequence data from two mitochondrial DNA regions. Our results indicated several lineages within M. commersoni. Individuals collected from northern Madagascar formed a single monophyletic clade (clade C). A second clade (clade B) included individuals collected from the south-western portion of the island. This second clade displayed more phylogeographical partitioning with differences in mtDNA haplotypes frequency detected between populations collected in different bioclimatic regions. Lineage dispersal, genetic divergence, and timing of expansion events of M. commersoni were probably associated with Pleistocene climate fluctuations. Our data suggest that the northern and the central western regions of Madagascar may have acted as refugia for this species during periods of cooler and drier climate conditions associated with the Pleistocene.
bibliographic citation: Rakotoarivelo et al. (2019) Phylogeography and population genetics of the endemic Malagasy bat, Macronycteris commersoni s.s. (Chiroptera: Hipposideridae). PeerJ 7:e5866 https://doi.org/10.7717/peerj.5866
date submitted: 2018-08-13
date accepted: 2018-10-03
issued: 2019-01-17
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Rakotoarivelo
  given name: Andrinajoro R.
author list: Agent
  family name: Goodman
  given name: Steven M.
author list: Agent
  family name: Schoeman
  given name: M. Corrie
author list: Agent
  family name: Willows-Munro
  given name: Sandi
doi: 10.7717/peerj.5866
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-01-17
copyright: ©2019 Rakotoarivelo et al.
attribution name: Rakotoarivelo et al.

Seasonality and trend prediction of scarlet fever incidence in mainland China from 2004 to 2018 using a hybrid SARIMA-NARX model
type: item
type: AcademicArticle
description: Background Scarlet fever is recognized as being a major public health issue owing to its increase in notifications in mainland China, and an advanced response based on forecasting techniques is being adopted to tackle this. Here, we construct a new hybrid method incorporating seasonal autoregressive integrated moving average (SARIMA) with a nonlinear autoregressive with external input(NARX) to analyze its seasonality and trend in order to efficiently prevent and control this re-emerging disease. Methods Four statistical models, including a basic SARIMA, basic nonlinear autoregressive (NAR) method, traditional SARIMA-NAR and new SARIMA-NARX hybrid approaches, were developed based on scarlet fever incidence data between January 2004 and July 2018 to evaluate its temporal patterns, and their mimic and predictive capacities were compared to discover the optimal using the mean absolute percentage error, root mean square error, mean error rate, and root mean square percentage error. Results The four preferred models identified were comprised of the SARIMA(0,1,0)(0,1,1)12, NAR with 14 hidden neurons and five delays, SARIMA-NAR with 33 hidden neurons and five delays, and SARIMA-NARX with 16 hidden neurons and 4 delays. Among which presenting the lowest values of the aforementioned indices in both simulation and prediction horizons is the SARIMA-NARX method. Analyses from the data suggested that scarlet fever was a seasonal disease with predominant peaks of summer and winter and a substantial rising trend in the scarlet fever notifications was observed with an acceleration of 9.641% annually, particularly since 2011 with 12.869%, and moreover such a trend will be projected to continue in the coming year. Conclusions The SARIMA-NARX technique has the promising ability to better consider both linearity and non-linearity behind scarlet fever data than the others, which significantly facilitates its prevention and intervention of scarlet fever. Besides, under current trend of on…
format: application/pdf
format: text/html
creator: Yongbin Wang
creator: Chunjie Xu
creator: Zhende Wang
creator: Juxiang Yuan
subject: Mathematical Biology
subject: Epidemiology
subject: Health Policy
subject: Infectious Diseases
subject: Public Health
description: doi:10.7717/peerj.6165
publisher: PeerJ Inc.
rights: © 2019 Wang et al.
abstract: Background Scarlet fever is recognized as being a major public health issue owing to its increase in notifications in mainland China, and an advanced response based on forecasting techniques is being adopted to tackle this. Here, we construct a new hybrid method incorporating seasonal autoregressive integrated moving average (SARIMA) with a nonlinear autoregressive with external input(NARX) to analyze its seasonality and trend in order to efficiently prevent and control this re-emerging disease. Methods Four statistical models, including a basic SARIMA, basic nonlinear autoregressive (NAR) method, traditional SARIMA-NAR and new SARIMA-NARX hybrid approaches, were developed based on scarlet fever incidence data between January 2004 and July 2018 to evaluate its temporal patterns, and their mimic and predictive capacities were compared to discover the optimal using the mean absolute percentage error, root mean square error, mean error rate, and root mean square percentage error. Results The four preferred models identified were comprised of the SARIMA(0,1,0)(0,1,1)12, NAR with 14 hidden neurons and five delays, SARIMA-NAR with 33 hidden neurons and five delays, and SARIMA-NARX with 16 hidden neurons and 4 delays. Among which presenting the lowest values of the aforementioned indices in both simulation and prediction horizons is the SARIMA-NARX method. Analyses from the data suggested that scarlet fever was a seasonal disease with predominant peaks of summer and winter and a substantial rising trend in the scarlet fever notifications was observed with an acceleration of 9.641% annually, particularly since 2011 with 12.869%, and moreover such a trend will be projected to continue in the coming year. Conclusions The SARIMA-NARX technique has the promising ability to better consider both linearity and non-linearity behind scarlet fever data than the others, which significantly facilitates its prevention and intervention of scarlet fever. Besides, under current trend of on…
bibliographic citation: Wang et al. (2019) Seasonality and trend prediction of scarlet fever incidence in mainland China from 2004 to 2018 using a hybrid SARIMA-NARX model. PeerJ 7:e6165 https://doi.org/10.7717/peerj.6165
date submitted: 2018-09-19
date accepted: 2018-11-27
issued: 2019-01-17
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Wang
  given name: Yongbin
author list: Agent
  family name: Xu
  given name: Chunjie
author list: Agent
  family name: Wang
  given name: Zhende
author list: Agent
  family name: Yuan
  given name: Juxiang
doi: 10.7717/peerj.6165
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-01-17
copyright: ©2019 Wang et al.
attribution name: Wang et al.

Outcomes of hospitalizations with atrial fibrillation-flutter on a weekday versus weekend: an analysis from a 2014 nationwide inpatient sample
type: item
type: AcademicArticle
description: Background Patients with atrial fibrillation-flutter (AF) admitted on the weekends were initially reported to have poor outcomes. The primary purpose of this study is to re-evaluate the outcomes for weekend versus weekday AF hospitalization using the 2014 Nationwide Inpatient Sample (NIS). Methods Included hospitalizations were aged above 18 years. The hospitalizations with AF were identified using the international classification of diseases 9 (ICD-9) codes (427.31, 427.32). In-hospital mortality, length of stay (LOS), other co-morbidities, cardioversion procedures, and time to cardioversion were recorded. All analysis was performed using SAS 9.4 statistical software (Cary, North Carolina). Results A total of 453,505 hospitalizations with atrial fibrillation and flutter as primary discharge diagnosis were identified. Among the total hospitalizations with a primary diagnosis of AF, 20.3% were admitted on the weekend. Among the weekend hospitalizations, 0.19% died in hospital compared to 0.74% among those admitted during the week. After adjusting for patient characteristics, hospital characteristics and disease severity, the adjusted odds for in-hospital mortality were not significantly different for weekend vs. weekday hospitalizations (OR = 0.91, 95% CI [0.77–1.11]; p = 0.33). The weekend admissions were associated with significantly lower odds of cardioversion procedures (OR = 0.72, 95% CI [0.69–0.76], P < 0.0001), lower cost of hospitalization (USD 8265.8 on weekends vs. USD 8966.5 on the weekdays, P < 0.001), slightly lower rate of anticoagulation (17.09% on the weekends vs. 18.73% on the weekdays. P < 0.0001), and slightly increased time to cardioversion (1.94 days on the weekend vs. 1.73 days on weekdays, P < 0.0005). The mean length of hospital stay (LOS) was statistically not different in both groups: (3.49 days ± 3.70 (SD) in the weekend group vs. 3.47 days ± 3.50 (SD) in the weekday group, P = 0.42) Discussion The weekend AF hospitalizations did not have a…
format: application/pdf
format: text/html
creator: Dinesh C. Voruganti
creator: Ghanshyam Palamaner Subash Shantha
creator: Abhishek Deshmukh
creator: Michael C. Giudici
subject: Cardiology
subject: Global Health
subject: Health Policy
description: doi:10.7717/peerj.6211
publisher: PeerJ Inc.
rights: © 2019 Voruganti et al.
abstract: Background Patients with atrial fibrillation-flutter (AF) admitted on the weekends were initially reported to have poor outcomes. The primary purpose of this study is to re-evaluate the outcomes for weekend versus weekday AF hospitalization using the 2014 Nationwide Inpatient Sample (NIS). Methods Included hospitalizations were aged above 18 years. The hospitalizations with AF were identified using the international classification of diseases 9 (ICD-9) codes (427.31, 427.32). In-hospital mortality, length of stay (LOS), other co-morbidities, cardioversion procedures, and time to cardioversion were recorded. All analysis was performed using SAS 9.4 statistical software (Cary, North Carolina). Results A total of 453,505 hospitalizations with atrial fibrillation and flutter as primary discharge diagnosis were identified. Among the total hospitalizations with a primary diagnosis of AF, 20.3% were admitted on the weekend. Among the weekend hospitalizations, 0.19% died in hospital compared to 0.74% among those admitted during the week. After adjusting for patient characteristics, hospital characteristics and disease severity, the adjusted odds for in-hospital mortality were not significantly different for weekend vs. weekday hospitalizations (OR = 0.91, 95% CI [0.77–1.11]; p = 0.33). The weekend admissions were associated with significantly lower odds of cardioversion procedures (OR = 0.72, 95% CI [0.69–0.76], P < 0.0001), lower cost of hospitalization (USD 8265.8 on weekends vs. USD 8966.5 on the weekdays, P < 0.001), slightly lower rate of anticoagulation (17.09% on the weekends vs. 18.73% on the weekdays. P < 0.0001), and slightly increased time to cardioversion (1.94 days on the weekend vs. 1.73 days on weekdays, P < 0.0005). The mean length of hospital stay (LOS) was statistically not different in both groups: (3.49 days ± 3.70 (SD) in the weekend group vs. 3.47 days ± 3.50 (SD) in the weekday group, P = 0.42) Discussion The weekend AF hospitalizations did not have a…
bibliographic citation: Voruganti et al. (2019) Outcomes of hospitalizations with atrial fibrillation-flutter on a weekday versus weekend: an analysis from a 2014 nationwide inpatient sample. PeerJ 7:e6211 https://doi.org/10.7717/peerj.6211
date submitted: 2018-08-14
date accepted: 2018-12-04
issued: 2019-01-17
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Voruganti
  given name: Dinesh C.
author list: Agent
  family name: Subash Shantha
  given name: Ghanshyam Palamaner
author list: Agent
  family name: Deshmukh
  given name: Abhishek
author list: Agent
  family name: Giudici
  given name: Michael C.
doi: 10.7717/peerj.6211
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-01-17
copyright: ©2019 Voruganti et al.
attribution name: Voruganti et al.

Extremely low levels of chloroplast genome sequence variability in Astelia pumila (Asteliaceae, Asparagales)
type: item
type: AcademicArticle
description: Astelia pumila (G.Forst.) Gaudich. (Asteliaceae, Asparagales) is a major element of West Patagonian cushion peat bog vegetation. With the aim to identify appropriate chloroplast markers for the use in a phylogeographic study, the complete chloroplast genomes of five A. pumila accessions from almost the entire geographical range of the species were assembled and screened for variable positions. The chloroplast genome sequence was obtained via a mapping approach, using Eustrephus latifolius (Asparagaceae) as a reference. The chloroplast genome of A. pumila varies in length from 158,215 bp to 158,221 bp, containing a large single copy region of 85,981–85,983 bp, a small single copy region of 18,182–18,186 bp and two inverted repeats of 27,026 bp. Genome annotation predicted a total of 113 genes, including 30 tRNA and four rRNA genes. Sequence comparisons revealed a very low degree of intraspecific genetic variability, as only 37 variable sites (18 indels, 18 single nucleotide polymorphisms, one 3-bp mutation)—most of them autapomorphies—were found among the five assembled chloroplast genomes. A Maximum Likelihood analysis, based on whole chloroplast genome sequences of several Asparagales accessions representing six of the currently recognized 14 families (sensu APG IV), confirmed the phylogenetic position of A. pumila. The chloroplast genome of A. pumila is the first to be reported for a member of the astelioid clade (14 genera with c. 215 species), a basally branching group within Asparagales.
format: application/pdf
format: text/html
creator: Simon Pfanzelt
creator: Dirk C. Albach
creator: K. Bernhard von Hagen
subject: Biogeography
subject: Plant Science
description: doi:10.7717/peerj.6244
publisher: PeerJ Inc.
rights: © 2019 Pfanzelt et al.
abstract: Astelia pumila (G.Forst.) Gaudich. (Asteliaceae, Asparagales) is a major element of West Patagonian cushion peat bog vegetation. With the aim to identify appropriate chloroplast markers for the use in a phylogeographic study, the complete chloroplast genomes of five A. pumila accessions from almost the entire geographical range of the species were assembled and screened for variable positions. The chloroplast genome sequence was obtained via a mapping approach, using Eustrephus latifolius (Asparagaceae) as a reference. The chloroplast genome of A. pumila varies in length from 158,215 bp to 158,221 bp, containing a large single copy region of 85,981–85,983 bp, a small single copy region of 18,182–18,186 bp and two inverted repeats of 27,026 bp. Genome annotation predicted a total of 113 genes, including 30 tRNA and four rRNA genes. Sequence comparisons revealed a very low degree of intraspecific genetic variability, as only 37 variable sites (18 indels, 18 single nucleotide polymorphisms, one 3-bp mutation)—most of them autapomorphies—were found among the five assembled chloroplast genomes. A Maximum Likelihood analysis, based on whole chloroplast genome sequences of several Asparagales accessions representing six of the currently recognized 14 families (sensu APG IV), confirmed the phylogenetic position of A. pumila. The chloroplast genome of A. pumila is the first to be reported for a member of the astelioid clade (14 genera with c. 215 species), a basally branching group within Asparagales.
bibliographic citation: Pfanzelt et al. (2019) Extremely low levels of chloroplast genome sequence variability in Astelia pumila (Asteliaceae, Asparagales). PeerJ 7:e6244 https://doi.org/10.7717/peerj.6244
date submitted: 2018-08-28
date accepted: 2018-12-08
issued: 2019-01-17
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Pfanzelt
  given name: Simon
author list: Agent
  family name: Albach
  given name: Dirk C.
author list: Agent
  family name: von Hagen
  given name: K. Bernhard
doi: 10.7717/peerj.6244
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-01-17
copyright: ©2019 Pfanzelt et al.
attribution name: Pfanzelt et al.

Effects of nickel and cobalt on methane production and methanogen abundance and diversity in paddy soil
type: item
type: AcademicArticle
description: Background Paddies are an important anthropogenic source of methane emissions to the atmosphere, and they are impacted by heavy metal pollution. Nickel (Ni) and cobalt (Co) pollution might either enhance or mitigate CH4 emission from paddy soils due to the total amounts of metals, bioavailability and functional microbial activity and composition. Methods An incubation experiment was conducted, and different Ni and Co concentrations were added to test the effects of trace metals on methane production in paddy soil. The archaea community structure and the abundance of methanogen functional groups in the paddy soil with added Ni and Co were detected using high-throughput sequencing and quantitative PCR based on the 16S rRNA and mcrA (methyl coenzyme M reductase) genes, respectively. Results The highest methane production rate was 561 mg CH4 kg−1 dry soil d−1 with the addition of 50 mg kg−1 Ni and 684 mg CH4 kg−1 dry soil d−1 with the addition of 25 mg kg−1 Co. Accordingly, the mcrA gene was most abundant in the 50 mg kg−1 Ni addition (3.1 × 106 ± 0.5 × 106 copies g−1 dry soil). The lowest mcrA gene abundance was detected in the 500 mg kg−1 Co addition (9.2× 105 ± 0.4 × 105 copies g−1 dry soil). The dominant methanogens were Methanobacterium, Methanosarcina, Methanocella, Methanomassiliicoccus, Bathyarchaeota, and Rice Cluster I (RC-I), and the relative abundances of these groups were higher than 1% in the Ni and Co treatments. Additionally, the archaeal compositions differed significantly in the soils with various Ni and Co additions. The most abundant Methanococcus spp. represented 51.3% of the composition in the 50 mg kg−1 Ni addition, which was significantly higher than that of the control (12.9% to 17.5%). Discussion Our results indicated that the contamination of soil by Ni and Co significantly affected total methanogens abundance and specific methanogen functional groups. Ni and Co additions to paddy soil promoted methanogenic activity at low concentrations, whil…
format: application/pdf
format: text/html
creator: Tianwei Wang
creator: Zhaoxia Li
creator: Xueping Chen
creator: Xi-En Long
subject: Soil Science
subject: Climate Change Biology
description: doi:10.7717/peerj.6274
publisher: PeerJ Inc.
rights: © 2019 Wang et al.
abstract: Background Paddies are an important anthropogenic source of methane emissions to the atmosphere, and they are impacted by heavy metal pollution. Nickel (Ni) and cobalt (Co) pollution might either enhance or mitigate CH4 emission from paddy soils due to the total amounts of metals, bioavailability and functional microbial activity and composition. Methods An incubation experiment was conducted, and different Ni and Co concentrations were added to test the effects of trace metals on methane production in paddy soil. The archaea community structure and the abundance of methanogen functional groups in the paddy soil with added Ni and Co were detected using high-throughput sequencing and quantitative PCR based on the 16S rRNA and mcrA (methyl coenzyme M reductase) genes, respectively. Results The highest methane production rate was 561 mg CH4 kg−1 dry soil d−1 with the addition of 50 mg kg−1 Ni and 684 mg CH4 kg−1 dry soil d−1 with the addition of 25 mg kg−1 Co. Accordingly, the mcrA gene was most abundant in the 50 mg kg−1 Ni addition (3.1 × 106 ± 0.5 × 106 copies g−1 dry soil). The lowest mcrA gene abundance was detected in the 500 mg kg−1 Co addition (9.2× 105 ± 0.4 × 105 copies g−1 dry soil). The dominant methanogens were Methanobacterium, Methanosarcina, Methanocella, Methanomassiliicoccus, Bathyarchaeota, and Rice Cluster I (RC-I), and the relative abundances of these groups were higher than 1% in the Ni and Co treatments. Additionally, the archaeal compositions differed significantly in the soils with various Ni and Co additions. The most abundant Methanococcus spp. represented 51.3% of the composition in the 50 mg kg−1 Ni addition, which was significantly higher than that of the control (12.9% to 17.5%). Discussion Our results indicated that the contamination of soil by Ni and Co significantly affected total methanogens abundance and specific methanogen functional groups. Ni and Co additions to paddy soil promoted methanogenic activity at low concentrations, whil…
bibliographic citation: Wang et al. (2019) Effects of nickel and cobalt on methane production and methanogen abundance and diversity in paddy soil. PeerJ 7:e6274 https://doi.org/10.7717/peerj.6274
date submitted: 2018-05-30
date accepted: 2018-12-07
issued: 2019-01-17
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Wang
  given name: Tianwei
author list: Agent
  family name: Li
  given name: Zhaoxia
author list: Agent
  family name: Chen
  given name: Xueping
author list: Agent
  family name: Long
  given name: Xi-En
doi: 10.7717/peerj.6274
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-01-17
copyright: ©2019 Wang et al.
attribution name: Wang et al.

Evaluation of AAV-DJ vector for retinal gene therapy
type: item
type: AcademicArticle
description: Purpose The most common virus vector used in gene therapy research for ophthalmologic diseases is the adeno-associated virus (AAV) vector, which has been used successfully in a number of preclinical and clinical studies. It is important to evaluate novel AAV vectors in animal models for application of clinical gene therapy. The AAV-DJ (type 2/type 8/type 9 chimera) was engineered from shuffling eight different wild-type native viruses. In this study, we investigated the efficiency of gene transfer by AAV-DJ injections into the retina. Methods One microliter of AAV-2-CAGGS-EGFP or AAV-DJ-CAGGS-EGFP vector at a titer of 1.4 × 10e12 vg/ml was injected intravitreally or subretinally in each eye of C57BL/6 mice. We evaluated the transduction characteristics of AAV-2 and -DJ vectors using fluorescence microscopy and electroretinography. Results The results confirmed that AAV-DJ could deeply transfer gene to photoreceptor layer with intravitreal injection and has an efficient gene transfer to various cell types especially the Mueller cells in the retina. Retinal function was not affected by AAV-DJ infection or ectopic EGFP expression. Conclusions The AAV-DJ vector efficiently induces the reporter gene in both the inner and outer murine retina without functional toxicity. These data indicated that the AAV-DJ vector is a useful tool for the gene therapy research targeting retinal disorders.
format: application/pdf
format: text/html
creator: Yusaku Katada
creator: Kenta Kobayashi
creator: Kazuo Tsubota
creator: Toshihide Kurihara
subject: Virology
subject: Ophthalmology
description: doi:10.7717/peerj.6317
publisher: PeerJ Inc.
rights: © 2019 Katada et al.
abstract: Purpose The most common virus vector used in gene therapy research for ophthalmologic diseases is the adeno-associated virus (AAV) vector, which has been used successfully in a number of preclinical and clinical studies. It is important to evaluate novel AAV vectors in animal models for application of clinical gene therapy. The AAV-DJ (type 2/type 8/type 9 chimera) was engineered from shuffling eight different wild-type native viruses. In this study, we investigated the efficiency of gene transfer by AAV-DJ injections into the retina. Methods One microliter of AAV-2-CAGGS-EGFP or AAV-DJ-CAGGS-EGFP vector at a titer of 1.4 × 10e12 vg/ml was injected intravitreally or subretinally in each eye of C57BL/6 mice. We evaluated the transduction characteristics of AAV-2 and -DJ vectors using fluorescence microscopy and electroretinography. Results The results confirmed that AAV-DJ could deeply transfer gene to photoreceptor layer with intravitreal injection and has an efficient gene transfer to various cell types especially the Mueller cells in the retina. Retinal function was not affected by AAV-DJ infection or ectopic EGFP expression. Conclusions The AAV-DJ vector efficiently induces the reporter gene in both the inner and outer murine retina without functional toxicity. These data indicated that the AAV-DJ vector is a useful tool for the gene therapy research targeting retinal disorders.
bibliographic citation: Katada et al. (2019) Evaluation of AAV-DJ vector for retinal gene therapy. PeerJ 7:e6317 https://doi.org/10.7717/peerj.6317
date submitted: 2018-10-15
date accepted: 2018-12-19
issued: 2019-01-17
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Katada
  given name: Yusaku
author list: Agent
  family name: Kobayashi
  given name: Kenta
author list: Agent
  family name: Tsubota
  given name: Kazuo
author list: Agent
  family name: Kurihara
  given name: Toshihide
doi: 10.7717/peerj.6317
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-01-17
copyright: ©2019 Katada et al.
attribution name: Katada et al.

Putatively asexual chrysophytes have meiotic genes: evidence from transcriptomic data
type: item
type: AcademicArticle
description: Chrysophytes are a large group of heterotrophic, phototrophic, or even mixotrophic protists that are abundant in aquatic as well as terrestrial environments. Although much is known about chrysophyte biology and ecology, it is unknown if they are sexual or not. Here we use available transcriptomes of 18 isolates of 15 putatively asexual species to inventory the presence of genes used in meiosis. Since we were able to detect a set of nine meiosis-specific and 29 meiosis-related genes shared by the chrysophytes, we conclude that they are secretively sexual and therefore should be investigated further using genome sequencing to uncover any missed genes from the transcriptomes.
format: application/pdf
format: text/html
creator: Diana Kraus
creator: Jingyun Chi
creator: Jens Boenigk
creator: Daniela Beisser
creator: Nadine Graupner
creator: Micah Dunthorn
subject: Biodiversity
subject: Evolutionary Studies
subject: Microbiology
description: doi:10.7717/peerj.5894
publisher: PeerJ Inc.
rights: © 2019 Kraus et al.
abstract: Chrysophytes are a large group of heterotrophic, phototrophic, or even mixotrophic protists that are abundant in aquatic as well as terrestrial environments. Although much is known about chrysophyte biology and ecology, it is unknown if they are sexual or not. Here we use available transcriptomes of 18 isolates of 15 putatively asexual species to inventory the presence of genes used in meiosis. Since we were able to detect a set of nine meiosis-specific and 29 meiosis-related genes shared by the chrysophytes, we conclude that they are secretively sexual and therefore should be investigated further using genome sequencing to uncover any missed genes from the transcriptomes.
bibliographic citation: Kraus et al. (2019) Putatively asexual chrysophytes have meiotic genes: evidence from transcriptomic data. PeerJ 6:e5894 https://doi.org/10.7717/peerj.5894
date submitted: 2018-07-05
date accepted: 2018-10-08
issued: 2019-01-16
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Kraus
  given name: Diana
author list: Agent
  family name: Chi
  given name: Jingyun
author list: Agent
  family name: Boenigk
  given name: Jens
author list: Agent
  family name: Beisser
  given name: Daniela
author list: Agent
  family name: Graupner
  given name: Nadine
author list: Agent
  family name: Dunthorn
  given name: Micah
doi: 10.7717/peerj.5894
volume: 6
issn: 2167-8359
publication name: PeerJ
publication date: 2019-01-16
copyright: © 2019 Kraus et al.
attribution name: Kraus et al.

Targeted inactivation of Salmonella Agona metabolic genes by group II introns and in vivo assessment of pathogenicity and anti-tumour activity in mouse model
type: item
type: AcademicArticle
description: The fight against cancer has been a never-ending battle. Limitations of conventional therapies include lack of selectivity, poor penetration and highly toxic to the host. Using genetically modified bacteria as a tumour therapy agent has gained the interest of scientist from the past few decades. Low virulence and highly tolerability of Salmonella spp. in animals and humans make it as the most studied pathogen with regards to anti-tumour therapy. The present study aims to construct a genetically modified S. Agona auxotroph as an anti-tumour agent. LeuB and ArgD metabolic genes in ΔSopBΔSopD double knockout S. Agona were successfully knocked out using a Targetron gene knockout system. The knockout was confirmed by colony PCR and the strains were characterized in vitro and in vivo. The knockout of metabolic genes causes significant growth defect in M9 minimal media. Quadruple knockout ΔSopBΔSopDΔLeuBΔArgD (BDLA) exhibited lowest virulence among all of the strains in all parameters including bacterial load, immunity profile and histopathology studies. In vivo anti-tumour study on colorectal tumour bearing-BALB/c mice revealed that all strains of S. Agona were able to suppress the growth of the large solid tumour as compared with negative control and ΔLeuBΔArgD (LA) and BDLA auxotroph showed better efficacy. Interestingly, higher level of tumour growth suppression was noticed in large tumour. However, multiple administration of bacteria dosage did not increase the tumour suppression efficacy. In this study, the virulence of BDLA knockout strain was slightly reduced and tumour growth suppression efficacy was successfully enhanced, which provide a valuable starting point for the development of S. Agona as anti-tumour agent.
format: application/pdf
format: text/html
creator: Chin Piaw Gwee
creator: Chai Hoon Khoo
creator: Swee Keong Yeap
creator: Geok Chin Tan
creator: Yoke Kqueen Cheah
subject: Bioengineering
subject: Biotechnology
subject: Microbiology
subject: Molecular Biology
subject: Oncology
description: doi:10.7717/peerj.5989
publisher: PeerJ Inc.
rights: © 2019 Gwee et al.
abstract: The fight against cancer has been a never-ending battle. Limitations of conventional therapies include lack of selectivity, poor penetration and highly toxic to the host. Using genetically modified bacteria as a tumour therapy agent has gained the interest of scientist from the past few decades. Low virulence and highly tolerability of Salmonella spp. in animals and humans make it as the most studied pathogen with regards to anti-tumour therapy. The present study aims to construct a genetically modified S. Agona auxotroph as an anti-tumour agent. LeuB and ArgD metabolic genes in ΔSopBΔSopD double knockout S. Agona were successfully knocked out using a Targetron gene knockout system. The knockout was confirmed by colony PCR and the strains were characterized in vitro and in vivo. The knockout of metabolic genes causes significant growth defect in M9 minimal media. Quadruple knockout ΔSopBΔSopDΔLeuBΔArgD (BDLA) exhibited lowest virulence among all of the strains in all parameters including bacterial load, immunity profile and histopathology studies. In vivo anti-tumour study on colorectal tumour bearing-BALB/c mice revealed that all strains of S. Agona were able to suppress the growth of the large solid tumour as compared with negative control and ΔLeuBΔArgD (LA) and BDLA auxotroph showed better efficacy. Interestingly, higher level of tumour growth suppression was noticed in large tumour. However, multiple administration of bacteria dosage did not increase the tumour suppression efficacy. In this study, the virulence of BDLA knockout strain was slightly reduced and tumour growth suppression efficacy was successfully enhanced, which provide a valuable starting point for the development of S. Agona as anti-tumour agent.
bibliographic citation: Gwee et al. (2019) Targeted inactivation of Salmonella Agona metabolic genes by group II introns and in vivo assessment of pathogenicity and anti-tumour activity in mouse model. PeerJ 7:e5989 https://doi.org/10.7717/peerj.5989
date submitted: 2018-05-21
date accepted: 2018-10-22
issued: 2019-01-16
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Gwee
  given name: Chin Piaw
author list: Agent
  family name: Khoo
  given name: Chai Hoon
author list: Agent
  family name: Yeap
  given name: Swee Keong
author list: Agent
  family name: Tan
  given name: Geok Chin
author list: Agent
  family name: Cheah
  given name: Yoke Kqueen
doi: 10.7717/peerj.5989
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-01-16
copyright: ©2019 Gwee et al.
attribution name: Gwee et al.

Inverse modelling for predicting both water and nitrate movement in a structured-clay soil (Red Ferrosol)
type: item
type: AcademicArticle
description: Soil physical parameter calculation by inverse modelling provides an indirect way of estimating the unsaturated hydraulic properties of soils. However many measurements are needed to provide sufficient data to determine unknown parameters. The objective of this research was to assess the use of unsaturated water flow and solute transport experiments, in horizontal packed soil columns, to estimate the parameters that govern water flow and solute transport. The derived parameters are then used to predict water infiltration and solute migration in a repacked soil wedge. Horizontal columns packed with Red Ferrosol were used in a nitrate diffusion experiment to estimate either three or six parameters of the van Genuchten–Mualem equation while keeping residual and saturated water content, and saturated hydraulic conductivity fixed to independently measured values. These parameters were calculated using the inverse optimisation routines in Hydrus 1D. Nitrate concentrations measured along the horizontal soil columns were used to independently determine the Langmuir adsorption isotherm. The soil hydraulic properties described by the van Genuchten–Mualem equation, and the NO3– adsorption isotherm, were then used to predict water and NO3– distributions from a point-source in two 3D flow scenarios. The use of horizontal columns of repacked soil and inverse modelling to quantify the soil water retention curve was found to be a simple and effective method for determining soil hydraulic properties of Red Ferrosols. These generated parameters supported subsequent testing of interactive flow and reactive transport processes under dynamic flow conditions.
format: application/pdf
format: text/html
creator: James M. Kirkham
creator: Christopher J. Smith
creator: Richard B. Doyle
creator: Philip H. Brown
subject: Agricultural Science
subject: Soil Science
subject: Environmental Impacts
description: doi:10.7717/peerj.6002
publisher: PeerJ Inc.
rights: © 2019 Kirkham et al.
abstract: Soil physical parameter calculation by inverse modelling provides an indirect way of estimating the unsaturated hydraulic properties of soils. However many measurements are needed to provide sufficient data to determine unknown parameters. The objective of this research was to assess the use of unsaturated water flow and solute transport experiments, in horizontal packed soil columns, to estimate the parameters that govern water flow and solute transport. The derived parameters are then used to predict water infiltration and solute migration in a repacked soil wedge. Horizontal columns packed with Red Ferrosol were used in a nitrate diffusion experiment to estimate either three or six parameters of the van Genuchten–Mualem equation while keeping residual and saturated water content, and saturated hydraulic conductivity fixed to independently measured values. These parameters were calculated using the inverse optimisation routines in Hydrus 1D. Nitrate concentrations measured along the horizontal soil columns were used to independently determine the Langmuir adsorption isotherm. The soil hydraulic properties described by the van Genuchten–Mualem equation, and the NO3– adsorption isotherm, were then used to predict water and NO3– distributions from a point-source in two 3D flow scenarios. The use of horizontal columns of repacked soil and inverse modelling to quantify the soil water retention curve was found to be a simple and effective method for determining soil hydraulic properties of Red Ferrosols. These generated parameters supported subsequent testing of interactive flow and reactive transport processes under dynamic flow conditions.
bibliographic citation: Kirkham et al. (2019) Inverse modelling for predicting both water and nitrate movement in a structured-clay soil (Red Ferrosol). PeerJ 6:e6002 https://doi.org/10.7717/peerj.6002
date submitted: 2018-03-30
date accepted: 2018-10-25
issued: 2019-01-16
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Kirkham
  given name: James M.
author list: Agent
  family name: Smith
  given name: Christopher J.
author list: Agent
  family name: Doyle
  given name: Richard B.
author list: Agent
  family name: Brown
  given name: Philip H.
doi: 10.7717/peerj.6002
volume: 6
issn: 2167-8359
publication name: PeerJ
publication date: 2019-01-16
copyright: © 2019 Kirkham et al.
attribution name: Kirkham et al.

Growth estimation of the larger foraminifer Heterostegina depressa by means of population dynamics
type: item
type: AcademicArticle
description: In Heterostegina depressa, the flagship species of laboratory investigations of larger benthic foraminifera (LBF) since the 70’s, the timing of reproduction, longevity and natural chamber building rates are still understudied. A recently developed method, the natural laboratory (sensu Hohenegger), has been applied on H. depressa populations from Sesoko Jima, NW Okinawa, Japan. An averaged chamber building rate and longevity of H. depressa were calculated based on 17 monthly samplings at fixed stations. All samples were collected at 20 and 50 m water depths using SCUBA. Live populations were dried and investigated by microCT. The monthly frequency distributions of chamber numbers and test diameters have been decomposed in normally distributed components. For each month, mean and standard deviations of the components were used to calculate the maximum chamber number and maximum test diameter. Based on these values, the natural chamber building rate (CBR) or diameter increase rate (DIR) could be estimated using the Michaelis-Menten function. CBR and DIR were inverted to estimate the ‘birthdate’ of all investigated individuals. Based on frequencies of these ‘birthdates’, main reproduction events could be detected and compared to the reproduction timing of other subtropical and tropical LBF taxa. Furthermore, peaks in reproduction could be linked to monsoon wet seasons (=“rainy seasons”) and winter rains.
format: application/pdf
format: text/html
creator: Wolfgang Eder
creator: Julia Woeger
creator: Shunichi Kinoshita
creator: Johann Hohenegger
creator: Antonino Briguglio
subject: Marine Biology
subject: Paleontology
subject: Population Biology
description: doi:10.7717/peerj.6096
publisher: PeerJ Inc.
rights: © 2019 Eder et al.
abstract: In Heterostegina depressa, the flagship species of laboratory investigations of larger benthic foraminifera (LBF) since the 70’s, the timing of reproduction, longevity and natural chamber building rates are still understudied. A recently developed method, the natural laboratory (sensu Hohenegger), has been applied on H. depressa populations from Sesoko Jima, NW Okinawa, Japan. An averaged chamber building rate and longevity of H. depressa were calculated based on 17 monthly samplings at fixed stations. All samples were collected at 20 and 50 m water depths using SCUBA. Live populations were dried and investigated by microCT. The monthly frequency distributions of chamber numbers and test diameters have been decomposed in normally distributed components. For each month, mean and standard deviations of the components were used to calculate the maximum chamber number and maximum test diameter. Based on these values, the natural chamber building rate (CBR) or diameter increase rate (DIR) could be estimated using the Michaelis-Menten function. CBR and DIR were inverted to estimate the ‘birthdate’ of all investigated individuals. Based on frequencies of these ‘birthdates’, main reproduction events could be detected and compared to the reproduction timing of other subtropical and tropical LBF taxa. Furthermore, peaks in reproduction could be linked to monsoon wet seasons (=“rainy seasons”) and winter rains.
bibliographic citation: Eder et al. (2019) Growth estimation of the larger foraminifer Heterostegina depressa by means of population dynamics. PeerJ 6:e6096 https://doi.org/10.7717/peerj.6096
date submitted: 2018-01-05
date accepted: 2018-11-08
issued: 2019-01-16
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Eder
  given name: Wolfgang
author list: Agent
  family name: Woeger
  given name: Julia
author list: Agent
  family name: Kinoshita
  given name: Shunichi
author list: Agent
  family name: Hohenegger
  given name: Johann
author list: Agent
  family name: Briguglio
  given name: Antonino
doi: 10.7717/peerj.6096
volume: 6
issn: 2167-8359
publication name: PeerJ
publication date: 2019-01-16
copyright: ©2019 Eder et al.
attribution name: Eder et al.

Recognition of species groups of Naupactus Dejean (Coleoptera: Curculionidae) from Argentina and neighboring countries
type: item
type: AcademicArticle
description: Naupactus Dejean is the most diverse genus of the tribe Naupactini (Curculionidae: Entiminae), with more than 200 species occurring in South America, of which about 40 range in Argentina and neighboring countries. The Argentinean species treated herein were classified into nine groups having different biogeographic patterns: (1) the groups of Naupactus xanthographus, N. delicatulus and N. auricinctus mainly occur in northeastern Argentina (Misiones province) and reach the highest species diversity in the Atlantic and Parana forests of Brazil; (2) the groups of N. hirtellus, N. cinereidorsum, N. rivulosus and N. tarsalis show the highest species diversity in the Chacoan biogeographic province and also occur in the Yungas, Espinal, Monte, Parana forest (Argentina) and Cerrado (Brazil); (3) the groups of N. leucoloma and N. purpureoviolaceus have the highest species diversity in the Pampean biogeographic province, being also present in adjoining areas, mainly Chaco, Espinal, Monte and Parana forest. We provide descriptions, a dichotomous key, habitus photographs and line drawings of genitalia for the identification of the nine species groups, and a list of the Argentinean species from each group, together with their abbreviated synonymies, updated geographic distributions (including six new country records and several state/province records) and host plant associations. We discuss the characters that allow the separation of the species groups in a geographic distribution context, and provide information on species reassigned to genera other than Naupactus; among these, we transferred N. cephalotes (Hustache) to the tribe Tanymecini, genus Eurymetopellus, establishing the new combination Eurymetopellus cephalotes.
format: application/pdf
format: text/html
creator: María G. del Río
creator: Analía A. Lanteri
subject: Entomology
subject: Taxonomy
description: doi:10.7717/peerj.6196
publisher: PeerJ Inc.
rights: © 2019 del Río and Lanteri
abstract: Naupactus Dejean is the most diverse genus of the tribe Naupactini (Curculionidae: Entiminae), with more than 200 species occurring in South America, of which about 40 range in Argentina and neighboring countries. The Argentinean species treated herein were classified into nine groups having different biogeographic patterns: (1) the groups of Naupactus xanthographus, N. delicatulus and N. auricinctus mainly occur in northeastern Argentina (Misiones province) and reach the highest species diversity in the Atlantic and Parana forests of Brazil; (2) the groups of N. hirtellus, N. cinereidorsum, N. rivulosus and N. tarsalis show the highest species diversity in the Chacoan biogeographic province and also occur in the Yungas, Espinal, Monte, Parana forest (Argentina) and Cerrado (Brazil); (3) the groups of N. leucoloma and N. purpureoviolaceus have the highest species diversity in the Pampean biogeographic province, being also present in adjoining areas, mainly Chaco, Espinal, Monte and Parana forest. We provide descriptions, a dichotomous key, habitus photographs and line drawings of genitalia for the identification of the nine species groups, and a list of the Argentinean species from each group, together with their abbreviated synonymies, updated geographic distributions (including six new country records and several state/province records) and host plant associations. We discuss the characters that allow the separation of the species groups in a geographic distribution context, and provide information on species reassigned to genera other than Naupactus; among these, we transferred N. cephalotes (Hustache) to the tribe Tanymecini, genus Eurymetopellus, establishing the new combination Eurymetopellus cephalotes.
bibliographic citation: del Río et al. (2019) Recognition of species groups of Naupactus Dejean (Coleoptera: Curculionidae) from Argentina and neighboring countries. PeerJ 6:e6196 https://doi.org/10.7717/peerj.6196
date submitted: 2018-09-27
date accepted: 2018-12-01
issued: 2019-01-16
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: del Río
  given name: María G.
author list: Agent
  family name: Lanteri
  given name: Analía A.
doi: 10.7717/peerj.6196
volume: 6
issn: 2167-8359
publication name: PeerJ
publication date: 2019-01-16
copyright: © 2019 del Río and Lanteri
attribution name: del Río and Lanteri

Registered reports: an early example and analysis
type: item
type: AcademicArticle
description: The recent ‘replication crisis’ in psychology has focused attention on ways of increasing methodological rigor within the behavioral sciences. Part of this work has involved promoting ‘Registered Reports’, wherein journals peer review papers prior to data collection and publication. Although this approach is usually seen as a relatively recent development, we note that a prototype of this publishing model was initiated in the mid-1970s by parapsychologist Martin Johnson in the European Journal of Parapsychology (EJP). A retrospective and observational comparison of Registered and non-Registered Reports published in the EJP during a seventeen-year period provides circumstantial evidence to suggest that the approach helped to reduce questionable research practices. This paper aims both to bring Johnson’s pioneering work to a wider audience, and to investigate the positive role that Registered Reports may play in helping to promote higher methodological and statistical standards.
format: application/pdf
format: text/html
creator: Richard Wiseman
creator: Caroline Watt
creator: Diana Kornbrot
subject: Psychiatry and Psychology
subject: Statistics
description: doi:10.7717/peerj.6232
publisher: PeerJ Inc.
rights: © 2019 Wiseman et al.
abstract: The recent ‘replication crisis’ in psychology has focused attention on ways of increasing methodological rigor within the behavioral sciences. Part of this work has involved promoting ‘Registered Reports’, wherein journals peer review papers prior to data collection and publication. Although this approach is usually seen as a relatively recent development, we note that a prototype of this publishing model was initiated in the mid-1970s by parapsychologist Martin Johnson in the European Journal of Parapsychology (EJP). A retrospective and observational comparison of Registered and non-Registered Reports published in the EJP during a seventeen-year period provides circumstantial evidence to suggest that the approach helped to reduce questionable research practices. This paper aims both to bring Johnson’s pioneering work to a wider audience, and to investigate the positive role that Registered Reports may play in helping to promote higher methodological and statistical standards.
bibliographic citation: Wiseman et al. (2019) Registered reports: an early example and analysis. PeerJ 7:e6232 https://doi.org/10.7717/peerj.6232
date submitted: 2018-09-10
date accepted: 2018-12-07
issued: 2019-01-16
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Wiseman
  given name: Richard
author list: Agent
  family name: Watt
  given name: Caroline
author list: Agent
  family name: Kornbrot
  given name: Diana
doi: 10.7717/peerj.6232
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-01-16
copyright: ©2019 Wiseman et al.
attribution name: Wiseman et al.

Termite mound architecture regulates nest temperature and correlates with species identities of symbiotic fungi
type: item
type: AcademicArticle
description: Background Large and complex mounds built by termites of the genus Macrotermes characterize many dry African landscapes, including the savannas, bushlands, and dry forests of the Tsavo Ecosystem in southern Kenya. The termites live in obligate symbiosis with filamentous fungi of the genus Termitomyces. The insects collect dead plant material from their environment and deposit it into their nests where indigestible cell wall compounds are effectively decomposed by the fungus. Above-ground mounds are built to enhance nest ventilation and to maintain nest interior microclimates favorable for fungal growth. Objectives In Tsavo Ecosystem two Macrotermes species associate with three different Termitomyces symbionts, always with a monoculture of one fungal species within each termite nest. As mound architecture differs considerably both between and within termite species we explored potential relationships between nest thermoregulatory strategies and species identity of fungal symbionts. Methods External dimensions were measured from 164 Macrotermes mounds and the cultivated Termitomyces species were identified by sequencing internal transcribed spacer (ITS) region of ribosomal DNA. We also recorded the annual temperature regimes of several termite mounds to determine relations between mound architecture and nest temperatures during different seasons. Results Mound architecture had a major effect on nest temperatures. Relatively cool temperatures were always recorded from large mounds with open ventilation systems, while the internal temperatures of mounds with closed ventilation systems and small mounds with open ventilation systems were consistently higher. The distribution of the three fungal symbionts in different mounds was not random, with one fungal species confined to “hot nests.” Conclusions Our results indicate that different Termitomyces species have different temperature requirements, and that one of the cultivated species is relatively intolerant of low temper…
format: application/pdf
format: text/html
creator: Risto Vesala
creator: Anni Harjuntausta
creator: Anu Hakkarainen
creator: Petri Rönnholm
creator: Petri Pellikka
creator: Jouko Rikkinen
subject: Animal Behavior
subject: Ecology
subject: Entomology
subject: Mycology
description: doi:10.7717/peerj.6237
publisher: PeerJ Inc.
rights: © 2019 Vesala et al.
abstract: Background Large and complex mounds built by termites of the genus Macrotermes characterize many dry African landscapes, including the savannas, bushlands, and dry forests of the Tsavo Ecosystem in southern Kenya. The termites live in obligate symbiosis with filamentous fungi of the genus Termitomyces. The insects collect dead plant material from their environment and deposit it into their nests where indigestible cell wall compounds are effectively decomposed by the fungus. Above-ground mounds are built to enhance nest ventilation and to maintain nest interior microclimates favorable for fungal growth. Objectives In Tsavo Ecosystem two Macrotermes species associate with three different Termitomyces symbionts, always with a monoculture of one fungal species within each termite nest. As mound architecture differs considerably both between and within termite species we explored potential relationships between nest thermoregulatory strategies and species identity of fungal symbionts. Methods External dimensions were measured from 164 Macrotermes mounds and the cultivated Termitomyces species were identified by sequencing internal transcribed spacer (ITS) region of ribosomal DNA. We also recorded the annual temperature regimes of several termite mounds to determine relations between mound architecture and nest temperatures during different seasons. Results Mound architecture had a major effect on nest temperatures. Relatively cool temperatures were always recorded from large mounds with open ventilation systems, while the internal temperatures of mounds with closed ventilation systems and small mounds with open ventilation systems were consistently higher. The distribution of the three fungal symbionts in different mounds was not random, with one fungal species confined to “hot nests.” Conclusions Our results indicate that different Termitomyces species have different temperature requirements, and that one of the cultivated species is relatively intolerant of low temper…
bibliographic citation: Vesala et al. (2019) Termite mound architecture regulates nest temperature and correlates with species identities of symbiotic fungi. PeerJ 6:e6237 https://doi.org/10.7717/peerj.6237
date submitted: 2018-04-17
date accepted: 2018-12-07
issued: 2019-01-16
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Vesala
  given name: Risto
author list: Agent
  family name: Harjuntausta
  given name: Anni
author list: Agent
  family name: Hakkarainen
  given name: Anu
author list: Agent
  family name: Rönnholm
  given name: Petri
author list: Agent
  family name: Pellikka
  given name: Petri
author list: Agent
  family name: Rikkinen
  given name: Jouko
doi: 10.7717/peerj.6237
volume: 6
issn: 2167-8359
publication name: PeerJ
publication date: 2019-01-16
copyright: © 2019 Vesala et al.
attribution name: Vesala et al.

Screening of reference genes in real-time PCR for Radopholus similis
type: item
type: AcademicArticle
description: Six candidate reference genes were chosen from the transcriptome database of Radopholus similis using the bioinformatics method, including four conventional reference genes (actin, Eukaryotic translation initiation factor 5A (eIF5A), Tubulin alpha (a-tubulin), ubiquitin (UBI)) and two new candidate reference genes (Ribosomal protein S21 (Rps21) and Serine/threonine protein phosphatase PP1-β catalytic subunit (β-PP1)). In addition, a traditional reference gene 18S ribosomal RNA (18S rRNA) obtained from NCBI databases was also added to the analysis. Real-time PCR was used to detect the expression of seven candidate reference genes in six populations of R. similis and four developmental stages (female, male, larva and egg) of a population. The stability of the expression of candidate genes was evaluated by three software programs, BestKeeper, geNorm and NormFinder. The results showed that eIF5A is the most suitable reference gene for gene functional research of different populations, while both Rps21 and eIF5A are the most suitable reference genes for different developmental stages of a population. Therefore, eIF5A is the best reference gene for studying R. similis. However, one defect of this study is that only seven candidate reference genes were analyzed; ideally, more genes should be tested.
format: application/pdf
format: text/html
creator: Jun-Yi Li
creator: Wan-Zhu Chen
creator: Si-Hua Yang
creator: Chun-Ling Xu
creator: Xin Huang
creator: Chun Chen
creator: Hui Xie
subject: Agricultural Science
subject: Bioinformatics
subject: Molecular Biology
description: doi:10.7717/peerj.6253
publisher: PeerJ Inc.
rights: © 2019 Li et al.
abstract: Six candidate reference genes were chosen from the transcriptome database of Radopholus similis using the bioinformatics method, including four conventional reference genes (actin, Eukaryotic translation initiation factor 5A (eIF5A), Tubulin alpha (a-tubulin), ubiquitin (UBI)) and two new candidate reference genes (Ribosomal protein S21 (Rps21) and Serine/threonine protein phosphatase PP1-β catalytic subunit (β-PP1)). In addition, a traditional reference gene 18S ribosomal RNA (18S rRNA) obtained from NCBI databases was also added to the analysis. Real-time PCR was used to detect the expression of seven candidate reference genes in six populations of R. similis and four developmental stages (female, male, larva and egg) of a population. The stability of the expression of candidate genes was evaluated by three software programs, BestKeeper, geNorm and NormFinder. The results showed that eIF5A is the most suitable reference gene for gene functional research of different populations, while both Rps21 and eIF5A are the most suitable reference genes for different developmental stages of a population. Therefore, eIF5A is the best reference gene for studying R. similis. However, one defect of this study is that only seven candidate reference genes were analyzed; ideally, more genes should be tested.
bibliographic citation: Li et al. (2019) Screening of reference genes in real-time PCR for Radopholus similis. PeerJ 7:e6253 https://doi.org/10.7717/peerj.6253
date submitted: 2018-09-28
date accepted: 2018-12-05
issued: 2019-01-16
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Li
  given name: Jun-Yi
author list: Agent
  family name: Chen
  given name: Wan-Zhu
author list: Agent
  family name: Yang
  given name: Si-Hua
author list: Agent
  family name: Xu
  given name: Chun-Ling
author list: Agent
  family name: Huang
  given name: Xin
author list: Agent
  family name: Chen
  given name: Chun
author list: Agent
  family name: Xie
  given name: Hui
doi: 10.7717/peerj.6253
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-01-16
copyright: ©2019 Li et al.
attribution name: Li et al.

Foraging habitat choice of White-tailed Tropicbirds revealed by fine-scale GPS tracking and remote sensing
type: item
type: AcademicArticle
description: Background The introduction of animal tracking technology has rapidly advanced our understanding of seabird foraging ecology. Tracking data is particularly powerful when combined with oceanographic information derived from satellite remote sensing, allowing insights into the functional mechanisms of marine ecosystems. While this framework has been used extensively over the last two decades, there are still vast ocean regions and many seabird species for which information is scarce, particularly in tropical oceans. Methods In this study we tracked the movement at high GPS recording frequency of 15 White-tailed Tropicbirds (Phaethon lepturus) during chick-rearing from a colony in Fernando de Noronha (offshore of Northeast Brazil). Flight behaviours of travelling and searching for food were derived from GPS data and examined in relation to satellite-sensed oceanographic variables (sea surface temperature, turbidity and chlorophyll-a concentration). Results White-tailed Tropicbirds showed marked preference for clear and warm sea surface waters, which are indicative of low primary productivity but are likely the best habitat for preying upon flying fish. Discussion These findings are consistent with previous studies showing that foraging habitat choices of tropical seabirds may not be driven by primary productivity, as has been widely shown for non-tropical species.
format: application/pdf
format: text/html
creator: Carlos D. Santos
creator: Leila F.A.S. Campos
creator: Márcio A. Efe
subject: Biogeography
subject: Conservation Biology
subject: Ecology
subject: Marine Biology
description: doi:10.7717/peerj.6261
publisher: PeerJ Inc.
rights: © 2019 Santos et al.
abstract: Background The introduction of animal tracking technology has rapidly advanced our understanding of seabird foraging ecology. Tracking data is particularly powerful when combined with oceanographic information derived from satellite remote sensing, allowing insights into the functional mechanisms of marine ecosystems. While this framework has been used extensively over the last two decades, there are still vast ocean regions and many seabird species for which information is scarce, particularly in tropical oceans. Methods In this study we tracked the movement at high GPS recording frequency of 15 White-tailed Tropicbirds (Phaethon lepturus) during chick-rearing from a colony in Fernando de Noronha (offshore of Northeast Brazil). Flight behaviours of travelling and searching for food were derived from GPS data and examined in relation to satellite-sensed oceanographic variables (sea surface temperature, turbidity and chlorophyll-a concentration). Results White-tailed Tropicbirds showed marked preference for clear and warm sea surface waters, which are indicative of low primary productivity but are likely the best habitat for preying upon flying fish. Discussion These findings are consistent with previous studies showing that foraging habitat choices of tropical seabirds may not be driven by primary productivity, as has been widely shown for non-tropical species.
bibliographic citation: Santos et al. (2019) Foraging habitat choice of White-tailed Tropicbirds revealed by fine-scale GPS tracking and remote sensing. PeerJ 7:e6261 https://doi.org/10.7717/peerj.6261
date submitted: 2018-09-13
date accepted: 2018-12-11
issued: 2019-01-16
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Santos
  given name: Carlos D.
author list: Agent
  family name: Campos
  given name: Leila F.A.S.
author list: Agent
  family name: Efe
  given name: Márcio A.
doi: 10.7717/peerj.6261
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-01-16
copyright: ©2019 Santos et al.
attribution name: Santos et al.

Effects of table tennis multi-ball training on dynamic posture control
type: item
type: AcademicArticle
description: Background Prior to the 2017 table tennis season, each participant performed the anterior, posteromedial, and posterolateral the star excursion balance test (SEBT) reach distances in a randomized order. The aim of this study was to assess the effects of table tennis multi-ball training and dynamic balance on performance measures of the SEBT for the male and female. Methods The limb lengths of the 12 table tennis athletes were measured bilaterally in the study. Besides warm-up end, the data of this study were recorded at a regular interval at approximately 16 min for the entire multi-ball training session, and they were defined as Phase I, Phase II, Phase II, respectively. The Borg rating of perceived exertion (RPE) scale was used to document the degree of physical strain. Results Reaching distances showed a decrease with training progression in all directions. Compared with the male table tennis athletes, the females showed poorer dynamic posture control, particularly when the free limb was considered with the right-leg stance toward posterolateral and posteromedial directions in phase I. Discussion This study suggests that during table tennis multi-ball training the male should have a regulatory protocol to compensate the deficit observed in phase II, but the females should be given the protocol in phase I.
format: application/pdf
format: text/html
creator: Yaodong Gu
creator: Changxiao Yu
creator: Shirui Shao
creator: Julien S. Baker
subject: Bioengineering
subject: Kinesiology
description: doi:10.7717/peerj.6262
publisher: PeerJ Inc.
rights: © 2019 Gu et al.
abstract: Background Prior to the 2017 table tennis season, each participant performed the anterior, posteromedial, and posterolateral the star excursion balance test (SEBT) reach distances in a randomized order. The aim of this study was to assess the effects of table tennis multi-ball training and dynamic balance on performance measures of the SEBT for the male and female. Methods The limb lengths of the 12 table tennis athletes were measured bilaterally in the study. Besides warm-up end, the data of this study were recorded at a regular interval at approximately 16 min for the entire multi-ball training session, and they were defined as Phase I, Phase II, Phase II, respectively. The Borg rating of perceived exertion (RPE) scale was used to document the degree of physical strain. Results Reaching distances showed a decrease with training progression in all directions. Compared with the male table tennis athletes, the females showed poorer dynamic posture control, particularly when the free limb was considered with the right-leg stance toward posterolateral and posteromedial directions in phase I. Discussion This study suggests that during table tennis multi-ball training the male should have a regulatory protocol to compensate the deficit observed in phase II, but the females should be given the protocol in phase I.
bibliographic citation: Gu et al. (2019) Effects of table tennis multi-ball training on dynamic posture control. PeerJ 6:e6262 https://doi.org/10.7717/peerj.6262
date submitted: 2018-10-24
date accepted: 2018-12-11
issued: 2019-01-16
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Gu
  given name: Yaodong
author list: Agent
  family name: Yu
  given name: Changxiao
author list: Agent
  family name: Shao
  given name: Shirui
author list: Agent
  family name: Baker
  given name: Julien S.
doi: 10.7717/peerj.6262
volume: 6
issn: 2167-8359
publication name: PeerJ
publication date: 2019-01-16
copyright: ©2019 Gu et al.
attribution name: Gu et al.

Individual and flock immunity responses of naïve ducks on smallholder farms after vaccination with H5N1 Avian Influenza vaccine: a study in a province of the Mekong Delta, Vietnam
type: item
type: AcademicArticle
description: In Vietnam, vaccination has played a crucial role in the national strategy for the prevention and control of H5 highly pathogenic avian influenza (HPAI). This study aimed to evaluate antibody responses of immunologically naïve domestic ducks to H5N1 avian influenza vaccine currently used in the national mass vaccination program of Vietnam. Blood samples of 166 ducks reared on smallholder farms were individually collected at three sampling time points, namely, right before vaccination, 21 days after primary vaccination, and 21 days after booster vaccination. Vaccine-induced antibody titers of duck sera were measured by the hemagglutination inhibition assay. Temporal differences in mean antibody titers were analyzed using the generalized least-squares method. No sampled ducks showed anti-H5 seropositivity pre-vaccination. The geometric mean titer (GMT) of the vaccinated ducks was 5.30 after primary vaccination, with 80% of the vaccinated ducks showing seropositivity. This result indicates that the immunity of duck flocks met the targets of the national poultry H5N1 HPAI mass vaccination program. GMT and seropositive rates of the ducks were 6.48 and 96.3%, respectively, after booster vaccination, which were significantly higher than those after primary vaccination. Flock-level seroprotection rate significantly increased from 68% to 84.7%, whereas variability in GMT titers decreased from 34.87% to 26.3%. This study provided important information on humoral immune responses of ducks to the currently used H5N1 vaccine under field conditions. Our findings may help guide veterinary authorities in planning effective vaccine protocols for the prevention and control of H5N1 in the target poultry population.
format: application/pdf
format: text/html
creator: Hoa Thi Thanh Huynh
creator: Liem Tan Truong
creator: Tongkorn Meeyam
creator: Hien Thanh Le
creator: Veerasak Punyapornwithaya
subject: Veterinary Medicine
subject: Immunology
description: doi:10.7717/peerj.6268
publisher: PeerJ Inc.
rights: © 2019 Huynh et al.
abstract: In Vietnam, vaccination has played a crucial role in the national strategy for the prevention and control of H5 highly pathogenic avian influenza (HPAI). This study aimed to evaluate antibody responses of immunologically naïve domestic ducks to H5N1 avian influenza vaccine currently used in the national mass vaccination program of Vietnam. Blood samples of 166 ducks reared on smallholder farms were individually collected at three sampling time points, namely, right before vaccination, 21 days after primary vaccination, and 21 days after booster vaccination. Vaccine-induced antibody titers of duck sera were measured by the hemagglutination inhibition assay. Temporal differences in mean antibody titers were analyzed using the generalized least-squares method. No sampled ducks showed anti-H5 seropositivity pre-vaccination. The geometric mean titer (GMT) of the vaccinated ducks was 5.30 after primary vaccination, with 80% of the vaccinated ducks showing seropositivity. This result indicates that the immunity of duck flocks met the targets of the national poultry H5N1 HPAI mass vaccination program. GMT and seropositive rates of the ducks were 6.48 and 96.3%, respectively, after booster vaccination, which were significantly higher than those after primary vaccination. Flock-level seroprotection rate significantly increased from 68% to 84.7%, whereas variability in GMT titers decreased from 34.87% to 26.3%. This study provided important information on humoral immune responses of ducks to the currently used H5N1 vaccine under field conditions. Our findings may help guide veterinary authorities in planning effective vaccine protocols for the prevention and control of H5N1 in the target poultry population.
bibliographic citation: Huynh et al. (2019) Individual and flock immunity responses of naïve ducks on smallholder farms after vaccination with H5N1 Avian Influenza vaccine: a study in a province of the Mekong Delta, Vietnam. PeerJ 7:e6268 https://doi.org/10.7717/peerj.6268
date submitted: 2018-10-09
date accepted: 2018-12-11
issued: 2019-01-16
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Huynh
  given name: Hoa Thi Thanh
author list: Agent
  family name: Truong
  given name: Liem Tan
author list: Agent
  family name: Meeyam
  given name: Tongkorn
author list: Agent
  family name: Le
  given name: Hien Thanh
author list: Agent
  family name: Punyapornwithaya
  given name: Veerasak
doi: 10.7717/peerj.6268
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-01-16
copyright: ©2019 Huynh et al.
attribution name: Huynh et al.

CRISPR/Cas9-mediated deletion of the Wiskott-Aldrich syndrome locus causes actin cytoskeleton disorganization in murine erythroleukemia cells
type: item
type: AcademicArticle
description: Wiskott-Aldrich syndrome (WAS) is a recessive X-linked inmmunodeficiency caused by loss-of-function mutations in the gene encoding the WAS protein (WASp). WASp plays an important role in the polymerization of the actin cytoskeleton in hematopoietic cells through activation of the Arp2/3 complex. In a previous study, we found that actin cytoskeleton proteins, including WASp, were silenced in murine erythroleukemia cells defective in differentiation. Here, we designed a CRISPR/Cas9 strategy to delete a 9.5-kb genomic region encompassing the Was gene in the X chromosome of murine erythroleukemia (MEL) cells. We show that Was-deficient MEL cells have a poor organization of the actin cytoskeleton that can be recovered by restoring Was expression. We found that whereas the total amount of actin protein was similar between wild-type and Was knockout MEL cells, the latter exhibited an altered ratio of monomeric G-actin to polymeric F-actin. We also demonstrate that Was overexpression can mediate the activation of Bruton’s tyrosine kinase. Overall, these findings support the role of WASp as a key regulator of F-actin in erythroid cells.
format: application/pdf
format: text/html
creator: Vanessa Fernández-Calleja
creator: María-José Fernández-Nestosa
creator: Pablo Hernández
creator: Jorge B. Schvartzman
creator: Dora B. Krimer
subject: Molecular Biology
subject: Hematology
description: doi:10.7717/peerj.6284
publisher: PeerJ Inc.
rights: © 2019 Fernández-Calleja et al.
abstract: Wiskott-Aldrich syndrome (WAS) is a recessive X-linked inmmunodeficiency caused by loss-of-function mutations in the gene encoding the WAS protein (WASp). WASp plays an important role in the polymerization of the actin cytoskeleton in hematopoietic cells through activation of the Arp2/3 complex. In a previous study, we found that actin cytoskeleton proteins, including WASp, were silenced in murine erythroleukemia cells defective in differentiation. Here, we designed a CRISPR/Cas9 strategy to delete a 9.5-kb genomic region encompassing the Was gene in the X chromosome of murine erythroleukemia (MEL) cells. We show that Was-deficient MEL cells have a poor organization of the actin cytoskeleton that can be recovered by restoring Was expression. We found that whereas the total amount of actin protein was similar between wild-type and Was knockout MEL cells, the latter exhibited an altered ratio of monomeric G-actin to polymeric F-actin. We also demonstrate that Was overexpression can mediate the activation of Bruton’s tyrosine kinase. Overall, these findings support the role of WASp as a key regulator of F-actin in erythroid cells.
bibliographic citation: Fernández-Calleja et al. (2019) CRISPR/Cas9-mediated deletion of the Wiskott-Aldrich syndrome locus causes actin cytoskeleton disorganization in murine erythroleukemia cells. PeerJ 7:e6284 https://doi.org/10.7717/peerj.6284
date submitted: 2018-08-30
date accepted: 2018-12-14
issued: 2019-01-16
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Fernández-Calleja
  given name: Vanessa
author list: Agent
  family name: Fernández-Nestosa
  given name: María-José
author list: Agent
  family name: Hernández
  given name: Pablo
author list: Agent
  family name: Schvartzman
  given name: Jorge B.
author list: Agent
  family name: Krimer
  given name: Dora B.
doi: 10.7717/peerj.6284
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-01-16
copyright: ©2019 Fernández-Calleja et al.
attribution name: Fernández-Calleja et al.

A new virus found in garlic virus complex is a member of possible novel genus of the family Betaflexiviridae (order Tymovirales)
type: item
type: AcademicArticle
description: Plant vegetative propagation strategies for agricultural crops cause the accumulation of viruses, resulting in the formation of virus complexes or communities. The cultivation of garlic is based on vegetative propagation and more than 13 virus species from the genera Potyvirus, Allexivirus and Carlavirus have been reported. Aiming for an unbiased identification of viruses from a garlic germplasm collection in Brazil, total RNA from eight garlic cultivars was sequenced by high-throughput sequencing (HTS) technology. Although most viruses found in this study were previously reported, one of them did not belong to any known genera. This putative new virus was found in seven out of eight garlic cultivars and phylogenetic data positioned it as representative of an independent evolutionary lineage within family Betaflexiviridae. This virus has been tentatively named garlic yellow mosaic-associated virus (GYMaV), sharing highest nucleotide identities with African oil palm ringspot virus (genus Robigovirus) and potato virus T (genus Tepovirus) for the replicase gene, and with viruses classified within genus Foveavirus for the coat protein gene. Due to its high frequency in garlic cultivars, GYMaV should be considered in upcoming surveys of pathogens in this crop and in the development of virus-free garlic plants.
format: application/pdf
format: text/html
creator: Leonardo A. Da Silva
creator: Athos S. Oliveira
creator: Fernando L. Melo
creator: Daniel M.P. Ardisson-Araújo
creator: Francisco V. Resende
creator: Renato O. Resende
creator: Bergmann M. Ribeiro
subject: Agricultural Science
subject: Microbiology
subject: Virology
description: doi:10.7717/peerj.6285
publisher: PeerJ Inc.
rights: © 2019 Da Silva et al.
abstract: Plant vegetative propagation strategies for agricultural crops cause the accumulation of viruses, resulting in the formation of virus complexes or communities. The cultivation of garlic is based on vegetative propagation and more than 13 virus species from the genera Potyvirus, Allexivirus and Carlavirus have been reported. Aiming for an unbiased identification of viruses from a garlic germplasm collection in Brazil, total RNA from eight garlic cultivars was sequenced by high-throughput sequencing (HTS) technology. Although most viruses found in this study were previously reported, one of them did not belong to any known genera. This putative new virus was found in seven out of eight garlic cultivars and phylogenetic data positioned it as representative of an independent evolutionary lineage within family Betaflexiviridae. This virus has been tentatively named garlic yellow mosaic-associated virus (GYMaV), sharing highest nucleotide identities with African oil palm ringspot virus (genus Robigovirus) and potato virus T (genus Tepovirus) for the replicase gene, and with viruses classified within genus Foveavirus for the coat protein gene. Due to its high frequency in garlic cultivars, GYMaV should be considered in upcoming surveys of pathogens in this crop and in the development of virus-free garlic plants.
bibliographic citation: Da Silva et al. (2019) A new virus found in garlic virus complex is a member of possible novel genus of the family Betaflexiviridae (order Tymovirales). PeerJ 7:e6285 https://doi.org/10.7717/peerj.6285
date submitted: 2018-07-31
date accepted: 2018-12-14
issued: 2019-01-16
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Da Silva
  given name: Leonardo A.
author list: Agent
  family name: Oliveira
  given name: Athos S.
author list: Agent
  family name: Melo
  given name: Fernando L.
author list: Agent
  family name: Ardisson-Araújo
  given name: Daniel M.P.
author list: Agent
  family name: Resende
  given name: Francisco V.
author list: Agent
  family name: Resende
  given name: Renato O.
author list: Agent
  family name: Ribeiro
  given name: Bergmann M.
doi: 10.7717/peerj.6285
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-01-16
copyright: ©2019 Da Silva et al.
attribution name: Da Silva et al.

The expression of chondrogenesis-related and arthritis-related genes in human ONFH cartilage with different Ficat stages
type: item
type: AcademicArticle
description: Background It has been well known that the degeneration of hip articular cartilage with osteonecrosis of the femoral head (ONFH) increases the instability of hip and accelerates the development process of ONFH. A better understanding of the expression of chondrogenesis-related and arthritis-related genes of cartilage along with the progression of ONFH seems to be essential for further insight into the molecular mechanisms of ONFH pathogenesis. Methods We analyzed the differentially expressed gene profile (GSE74089) of human hip articular cartilage with ONFH. The functions and pathway enrichments of differentially expressed genes (DEGs) were analyzed via GO and KEGG analysis. The expression of six selected critical chondrogenesis-related and four arthritis-related genes in eight human hip articular cartilage with femoral neck fracture (FNF) and 26 human hip articular cartilage with different stages ONFH (6 cases of Ficat stage II, 10 cases of Ficat stage III and 10 cases of Ficat stage IV) were detected. Results A total of 2,174 DEGs, including 1,482 up-regulated and 692 down-regulated ones, were obtained in the ONFH cartilage specimens compared to the control group. The GO and KEGG enrichment analysis indicated that the function of these DEGs mainly enriched in extracellular matrix, angiogenesis, antigen processing and presentation. The results showed a significant stepwise up-expression of chondrogenesis-related genes, including MMP13, ASPN, COL1A1, OGN, COL2A1 and BMP2, along with the progression of ONFH. The arthritis-related genes IL1β, IL6 and TNFα were only found up-expressed in Ficat IV stage which indicated that the arthritis-related molecular changes were not significant in the progression of ONFH before Ficat III stage. However, the arthritis-related gene PTGS2 was significant stepwise up-expression along with the progression of ONFH which makes it to be a sensitive arthritis-related biomarker of ONFH. Conclusion Expression changes of six chondrogenesis-re…
format: application/pdf
format: text/html
creator: Gaoyang Chen
creator: Lei Zhong
creator: Qingyu Wang
creator: Zhaoyan Li
creator: Jing Shang
creator: Qiwei Yang
creator: Zhenwu Du
creator: Jincheng Wang
creator: Yang Song
creator: Guizhen Zhang
subject: Bioinformatics
subject: Orthopedics
description: doi:10.7717/peerj.6306
publisher: PeerJ Inc.
rights: © 2019 Chen et al.
abstract: Background It has been well known that the degeneration of hip articular cartilage with osteonecrosis of the femoral head (ONFH) increases the instability of hip and accelerates the development process of ONFH. A better understanding of the expression of chondrogenesis-related and arthritis-related genes of cartilage along with the progression of ONFH seems to be essential for further insight into the molecular mechanisms of ONFH pathogenesis. Methods We analyzed the differentially expressed gene profile (GSE74089) of human hip articular cartilage with ONFH. The functions and pathway enrichments of differentially expressed genes (DEGs) were analyzed via GO and KEGG analysis. The expression of six selected critical chondrogenesis-related and four arthritis-related genes in eight human hip articular cartilage with femoral neck fracture (FNF) and 26 human hip articular cartilage with different stages ONFH (6 cases of Ficat stage II, 10 cases of Ficat stage III and 10 cases of Ficat stage IV) were detected. Results A total of 2,174 DEGs, including 1,482 up-regulated and 692 down-regulated ones, were obtained in the ONFH cartilage specimens compared to the control group. The GO and KEGG enrichment analysis indicated that the function of these DEGs mainly enriched in extracellular matrix, angiogenesis, antigen processing and presentation. The results showed a significant stepwise up-expression of chondrogenesis-related genes, including MMP13, ASPN, COL1A1, OGN, COL2A1 and BMP2, along with the progression of ONFH. The arthritis-related genes IL1β, IL6 and TNFα were only found up-expressed in Ficat IV stage which indicated that the arthritis-related molecular changes were not significant in the progression of ONFH before Ficat III stage. However, the arthritis-related gene PTGS2 was significant stepwise up-expression along with the progression of ONFH which makes it to be a sensitive arthritis-related biomarker of ONFH. Conclusion Expression changes of six chondrogenesis-re…
bibliographic citation: Chen et al. (2019) The expression of chondrogenesis-related and arthritis-related genes in human ONFH cartilage with different Ficat stages. PeerJ 7:e6306 https://doi.org/10.7717/peerj.6306
date submitted: 2018-10-02
date accepted: 2018-12-18
issued: 2019-01-16
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Chen
  given name: Gaoyang
author list: Agent
  family name: Zhong
  given name: Lei
author list: Agent
  family name: Wang
  given name: Qingyu
author list: Agent
  family name: Li
  given name: Zhaoyan
author list: Agent
  family name: Shang
  given name: Jing
author list: Agent
  family name: Yang
  given name: Qiwei
author list: Agent
  family name: Du
  given name: Zhenwu
author list: Agent
  family name: Wang
  given name: Jincheng
author list: Agent
  family name: Song
  given name: Yang
author list: Agent
  family name: Zhang
  given name: Guizhen
doi: 10.7717/peerj.6306
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-01-16
copyright: ©2019 Chen et al.
attribution name: Chen et al.

Influence of light intensity, fertilizing and season on the cirsiliol content, a chemical marker of Leonotis nepetifolia (Lamiaceae)
type: item
type: AcademicArticle
description: Background Leonotis nepetifolia (Family Lamiaceae) is a medicinal plant from which the flavonoid cirsiliol with sedative, hypnotic, anti-inflammatory and cytotoxic activity has been extracted. Methods Seedlings were cultivated under different levels of shade in native or fertilized modes. The content of cirsiliol was measured monthly by high-performance liquid chromatography and the total phenolic content by the Folin-Ciocalteu method. Monitoring of growth was carried out with the weekly measurement of height until the stabilization of growth. Results The application of fertilizing and/or shading does not alter significantly the cirsiliol content. However, this content varies throughout the year, reaching the peak production in the summer, independently of the treatment applied. This same profile, with production in the summer, was also verified for phenolic compounds, reaching 58.15 ± 9.35 mg of equivalents of gallic acid per g of extract in the summer, content 1.84 times greater than the content verified in winter (31.56 ± 4.09 mg of gallic acid/g of extract). Although shading and fertilizing had no effect on cirsiliol content, the results also showed a positive influence on the height and biomass of the plant, which can causes a higher yield of extractable material. Discussion Biotic and abiotic stresses are able to increase or decrease the production of secondary metabolites, including phenolic compounds in medicinal plants and, as the stress response is peculiar to each species, cultivation studies become necessary. The present study reports by the first time the influence of shading, fertilizing and seasons in cirsiliol content in L. nepetifolia. Among analyzed variables, the seasons showed a larger influence in expression of cirsiliol and among seasons, our results showed that the summer is the ideal season for collections. In summer, the photoperiod is larger than in other seasons of the year and due to that, the plants need greater protection against the lo…
format: application/pdf
format: text/html
creator: Ana Paula de Oliveira
creator: Ivanildo Viana Borges
creator: Emanuella Chiara Valença Pereira
creator: Thiala Alves Feitosa
creator: Raira Feitosa dos Santos
creator: Raimundo Gonçalves de Oliveira-Junior
creator: Larissa Araújo Rolim
creator: Lucas Gustavo Ferreira Cordeiro Viana
creator: Luciano Augusto de Araújo Ribeiro
creator: Alan Diego da Conceição Santos
creator: Pedro José Rolim-Neto
creator: Jackson Roberto Guedes da Silva Almeida
subject: Agricultural Science
subject: Ecosystem Science
subject: Plant Science
description: doi:10.7717/peerj.6187
publisher: PeerJ Inc.
rights: © 2019 de Oliveira et al.
abstract: Background Leonotis nepetifolia (Family Lamiaceae) is a medicinal plant from which the flavonoid cirsiliol with sedative, hypnotic, anti-inflammatory and cytotoxic activity has been extracted. Methods Seedlings were cultivated under different levels of shade in native or fertilized modes. The content of cirsiliol was measured monthly by high-performance liquid chromatography and the total phenolic content by the Folin-Ciocalteu method. Monitoring of growth was carried out with the weekly measurement of height until the stabilization of growth. Results The application of fertilizing and/or shading does not alter significantly the cirsiliol content. However, this content varies throughout the year, reaching the peak production in the summer, independently of the treatment applied. This same profile, with production in the summer, was also verified for phenolic compounds, reaching 58.15 ± 9.35 mg of equivalents of gallic acid per g of extract in the summer, content 1.84 times greater than the content verified in winter (31.56 ± 4.09 mg of gallic acid/g of extract). Although shading and fertilizing had no effect on cirsiliol content, the results also showed a positive influence on the height and biomass of the plant, which can causes a higher yield of extractable material. Discussion Biotic and abiotic stresses are able to increase or decrease the production of secondary metabolites, including phenolic compounds in medicinal plants and, as the stress response is peculiar to each species, cultivation studies become necessary. The present study reports by the first time the influence of shading, fertilizing and seasons in cirsiliol content in L. nepetifolia. Among analyzed variables, the seasons showed a larger influence in expression of cirsiliol and among seasons, our results showed that the summer is the ideal season for collections. In summer, the photoperiod is larger than in other seasons of the year and due to that, the plants need greater protection against the lo…
bibliographic citation: de Oliveira et al. (2019) Influence of light intensity, fertilizing and season on the cirsiliol content, a chemical marker of Leonotis nepetifolia (Lamiaceae). PeerJ 7:e6187 https://doi.org/10.7717/peerj.6187
date submitted: 2018-05-23
date accepted: 2018-11-30
issued: 2019-01-15
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: de Oliveira
  given name: Ana Paula
author list: Agent
  family name: Borges
  given name: Ivanildo Viana
author list: Agent
  family name: Pereira
  given name: Emanuella Chiara Valença
author list: Agent
  family name: Feitosa
  given name: Thiala Alves
author list: Agent
  family name: dos Santos
  given name: Raira Feitosa
author list: Agent
  family name: de Oliveira-Junior
  given name: Raimundo Gonçalves
author list: Agent
  family name: Rolim
  given name: Larissa Araújo
author list: Agent
  family name: Cordeiro Viana
  given name: Lucas Gustavo Ferreira
author list: Agent
  family name: Ribeiro
  given name: Luciano Augusto de Araújo
author list: Agent
  family name: Santos
  given name: Alan Diego da Conceição
author list: Agent
  family name: Rolim-Neto
  given name: Pedro José
author list: Agent
  family name: Almeida
  given name: Jackson Roberto Guedes da Silva
doi: 10.7717/peerj.6187
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-01-15
copyright: ©2019 de Oliveira et al.
attribution name: de Oliveira et al.

Awareness, behavior and attitudes concerning sun exposure among beachgoers in the northern coast of Peru
type: item
type: AcademicArticle
description: Background Skin cancer incidence has increased over the last years, becoming a major public health problem. Objective To describe the awareness, behavior and attitudes concerning sun exposure among beachgoers in the northern coast of Peru. Methods We conducted a cross-sectional study in the Pimentel beach, Peru. The “Beach Questionnaire” was used and we surveyed all the beachgoers from 8 a.m. to 4 p.m. and from March 5 to March 19. For the statistical analysis, sun exposure habits, sunburns history, knowledge, attitudes and practices were crossed with sex using the chi2 test. Results We surveyed 410 beachgoers, the most frequent phototype was type III (40.5%). Only the 13.66% of the respondents correctly answered the seven knowledge questions related to sun exposure and skin cancer. Men more frequently agreed that “when they are tanned their clothes looks nicer” (p = 0.048). Likewise, regarding the questions “Sunbathing is relaxing” and “Sunbathing improves my mood”, men agreed or totally agreed with more frequency than women (63.64% vs. 46.15%, p < 0.001; and 61.36% vs 49.15%, p = 0.014, respectively). Regarding sun protection practices, women more frequently used sunshade (p = 0.001) and sunscreen (SPF ≥ 15) (p < 0.001) when compared to the male group. Conclusion Sun exposure is a potentially preventable risk factor for skin cancer. Thus, awareness of the risks of UVR overexposure and adequate sun-protective behaviors and attitudes are essential. Our results, however, are not as favorable as expected. Public health efforts should encourage sun-safety precautions and intervention campaigns should be carried out in recreational settings, such as the beaches.
format: application/pdf
format: text/html
creator: Carlos J. Toro-Huamanchumo
creator: Sara J. Burgos-Muñoz
creator: Luz M. Vargas-Tineo
creator: Jhosuny Perez-Fernandez
creator: Otto W. Vargas-Tineo
creator: Ruth M. Burgos-Muñoz
creator: Javier A. Zentner-Guevara
creator: Carlos Bada
subject: Dermatology
subject: Epidemiology
subject: Public Health
description: doi:10.7717/peerj.6189
publisher: PeerJ Inc.
rights: © 2019 Toro-Huamanchumo et al.
abstract: Background Skin cancer incidence has increased over the last years, becoming a major public health problem. Objective To describe the awareness, behavior and attitudes concerning sun exposure among beachgoers in the northern coast of Peru. Methods We conducted a cross-sectional study in the Pimentel beach, Peru. The “Beach Questionnaire” was used and we surveyed all the beachgoers from 8 a.m. to 4 p.m. and from March 5 to March 19. For the statistical analysis, sun exposure habits, sunburns history, knowledge, attitudes and practices were crossed with sex using the chi2 test. Results We surveyed 410 beachgoers, the most frequent phototype was type III (40.5%). Only the 13.66% of the respondents correctly answered the seven knowledge questions related to sun exposure and skin cancer. Men more frequently agreed that “when they are tanned their clothes looks nicer” (p = 0.048). Likewise, regarding the questions “Sunbathing is relaxing” and “Sunbathing improves my mood”, men agreed or totally agreed with more frequency than women (63.64% vs. 46.15%, p < 0.001; and 61.36% vs 49.15%, p = 0.014, respectively). Regarding sun protection practices, women more frequently used sunshade (p = 0.001) and sunscreen (SPF ≥ 15) (p < 0.001) when compared to the male group. Conclusion Sun exposure is a potentially preventable risk factor for skin cancer. Thus, awareness of the risks of UVR overexposure and adequate sun-protective behaviors and attitudes are essential. Our results, however, are not as favorable as expected. Public health efforts should encourage sun-safety precautions and intervention campaigns should be carried out in recreational settings, such as the beaches.
bibliographic citation: Toro-Huamanchumo et al. (2019) Awareness, behavior and attitudes concerning sun exposure among beachgoers in the northern coast of Peru. PeerJ 7:e6189 https://doi.org/10.7717/peerj.6189
date submitted: 2018-07-17
date accepted: 2018-11-30
issued: 2019-01-15
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Toro-Huamanchumo
  given name: Carlos J.
author list: Agent
  family name: Burgos-Muñoz
  given name: Sara J.
author list: Agent
  family name: Vargas-Tineo
  given name: Luz M.
author list: Agent
  family name: Perez-Fernandez
  given name: Jhosuny
author list: Agent
  family name: Vargas-Tineo
  given name: Otto W.
author list: Agent
  family name: Burgos-Muñoz
  given name: Ruth M.
author list: Agent
  family name: Zentner-Guevara
  given name: Javier A.
author list: Agent
  family name: Bada
  given name: Carlos
doi: 10.7717/peerj.6189
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-01-15
copyright: ©2019 Toro-Huamanchumo et al.
attribution name: Toro-Huamanchumo et al.

TGF-beta signalling in bovine mammary gland involution and a comparative assessment of MAC-T and BME-UV1 cells as in vitro models for its study
type: item
type: AcademicArticle
description: The goal of the dairy industry is ultimately to increase lactation persistency, which is the length of time during which peak milk yield is sustained. Lactation persistency is determined by the balance of cell apoptosis and cell proliferation; when the balance is skewed toward the latter, this results in greater persistency. Thus, we can potentially increase milk production in dairy cows through manipulating apoptogenic and antiproliferative cellular signaling that occurs in the bovine mammary gland. Transforming growth factor beta 1 (TGFβ1) is an antiproliferative and apoptogenic cytokine that is upregulated during bovine mammary gland involution. Here, we discuss possible applications of TGFβ1 signaling for the purposes of increasing lactation persistency. We also compare the features of mammary alveolar cells expressing SV-40 large T antigen (MAC-T) and bovine mammary epithelial cells-clone UV1 (BME-UV1) cells, two extensively used bovine mammary epithelial cell lines, to assess their appropriateness for the study of TGFβ1 signaling. TGFβ1 induces apoptosis and arrests cell growth in BME-UV1 cells, and this was reported to involve suppression of the somatotropic axis. Conversely, there is no proof that exogenous TGFβ1 induces apoptosis of MAC-T cells. In addition to TGFβ1’s different effects on apoptosis in these cell lines, hormones and growth factors have distinct effects on TGFβ1 secretion and synthesis in MAC-T and BME-UV1 cells as well. MAC-T and BME-UV1 cells may behave differently in response to TGFβ1 due to their contrasting phenotypes; MAC-T cells have a profile indicative of both myoepithelial and luminal populations, while the BME-UV1 cells exclusively contain a luminal-like profile. Depending on the nature of the research question, the use of these cell lines as models to study TGFβ1 signaling should be carefully tailored to the questions asked.
format: application/pdf
format: text/html
creator: Charlotte Alexandra Mitz
creator: Alicia Mercedes Viloria-Petit
subject: Agricultural Science
subject: Cell Biology
subject: Food Science and Technology
subject: Veterinary Medicine
description: doi:10.7717/peerj.6210
publisher: PeerJ Inc.
rights: © 2019 Mitz and Viloria-Petit
abstract: The goal of the dairy industry is ultimately to increase lactation persistency, which is the length of time during which peak milk yield is sustained. Lactation persistency is determined by the balance of cell apoptosis and cell proliferation; when the balance is skewed toward the latter, this results in greater persistency. Thus, we can potentially increase milk production in dairy cows through manipulating apoptogenic and antiproliferative cellular signaling that occurs in the bovine mammary gland. Transforming growth factor beta 1 (TGFβ1) is an antiproliferative and apoptogenic cytokine that is upregulated during bovine mammary gland involution. Here, we discuss possible applications of TGFβ1 signaling for the purposes of increasing lactation persistency. We also compare the features of mammary alveolar cells expressing SV-40 large T antigen (MAC-T) and bovine mammary epithelial cells-clone UV1 (BME-UV1) cells, two extensively used bovine mammary epithelial cell lines, to assess their appropriateness for the study of TGFβ1 signaling. TGFβ1 induces apoptosis and arrests cell growth in BME-UV1 cells, and this was reported to involve suppression of the somatotropic axis. Conversely, there is no proof that exogenous TGFβ1 induces apoptosis of MAC-T cells. In addition to TGFβ1’s different effects on apoptosis in these cell lines, hormones and growth factors have distinct effects on TGFβ1 secretion and synthesis in MAC-T and BME-UV1 cells as well. MAC-T and BME-UV1 cells may behave differently in response to TGFβ1 due to their contrasting phenotypes; MAC-T cells have a profile indicative of both myoepithelial and luminal populations, while the BME-UV1 cells exclusively contain a luminal-like profile. Depending on the nature of the research question, the use of these cell lines as models to study TGFβ1 signaling should be carefully tailored to the questions asked.
bibliographic citation: Mitz et al. (2019) TGF-beta signalling in bovine mammary gland involution and a comparative assessment of MAC-T and BME-UV1 cells as in vitro models for its study. PeerJ 6:e6210 https://doi.org/10.7717/peerj.6210
date submitted: 2018-07-10
date accepted: 2018-12-04
issued: 2019-01-15
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Mitz
  given name: Charlotte Alexandra
author list: Agent
  family name: Viloria-Petit
  given name: Alicia Mercedes
doi: 10.7717/peerj.6210
volume: 6
issn: 2167-8359
publication name: PeerJ
publication date: 2019-01-15
copyright: © 2019 Mitz and Viloria-Petit
attribution name: Mitz and Viloria-Petit

Common garden comparisons confirm inherited differences in sensitivity to climate change between forest tree species
type: item
type: AcademicArticle
description: The natural distribution, habitat, growth and evolutionary history of tree species are strongly dependent on ecological and genetic processes in ecosystems subject to fluctuating climatic conditions, but there have been few experimental comparisons of sensitivity between species. We compared the responses of two broadleaved tree species (Fagus sylvatica and Quercus petraea) and two conifer tree species (Pinus sylvestris and Picea abies) to climatic transfers by fitting models containing the same climatic variables. We used published data from European provenance test networks to model the responses of individual populations nested within species. A mixed model approach was applied to develop a response function for tree height over climatic transfer distance, taking into account the climatic conditions at both the seed source and the test location. The two broadleaved species had flat climatic response curves, indicating high levels of plasticity in populations, facilitating adaptation to a broader range of environments, and conferring a high potential for resilience in the face of climatic change. By contrast, the two conifer species had response curves with more pronounced slopes, indicating a lower resilience to climate change. This finding may reflect stronger genetic clines in P. sylvestris and P. abies, which constrain their climate responses to narrower climatic ranges. The response functions had maxima that deviated from the expected maximum productivity in the climate of provenance towards cooler/moister climate conditions, which we interpreted as an adaptation lag. Unilateral, linear regression analyses following transfer to warmer and drier sites confirmed a decline in productivity, predictive of the likely impact of ongoing climate change on forest populations. The responses to mimicked climate change evaluated here are of considerable interest for forestry and ecology, supporting projections of expected performance based on “real-time” field data.
format: application/pdf
format: text/html
creator: Cuauhtémoc Sáenz-Romero
creator: Antoine Kremer
creator: László Nagy
creator: Éva Újvári-Jármay
creator: Alexis Ducousso
creator: Anikó Kóczán-Horváth
creator: Jon Kehlet Hansen
creator: Csaba Mátyás
subject: Climate Change Biology
subject: Forestry
subject: Ecology
description: doi:10.7717/peerj.6213
publisher: PeerJ Inc.
rights: © 2019 Sáenz-Romero et al.
abstract: The natural distribution, habitat, growth and evolutionary history of tree species are strongly dependent on ecological and genetic processes in ecosystems subject to fluctuating climatic conditions, but there have been few experimental comparisons of sensitivity between species. We compared the responses of two broadleaved tree species (Fagus sylvatica and Quercus petraea) and two conifer tree species (Pinus sylvestris and Picea abies) to climatic transfers by fitting models containing the same climatic variables. We used published data from European provenance test networks to model the responses of individual populations nested within species. A mixed model approach was applied to develop a response function for tree height over climatic transfer distance, taking into account the climatic conditions at both the seed source and the test location. The two broadleaved species had flat climatic response curves, indicating high levels of plasticity in populations, facilitating adaptation to a broader range of environments, and conferring a high potential for resilience in the face of climatic change. By contrast, the two conifer species had response curves with more pronounced slopes, indicating a lower resilience to climate change. This finding may reflect stronger genetic clines in P. sylvestris and P. abies, which constrain their climate responses to narrower climatic ranges. The response functions had maxima that deviated from the expected maximum productivity in the climate of provenance towards cooler/moister climate conditions, which we interpreted as an adaptation lag. Unilateral, linear regression analyses following transfer to warmer and drier sites confirmed a decline in productivity, predictive of the likely impact of ongoing climate change on forest populations. The responses to mimicked climate change evaluated here are of considerable interest for forestry and ecology, supporting projections of expected performance based on “real-time” field data.
bibliographic citation: Sáenz-Romero et al. (2019) Common garden comparisons confirm inherited differences in sensitivity to climate change between forest tree species. PeerJ 7:e6213 https://doi.org/10.7717/peerj.6213
date submitted: 2018-07-12
date accepted: 2018-12-04
issued: 2019-01-15
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Sáenz-Romero
  given name: Cuauhtémoc
author list: Agent
  family name: Kremer
  given name: Antoine
author list: Agent
  family name: Nagy
  given name: László
author list: Agent
  family name: Újvári-Jármay
  given name: Éva
author list: Agent
  family name: Ducousso
  given name: Alexis
author list: Agent
  family name: Kóczán-Horváth
  given name: Anikó
author list: Agent
  family name: Hansen
  given name: Jon Kehlet
author list: Agent
  family name: Mátyás
  given name: Csaba
doi: 10.7717/peerj.6213
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-01-15
copyright: ©2019 Sáenz-Romero et al.
attribution name: Sáenz-Romero et al.

The sinemydid turtle Ordosemys from the Lower Cretaceous Mengyin Formation of Shandong, China and its implication for the age of the Luohandong Formation of the Ordos Basin
type: item
type: AcademicArticle
description: Chronostratigraphic correlation of terrestrial Early Cretaceous biotas in China is highly problematic due to the lack of marine deposits, few absolute dates, and limited number of index fossils. This often leaves vertebrate faunas as one of the few potential tools for a preliminary biostratigraphy. Taxonomic identity of fragmentary fossils is, however, often uncertain and many faunas are insufficiently sampled. Turtles are one of the most common elements of Early Cretaceous biotas of Asia and their skeleton is frequently preserved more completely than that of other vertebrates- they yet receive little attention from vertebrate paleontologists. We here record the presence of the sinemydid turtle Ordosemys leios from the Lower Cretaceous Mengyin Formation of Shandong Province, China, best known for the first dinosaurs and Mesozoic turtles described from the country. Ordosemys is the third turtle reported from the Mengyin Formation along with Sinemys lens and Sinochelys applanata and the only other formation where Ordosemys is known to co-occur with Sinemys is the Luohandong Formation of the Ordos Basin (Inner Mongolia), the type and so far only horizon of Ordosemys leios. The presence of the crocodyliform Shantungosuchus may further define a fauna that is so far only known from these two formations. The stratigraphic position of the Luohandong Formation is poorly controlled and it has been placed anywhere between the Valanginian and Aptian. Published absolute dates from the Mengyin Formation and the numerous shared vertebrate and invertebrate taxa (now also including turtles) implies a Valanginian—early Hauterivian age for the Luohandong Formation—in contrast to late Hauterivian-Albian as previously proposed using the temporal distribution of Psittacosaurus. The new specimen of Ordosemys leios preserves the only known manus of this species and ecomorphological analysis of limb proportions implies that it was a less capable swimmer compared to Ordosemys liaoxiensis com…
format: application/pdf
format: text/html
creator: Da-Qing Li
creator: Chang-Fu Zhou
creator: Lan Li
creator: Jing-Tao Yang
creator: Longfeng Li
creator: Márton Rabi
subject: Ecology
subject: Paleontology
subject: Taxonomy
description: doi:10.7717/peerj.6229
publisher: PeerJ Inc.
rights: © 2019 Li et al.
abstract: Chronostratigraphic correlation of terrestrial Early Cretaceous biotas in China is highly problematic due to the lack of marine deposits, few absolute dates, and limited number of index fossils. This often leaves vertebrate faunas as one of the few potential tools for a preliminary biostratigraphy. Taxonomic identity of fragmentary fossils is, however, often uncertain and many faunas are insufficiently sampled. Turtles are one of the most common elements of Early Cretaceous biotas of Asia and their skeleton is frequently preserved more completely than that of other vertebrates- they yet receive little attention from vertebrate paleontologists. We here record the presence of the sinemydid turtle Ordosemys leios from the Lower Cretaceous Mengyin Formation of Shandong Province, China, best known for the first dinosaurs and Mesozoic turtles described from the country. Ordosemys is the third turtle reported from the Mengyin Formation along with Sinemys lens and Sinochelys applanata and the only other formation where Ordosemys is known to co-occur with Sinemys is the Luohandong Formation of the Ordos Basin (Inner Mongolia), the type and so far only horizon of Ordosemys leios. The presence of the crocodyliform Shantungosuchus may further define a fauna that is so far only known from these two formations. The stratigraphic position of the Luohandong Formation is poorly controlled and it has been placed anywhere between the Valanginian and Aptian. Published absolute dates from the Mengyin Formation and the numerous shared vertebrate and invertebrate taxa (now also including turtles) implies a Valanginian—early Hauterivian age for the Luohandong Formation—in contrast to late Hauterivian-Albian as previously proposed using the temporal distribution of Psittacosaurus. The new specimen of Ordosemys leios preserves the only known manus of this species and ecomorphological analysis of limb proportions implies that it was a less capable swimmer compared to Ordosemys liaoxiensis com…
bibliographic citation: Li et al. (2019) The sinemydid turtle Ordosemys from the Lower Cretaceous Mengyin Formation of Shandong, China and its implication for the age of the Luohandong Formation of the Ordos Basin. PeerJ 7:e6229 https://doi.org/10.7717/peerj.6229
date submitted: 2018-09-14
date accepted: 2018-12-07
issued: 2019-01-15
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Li
  given name: Da-Qing
author list: Agent
  family name: Zhou
  given name: Chang-Fu
author list: Agent
  family name: Li
  given name: Lan
author list: Agent
  family name: Yang
  given name: Jing-Tao
author list: Agent
  family name: Li
  given name: Longfeng
author list: Agent
  family name: Rabi
  given name: Márton
doi: 10.7717/peerj.6229
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-01-15
copyright: ©2019 Li et al.
attribution name: Li et al.

Serverless OpenHealth at data commons scale—traversing the 20 million patient records of New York’s SPARCS dataset in real-time
type: item
type: AcademicArticle
description: In a previous report, we explored the serverless OpenHealth approach to the Web as a Global Compute space. That approach relies on the modern browser full stack, and, in particular, its configuration for application assembly by code injection. The opportunity, and need, to expand this approach has since increased markedly, reflecting a wider adoption of Open Data policies by Public Health Agencies. Here, we describe how the serverless scaling challenge can be achieved by the isomorphic mapping between the remote data layer API and a local (client-side, in-browser) operator. This solution is validated with an accompanying interactive web application (bit.ly/loadsparcs) capable of real-time traversal of New York’s 20 million patient records of the Statewide Planning and Research Cooperative System (SPARCS), and is compared with alternative approaches. The results obtained strengthen the argument that the FAIR reproducibility needed for Population Science applications in the age of P4 Medicine is particularly well served by the Web platform.
format: application/pdf
format: text/html
creator: Jonas S. Almeida
creator: Janos Hajagos
creator: Joel Saltz
creator: Mary Saltz
subject: Bioinformatics
subject: Epidemiology
subject: Public Health
subject: Computational Science
subject: Data Science
description: doi:10.7717/peerj.6230
publisher: PeerJ Inc.
rights: © 2019 Almeida et al.
abstract: In a previous report, we explored the serverless OpenHealth approach to the Web as a Global Compute space. That approach relies on the modern browser full stack, and, in particular, its configuration for application assembly by code injection. The opportunity, and need, to expand this approach has since increased markedly, reflecting a wider adoption of Open Data policies by Public Health Agencies. Here, we describe how the serverless scaling challenge can be achieved by the isomorphic mapping between the remote data layer API and a local (client-side, in-browser) operator. This solution is validated with an accompanying interactive web application (bit.ly/loadsparcs) capable of real-time traversal of New York’s 20 million patient records of the Statewide Planning and Research Cooperative System (SPARCS), and is compared with alternative approaches. The results obtained strengthen the argument that the FAIR reproducibility needed for Population Science applications in the age of P4 Medicine is particularly well served by the Web platform.
bibliographic citation: Almeida et al. (2019) Serverless OpenHealth at data commons scale—traversing the 20 million patient records of New York’s SPARCS dataset in real-time. PeerJ 7:e6230 https://doi.org/10.7717/peerj.6230
date submitted: 2018-09-05
date accepted: 2018-12-07
issued: 2019-01-15
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Almeida
  given name: Jonas S.
author list: Agent
  family name: Hajagos
  given name: Janos
author list: Agent
  family name: Saltz
  given name: Joel
author list: Agent
  family name: Saltz
  given name: Mary
doi: 10.7717/peerj.6230
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-01-15
copyright: ©2019 Almeida et al.
attribution name: Almeida et al.

Duplicated flavonoid 3’-hydroxylase and flavonoid 3’, 5’-hydroxylase genes in barley genome
type: item
type: AcademicArticle
description: Background Anthocyanin compounds playing multiple biological functions can be synthesized in different parts of barley (Hordeum vulgare L.) plant. The diversity of anthocyanin molecules is related with branching the pathway to alternative ways in which dihydroflavonols may be modified either with the help of flavonoid 3′-hydroxylase (F3′H) or flavonoid 3′,5′-hydroxylase (F3′5′H)—the cytochrome P450-dependent monooxygenases. The F3′H and F3′5′H gene families are among the least studied anthocyanin biosynthesis structural genes in barley. The aim of this study was to identify and characterise duplicated copies of the F3′H and F3′5′H genes in the barley genome. Results Four copies of the F3′5′H gene (on chromosomes 4HL, 6HL, 6HS and 7HS) and two copies of the F3′H gene (on chromosomes 1HL and 6HS) were identified in barley genome. These copies have either one or two introns. Amino acid sequences analysis demonstrated the presence of the flavonoid hydroxylase-featured conserved motifs in all copies of the F3′H and F3′5′H genes with the exception of F3′5′H-3 carrying a loss-of-function mutation in a conservative cytochrome P450 domain. It was shown that the divergence between F3′H and F3′5′H genes occurred 129 million years ago (MYA) before the emergence of monocot and dicot plant species. The F3′H copy approximately occurred 80 MYA; the appearance of F3′5′H copies occurred 8, 36 and 91 MYA. qRT-PCR analysis revealed the tissue-specific activity for some copies of the studied genes. The F3′H-1 gene was transcribed in aleurone layer, lemma and pericarp (with an increased level in the coloured pericarp), whereas the F3′H-2 gene was expressed in stems only. The F3′5′H-1 gene was expressed only in the aleurone layer, and in a coloured aleurone its expression was 30-fold higher. The transcriptional activity of F3′5′H-2 was detected in different tissues with significantly higher level in uncoloured genotype in contrast to coloured ones. The F3′5′H-3 gene expressed neither in s…
format: application/pdf
format: text/html
creator: Alexander V. Vikhorev
creator: Ksenia V. Strygina
creator: Elena K. Khlestkina
subject: Genetics
subject: Molecular Biology
subject: Plant Science
description: doi:10.7717/peerj.6266
publisher: PeerJ Inc.
rights: © 2019 Vikhorev et al.
abstract: Background Anthocyanin compounds playing multiple biological functions can be synthesized in different parts of barley (Hordeum vulgare L.) plant. The diversity of anthocyanin molecules is related with branching the pathway to alternative ways in which dihydroflavonols may be modified either with the help of flavonoid 3′-hydroxylase (F3′H) or flavonoid 3′,5′-hydroxylase (F3′5′H)—the cytochrome P450-dependent monooxygenases. The F3′H and F3′5′H gene families are among the least studied anthocyanin biosynthesis structural genes in barley. The aim of this study was to identify and characterise duplicated copies of the F3′H and F3′5′H genes in the barley genome. Results Four copies of the F3′5′H gene (on chromosomes 4HL, 6HL, 6HS and 7HS) and two copies of the F3′H gene (on chromosomes 1HL and 6HS) were identified in barley genome. These copies have either one or two introns. Amino acid sequences analysis demonstrated the presence of the flavonoid hydroxylase-featured conserved motifs in all copies of the F3′H and F3′5′H genes with the exception of F3′5′H-3 carrying a loss-of-function mutation in a conservative cytochrome P450 domain. It was shown that the divergence between F3′H and F3′5′H genes occurred 129 million years ago (MYA) before the emergence of monocot and dicot plant species. The F3′H copy approximately occurred 80 MYA; the appearance of F3′5′H copies occurred 8, 36 and 91 MYA. qRT-PCR analysis revealed the tissue-specific activity for some copies of the studied genes. The F3′H-1 gene was transcribed in aleurone layer, lemma and pericarp (with an increased level in the coloured pericarp), whereas the F3′H-2 gene was expressed in stems only. The F3′5′H-1 gene was expressed only in the aleurone layer, and in a coloured aleurone its expression was 30-fold higher. The transcriptional activity of F3′5′H-2 was detected in different tissues with significantly higher level in uncoloured genotype in contrast to coloured ones. The F3′5′H-3 gene expressed neither in s…
bibliographic citation: Vikhorev et al. (2019) Duplicated flavonoid 3’-hydroxylase and flavonoid 3’, 5’-hydroxylase genes in barley genome. PeerJ 7:e6266 https://doi.org/10.7717/peerj.6266
date submitted: 2018-11-02
date accepted: 2018-12-11
issued: 2019-01-15
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Vikhorev
  given name: Alexander V.
author list: Agent
  family name: Strygina
  given name: Ksenia V.
author list: Agent
  family name: Khlestkina
  given name: Elena K.
doi: 10.7717/peerj.6266
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-01-15
copyright: ©2019 Vikhorev et al.
attribution name: Vikhorev et al.

Opioid distribution trends (2006–2017) in the US Territories
type: item
type: AcademicArticle
description: Background The US mainland is experiencing an epidemic of opioid overdoses. Unfortunately, the US Territories (Guam, Puerto Rico, and the Virgin Islands) have often been overlooked in opioid pharmacoepidemiology research. This study examined common prescription opioids over the last decade. Methods The United States Drug Enforcement Administration’s Automation of Reports and Consolidated Orders System (ARCOS) was used to report on ten medical opioids: buprenorphine, codeine, fentanyl, hydrocodone, hydromorphone, meperidine, methadone, morphine, oxycodone, and oxymorphone, by weight from 2006 to 2017. Florida and Hawaii were selected as comparison areas. Results Puerto Rico had the greatest Territorial oral morphine mg equivalent (MME) per capita (421.5) which was significantly higher (p < .005) than the Virgin Islands (139.2) and Guam (118.9) but significantly lower than that of Hawaii (794.6) or Florida (1,509.8). Methadone was the largest opioid by MMEs in 2017 in most municipalities, accounting for 41.1% of the total in the Virgin Islands, 37.9% in Florida, 36.6% in Hawaii but 80.8% in Puerto Rico. Puerto Rico and Florida showed pronounced differences in the distribution patterns by pharmacies, hospitals, and narcotic treatment programs for opioids. Conclusions Continued monitoring of the US Territories is needed to provide a balance between appropriate access to these important agents for cancer related and acute pain while also minimizing diversion and avoiding the opioid epidemic which has adversely impacted the US mainland.
format: application/pdf
format: text/html
creator: Fedor F. Cabrera
creator: Erik R. Gamarra
creator: Tiffany E. Garcia
creator: Ashanti D. Littlejohn
creator: Poul A. Chinga
creator: Luis D. Pinentel-Morillo
creator: Jorge R. Tirado
creator: Daniel Y. Chung
creator: Leana J. Pande
creator: Kenneth L. McCall
creator: Stephanie D. Nichols
creator: Brian J. Piper
subject: Drugs and Devices
subject: Epidemiology
subject: Health Policy
subject: Pharmacology
subject: Public Health
description: doi:10.7717/peerj.6272
publisher: PeerJ Inc.
rights: © 2019 Cabrera et al.
abstract: Background The US mainland is experiencing an epidemic of opioid overdoses. Unfortunately, the US Territories (Guam, Puerto Rico, and the Virgin Islands) have often been overlooked in opioid pharmacoepidemiology research. This study examined common prescription opioids over the last decade. Methods The United States Drug Enforcement Administration’s Automation of Reports and Consolidated Orders System (ARCOS) was used to report on ten medical opioids: buprenorphine, codeine, fentanyl, hydrocodone, hydromorphone, meperidine, methadone, morphine, oxycodone, and oxymorphone, by weight from 2006 to 2017. Florida and Hawaii were selected as comparison areas. Results Puerto Rico had the greatest Territorial oral morphine mg equivalent (MME) per capita (421.5) which was significantly higher (p < .005) than the Virgin Islands (139.2) and Guam (118.9) but significantly lower than that of Hawaii (794.6) or Florida (1,509.8). Methadone was the largest opioid by MMEs in 2017 in most municipalities, accounting for 41.1% of the total in the Virgin Islands, 37.9% in Florida, 36.6% in Hawaii but 80.8% in Puerto Rico. Puerto Rico and Florida showed pronounced differences in the distribution patterns by pharmacies, hospitals, and narcotic treatment programs for opioids. Conclusions Continued monitoring of the US Territories is needed to provide a balance between appropriate access to these important agents for cancer related and acute pain while also minimizing diversion and avoiding the opioid epidemic which has adversely impacted the US mainland.
bibliographic citation: Cabrera et al. (2019) Opioid distribution trends (2006–2017) in the US Territories. PeerJ 7:e6272 https://doi.org/10.7717/peerj.6272
date submitted: 2018-08-22
date accepted: 2018-12-10
issued: 2019-01-15
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Cabrera
  given name: Fedor F.
author list: Agent
  family name: Gamarra
  given name: Erik R.
author list: Agent
  family name: Garcia
  given name: Tiffany E.
author list: Agent
  family name: Littlejohn
  given name: Ashanti D.
author list: Agent
  family name: Chinga
  given name: Poul A.
author list: Agent
  family name: Pinentel-Morillo
  given name: Luis D.
author list: Agent
  family name: Tirado
  given name: Jorge R.
author list: Agent
  family name: Chung
  given name: Daniel Y.
author list: Agent
  family name: Pande
  given name: Leana J.
author list: Agent
  family name: McCall
  given name: Kenneth L.
author list: Agent
  family name: Nichols
  given name: Stephanie D.
author list: Agent
  family name: Piper
  given name: Brian J.
doi: 10.7717/peerj.6272
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-01-15
copyright: ©2019 Cabrera et al.
attribution name: Cabrera et al.

Estimating the incidence and diagnosed proportion of HIV infections in Japan: a statistical modeling study
type: item
type: AcademicArticle
description: Background Epidemiological surveillance of HIV infection in Japan involves two technical problems for directly applying a classical backcalculation method, i.e., (i) all AIDS cases are not counted over time and (ii) people diagnosed with HIV have received antiretroviral therapy, extending the incubation period. The present study aimed to address these issues and estimate the HIV incidence and the proportion of diagnosed HIV infections, using a simple statistical model. Methods From among Japanese nationals, yearly incidence data of HIV diagnoses and patients with AIDS who had not previously been diagnosed as HIV positive, from 1985 to 2017, were analyzed. Using the McKendrick partial differential equation, general convolution-like equations were derived, allowing estimation of the HIV incidence and the time-dependent rate of diagnosis. A likelihood-based approach was used to obtain parameter estimates. Results Assuming that the median incubation period was 10.0 years, the cumulative number of HIV infections was estimated to be 29,613 (95% confidence interval (CI): 29,059, 30,167) by the end of 2017, and the proportion of diagnosed HIV infections was estimated at 80.3% (95% CI [78.7%–82.0%]). Allowing the median incubation period to range from 7.5 to 12.3 years, the estimate of the proportion diagnosed can vary from 77% to 84%. Discussion The proportion of diagnosed HIV infections appears to have not yet reached 90% among Japanese nationals. Compared with the peak incidence from 2005–2008, new HIV infections have clearly been in a declining trend; however, there are still more than 1,000 new HIV infections per year in Japan. To increase the diagnosed proportion of HIV infections, it is critical to identify people who have difficulty accessing consultation, testing, and care, and to explore heterogeneous patterns of infection.
format: application/pdf
format: text/html
creator: Hiroshi Nishiura
subject: Epidemiology
subject: HIV
subject: Infectious Diseases
subject: Public Health
subject: Statistics
description: doi:10.7717/peerj.6275
publisher: PeerJ Inc.
rights: © 2019 Nishiura
abstract: Background Epidemiological surveillance of HIV infection in Japan involves two technical problems for directly applying a classical backcalculation method, i.e., (i) all AIDS cases are not counted over time and (ii) people diagnosed with HIV have received antiretroviral therapy, extending the incubation period. The present study aimed to address these issues and estimate the HIV incidence and the proportion of diagnosed HIV infections, using a simple statistical model. Methods From among Japanese nationals, yearly incidence data of HIV diagnoses and patients with AIDS who had not previously been diagnosed as HIV positive, from 1985 to 2017, were analyzed. Using the McKendrick partial differential equation, general convolution-like equations were derived, allowing estimation of the HIV incidence and the time-dependent rate of diagnosis. A likelihood-based approach was used to obtain parameter estimates. Results Assuming that the median incubation period was 10.0 years, the cumulative number of HIV infections was estimated to be 29,613 (95% confidence interval (CI): 29,059, 30,167) by the end of 2017, and the proportion of diagnosed HIV infections was estimated at 80.3% (95% CI [78.7%–82.0%]). Allowing the median incubation period to range from 7.5 to 12.3 years, the estimate of the proportion diagnosed can vary from 77% to 84%. Discussion The proportion of diagnosed HIV infections appears to have not yet reached 90% among Japanese nationals. Compared with the peak incidence from 2005–2008, new HIV infections have clearly been in a declining trend; however, there are still more than 1,000 new HIV infections per year in Japan. To increase the diagnosed proportion of HIV infections, it is critical to identify people who have difficulty accessing consultation, testing, and care, and to explore heterogeneous patterns of infection.
bibliographic citation: Nishiura (2019) Estimating the incidence and diagnosed proportion of HIV infections in Japan: a statistical modeling study. PeerJ 7:e6275 https://doi.org/10.7717/peerj.6275
date submitted: 2018-10-12
date accepted: 2018-12-09
issued: 2019-01-15
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Nishiura
  given name: Hiroshi
doi: 10.7717/peerj.6275
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-01-15
copyright: ©2019 Nishiura
attribution name: Nishiura

Identification and characterization of capsule depolymerase Dpo48 from Acinetobacter baumannii phage IME200
type: item
type: AcademicArticle
description: Background The emergence of multidrug- or extensively drug-resistant Acinetobacter baumannii has made it difficult to treat and control infections caused by this bacterium. It is urgently necessary to search for alternatives to conventional antibiotics for control of severe A. baumannii infections. In recent years, bacteriophages and their derivatives, such as depolymerases, showed great potential as antibacterial or antivirulence agents against bacterial infections. Nonetheless, unlike broad-spectrum bactericidal antibiotics, phage-encoded depolymerase targets only a limited number of bacterial strains. Therefore, identification of novel depolymerases and evaluation of their ability to control A. baumannii infections is important. Methods A bacteriophage was isolated from hospital sewage using an extensively drug-resistant A. baumannii strain as the host bacterium, and the phage’s plaque morphology and genomic composition were studied. A polysaccharide depolymerase (Dpo48) was expressed and identified, and the effects of pH and temperature on its activity were determined. Besides, a serum killing assay was conducted, and amino acid sequences homologous to those of putative polysaccharide depolymerases were compared. Results Phage IME200 yielded clear plaques surrounded by enlarged halos, with polysaccharide depolymerase activity against the host bacterium. A tail fiber protein with a Pectate_lyase_3 domain was identified as Dpo48 and characterized . Dpo48 was found to degrade the capsule polysaccharide of the bacterial surface, as revealed by Alcian blue staining. Dpo48 manifested stable activity over a broad range of pH (5.0–9.0) and temperatures (20–70 °C). Results from in vitro serum killing assays indicated that 50% serum was sufficient to cause a five log reduction of overnight enzyme-treated bacteria, with serum complement playing an important role in these killing assays. Moreover, Dpo48 had a spectrum of activity exactly the same as its parental phage IME20…
format: application/pdf
format: text/html
creator: Yannan Liu
creator: Zhiqiang Mi
creator: Liyuan Mi
creator: Yong Huang
creator: Puyuan Li
creator: Huiying Liu
creator: Xin Yuan
creator: Wenkai Niu
creator: Ning Jiang
creator: Changqing Bai
creator: Zhancheng Gao
subject: Microbiology
subject: Molecular Biology
subject: Virology
description: doi:10.7717/peerj.6173
publisher: PeerJ Inc.
rights: © 2019 Liu et al.
abstract: Background The emergence of multidrug- or extensively drug-resistant Acinetobacter baumannii has made it difficult to treat and control infections caused by this bacterium. It is urgently necessary to search for alternatives to conventional antibiotics for control of severe A. baumannii infections. In recent years, bacteriophages and their derivatives, such as depolymerases, showed great potential as antibacterial or antivirulence agents against bacterial infections. Nonetheless, unlike broad-spectrum bactericidal antibiotics, phage-encoded depolymerase targets only a limited number of bacterial strains. Therefore, identification of novel depolymerases and evaluation of their ability to control A. baumannii infections is important. Methods A bacteriophage was isolated from hospital sewage using an extensively drug-resistant A. baumannii strain as the host bacterium, and the phage’s plaque morphology and genomic composition were studied. A polysaccharide depolymerase (Dpo48) was expressed and identified, and the effects of pH and temperature on its activity were determined. Besides, a serum killing assay was conducted, and amino acid sequences homologous to those of putative polysaccharide depolymerases were compared. Results Phage IME200 yielded clear plaques surrounded by enlarged halos, with polysaccharide depolymerase activity against the host bacterium. A tail fiber protein with a Pectate_lyase_3 domain was identified as Dpo48 and characterized . Dpo48 was found to degrade the capsule polysaccharide of the bacterial surface, as revealed by Alcian blue staining. Dpo48 manifested stable activity over a broad range of pH (5.0–9.0) and temperatures (20–70 °C). Results from in vitro serum killing assays indicated that 50% serum was sufficient to cause a five log reduction of overnight enzyme-treated bacteria, with serum complement playing an important role in these killing assays. Moreover, Dpo48 had a spectrum of activity exactly the same as its parental phage IME20…
bibliographic citation: Liu et al. (2019) Identification and characterization of capsule depolymerase Dpo48 from Acinetobacter baumannii phage IME200. PeerJ 7:e6173 https://doi.org/10.7717/peerj.6173
date submitted: 2018-05-11
date accepted: 2018-11-28
issued: 2019-01-14
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Liu
  given name: Yannan
author list: Agent
  family name: Mi
  given name: Zhiqiang
author list: Agent
  family name: Mi
  given name: Liyuan
author list: Agent
  family name: Huang
  given name: Yong
author list: Agent
  family name: Li
  given name: Puyuan
author list: Agent
  family name: Liu
  given name: Huiying
author list: Agent
  family name: Yuan
  given name: Xin
author list: Agent
  family name: Niu
  given name: Wenkai
author list: Agent
  family name: Jiang
  given name: Ning
author list: Agent
  family name: Bai
  given name: Changqing
author list: Agent
  family name: Gao
  given name: Zhancheng
doi: 10.7717/peerj.6173
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-01-14
copyright: ©2019 Liu et al.
attribution name: Liu et al.

Application of built-in adjuvants for epitope-based vaccines
type: item
type: AcademicArticle
description: Several studies have shown that epitope vaccines exhibit substantial advantages over conventional vaccines. However, epitope vaccines are associated with limited immunity, which can be overcome by conjugating antigenic epitopes with built-in adjuvants (e.g., some carrier proteins or new biomaterials) with special properties, including immunologic specificity, good biosecurity and biocompatibility, and the ability to vastly improve the immune response of epitope vaccines. When designing epitope vaccines, the following types of built-in adjuvants are typically considered: (1) pattern recognition receptor ligands (i.e., toll-like receptors); (2) virus-like particle carrier platforms; (3) bacterial toxin proteins; and (4) novel potential delivery systems (e.g., self-assembled peptide nanoparticles, lipid core peptides, and polymeric or inorganic nanoparticles). This review primarily discusses the current and prospective applications of these built-in adjuvants (i.e., biological carriers) to provide some references for the future design of epitope-based vaccines.
format: application/pdf
format: text/html
creator: Yao Lei
creator: Furong Zhao
creator: Junjun Shao
creator: Yangfan Li
creator: Shifang Li
creator: Huiyun Chang
creator: Yongguang Zhang
subject: Biotechnology
subject: Veterinary Medicine
subject: Immunology
description: doi:10.7717/peerj.6185
publisher: PeerJ Inc.
rights: © 2019 Lei et al.
abstract: Several studies have shown that epitope vaccines exhibit substantial advantages over conventional vaccines. However, epitope vaccines are associated with limited immunity, which can be overcome by conjugating antigenic epitopes with built-in adjuvants (e.g., some carrier proteins or new biomaterials) with special properties, including immunologic specificity, good biosecurity and biocompatibility, and the ability to vastly improve the immune response of epitope vaccines. When designing epitope vaccines, the following types of built-in adjuvants are typically considered: (1) pattern recognition receptor ligands (i.e., toll-like receptors); (2) virus-like particle carrier platforms; (3) bacterial toxin proteins; and (4) novel potential delivery systems (e.g., self-assembled peptide nanoparticles, lipid core peptides, and polymeric or inorganic nanoparticles). This review primarily discusses the current and prospective applications of these built-in adjuvants (i.e., biological carriers) to provide some references for the future design of epitope-based vaccines.
bibliographic citation: Lei et al. (2019) Application of built-in adjuvants for epitope-based vaccines. PeerJ 6:e6185 https://doi.org/10.7717/peerj.6185
date submitted: 2018-09-04
date accepted: 2018-11-29
issued: 2019-01-14
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Lei
  given name: Yao
author list: Agent
  family name: Zhao
  given name: Furong
author list: Agent
  family name: Shao
  given name: Junjun
author list: Agent
  family name: Li
  given name: Yangfan
author list: Agent
  family name: Li
  given name: Shifang
author list: Agent
  family name: Chang
  given name: Huiyun
author list: Agent
  family name: Zhang
  given name: Yongguang
doi: 10.7717/peerj.6185
volume: 6
issn: 2167-8359
publication name: PeerJ
publication date: 2019-01-14
copyright: © 2019 Lei et al.
attribution name: Lei et al.

Worldwide co-occurrence analysis of 17 species of the genus Brachypodium using data mining
type: item
type: AcademicArticle
description: The co-occurrence of plant species is a fundamental aspect of plant ecology that contributes to understanding ecological processes, including the establishment of ecological communities and its applications in biological conservation. A priori algorithms can be used to measure the co-occurrence of species in a spatial distribution given by coordinates. We used 17 species of the genus Brachypodium, downloaded from the Global Biodiversity Information Facility data repository or obtained from bibliographical sources, to test an algorithm with the spatial points process technique used by Silva et al. (2016), generating association rules for co-occurrence analysis. Brachypodium spp. has emerged as an effective model for monocot species, growing in different environments, latitudes, and elevations; thereby, representing a wide range of biotic and abiotic conditions that may be associated with adaptive natural genetic variation. We created seven datasets of two, three, four, six, seven, 15, and 17 species in order to test the algorithm with four different distances (1, 5, 10, and 20 km). Several measurements (support, confidence, lift, Chi-square, and p-value) were used to evaluate the quality of the results generated by the algorithm. No negative association rules were created in the datasets, while 95 positive co-occurrences rules were found for datasets with six, seven, 15, and 17 species. Using 20 km in the dataset with 17 species, we found 16 positive co-occurrences involving five species, suggesting that these species are coexisting. These findings are corroborated by the results obtained in the dataset with 15 species, where two species with broad range distributions present in the previous dataset are eliminated, obtaining seven positive co-occurrences. We found that B. sylvaticum has co-occurrence relations with several species, such as B. pinnatum, B. rupestre, B. retusum, and B. phoenicoides, due to its wide distribution in Europe, Asia, and north of Africa. We …
format: application/pdf
format: text/html
creator: Simon Orozco-Arias
creator: Ana María Núñez-Rincón
creator: Reinel Tabares-Soto
creator: Diana López-Álvarez
subject: Bioinformatics
subject: Ecology
subject: Computational Science
subject: Data Mining and Machine Learning
subject: Spatial and Geographic Information Science
description: doi:10.7717/peerj.6193
publisher: PeerJ Inc.
rights: © 2019 Orozco-Arias et al.
abstract: The co-occurrence of plant species is a fundamental aspect of plant ecology that contributes to understanding ecological processes, including the establishment of ecological communities and its applications in biological conservation. A priori algorithms can be used to measure the co-occurrence of species in a spatial distribution given by coordinates. We used 17 species of the genus Brachypodium, downloaded from the Global Biodiversity Information Facility data repository or obtained from bibliographical sources, to test an algorithm with the spatial points process technique used by Silva et al. (2016), generating association rules for co-occurrence analysis. Brachypodium spp. has emerged as an effective model for monocot species, growing in different environments, latitudes, and elevations; thereby, representing a wide range of biotic and abiotic conditions that may be associated with adaptive natural genetic variation. We created seven datasets of two, three, four, six, seven, 15, and 17 species in order to test the algorithm with four different distances (1, 5, 10, and 20 km). Several measurements (support, confidence, lift, Chi-square, and p-value) were used to evaluate the quality of the results generated by the algorithm. No negative association rules were created in the datasets, while 95 positive co-occurrences rules were found for datasets with six, seven, 15, and 17 species. Using 20 km in the dataset with 17 species, we found 16 positive co-occurrences involving five species, suggesting that these species are coexisting. These findings are corroborated by the results obtained in the dataset with 15 species, where two species with broad range distributions present in the previous dataset are eliminated, obtaining seven positive co-occurrences. We found that B. sylvaticum has co-occurrence relations with several species, such as B. pinnatum, B. rupestre, B. retusum, and B. phoenicoides, due to its wide distribution in Europe, Asia, and north of Africa. We …
bibliographic citation: Orozco-Arias et al. (2019) Worldwide co-occurrence analysis of 17 species of the genus Brachypodium using data mining. PeerJ 6:e6193 https://doi.org/10.7717/peerj.6193
date submitted: 2018-05-24
date accepted: 2018-11-29
issued: 2019-01-14
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Orozco-Arias
  given name: Simon
author list: Agent
  family name: Núñez-Rincón
  given name: Ana María
author list: Agent
  family name: Tabares-Soto
  given name: Reinel
author list: Agent
  family name: López-Álvarez
  given name: Diana
doi: 10.7717/peerj.6193
volume: 6
issn: 2167-8359
publication name: PeerJ
publication date: 2019-01-14
copyright: © 2019 Orozco-Arias et al.
attribution name: Orozco-Arias et al.

Combining legacy data with new drone and DGPS mapping to identify the provenance of Plio-Pleistocene fossils from Bolt’s Farm, Cradle of Humankind (South Africa)
type: item
type: AcademicArticle
description: Bolt’s Farm is a Plio-Pleistocene fossil site located within the southwestern corner of the UNESCO Hominid Fossil Sites of South Africa World Heritage Site. The site is a complex of active caves and more than 20 palaeokarst deposits or pits, many of which were exposed through the action of lime mining in the early 20th century. The pits represent heavily eroded cave systems, and as such associating the palaeocave sediments within and between the pits is difficult, especially as little geochronological data exists. These pits and the associated lime miner’s rubble were first explored by palaeoanthropologists in the late 1930s, but as yet no hominin material has been recovered. The first systematic mapping was undertaken by Frank Peabody as part of the University of California Africa Expedition (UCAE) in 1947–1948. A redrawn version of the map was not published until 1991 by Basil Cooke and this has subsequently been used and modified by recent researchers. Renewed work in the 2000s used Cooke’s map to try and relocate the original fossil deposits. However, Peabody’s map does not include all the pits and caves, and thus in some cases this was successful, while in others previously sampled pits were inadvertently given new names. This was compounded by the fact that new fossil bearing deposits were discovered in this new phase, causing confusion in associating the 1940s fossils with the deposits from which they originated; as well as associating them with the recently excavated material. To address this, we have used a Geographic Information System (GIS) to compare Peabody’s original map with subsequently published maps. This highlighted transcription errors between maps, most notably the location of Pit 23, an important palaeontological deposit given the recovery of well-preserved primate crania (Parapapio, Cercopithecoides) and partial skeletons of the extinct felid Dinofelis. We conducted the first drone and Differential Global Positioning System (DGPS) survey of Bo…
format: application/pdf
format: text/html
creator: Tara R. Edwards
creator: Brian J. Armstrong
creator: Jessie Birkett-Rees
creator: Alexander F. Blackwood
creator: Andy I.R. Herries
creator: Paul Penzo-Kajewski
creator: Robyn Pickering
creator: Justin W. Adams
subject: Evolutionary Studies
subject: Paleontology
subject: Spatial and Geographic Information Science
description: doi:10.7717/peerj.6202
publisher: PeerJ Inc.
rights: © 2019 Edwards et al.
abstract: Bolt’s Farm is a Plio-Pleistocene fossil site located within the southwestern corner of the UNESCO Hominid Fossil Sites of South Africa World Heritage Site. The site is a complex of active caves and more than 20 palaeokarst deposits or pits, many of which were exposed through the action of lime mining in the early 20th century. The pits represent heavily eroded cave systems, and as such associating the palaeocave sediments within and between the pits is difficult, especially as little geochronological data exists. These pits and the associated lime miner’s rubble were first explored by palaeoanthropologists in the late 1930s, but as yet no hominin material has been recovered. The first systematic mapping was undertaken by Frank Peabody as part of the University of California Africa Expedition (UCAE) in 1947–1948. A redrawn version of the map was not published until 1991 by Basil Cooke and this has subsequently been used and modified by recent researchers. Renewed work in the 2000s used Cooke’s map to try and relocate the original fossil deposits. However, Peabody’s map does not include all the pits and caves, and thus in some cases this was successful, while in others previously sampled pits were inadvertently given new names. This was compounded by the fact that new fossil bearing deposits were discovered in this new phase, causing confusion in associating the 1940s fossils with the deposits from which they originated; as well as associating them with the recently excavated material. To address this, we have used a Geographic Information System (GIS) to compare Peabody’s original map with subsequently published maps. This highlighted transcription errors between maps, most notably the location of Pit 23, an important palaeontological deposit given the recovery of well-preserved primate crania (Parapapio, Cercopithecoides) and partial skeletons of the extinct felid Dinofelis. We conducted the first drone and Differential Global Positioning System (DGPS) survey of Bo…
bibliographic citation: Edwards et al. (2019) Combining legacy data with new drone and DGPS mapping to identify the provenance of Plio-Pleistocene fossils from Bolt’s Farm, Cradle of Humankind (South Africa). PeerJ 7:e6202 https://doi.org/10.7717/peerj.6202
date submitted: 2018-10-25
date accepted: 2018-12-03
issued: 2019-01-14
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Edwards
  given name: Tara R.
author list: Agent
  family name: Armstrong
  given name: Brian J.
author list: Agent
  family name: Birkett-Rees
  given name: Jessie
author list: Agent
  family name: Blackwood
  given name: Alexander F.
author list: Agent
  family name: Herries
  given name: Andy I.R.
author list: Agent
  family name: Penzo-Kajewski
  given name: Paul
author list: Agent
  family name: Pickering
  given name: Robyn
author list: Agent
  family name: Adams
  given name: Justin W.
doi: 10.7717/peerj.6202
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-01-14
copyright: ©2019 Edwards et al.
attribution name: Edwards et al.

Using lidar to assess the development of structural diversity in forests undergoing passive rewilding in temperate Northern Europe
type: item
type: AcademicArticle
description: Forested areas are increasing across Europe, driven by both reforestation programs and farmland abandonment. While tree planting remains the standard reforestation strategy, there is increased interest in spontaneous regeneration as a cost-effective method with equal or potentially greater benefits. Furthermore, expanding areas of already established forests are left for passive rewilding to promote biodiversity conservation. Effective and objective methods are needed for monitoring and analyzing the development of forest structure under these management scenarios, with airborne laser scanning (lidar: light detection and ranging) being a promising methodology. Here, we assess the structural characteristics and development of unmanaged forests and 28- to 78-year old spontaneously regenerated forests on former agricultural land, relative to managed forests of similar age in Denmark, using 25 lidar-derived metrics in 10- and 30-m grid cells. We analyzed the lidar-derived cell values in a principal component analysis (PCA) and interpreted the axes ecologically, in conjunction with pairwise tests of median and variance of PCA-values for each forest. Spontaneously regenerated forest in general had increased structural heterogeneity compared to planted and managed forests. Furthermore, structural heterogeneity kept increasing in spontaneously regenerated forest across the maximal 78-year timespan investigated. Natural disturbances showed strong impacts on vegetation structure, leading to both structural homogeneity and heterogeneity. The results illustrate the utility of passive rewilding for generating structurally heterogeneous forested nature areas, and the utility of lidar surveys for monitoring and interpreting structural development of such forests.
format: application/pdf
format: text/html
creator: Henrik Thers
creator: Peder Klith Bøcher
creator: Jens-Christian Svenning
subject: Computational Biology
subject: Conservation Biology
subject: Ecology
subject: Forestry
subject: Spatial and Geographic Information Science
description: doi:10.7717/peerj.6219
publisher: PeerJ Inc.
rights: © 2019 Thers et al.
abstract: Forested areas are increasing across Europe, driven by both reforestation programs and farmland abandonment. While tree planting remains the standard reforestation strategy, there is increased interest in spontaneous regeneration as a cost-effective method with equal or potentially greater benefits. Furthermore, expanding areas of already established forests are left for passive rewilding to promote biodiversity conservation. Effective and objective methods are needed for monitoring and analyzing the development of forest structure under these management scenarios, with airborne laser scanning (lidar: light detection and ranging) being a promising methodology. Here, we assess the structural characteristics and development of unmanaged forests and 28- to 78-year old spontaneously regenerated forests on former agricultural land, relative to managed forests of similar age in Denmark, using 25 lidar-derived metrics in 10- and 30-m grid cells. We analyzed the lidar-derived cell values in a principal component analysis (PCA) and interpreted the axes ecologically, in conjunction with pairwise tests of median and variance of PCA-values for each forest. Spontaneously regenerated forest in general had increased structural heterogeneity compared to planted and managed forests. Furthermore, structural heterogeneity kept increasing in spontaneously regenerated forest across the maximal 78-year timespan investigated. Natural disturbances showed strong impacts on vegetation structure, leading to both structural homogeneity and heterogeneity. The results illustrate the utility of passive rewilding for generating structurally heterogeneous forested nature areas, and the utility of lidar surveys for monitoring and interpreting structural development of such forests.
bibliographic citation: Thers et al. (2019) Using lidar to assess the development of structural diversity in forests undergoing passive rewilding in temperate Northern Europe. PeerJ 6:e6219 https://doi.org/10.7717/peerj.6219
date submitted: 2018-06-04
date accepted: 2018-12-05
issued: 2019-01-14
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Thers
  given name: Henrik
author list: Agent
  family name: Bøcher
  given name: Peder Klith
author list: Agent
  family name: Svenning
  given name: Jens-Christian
doi: 10.7717/peerj.6219
volume: 6
issn: 2167-8359
publication name: PeerJ
publication date: 2019-01-14
copyright: © 2019 Thers et al.
attribution name: Thers et al.

Global genomic similarity and core genome sequence diversity of the Streptococcus genus as a toolkit to identify closely related bacterial species in complex environments
type: item
type: AcademicArticle
description: Background The Streptococcus genus is relevant to both public health and food safety because of its ability to cause pathogenic infections. It is well-represented (>100 genomes) in publicly available databases. Streptococci are ubiquitous, with multiple sources of isolation, from human pathogens to dairy products. The Streptococcus genus has traditionally been classified by morphology, serum types, the 16S ribosomal RNA (rRNA) gene, and multi-locus sequence types subject to in-depth comparative genomic analysis. Methods Core and pan-genomes described the genomic diversity of 108 strains belonging to 16 Streptococcus species. The core genome nucleotide diversity was calculated and compared to phylogenomic distances within the genus Streptococcus. The core genome was also used as a resource to recruit metagenomic fragment reads from streptococci dominated environments. A conventional 16S rRNA gene phylogeny reconstruction was used as a reference to compare the resulting dendrograms of average nucleotide identity (ANI) and genome similarity score (GSS) dendrograms. Results The core genome, in this work, consists of 404 proteins that are shared by all 108 Streptococcus. The average identity of the pairwise compared core proteins decreases proportionally to GSS lower scores, across species. The GSS dendrogram recovers most of the clades in the 16S rRNA gene phylogeny while distinguishing between 16S polytomies (unresolved nodes). The GSS is a distance metric that can reflect evolutionary history comparing orthologous proteins. Additionally, GSS resulted in the most useful metric for genus and species comparisons, where ANI metrics failed due to false positives when comparing different species. Discussion Understanding of genomic variability and species relatedness is the goal of tools like GSS, which makes use of the maximum pairwise shared orthologous sequences for its calculation. It allows for long evolutionary distances (above species) to be included because of the u…
format: application/pdf
format: text/html
creator: Hugo R. Barajas
creator: Miguel F. Romero
creator: Shamayim Martínez-Sánchez
creator: Luis D. Alcaraz
subject: Biodiversity
subject: Bioinformatics
subject: Genomics
subject: Microbiology
subject: Molecular Biology
description: doi:10.7717/peerj.6233
publisher: PeerJ Inc.
rights: © 2019 Barajas et al.
abstract: Background The Streptococcus genus is relevant to both public health and food safety because of its ability to cause pathogenic infections. It is well-represented (>100 genomes) in publicly available databases. Streptococci are ubiquitous, with multiple sources of isolation, from human pathogens to dairy products. The Streptococcus genus has traditionally been classified by morphology, serum types, the 16S ribosomal RNA (rRNA) gene, and multi-locus sequence types subject to in-depth comparative genomic analysis. Methods Core and pan-genomes described the genomic diversity of 108 strains belonging to 16 Streptococcus species. The core genome nucleotide diversity was calculated and compared to phylogenomic distances within the genus Streptococcus. The core genome was also used as a resource to recruit metagenomic fragment reads from streptococci dominated environments. A conventional 16S rRNA gene phylogeny reconstruction was used as a reference to compare the resulting dendrograms of average nucleotide identity (ANI) and genome similarity score (GSS) dendrograms. Results The core genome, in this work, consists of 404 proteins that are shared by all 108 Streptococcus. The average identity of the pairwise compared core proteins decreases proportionally to GSS lower scores, across species. The GSS dendrogram recovers most of the clades in the 16S rRNA gene phylogeny while distinguishing between 16S polytomies (unresolved nodes). The GSS is a distance metric that can reflect evolutionary history comparing orthologous proteins. Additionally, GSS resulted in the most useful metric for genus and species comparisons, where ANI metrics failed due to false positives when comparing different species. Discussion Understanding of genomic variability and species relatedness is the goal of tools like GSS, which makes use of the maximum pairwise shared orthologous sequences for its calculation. It allows for long evolutionary distances (above species) to be included because of the u…
bibliographic citation: Barajas et al. (2019) Global genomic similarity and core genome sequence diversity of the Streptococcus genus as a toolkit to identify closely related bacterial species in complex environments. PeerJ 6:e6233 https://doi.org/10.7717/peerj.6233
date submitted: 2018-03-09
date accepted: 2018-12-07
issued: 2019-01-14
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Barajas
  given name: Hugo R.
author list: Agent
  family name: Romero
  given name: Miguel F.
author list: Agent
  family name: Martínez-Sánchez
  given name: Shamayim
author list: Agent
  family name: Alcaraz
  given name: Luis D.
doi: 10.7717/peerj.6233
volume: 6
issn: 2167-8359
publication name: PeerJ
publication date: 2019-01-14
copyright: © 2019 Barajas et al.
attribution name: Barajas et al.

Method for the quantitative evaluation of ecosystem services in coastal regions
type: item
type: AcademicArticle
description: Wetlands, tidal flats, seaweed beds, and coral reefs are valuable not only as habitats for many species, but also as places where people interact with the sea. Unfortunately, these areas have declined in recent years, so environmental improvement projects to conserve and restore them are being carried out across the world. In this study, we propose a method for quantifying ecosystem services, that is, useful for the proper maintenance and management of artificial tidal flats, a type of environmental improvement project. With this method, a conceptual model of the relationship between each service and related environmental factors in natural and social systems was created, and the relationships between services and environmental factors were clarified. The state of the environmental factors affecting each service was quantified, and the state of those factors was reflected in the evaluation value of the service. As a result, the method can identify which environmental factors need to be improved and if the goal is to increase the value of the targeted tidal flat. The method demonstrates an effective approach in environmental conservation for the restoration and preservation of coastal areas.
format: application/pdf
format: text/html
creator: Tomonari Okada
creator: Yugo Mito
creator: Erina Iseri
creator: Toshiyuki Takahashi
creator: Takanori Sugano
creator: Yoshihiro B. Akiyama
creator: Kenta Watanabe
creator: Toko Tanaya
creator: Hiroaki Sugino
creator: Kanae Tokunaga
creator: Takahiro Kubo
creator: Tomohiro Kuwae
subject: Conservation Biology
subject: Ecology
subject: Ecosystem Science
subject: Science Policy
subject: Coupled Natural and Human Systems
description: doi:10.7717/peerj.6234
publisher: PeerJ Inc.
rights: © 2019 Okada et al.
abstract: Wetlands, tidal flats, seaweed beds, and coral reefs are valuable not only as habitats for many species, but also as places where people interact with the sea. Unfortunately, these areas have declined in recent years, so environmental improvement projects to conserve and restore them are being carried out across the world. In this study, we propose a method for quantifying ecosystem services, that is, useful for the proper maintenance and management of artificial tidal flats, a type of environmental improvement project. With this method, a conceptual model of the relationship between each service and related environmental factors in natural and social systems was created, and the relationships between services and environmental factors were clarified. The state of the environmental factors affecting each service was quantified, and the state of those factors was reflected in the evaluation value of the service. As a result, the method can identify which environmental factors need to be improved and if the goal is to increase the value of the targeted tidal flat. The method demonstrates an effective approach in environmental conservation for the restoration and preservation of coastal areas.
bibliographic citation: Okada et al. (2019) Method for the quantitative evaluation of ecosystem services in coastal regions. PeerJ 6:e6234 https://doi.org/10.7717/peerj.6234
date submitted: 2018-05-01
date accepted: 2018-12-07
issued: 2019-01-14
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Okada
  given name: Tomonari
author list: Agent
  family name: Mito
  given name: Yugo
author list: Agent
  family name: Iseri
  given name: Erina
author list: Agent
  family name: Takahashi
  given name: Toshiyuki
author list: Agent
  family name: Sugano
  given name: Takanori
author list: Agent
  family name: Akiyama
  given name: Yoshihiro B.
author list: Agent
  family name: Watanabe
  given name: Kenta
author list: Agent
  family name: Tanaya
  given name: Toko
author list: Agent
  family name: Sugino
  given name: Hiroaki
author list: Agent
  family name: Tokunaga
  given name: Kanae
author list: Agent
  family name: Kubo
  given name: Takahiro
author list: Agent
  family name: Kuwae
  given name: Tomohiro
doi: 10.7717/peerj.6234
volume: 6
issn: 2167-8359
publication name: PeerJ
publication date: 2019-01-14
copyright: © 2019 Okada et al.
attribution name: Okada et al.

Mantle transcriptome sequencing of Mytilus spp. and identification of putative biomineralization genes
type: item
type: AcademicArticle
description: In molluscs, the shell secreted by mantle tissue during the biomineralization process is the first barrier against predators and mechanical damage. Changing environmental conditions, such as ocean acidification, influence shell strength and thus protection of the soft body within. Mussels are marine bivalves with important commercial and ecological value worldwide. Despite this importance, the proteins involved in the biomineralization and pigmentation processes in Mytilus spp. remain unclear, as does taxonomy of Mytilus taxa, though there have been many molecular studies. To further understanding in these areas, this study aimed to characterize and compare mantle transcriptomes of four mussel taxa using next generation sequencing. Mussels representing four taxa, were collected from several localities and RNA from mantle tissue was extracted. RNA sequences obtained were assembled, annotated and potential molecular markers, including simple sequence repeats (SSRs) and single nucleotide polymorphisms (SNPs) were identified. Candidate contigs putatively related to biomineralization and pigmentation processes were then selected and several transcripts were chosen for phylogenetic analyses from the Bivalvia class. Transcriptome comparisons between Mytilus taxa, including gene ontology (GO) enrichment analysis and orthologues identification were performed. Of assembled contigs, 46.57%, 37.28% and 17.53% were annotated using NCBI NR, GO and Kyoto Encyclopedia of Genes and Genomes databases, respectively. Potential SSRs (483) and SNPs (1,497) were identified. Results presented a total of 1,292 contigs putatively involved in biomineralization and melanogenesis. Phylogenetic analyses of α-carbonic anhydrase, chitinase and tyrosinase revealed complex evolutionary history and diversity of these genes, which may be a result of duplication events or adaptation to different environments in mussels and other bivalves. Enrichment analyses revealed GO terms associated with pH and the…
format: application/pdf
format: text/html
creator: Magdalena Malachowicz
creator: Roman Wenne
subject: Aquaculture, Fisheries and Fish Science
subject: Genetics
subject: Marine Biology
description: doi:10.7717/peerj.6245
publisher: PeerJ Inc.
rights: © 2019 Malachowicz and Wenne
abstract: In molluscs, the shell secreted by mantle tissue during the biomineralization process is the first barrier against predators and mechanical damage. Changing environmental conditions, such as ocean acidification, influence shell strength and thus protection of the soft body within. Mussels are marine bivalves with important commercial and ecological value worldwide. Despite this importance, the proteins involved in the biomineralization and pigmentation processes in Mytilus spp. remain unclear, as does taxonomy of Mytilus taxa, though there have been many molecular studies. To further understanding in these areas, this study aimed to characterize and compare mantle transcriptomes of four mussel taxa using next generation sequencing. Mussels representing four taxa, were collected from several localities and RNA from mantle tissue was extracted. RNA sequences obtained were assembled, annotated and potential molecular markers, including simple sequence repeats (SSRs) and single nucleotide polymorphisms (SNPs) were identified. Candidate contigs putatively related to biomineralization and pigmentation processes were then selected and several transcripts were chosen for phylogenetic analyses from the Bivalvia class. Transcriptome comparisons between Mytilus taxa, including gene ontology (GO) enrichment analysis and orthologues identification were performed. Of assembled contigs, 46.57%, 37.28% and 17.53% were annotated using NCBI NR, GO and Kyoto Encyclopedia of Genes and Genomes databases, respectively. Potential SSRs (483) and SNPs (1,497) were identified. Results presented a total of 1,292 contigs putatively involved in biomineralization and melanogenesis. Phylogenetic analyses of α-carbonic anhydrase, chitinase and tyrosinase revealed complex evolutionary history and diversity of these genes, which may be a result of duplication events or adaptation to different environments in mussels and other bivalves. Enrichment analyses revealed GO terms associated with pH and the…
bibliographic citation: Malachowicz et al. (2019) Mantle transcriptome sequencing of Mytilus spp. and identification of putative biomineralization genes. PeerJ 6:e6245 https://doi.org/10.7717/peerj.6245
date submitted: 2018-08-23
date accepted: 2018-12-09
issued: 2019-01-14
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Malachowicz
  given name: Magdalena
author list: Agent
  family name: Wenne
  given name: Roman
doi: 10.7717/peerj.6245
volume: 6
issn: 2167-8359
publication name: PeerJ
publication date: 2019-01-14
copyright: © 2019 Malachowicz and Wenne
attribution name: Malachowicz and Wenne

Effect of agricultural land-use change on ant dominance hierarchy and food preferences in a temperate oak forest
type: item
type: AcademicArticle
description: Background The discovery-dominance trade-off is the inverse relationship between the ability of a species to discover resources and the species’ dominance of those resources; a paradigm used to explain species coexistence in ant communities dependent on similar resources. However, factors such as stress (e.g., temperature) or disturbance (e.g., removal of biomass) associated with the change in land use, can modify this trade-off. Here, we aimed to determine the potential effects of land use change on dominance hierarchy, food preferences and on the discovery-dominance trade-off. Methods An experiment with baits was used to investigate the dominance hierarchies of ant communities in a temperate mountain habitat in central Mexico. We evaluated the dominance index (DI), food preferences and discovery-dominance trade-offs of ants inhabiting two types of vegetation: a native oak forest and agricultural land resulting from agricultural land use and grazing. Results The ant communities in both environments were comprised of three species of ants (Monomorium minimum, Myrmica mexicana, and Camponotus picipes pilosulus), four morphospecies (Pheidole sp.1 and Pheidole sp.2, Temnothorax sp. and Lasius sp.) and one genus (Formica spp.). All Formicidae showed values of intermediate to low DI, and this factor did not seem to be influenced by the change in land use. Ants in the modified vegetation (i.e., agricultural land) were found to be numerically greater. Overall, a higher number of visits were registered to the tuna bait, although the duration of foraging events to the honey baits was longer. However, foraging times were dependent on the species considered: the generalized Myrmicinae, M. minimum, the ant species with highest DI, foraged for longer periods of time in the agricultural land and on the tuna bait. Meanwhile, the cold-climate specialist Formica spp., with a lower DI, foraged for longer periods of time in the oak (although not significant) and on the honey bait. We …
format: application/pdf
format: text/html
creator: Citlalli Castillo-Guevara
creator: Mariana Cuautle
creator: Carlos Lara
creator: Brenda Juárez-Juárez
subject: Animal Behavior
subject: Biodiversity
subject: Conservation Biology
subject: Ecology
description: doi:10.7717/peerj.6255
publisher: PeerJ Inc.
rights: © 2019 Castillo-Guevara et al.
abstract: Background The discovery-dominance trade-off is the inverse relationship between the ability of a species to discover resources and the species’ dominance of those resources; a paradigm used to explain species coexistence in ant communities dependent on similar resources. However, factors such as stress (e.g., temperature) or disturbance (e.g., removal of biomass) associated with the change in land use, can modify this trade-off. Here, we aimed to determine the potential effects of land use change on dominance hierarchy, food preferences and on the discovery-dominance trade-off. Methods An experiment with baits was used to investigate the dominance hierarchies of ant communities in a temperate mountain habitat in central Mexico. We evaluated the dominance index (DI), food preferences and discovery-dominance trade-offs of ants inhabiting two types of vegetation: a native oak forest and agricultural land resulting from agricultural land use and grazing. Results The ant communities in both environments were comprised of three species of ants (Monomorium minimum, Myrmica mexicana, and Camponotus picipes pilosulus), four morphospecies (Pheidole sp.1 and Pheidole sp.2, Temnothorax sp. and Lasius sp.) and one genus (Formica spp.). All Formicidae showed values of intermediate to low DI, and this factor did not seem to be influenced by the change in land use. Ants in the modified vegetation (i.e., agricultural land) were found to be numerically greater. Overall, a higher number of visits were registered to the tuna bait, although the duration of foraging events to the honey baits was longer. However, foraging times were dependent on the species considered: the generalized Myrmicinae, M. minimum, the ant species with highest DI, foraged for longer periods of time in the agricultural land and on the tuna bait. Meanwhile, the cold-climate specialist Formica spp., with a lower DI, foraged for longer periods of time in the oak (although not significant) and on the honey bait. We …
bibliographic citation: Castillo-Guevara et al. (2019) Effect of agricultural land-use change on ant dominance hierarchy and food preferences in a temperate oak forest. PeerJ 7:e6255 https://doi.org/10.7717/peerj.6255
date submitted: 2018-06-28
date accepted: 2018-12-10
issued: 2019-01-14
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Castillo-Guevara
  given name: Citlalli
author list: Agent
  family name: Cuautle
  given name: Mariana
author list: Agent
  family name: Lara
  given name: Carlos
author list: Agent
  family name: Juárez-Juárez
  given name: Brenda
doi: 10.7717/peerj.6255
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-01-14
copyright: ©2019 Castillo-Guevara et al.
attribution name: Castillo-Guevara et al.

Comparative genomics of 16 Microbacterium spp. that tolerate multiple heavy metals and antibiotics
type: item
type: AcademicArticle
description: A total of 16 different strains of Microbacterium spp. were isolated from contaminated soil and enriched on the carcinogen, hexavalent chromium [Cr(VI)]. The majority of the isolates (11 of the 16) were able to tolerate concentrations (0.1 mM) of cobalt, cadmium, and nickel, in addition to Cr(VI) (0.5–20 mM). Interestingly, these bacteria were also able to tolerate three different antibiotics (ranges: ampicillin 0–16 μg ml−1, chloramphenicol 0–24 μg ml−1, and vancomycin 0–24 μg ml−1). To gain genetic insight into these tolerance pathways, the genomes of these isolates were assembled and annotated. The genomes of these isolates not only have some shared genes (core genome) but also have a large amount of variability. The genomes also contained an annotated Cr(VI) reductase (chrR) that could be related to Cr(VI) reduction. Further, various heavy metal tolerance (e.g., Co/Zn/Cd efflux system) and antibiotic resistance genes were identified, which provide insight into the isolates’ ability to tolerate metals and antibiotics. Overall, these isolates showed a wide range of tolerances to heavy metals and antibiotics and genetic diversity, which was likely required of this population to thrive in a contaminated environment.
format: application/pdf
format: text/html
creator: Deric R. Learman
creator: Zahra Ahmad
creator: Allison Brookshier
creator: Michael W. Henson
creator: Victoria Hewitt
creator: Amanda Lis
creator: Cody Morrison
creator: Autumn Robinson
creator: Emily Todaro
creator: Ethan Wologo
creator: Sydney Wynne
creator: Elizabeth W. Alm
creator: Peter S. Kourtev
subject: Genomics
subject: Microbiology
subject: Biogeochemistry
subject: Environmental Contamination and Remediation
description: doi:10.7717/peerj.6258
publisher: PeerJ Inc.
rights: © 2019 Learman et al.
abstract: A total of 16 different strains of Microbacterium spp. were isolated from contaminated soil and enriched on the carcinogen, hexavalent chromium [Cr(VI)]. The majority of the isolates (11 of the 16) were able to tolerate concentrations (0.1 mM) of cobalt, cadmium, and nickel, in addition to Cr(VI) (0.5–20 mM). Interestingly, these bacteria were also able to tolerate three different antibiotics (ranges: ampicillin 0–16 μg ml−1, chloramphenicol 0–24 μg ml−1, and vancomycin 0–24 μg ml−1). To gain genetic insight into these tolerance pathways, the genomes of these isolates were assembled and annotated. The genomes of these isolates not only have some shared genes (core genome) but also have a large amount of variability. The genomes also contained an annotated Cr(VI) reductase (chrR) that could be related to Cr(VI) reduction. Further, various heavy metal tolerance (e.g., Co/Zn/Cd efflux system) and antibiotic resistance genes were identified, which provide insight into the isolates’ ability to tolerate metals and antibiotics. Overall, these isolates showed a wide range of tolerances to heavy metals and antibiotics and genetic diversity, which was likely required of this population to thrive in a contaminated environment.
bibliographic citation: Learman et al. (2019) Comparative genomics of 16 Microbacterium spp. that tolerate multiple heavy metals and antibiotics. PeerJ 6:e6258 https://doi.org/10.7717/peerj.6258
date submitted: 2018-08-02
date accepted: 2018-12-06
issued: 2019-01-14
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Learman
  given name: Deric R.
author list: Agent
  family name: Ahmad
  given name: Zahra
author list: Agent
  family name: Brookshier
  given name: Allison
author list: Agent
  family name: Henson
  given name: Michael W.
author list: Agent
  family name: Hewitt
  given name: Victoria
author list: Agent
  family name: Lis
  given name: Amanda
author list: Agent
  family name: Morrison
  given name: Cody
author list: Agent
  family name: Robinson
  given name: Autumn
author list: Agent
  family name: Todaro
  given name: Emily
author list: Agent
  family name: Wologo
  given name: Ethan
author list: Agent
  family name: Wynne
  given name: Sydney
author list: Agent
  family name: Alm
  given name: Elizabeth W.
author list: Agent
  family name: Kourtev
  given name: Peter S.
doi: 10.7717/peerj.6258
volume: 6
issn: 2167-8359
publication name: PeerJ
publication date: 2019-01-14
copyright: © 2019 Learman et al.
attribution name: Learman et al.

Variation in wild pea (Pisum sativum subsp. elatius) seed dormancy and its relationship to the environment and seed coat traits
type: item
type: AcademicArticle
description: Background Seed germination is one of the earliest key events in the plant life cycle. The timing of transition from seed to seedling is an important developmental stage determining the survival of individuals that influences the status of populations and species. Because of wide geographical distribution and occurrence in diverse habitats, wild pea (Pisum sativum subsp. elatius) offers an excellent model to study physical type of seed dormancy in an ecological context. This study addresses the gap in knowledge of association between the seed dormancy, seed properties and environmental factors, experimentally testing oscillating temperature as dormancy release clue. Methods Seeds of 97 pea accessions were subjected to two germination treatments (oscillating temperatures of 25/15 °C and 35/15 °C) over 28 days. Germination pattern was described using B-spline coefficients that aggregate both final germination and germination speed. Relationships between germination pattern and environmental conditions at the site of origin (soil and bioclimatic variables extracted from WorldClim 2.0 and SoilGrids databases) were studied using principal component analysis, redundancy analysis and ecological niche modelling. Seeds were analyzed for the seed coat thickness, seed morphology, weight and content of proanthocyanidins (PA). Results Seed total germination ranged from 0% to 100%. Cluster analysis of germination patterns of seeds under two temperature treatments differentiated the accessions into three groups: (1) non-dormant (28 accessions, mean germination of 92%), (2) dormant at both treatments (29 acc., 15%) and (3) responsive to increasing temperature range (41 acc., with germination change from 15 to 80%). Seed coat thickness differed between groups with dormant and responsive accessions having thicker testa (median 138 and 140 µm) than non-dormant ones (median 84 mm). The total PA content showed to be higher in the seed coat of dormant (mean 2.18 mg g−1) than those of non…
format: application/pdf
format: text/html
creator: Iveta Hradilová
creator: Martin Duchoslav
creator: Jan Brus
creator: Vilém Pechanec
creator: Miroslav Hýbl
creator: Pavel Kopecký
creator: Lucie Smržová
creator: Nikola Štefelová
creator: Tadeáš Vaclávek
creator: Michael Bariotakis
creator: Jitka Machalová
creator: Karel Hron
creator: Stergios Pirintsos
creator: Petr Smýkal
subject: Plant Science
subject: Spatial and Geographic Information Science
description: doi:10.7717/peerj.6263
publisher: PeerJ Inc.
rights: © 2019 Hradilová et al.
abstract: Background Seed germination is one of the earliest key events in the plant life cycle. The timing of transition from seed to seedling is an important developmental stage determining the survival of individuals that influences the status of populations and species. Because of wide geographical distribution and occurrence in diverse habitats, wild pea (Pisum sativum subsp. elatius) offers an excellent model to study physical type of seed dormancy in an ecological context. This study addresses the gap in knowledge of association between the seed dormancy, seed properties and environmental factors, experimentally testing oscillating temperature as dormancy release clue. Methods Seeds of 97 pea accessions were subjected to two germination treatments (oscillating temperatures of 25/15 °C and 35/15 °C) over 28 days. Germination pattern was described using B-spline coefficients that aggregate both final germination and germination speed. Relationships between germination pattern and environmental conditions at the site of origin (soil and bioclimatic variables extracted from WorldClim 2.0 and SoilGrids databases) were studied using principal component analysis, redundancy analysis and ecological niche modelling. Seeds were analyzed for the seed coat thickness, seed morphology, weight and content of proanthocyanidins (PA). Results Seed total germination ranged from 0% to 100%. Cluster analysis of germination patterns of seeds under two temperature treatments differentiated the accessions into three groups: (1) non-dormant (28 accessions, mean germination of 92%), (2) dormant at both treatments (29 acc., 15%) and (3) responsive to increasing temperature range (41 acc., with germination change from 15 to 80%). Seed coat thickness differed between groups with dormant and responsive accessions having thicker testa (median 138 and 140 µm) than non-dormant ones (median 84 mm). The total PA content showed to be higher in the seed coat of dormant (mean 2.18 mg g−1) than those of non…
bibliographic citation: Hradilová et al. (2019) Variation in wild pea (Pisum sativum subsp. elatius) seed dormancy and its relationship to the environment and seed coat traits. PeerJ 7:e6263 https://doi.org/10.7717/peerj.6263
date submitted: 2018-11-14
date accepted: 2018-12-11
issued: 2019-01-14
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Hradilová
  given name: Iveta
author list: Agent
  family name: Duchoslav
  given name: Martin
author list: Agent
  family name: Brus
  given name: Jan
author list: Agent
  family name: Pechanec
  given name: Vilém
author list: Agent
  family name: Hýbl
  given name: Miroslav
author list: Agent
  family name: Kopecký
  given name: Pavel
author list: Agent
  family name: Smržová
  given name: Lucie
author list: Agent
  family name: Štefelová
  given name: Nikola
author list: Agent
  family name: Vaclávek
  given name: Tadeáš
author list: Agent
  family name: Bariotakis
  given name: Michael
author list: Agent
  family name: Machalová
  given name: Jitka
author list: Agent
  family name: Hron
  given name: Karel
author list: Agent
  family name: Pirintsos
  given name: Stergios
author list: Agent
  family name: Smýkal
  given name: Petr
doi: 10.7717/peerj.6263
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-01-14
copyright: ©2019 Hradilová et al.
attribution name: Hradilová et al.

The effects of afforestation on soil bacterial communities in temperate grassland are modulated by soil chemical properties
type: item
type: AcademicArticle
description: Grassland afforestation dramatically affects the abiotic, biotic, and ecological function properties of the original ecosystems. Interference from afforestation might disrupt the stasis of soil physicochemical properties and the dynamic balance of microbiota. Some studies have suggested low sensitivity of soil properties and bacterial community to afforestation, but the apparent lack of a significant relationship is probably due to the confounding effects of the generalist habitat and rare bacterial communities. In this study, soil chemical and prokaryotic properties in a 30-year-old Mongolia pine (Pinus sylvestris var. mongolica Litv.) afforested region and adjacent grassland in Inner Mongolia were classified and quantified. Our results indicate that the high richness of rare microbes accounts for the alpha-diversity of the soil microbiome. Few OTUs of generalist (core bacteria) and habitat-specialist bacteria are present. However, the high abundance of this small number of OTUs governs the beta-diversity of the grassland and afforested land bacterial communities. Afforestation has changed the soil chemical properties, thus indirectly affecting the soil bacterial composition rather than richness. The contents of soil P, Ca2+, and Fe3+ account for differentially abundant OTUs such as Planctomycetes and subsequent changes in the ecologically functional potential of soil bacterial communities due to grassland afforestation. We conclude that grassland afforestation has changed the chemical properties and composition of the soil and ecological functions of the soil bacterial community and that these effects of afforestation on the microbiome have been modulated by changes in soil chemical properties.
format: application/pdf
format: text/html
creator: Shu-Hong Wu
creator: Bing-Hong Huang
creator: Jian Gao
creator: Siqi Wang
creator: Pei-Chun Liao
subject: Agricultural Science
subject: Conservation Biology
subject: Ecology
subject: Microbiology
subject: Forestry
description: doi:10.7717/peerj.6147
publisher: PeerJ Inc.
rights: © 2019 Wu et al.
abstract: Grassland afforestation dramatically affects the abiotic, biotic, and ecological function properties of the original ecosystems. Interference from afforestation might disrupt the stasis of soil physicochemical properties and the dynamic balance of microbiota. Some studies have suggested low sensitivity of soil properties and bacterial community to afforestation, but the apparent lack of a significant relationship is probably due to the confounding effects of the generalist habitat and rare bacterial communities. In this study, soil chemical and prokaryotic properties in a 30-year-old Mongolia pine (Pinus sylvestris var. mongolica Litv.) afforested region and adjacent grassland in Inner Mongolia were classified and quantified. Our results indicate that the high richness of rare microbes accounts for the alpha-diversity of the soil microbiome. Few OTUs of generalist (core bacteria) and habitat-specialist bacteria are present. However, the high abundance of this small number of OTUs governs the beta-diversity of the grassland and afforested land bacterial communities. Afforestation has changed the soil chemical properties, thus indirectly affecting the soil bacterial composition rather than richness. The contents of soil P, Ca2+, and Fe3+ account for differentially abundant OTUs such as Planctomycetes and subsequent changes in the ecologically functional potential of soil bacterial communities due to grassland afforestation. We conclude that grassland afforestation has changed the chemical properties and composition of the soil and ecological functions of the soil bacterial community and that these effects of afforestation on the microbiome have been modulated by changes in soil chemical properties.
bibliographic citation: Wu et al. (2019) The effects of afforestation on soil bacterial communities in temperate grassland are modulated by soil chemical properties. PeerJ 7:e6147 https://doi.org/10.7717/peerj.6147
date submitted: 2018-05-30
date accepted: 2018-11-21
issued: 2019-01-11
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Wu
  given name: Shu-Hong
author list: Agent
  family name: Huang
  given name: Bing-Hong
author list: Agent
  family name: Gao
  given name: Jian
author list: Agent
  family name: Wang
  given name: Siqi
author list: Agent
  family name: Liao
  given name: Pei-Chun
doi: 10.7717/peerj.6147
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-01-11
copyright: ©2019 Wu et al.
attribution name: Wu et al.

Effects of Trichoderma seedling treatment with System of Rice Intensification management and with conventional management of transplanted rice
type: item
type: AcademicArticle
description: Many benefits of Trichoderma inoculation for improving crop production have been documented, including growth and yield enhancement and the alleviation of biotic and abiotic stresses. However, because rice is usually cultivated under continuous flooding that creates anaerobic soil conditions, this limits the benefits of these beneficial fungi. Cultivating rice with the methods of the System of Rice Intensification (SRI) provides rice plants with a more favorable environment for their colonization by beneficial microbes in the soil because the soil is more aerobic under SRI management and contains more organic matter. This study evaluated the effects of Trichoderma inoculation of rice plants under SRI management compared with transplanted and flooded rice plants, considering also the effects of different means of fertilization and different varieties in rice. Experiments were conducted in 2015 and 2016 under the tropical climate of Nepal’s western terai (plains) during both the rainy season (July to November) and the dry season (March to July). The results indicated significantly better performance (P = 0.01) associated with Trichoderma inoculation for both seasons and for both systems of crop management in terms of grain yield and other growth-contributing factors, compared to non-inoculated rice cropping. Relatively higher effects on grain yield were recorded also with organic compared to inorganic fertilization; for unimproved (heirloom) varieties compared with improved varieties; and from SRI vs. conventional flooded crop management. The yield increase with Trichoderma treatments across all trials was 31% higher than in untreated plots (4.9 vs 4.5 mt ha−1). With Trichoderma treatment, yields compared with non-treated plots were 24% higher with organic SRI (6.38 vs 5.13 mt ha−1) and 52% higher with non-organic SRI (6.38 vs 3.53 mt ha−1). With regard to varietal differences, under SRI management Trichoderma inoculation of the improved variety Sukhadhan-3 led to 26%…
format: application/pdf
format: text/html
creator: Ram B. Khadka
creator: Norman Uphoff
subject: Agricultural Science
subject: Microbiology
subject: Mycology
subject: Soil Science
subject: Food, Water and Energy Nexus
description: doi:10.7717/peerj.5877
publisher: PeerJ Inc.
rights: © 2019 Khadka and Uphoff
abstract: Many benefits of Trichoderma inoculation for improving crop production have been documented, including growth and yield enhancement and the alleviation of biotic and abiotic stresses. However, because rice is usually cultivated under continuous flooding that creates anaerobic soil conditions, this limits the benefits of these beneficial fungi. Cultivating rice with the methods of the System of Rice Intensification (SRI) provides rice plants with a more favorable environment for their colonization by beneficial microbes in the soil because the soil is more aerobic under SRI management and contains more organic matter. This study evaluated the effects of Trichoderma inoculation of rice plants under SRI management compared with transplanted and flooded rice plants, considering also the effects of different means of fertilization and different varieties in rice. Experiments were conducted in 2015 and 2016 under the tropical climate of Nepal’s western terai (plains) during both the rainy season (July to November) and the dry season (March to July). The results indicated significantly better performance (P = 0.01) associated with Trichoderma inoculation for both seasons and for both systems of crop management in terms of grain yield and other growth-contributing factors, compared to non-inoculated rice cropping. Relatively higher effects on grain yield were recorded also with organic compared to inorganic fertilization; for unimproved (heirloom) varieties compared with improved varieties; and from SRI vs. conventional flooded crop management. The yield increase with Trichoderma treatments across all trials was 31% higher than in untreated plots (4.9 vs 4.5 mt ha−1). With Trichoderma treatment, yields compared with non-treated plots were 24% higher with organic SRI (6.38 vs 5.13 mt ha−1) and 52% higher with non-organic SRI (6.38 vs 3.53 mt ha−1). With regard to varietal differences, under SRI management Trichoderma inoculation of the improved variety Sukhadhan-3 led to 26%…
bibliographic citation: Khadka et al. (2019) Effects of Trichoderma seedling treatment with System of Rice Intensification management and with conventional management of transplanted rice. PeerJ 7:e5877 https://doi.org/10.7717/peerj.5877
date submitted: 2018-06-07
date accepted: 2018-10-05
issued: 2019-01-11
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Khadka
  given name: Ram B.
author list: Agent
  family name: Uphoff
  given name: Norman
doi: 10.7717/peerj.5877
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-01-11
copyright: ©2019 Khadka and Uphoff
attribution name: Khadka and Uphoff

A miniature inverted-repeat transposable element, AddIn-MITE, located inside a WD40 gene is conserved in Andropogoneae grasses
type: item
type: AcademicArticle
description: Miniature inverted-repeat transposable elements (MITEs) have been associated with genic regions in plant genomes and may play important roles in the regulation of nearby genes via recruitment of small RNAs (sRNA) to the MITEs loci. We identified eight families of MITEs in the sugarcane genome assembly with MITE-Hunter pipeline. These sequences were found to be upstream, downstream or inserted into 67 genic regions in the genome. The position of the most abundant MITE (Stowaway-like) in genic regions, which we call AddIn-MITE, was confirmed in a WD40 gene. The analysis of four monocot species showed conservation of the AddIn-MITE sequence, with a large number of copies in their genomes. We also investigated the conservation of the AddIn-MITE’ position in the WD40 genes from sorghum, maize and, in sugarcane cultivars and wild Saccharum species. In all analyzed plants, AddIn-MITE has located in WD40 intronic region. Furthermore, the role of AddIn-MITE-related sRNA in WD40 genic region was investigated. We found sRNAs preferentially mapped to the AddIn-MITE than to other regions in the WD40 gene in sugarcane. In addition, the analysis of the small RNA distribution patterns in the WD40 gene and the structure of AddIn-MITE, suggests that the MITE region is a proto-miRNA locus in sugarcane. Together, these data provide insights into the AddIn-MITE role in Andropogoneae grasses.
format: application/pdf
format: text/html
creator: Clicia Grativol
creator: Flavia Thiebaut
creator: Sara Sangi
creator: Patricia Montessoro
creator: Walaci da Silva Santos
creator: Adriana S. Hemerly
creator: Paulo C.G. Ferreira
subject: Bioinformatics
subject: Genomics
subject: Plant Science
description: doi:10.7717/peerj.6080
publisher: PeerJ Inc.
rights: © 2019 Grativol et al.
abstract: Miniature inverted-repeat transposable elements (MITEs) have been associated with genic regions in plant genomes and may play important roles in the regulation of nearby genes via recruitment of small RNAs (sRNA) to the MITEs loci. We identified eight families of MITEs in the sugarcane genome assembly with MITE-Hunter pipeline. These sequences were found to be upstream, downstream or inserted into 67 genic regions in the genome. The position of the most abundant MITE (Stowaway-like) in genic regions, which we call AddIn-MITE, was confirmed in a WD40 gene. The analysis of four monocot species showed conservation of the AddIn-MITE sequence, with a large number of copies in their genomes. We also investigated the conservation of the AddIn-MITE’ position in the WD40 genes from sorghum, maize and, in sugarcane cultivars and wild Saccharum species. In all analyzed plants, AddIn-MITE has located in WD40 intronic region. Furthermore, the role of AddIn-MITE-related sRNA in WD40 genic region was investigated. We found sRNAs preferentially mapped to the AddIn-MITE than to other regions in the WD40 gene in sugarcane. In addition, the analysis of the small RNA distribution patterns in the WD40 gene and the structure of AddIn-MITE, suggests that the MITE region is a proto-miRNA locus in sugarcane. Together, these data provide insights into the AddIn-MITE role in Andropogoneae grasses.
bibliographic citation: Grativol et al. (2019) A miniature inverted-repeat transposable element, AddIn-MITE, located inside a WD40 gene is conserved in Andropogoneae grasses. PeerJ 7:e6080 https://doi.org/10.7717/peerj.6080
date submitted: 2018-03-15
date accepted: 2018-11-07
issued: 2019-01-11
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Grativol
  given name: Clicia
author list: Agent
  family name: Thiebaut
  given name: Flavia
author list: Agent
  family name: Sangi
  given name: Sara
author list: Agent
  family name: Montessoro
  given name: Patricia
author list: Agent
  family name: Santos
  given name: Walaci da Silva
author list: Agent
  family name: Hemerly
  given name: Adriana S.
author list: Agent
  family name: Ferreira
  given name: Paulo C.G.
doi: 10.7717/peerj.6080
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-01-11
copyright: ©2019 Grativol et al.
attribution name: Grativol et al.

Diverse and variable virus communities in wild plant populations revealed by metagenomic tools
type: item
type: AcademicArticle
description: Wild plant populations may harbour a myriad of unknown viruses. As the majority of research efforts have targeted economically important plant species, the diversity and prevalence of viruses in the wild has remained largely unknown. However, the recent shift towards metagenomics-based sequencing methodologies, especially those targeting small RNAs, is finally enabling virus discovery from wild hosts. Understanding this diversity of potentially pathogenic microbes in the wild can offer insights into the components of natural biodiversity that promotes long-term coexistence between hosts and parasites in nature, and help predict when and where risks of disease emergence are highest. Here, we used small RNA deep sequencing to identify viruses in Plantago lanceolata populations, and to understand the variation in their prevalence and distribution across the Åland Islands, South-West Finland. By subsequent design of PCR primers, we screened the five most common viruses from two sets of P. lanceolata plants: 164 plants collected from 12 populations irrespective of symptoms, and 90 plants collected from five populations showing conspicuous viral symptoms. In addition to the previously reported species Plantago lanceolata latent virus (PlLV), we found four potentially novel virus species belonging to Caulimovirus, Betapartitivirus, Enamovirus, and Closterovirus genera. Our results show that virus prevalence and diversity varied among the sampled host populations. In six of the virus infected populations only a single virus species was detected, while five of the populations supported between two to five of the studied virus species. In 20% of the infected plants, viruses occurred as coinfections. When the relationship between conspicuous viral symptoms and virus infection was investigated, we found that plants showing symptoms were usually infected (84%), but virus infections were also detected from asymptomatic plants (44%). Jointly, these results reveal a diverse virus c…
format: application/pdf
format: text/html
creator: Hanna Susi
creator: Denis Filloux
creator: Mikko J. Frilander
creator: Philippe Roumagnac
creator: Anna-Liisa Laine
subject: Bioinformatics
subject: Ecology
subject: Plant Science
subject: Virology
subject: Population Biology
description: doi:10.7717/peerj.6140
publisher: PeerJ Inc.
rights: © 2019 Susi et al.
abstract: Wild plant populations may harbour a myriad of unknown viruses. As the majority of research efforts have targeted economically important plant species, the diversity and prevalence of viruses in the wild has remained largely unknown. However, the recent shift towards metagenomics-based sequencing methodologies, especially those targeting small RNAs, is finally enabling virus discovery from wild hosts. Understanding this diversity of potentially pathogenic microbes in the wild can offer insights into the components of natural biodiversity that promotes long-term coexistence between hosts and parasites in nature, and help predict when and where risks of disease emergence are highest. Here, we used small RNA deep sequencing to identify viruses in Plantago lanceolata populations, and to understand the variation in their prevalence and distribution across the Åland Islands, South-West Finland. By subsequent design of PCR primers, we screened the five most common viruses from two sets of P. lanceolata plants: 164 plants collected from 12 populations irrespective of symptoms, and 90 plants collected from five populations showing conspicuous viral symptoms. In addition to the previously reported species Plantago lanceolata latent virus (PlLV), we found four potentially novel virus species belonging to Caulimovirus, Betapartitivirus, Enamovirus, and Closterovirus genera. Our results show that virus prevalence and diversity varied among the sampled host populations. In six of the virus infected populations only a single virus species was detected, while five of the populations supported between two to five of the studied virus species. In 20% of the infected plants, viruses occurred as coinfections. When the relationship between conspicuous viral symptoms and virus infection was investigated, we found that plants showing symptoms were usually infected (84%), but virus infections were also detected from asymptomatic plants (44%). Jointly, these results reveal a diverse virus c…
bibliographic citation: Susi et al. (2019) Diverse and variable virus communities in wild plant populations revealed by metagenomic tools. PeerJ 7:e6140 https://doi.org/10.7717/peerj.6140
date submitted: 2018-07-12
date accepted: 2018-11-20
issued: 2019-01-11
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Susi
  given name: Hanna
author list: Agent
  family name: Filloux
  given name: Denis
author list: Agent
  family name: Frilander
  given name: Mikko J.
author list: Agent
  family name: Roumagnac
  given name: Philippe
author list: Agent
  family name: Laine
  given name: Anna-Liisa
doi: 10.7717/peerj.6140
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-01-11
copyright: ©2019 Susi et al.
attribution name: Susi et al.

Life history responses of two ephemeral plant species to increased precipitation and nitrogen in the Gurbantunggut Desert
type: item
type: AcademicArticle
description: Precipitation change and nitrogen deposition are not only hot topics of current global change but also the main environmental factors affecting plant growth in desert ecosystems. Thus, we performed an experiment of increased precipitation, nitrogen, and precipitation plus nitrogen on the ephemeral annual species Nepeta micrantha and Eremopyrum distans in the Gurbantunggut Desert. We aimed to determine the life history responses of N. micrantha and E. distans to environment changes, and the germination percentage of the offspring (seeds) was also tested in the laboratory. The results showed that increased nitrogen and precipitation plus nitrogen increased the growth of both plant species, whereas increased precipitation inhibited the growth of N. micrantha but increased the growth of E. distans. This differential response of these two species to precipitation and nitrogen also affected the germination of their offspring. In response to increased nitrogen and precipitation plus nitrogen, the germination percentage of the offspring produced by two species decreased in conjunction with the plants exhibiting high reproduction, which may prevent overcrowding during the following year; however, the N. micrantha plants produced more nondormant offspring in conjunction with low reproduction under relatively greater amounts of precipitation, and N. micrantha offspring could occupy their habitat via rapid germination in suitable environments. Therefore, with increased precipitation and nitrogen deposition, these differences in offspring dormancy may affect their ecological niche in the community.
format: application/pdf
format: text/html
creator: Yanfeng Chen
creator: Lingwei Zhang
creator: Xiang Shi
creator: Huiliang Liu
creator: Daoyuan Zhang
subject: Ecology
subject: Plant Science
subject: Climate Change Biology
description: doi:10.7717/peerj.6158
publisher: PeerJ Inc.
rights: © 2019 Chen et al.
abstract: Precipitation change and nitrogen deposition are not only hot topics of current global change but also the main environmental factors affecting plant growth in desert ecosystems. Thus, we performed an experiment of increased precipitation, nitrogen, and precipitation plus nitrogen on the ephemeral annual species Nepeta micrantha and Eremopyrum distans in the Gurbantunggut Desert. We aimed to determine the life history responses of N. micrantha and E. distans to environment changes, and the germination percentage of the offspring (seeds) was also tested in the laboratory. The results showed that increased nitrogen and precipitation plus nitrogen increased the growth of both plant species, whereas increased precipitation inhibited the growth of N. micrantha but increased the growth of E. distans. This differential response of these two species to precipitation and nitrogen also affected the germination of their offspring. In response to increased nitrogen and precipitation plus nitrogen, the germination percentage of the offspring produced by two species decreased in conjunction with the plants exhibiting high reproduction, which may prevent overcrowding during the following year; however, the N. micrantha plants produced more nondormant offspring in conjunction with low reproduction under relatively greater amounts of precipitation, and N. micrantha offspring could occupy their habitat via rapid germination in suitable environments. Therefore, with increased precipitation and nitrogen deposition, these differences in offspring dormancy may affect their ecological niche in the community.
bibliographic citation: Chen et al. (2019) Life history responses of two ephemeral plant species to increased precipitation and nitrogen in the Gurbantunggut Desert. PeerJ 7:e6158 https://doi.org/10.7717/peerj.6158
date submitted: 2018-08-28
date accepted: 2018-11-26
issued: 2019-01-11
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Chen
  given name: Yanfeng
author list: Agent
  family name: Zhang
  given name: Lingwei
author list: Agent
  family name: Shi
  given name: Xiang
author list: Agent
  family name: Liu
  given name: Huiliang
author list: Agent
  family name: Zhang
  given name: Daoyuan
doi: 10.7717/peerj.6158
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-01-11
copyright: ©2019 Chen et al.
attribution name: Chen et al.

Impact of inter- and intra-individual variation, sample storage and sampling fraction on human stool microbial community profiles
type: item
type: AcademicArticle
description: Stools are commonly used as proxies for studying human gut microbial communities as sample collection is straightforward, cheap and non-invasive. In large-scale human population surveys, however, sample integrity becomes an issue as it is not logistically feasible for researchers to personally collect stools from every participant. Instead, participants are usually given guidelines on sample packaging and storage, and asked to deliver their stools to a centralised facility. Here, we tested a number of delivery conditions (temperature, duration and addition of preservative medium) and assessed their effects on stool microbial community composition using 16S rRNA gene amplicon sequencing. The largest source of variability in stool community composition was attributable to inter-individual differences regardless of delivery condition. Although the relative effect of delivery condition on community composition was small compared to inter-individual variability (1.6% vs. 60.5%, permutational multivariate analysis of variance [PERMANOVA]) and temporal variation within subjects over 10 weeks (5.2%), shifts in microbial taxa associated with delivery conditions were non-systematic and subject-specific. These findings indicated that it is not possible to model or accurately predict shifts in stool community composition associated with sampling logistics. Based on our findings, we recommend delivery of fresh, preservative-free stool samples to laboratories within 2 hr either at ambient or chilled temperatures to minimise perturbations to microbial community composition. In addition, subsamples from different fractions of the same stool displayed a small (3.3% vs. 72.6% inter-individual variation, PERMANOVA) but significant effect on community composition. Collection of larger sample volumes for homogenisation is recommended.
format: application/pdf
format: text/html
creator: Yun Kit Yeoh
creator: Zigui Chen
creator: Mamie Hui
creator: Martin C.S. Wong
creator: Wendy C.S. Ho
creator: Miu Ling Chin
creator: Siew C. Ng
creator: Francis K.L. Chan
creator: Paul K.S. Chan
subject: Microbiology
subject: Gastroenterology and Hepatology
subject: Public Health
description: doi:10.7717/peerj.6172
publisher: PeerJ Inc.
rights: © 2019 Yeoh et al.
abstract: Stools are commonly used as proxies for studying human gut microbial communities as sample collection is straightforward, cheap and non-invasive. In large-scale human population surveys, however, sample integrity becomes an issue as it is not logistically feasible for researchers to personally collect stools from every participant. Instead, participants are usually given guidelines on sample packaging and storage, and asked to deliver their stools to a centralised facility. Here, we tested a number of delivery conditions (temperature, duration and addition of preservative medium) and assessed their effects on stool microbial community composition using 16S rRNA gene amplicon sequencing. The largest source of variability in stool community composition was attributable to inter-individual differences regardless of delivery condition. Although the relative effect of delivery condition on community composition was small compared to inter-individual variability (1.6% vs. 60.5%, permutational multivariate analysis of variance [PERMANOVA]) and temporal variation within subjects over 10 weeks (5.2%), shifts in microbial taxa associated with delivery conditions were non-systematic and subject-specific. These findings indicated that it is not possible to model or accurately predict shifts in stool community composition associated with sampling logistics. Based on our findings, we recommend delivery of fresh, preservative-free stool samples to laboratories within 2 hr either at ambient or chilled temperatures to minimise perturbations to microbial community composition. In addition, subsamples from different fractions of the same stool displayed a small (3.3% vs. 72.6% inter-individual variation, PERMANOVA) but significant effect on community composition. Collection of larger sample volumes for homogenisation is recommended.
bibliographic citation: Yeoh et al. (2019) Impact of inter- and intra-individual variation, sample storage and sampling fraction on human stool microbial community profiles. PeerJ 7:e6172 https://doi.org/10.7717/peerj.6172
date submitted: 2018-08-28
date accepted: 2018-11-28
issued: 2019-01-11
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Yeoh
  given name: Yun Kit
author list: Agent
  family name: Chen
  given name: Zigui
author list: Agent
  family name: Hui
  given name: Mamie
author list: Agent
  family name: Wong
  given name: Martin C.S.
author list: Agent
  family name: Ho
  given name: Wendy C.S.
author list: Agent
  family name: Chin
  given name: Miu Ling
author list: Agent
  family name: Ng
  given name: Siew C.
author list: Agent
  family name: Chan
  given name: Francis K.L.
author list: Agent
  family name: Chan
  given name: Paul K.S.
doi: 10.7717/peerj.6172
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-01-11
copyright: ©2019 Yeoh et al.
attribution name: Yeoh et al.

Artificial liver research output and citations from 2004 to 2017: a bibliometric analysis
type: item
type: AcademicArticle
description: Background Researches on artificial livers greatly contribute to the clinical treatments for liver failure. This study aimed to evaluate the research output of artificial livers and citations from 2004 to 2017 through a bibliometric analysis. Methods A list of included articles on artificial livers were generated after a comprehensive search of the Web of Science Core Collection (from 2004 to 2017) with the following basic information: number of publications, citations, publication year, country of origin, authors and authorship, funding source, journals, institutions, keywords, and research area. Results A total of 968 included articles ranged from 47 citations to 394 citations with a fluctuation. The publications were distributed in 12 countries, led by China (n = 212) and the US (n = 207). There were strong correlations of the number of citations with authors (r2 = 0.133, p < 0.001), and countries (r2 = 0.275, p < 0.001), while no correlations of the number of citations with the years since publication (r2 = 0.016, p = 0.216), and funding (r2 < 0.001, p = 0.770) were identified. Keyword analysis demonstrated that with the specific change of “acute liver failure,” decrease in “bioartificial livers” and “hepatocyte,” and increase in “tissue engineering” were identified. The top 53 cited keyword and keyword plus (including some duplicates counts) were identified, led by bioartificial liver (405 citations) and hepatocyte (248 citations). The top 50 cited keywords bursts were mainly “Blood” (2004–2008), “hepatocyte like cell” (2008–2015), and “tissue engineering” (2014–2017). All keywords could be classified into four categories: bioartificial livers (57.40%), blood purification (25.00%), clinical (14.81%), and other artificial organs (2.78%). Discussion This study shows the process and tendency of artificial liver research with a comprehensive analysis on artificial livers. However, although it seems that the future of artificial livers seems brighter for hepatocyte …
format: application/pdf
format: text/html
creator: Yan Li
creator: Meizhi He
creator: Ziyuan Zou
creator: Xiaohui Bian
creator: Xiaowen Huang
creator: Chen Yang
creator: Shuyi Wei
creator: Shixue Dai
subject: Gastroenterology and Hepatology
subject: Statistics
subject: Data Science
description: doi:10.7717/peerj.6178
publisher: PeerJ Inc.
rights: © 2019 Li et al.
abstract: Background Researches on artificial livers greatly contribute to the clinical treatments for liver failure. This study aimed to evaluate the research output of artificial livers and citations from 2004 to 2017 through a bibliometric analysis. Methods A list of included articles on artificial livers were generated after a comprehensive search of the Web of Science Core Collection (from 2004 to 2017) with the following basic information: number of publications, citations, publication year, country of origin, authors and authorship, funding source, journals, institutions, keywords, and research area. Results A total of 968 included articles ranged from 47 citations to 394 citations with a fluctuation. The publications were distributed in 12 countries, led by China (n = 212) and the US (n = 207). There were strong correlations of the number of citations with authors (r2 = 0.133, p < 0.001), and countries (r2 = 0.275, p < 0.001), while no correlations of the number of citations with the years since publication (r2 = 0.016, p = 0.216), and funding (r2 < 0.001, p = 0.770) were identified. Keyword analysis demonstrated that with the specific change of “acute liver failure,” decrease in “bioartificial livers” and “hepatocyte,” and increase in “tissue engineering” were identified. The top 53 cited keyword and keyword plus (including some duplicates counts) were identified, led by bioartificial liver (405 citations) and hepatocyte (248 citations). The top 50 cited keywords bursts were mainly “Blood” (2004–2008), “hepatocyte like cell” (2008–2015), and “tissue engineering” (2014–2017). All keywords could be classified into four categories: bioartificial livers (57.40%), blood purification (25.00%), clinical (14.81%), and other artificial organs (2.78%). Discussion This study shows the process and tendency of artificial liver research with a comprehensive analysis on artificial livers. However, although it seems that the future of artificial livers seems brighter for hepatocyte …
bibliographic citation: Li et al. (2019) Artificial liver research output and citations from 2004 to 2017: a bibliometric analysis. PeerJ 6:e6178 https://doi.org/10.7717/peerj.6178
date submitted: 2018-09-24
date accepted: 2018-11-28
issued: 2019-01-11
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Li
  given name: Yan
author list: Agent
  family name: He
  given name: Meizhi
author list: Agent
  family name: Zou
  given name: Ziyuan
author list: Agent
  family name: Bian
  given name: Xiaohui
author list: Agent
  family name: Huang
  given name: Xiaowen
author list: Agent
  family name: Yang
  given name: Chen
author list: Agent
  family name: Wei
  given name: Shuyi
author list: Agent
  family name: Dai
  given name: Shixue
doi: 10.7717/peerj.6178
volume: 6
issn: 2167-8359
publication name: PeerJ
publication date: 2019-01-11
copyright: © 2019 Li et al.
attribution name: Li et al.

Non-H3 CDR template selection in antibody modeling through machine learning
type: item
type: AcademicArticle
description: Antibodies are proteins generated by the adaptive immune system to recognize and counteract a plethora of pathogens through specific binding. This adaptive binding is mediated by structural diversity in the six complementary determining region (CDR) loops (H1, H2, H3, L1, L2 and L3), which also makes accurate structural modeling of CDRs challenging. Both homology and de novo modeling approaches have been used; to date, the former has achieved greater accuracy for the non-H3 loops. The homology modeling of non-H3 CDRs is more accurate because non-H3 CDR loops of the same length and type can be grouped into a few structural clusters. Most antibody-modeling suites utilize homology modeling for the non-H3 CDRs, differing only in the alignment algorithm and how/if they utilize structural clusters. While RosettaAntibody and SAbPred do not explicitly assign query CDR sequences to clusters, two other approaches, PIGS and Kotai Antibody Builder, utilize sequence-based rules to assign CDR sequences to clusters. While the manually curated sequence rules can identify better structural templates, because their curation requires extensive literature search and human effort, they lag behind the deposition of new antibody structures and are infrequently updated. In this study, we propose a machine learning approach (Gradient Boosting Machine [GBM]) to learn the structural clusters of non-H3 CDRs from sequence alone. The GBM method simplifies feature selection and can easily integrate new data, compared to manual sequence rule curation. We compare the classification results using the GBM method to that of RosettaAntibody in a 3-repeat 10-fold cross-validation (CV) scheme on the cluster-annotated antibody database PyIgClassify and we observe an improvement in the classification accuracy of the concerned loops from 84.5% ± 0.24% to 88.16% ± 0.056%. The GBM models reduce the errors in specific cluster membership misclassifications when the involved clusters have relatively abundant dat…
format: application/pdf
format: text/html
creator: Xiyao Long
creator: Jeliazko R. Jeliazkov
creator: Jeffrey J. Gray
subject: Bioinformatics
subject: Computational Biology
description: doi:10.7717/peerj.6179
publisher: PeerJ Inc.
rights: © 2019 Long et al.
abstract: Antibodies are proteins generated by the adaptive immune system to recognize and counteract a plethora of pathogens through specific binding. This adaptive binding is mediated by structural diversity in the six complementary determining region (CDR) loops (H1, H2, H3, L1, L2 and L3), which also makes accurate structural modeling of CDRs challenging. Both homology and de novo modeling approaches have been used; to date, the former has achieved greater accuracy for the non-H3 loops. The homology modeling of non-H3 CDRs is more accurate because non-H3 CDR loops of the same length and type can be grouped into a few structural clusters. Most antibody-modeling suites utilize homology modeling for the non-H3 CDRs, differing only in the alignment algorithm and how/if they utilize structural clusters. While RosettaAntibody and SAbPred do not explicitly assign query CDR sequences to clusters, two other approaches, PIGS and Kotai Antibody Builder, utilize sequence-based rules to assign CDR sequences to clusters. While the manually curated sequence rules can identify better structural templates, because their curation requires extensive literature search and human effort, they lag behind the deposition of new antibody structures and are infrequently updated. In this study, we propose a machine learning approach (Gradient Boosting Machine [GBM]) to learn the structural clusters of non-H3 CDRs from sequence alone. The GBM method simplifies feature selection and can easily integrate new data, compared to manual sequence rule curation. We compare the classification results using the GBM method to that of RosettaAntibody in a 3-repeat 10-fold cross-validation (CV) scheme on the cluster-annotated antibody database PyIgClassify and we observe an improvement in the classification accuracy of the concerned loops from 84.5% ± 0.24% to 88.16% ± 0.056%. The GBM models reduce the errors in specific cluster membership misclassifications when the involved clusters have relatively abundant dat…
bibliographic citation: Long et al. (2019) Non-H3 CDR template selection in antibody modeling through machine learning. PeerJ 7:e6179 https://doi.org/10.7717/peerj.6179
date submitted: 2018-06-19
date accepted: 2018-11-28
issued: 2019-01-11
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Long
  given name: Xiyao
author list: Agent
  family name: Jeliazkov
  given name: Jeliazko R.
author list: Agent
  family name: Gray
  given name: Jeffrey J.
doi: 10.7717/peerj.6179
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-01-11
copyright: ©2019 Long et al.
attribution name: Long et al.

Genetic diversity and its conservation implications of Vitex rotundifolia (Lamiaceae) populations in East Asia
type: item
type: AcademicArticle
description: Vitex rotundifolia is an important coastal and medicinal plant, and is recorded in the List of the Important Wild Plants for Conservation in China and Japan. However, an effective conservation strategy is lacking. In the present study, the genetic diversity and population structure were analyzed using phylogeographical methods based on the trnH-psbA and trnG-trnS intergenic spacers of the chloroplast DNA (cpDNA) sequences from 157 individuals from 25 sampling sites for V. rotundifolia and V. trifolia plus the internal transcribed spacer (ITS) of the nuclear ribosomal DNA (nrDNA) sequences of 177 individuals from 27 sampling sites. The results showed that V. rotundifolia and V. trifolia had eight cpDNA and two nrDNA haplotypes, respectively, and the V. rotundifolia has a low level of genetic diversity (haplotype diversity hd,cp = 0.360, hd,nr = 0.440), a more pronounced genetic differentiation among populations (population differentiation at the species level (GST) = 0.201, population differentiation at the allele level (NST) = 0.462), and an insignificantly different phylogeographical structure (NST > GST, P > 0.05). In addition, haplotype network analyses indicated that V. rotundifolia and V. trifolia have distinct haplotypes. Divergence dating based on BEAST software analyses showed that most cpDNA clades diverged in the late Pleistocene era. Demographic analysis indicated that V. rotundifolia underwent a rapid demographic expansion. Some scientific strategies are suggested for resource conservation of V. rotundifolia based on its genetic diversity and population structure.
format: application/pdf
format: text/html
creator: Yiqi Sun
creator: Hong Yang
creator: Qiaoyan Zhang
creator: Luping Qin
creator: Pan Li
creator: Joongku Lee
creator: Shichao Chen
creator: Khalid Rahman
creator: Tingguo Kang
creator: Min Jia
subject: Biodiversity
subject: Biogeography
subject: Conservation Biology
subject: Evolutionary Studies
subject: Plant Science
description: doi:10.7717/peerj.6194
publisher: PeerJ Inc.
rights: © 2019 Sun et al.
abstract: Vitex rotundifolia is an important coastal and medicinal plant, and is recorded in the List of the Important Wild Plants for Conservation in China and Japan. However, an effective conservation strategy is lacking. In the present study, the genetic diversity and population structure were analyzed using phylogeographical methods based on the trnH-psbA and trnG-trnS intergenic spacers of the chloroplast DNA (cpDNA) sequences from 157 individuals from 25 sampling sites for V. rotundifolia and V. trifolia plus the internal transcribed spacer (ITS) of the nuclear ribosomal DNA (nrDNA) sequences of 177 individuals from 27 sampling sites. The results showed that V. rotundifolia and V. trifolia had eight cpDNA and two nrDNA haplotypes, respectively, and the V. rotundifolia has a low level of genetic diversity (haplotype diversity hd,cp = 0.360, hd,nr = 0.440), a more pronounced genetic differentiation among populations (population differentiation at the species level (GST) = 0.201, population differentiation at the allele level (NST) = 0.462), and an insignificantly different phylogeographical structure (NST > GST, P > 0.05). In addition, haplotype network analyses indicated that V. rotundifolia and V. trifolia have distinct haplotypes. Divergence dating based on BEAST software analyses showed that most cpDNA clades diverged in the late Pleistocene era. Demographic analysis indicated that V. rotundifolia underwent a rapid demographic expansion. Some scientific strategies are suggested for resource conservation of V. rotundifolia based on its genetic diversity and population structure.
bibliographic citation: Sun et al. (2019) Genetic diversity and its conservation implications of Vitex rotundifolia (Lamiaceae) populations in East Asia. PeerJ 7:e6194 https://doi.org/10.7717/peerj.6194
date submitted: 2018-08-07
date accepted: 2018-12-01
issued: 2019-01-11
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Sun
  given name: Yiqi
author list: Agent
  family name: Yang
  given name: Hong
author list: Agent
  family name: Zhang
  given name: Qiaoyan
author list: Agent
  family name: Qin
  given name: Luping
author list: Agent
  family name: Li
  given name: Pan
author list: Agent
  family name: Lee
  given name: Joongku
author list: Agent
  family name: Chen
  given name: Shichao
author list: Agent
  family name: Rahman
  given name: Khalid
author list: Agent
  family name: Kang
  given name: Tingguo
author list: Agent
  family name: Jia
  given name: Min
doi: 10.7717/peerj.6194
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-01-11
copyright: ©2019 Sun et al.
attribution name: Sun et al.

Local fishermen’s perceptions of the usefulness of artificial reef ecosystem services in Portugal
type: item
type: AcademicArticle
description: Proponents of artificial reef (AR) deployment are often motivated by the usefulness of such structures. The usefulness of ARs is related to their capability of providing ecosystem services/additional functions. We present two distinct Portuguese AR case studies: (1) The Nazaré reef off the central coast of Portugal and (2) the Oura reef off the Algarve coast. Semi-structured interviews were conducted with local fishermen in the fishing towns of Nazaré and Quarteira pre-and post-AR deployment. The main focus of the interviews was to understand fishermen’s perception of AR usefulness (or lack thereof) in terms of nine ecosystem services/additional functions potentially provided by the ARs. We tested the null hypothesis that ARs do not provide additional ecosystem services/additional functions. When queried pre-AR deployment, fishermen indicated that ARs are most likely to provide three ecosystem services: “habitat and refuge,” “biodiversity preservation” and “food production.” Fishermen had similar perceptions post-deployment. For the Nazaré reef, fishermen tended to have a positive or neutral perception of ecosystem services/additional functions being provided by ARs. For the Oura reef, fishermen tended to have a mostly neutral perception of AR ecosystem services; however, there were also some positive and other negative perceptions. It was difficult for stakeholders to conceptualize some of the ecosystem services/additional functions provided by ARs prior to actively using them. As a result, some stakeholders changed their perception of the ecosystem services/additional functions after using the structures. These results indicate that stakeholders likely need to perceive ARs as useful in order for them to provide their support for AR installation. Likewise, their support is often needed to justify the use of public funds to install ARs, therefore making it imperative for resource managers to undertake similar interviews with fishermen when considering the use of ARs…
format: application/pdf
format: text/html
creator: Jorge Ramos
creator: Pedro G. Lino
creator: Amber Himes-Cornell
creator: Miguel N. Santos
subject: Aquaculture, Fisheries and Fish Science
subject: Ecosystem Science
description: doi:10.7717/peerj.6206
publisher: PeerJ Inc.
rights: © 2019 Ramos et al.
abstract: Proponents of artificial reef (AR) deployment are often motivated by the usefulness of such structures. The usefulness of ARs is related to their capability of providing ecosystem services/additional functions. We present two distinct Portuguese AR case studies: (1) The Nazaré reef off the central coast of Portugal and (2) the Oura reef off the Algarve coast. Semi-structured interviews were conducted with local fishermen in the fishing towns of Nazaré and Quarteira pre-and post-AR deployment. The main focus of the interviews was to understand fishermen’s perception of AR usefulness (or lack thereof) in terms of nine ecosystem services/additional functions potentially provided by the ARs. We tested the null hypothesis that ARs do not provide additional ecosystem services/additional functions. When queried pre-AR deployment, fishermen indicated that ARs are most likely to provide three ecosystem services: “habitat and refuge,” “biodiversity preservation” and “food production.” Fishermen had similar perceptions post-deployment. For the Nazaré reef, fishermen tended to have a positive or neutral perception of ecosystem services/additional functions being provided by ARs. For the Oura reef, fishermen tended to have a mostly neutral perception of AR ecosystem services; however, there were also some positive and other negative perceptions. It was difficult for stakeholders to conceptualize some of the ecosystem services/additional functions provided by ARs prior to actively using them. As a result, some stakeholders changed their perception of the ecosystem services/additional functions after using the structures. These results indicate that stakeholders likely need to perceive ARs as useful in order for them to provide their support for AR installation. Likewise, their support is often needed to justify the use of public funds to install ARs, therefore making it imperative for resource managers to undertake similar interviews with fishermen when considering the use of ARs…
bibliographic citation: Ramos et al. (2019) Local fishermen’s perceptions of the usefulness of artificial reef ecosystem services in Portugal. PeerJ 6:e6206 https://doi.org/10.7717/peerj.6206
date submitted: 2018-04-23
date accepted: 2018-11-22
issued: 2019-01-11
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Ramos
  given name: Jorge
author list: Agent
  family name: Lino
  given name: Pedro G.
author list: Agent
  family name: Himes-Cornell
  given name: Amber
author list: Agent
  family name: Santos
  given name: Miguel N.
doi: 10.7717/peerj.6206
volume: 6
issn: 2167-8359
publication name: PeerJ
publication date: 2019-01-11
copyright: © 2019 Ramos et al.
attribution name: Ramos et al.

Anuran diversity indicates that Caatinga relictual Neotropical forests are more related to the Atlantic Forest than to the Amazon
type: item
type: AcademicArticle
description: The relationships among the morphoclimatic domains of South America have been a major biogeographical issue of recent years. Palynological, geological and phytogeographical data suggest that the Amazon Forest and the Atlantic Forest were connected during part of the Tertiary and Quaternary periods. This study uses amphibians as model organisms to investigate whether relict northeastern forests are a transition between the Amazon Forest and the Atlantic Forest. We compiled matrices of species composition for four different phytogeographic formations and “Brejos de Altitude,” and analyzed them using clustering methods and Cladistic Analysis of Distributions and Endemism. Our results indicate that the anurofauna of these northeastern forest relicts is most similar in composition to the areas of the Atlantic Forest included in this study, and most dissimilar to the Amazon Forest, which leads us to affirm that events of biotic exchange were more frequent within the Atlantic Forest areas.
format: application/pdf
format: text/html
creator: Deborah P. Castro
creator: João Fabrício M. Rodrigues
creator: Maria Juliana Borges-Leite
creator: Daniel Cassiano Lima
creator: Diva Maria Borges-Nojosa
subject: Biodiversity
subject: Biogeography
subject: Ecology
subject: Zoology
description: doi:10.7717/peerj.6208
publisher: PeerJ Inc.
rights: © 2019 Castro et al.
abstract: The relationships among the morphoclimatic domains of South America have been a major biogeographical issue of recent years. Palynological, geological and phytogeographical data suggest that the Amazon Forest and the Atlantic Forest were connected during part of the Tertiary and Quaternary periods. This study uses amphibians as model organisms to investigate whether relict northeastern forests are a transition between the Amazon Forest and the Atlantic Forest. We compiled matrices of species composition for four different phytogeographic formations and “Brejos de Altitude,” and analyzed them using clustering methods and Cladistic Analysis of Distributions and Endemism. Our results indicate that the anurofauna of these northeastern forest relicts is most similar in composition to the areas of the Atlantic Forest included in this study, and most dissimilar to the Amazon Forest, which leads us to affirm that events of biotic exchange were more frequent within the Atlantic Forest areas.
bibliographic citation: Castro et al. (2019) Anuran diversity indicates that Caatinga relictual Neotropical forests are more related to the Atlantic Forest than to the Amazon. PeerJ 6:e6208 https://doi.org/10.7717/peerj.6208
date submitted: 2018-03-19
date accepted: 2018-12-04
issued: 2019-01-11
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Castro
  given name: Deborah P.
author list: Agent
  family name: Rodrigues
  given name: João Fabrício M.
author list: Agent
  family name: Borges-Leite
  given name: Maria Juliana
author list: Agent
  family name: Lima
  given name: Daniel Cassiano
author list: Agent
  family name: Borges-Nojosa
  given name: Diva Maria
doi: 10.7717/peerj.6208
volume: 6
issn: 2167-8359
publication name: PeerJ
publication date: 2019-01-11
copyright: © 2019 Authors.
attribution name: Castro et al.

Immunohistochemical analysis of cyclin A expression in Wilms tumor
type: item
type: AcademicArticle
description: Background Cyclin A overexpression is found in a variety of human tumors and correlates with unfavorable outcome. We analyzed immunohistochemical expression of cyclin A in Wilms tumor (WT) in relation to clinicopathological characteristics, preoperative chemotherapy (PrOpChTh), and overall survival (OS). Methods This retrospective study involved 43 patients who underwent nephrectomy from January 1996 to October 2010. Tumor stage and histological subtype were determined by revised Societé International d’Oncologie Pediatrique protocol, based on histological components/alterations caused by PrOpChTh, within the prognostic group of low, intermediate and high risk, and with criteria for anaplasia. The regressive/necrotic changes in total tumor mass of primary tumor and the proportion of epithelial, blastemal, and stromal components in the remaining viable tumor tissue were also determined. Cyclin A expression was evaluated by immunohistochemistry using a polyclonal rabbit, antihuman antibody (H-432). Results Cyclin A overexpression was found in 34.3% of WTs, with higher frequency in tumors with epithelial (31.3%) and blastemal (37.1%) components than those with stromal component (17.7%). Regarding histological type, cyclin A overexpression was found most often in focal anaplasia (100%), stromal (60%), and diffuse anaplastic (66.7) WTs. The overexpression was also more frequent in stages 3 and 4 (77.8% and 66.7%, respectively) compared to tumors in stages 1 and 2 (13.3% and 12.5%, respectively; p = 0.004) in all components, as well as in blastemal component in stages 3 and 4 (77.8% and 66.7%, respectively) vs. stages 1 and 2 (13.3% and 25%, respectively, p = 0.009). Cyclin A overexpression in all components was 66.7% in WTs with metastasis and 31.3% in WTs without metastasis (p = 0.265, Fisher test). Log-rank testing revealed differences of OS regarding stage (p = 0.000), prognostic groups (p = 0.001), and cyclin A expression in blastemal component (p = 0.025). After uni…
format: application/pdf
format: text/html
creator: Sanja Radojević-Škodrić
creator: Dimitrije Brašanac
creator: Slaviša M. Đuričić
creator: Sofija Glumac
creator: Zlatibor Lončar
creator: Ivan Pavlović
creator: Ana Todorović
creator: Gorana Nikolić
creator: Ivana Baralić
creator: Snežana Pejić
subject: Nephrology
subject: Oncology
subject: Pathology
subject: Pediatrics
subject: Urology
description: doi:10.7717/peerj.6212
publisher: PeerJ Inc.
rights: © 2019 Radojević-Škodrić et al.
abstract: Background Cyclin A overexpression is found in a variety of human tumors and correlates with unfavorable outcome. We analyzed immunohistochemical expression of cyclin A in Wilms tumor (WT) in relation to clinicopathological characteristics, preoperative chemotherapy (PrOpChTh), and overall survival (OS). Methods This retrospective study involved 43 patients who underwent nephrectomy from January 1996 to October 2010. Tumor stage and histological subtype were determined by revised Societé International d’Oncologie Pediatrique protocol, based on histological components/alterations caused by PrOpChTh, within the prognostic group of low, intermediate and high risk, and with criteria for anaplasia. The regressive/necrotic changes in total tumor mass of primary tumor and the proportion of epithelial, blastemal, and stromal components in the remaining viable tumor tissue were also determined. Cyclin A expression was evaluated by immunohistochemistry using a polyclonal rabbit, antihuman antibody (H-432). Results Cyclin A overexpression was found in 34.3% of WTs, with higher frequency in tumors with epithelial (31.3%) and blastemal (37.1%) components than those with stromal component (17.7%). Regarding histological type, cyclin A overexpression was found most often in focal anaplasia (100%), stromal (60%), and diffuse anaplastic (66.7) WTs. The overexpression was also more frequent in stages 3 and 4 (77.8% and 66.7%, respectively) compared to tumors in stages 1 and 2 (13.3% and 12.5%, respectively; p = 0.004) in all components, as well as in blastemal component in stages 3 and 4 (77.8% and 66.7%, respectively) vs. stages 1 and 2 (13.3% and 25%, respectively, p = 0.009). Cyclin A overexpression in all components was 66.7% in WTs with metastasis and 31.3% in WTs without metastasis (p = 0.265, Fisher test). Log-rank testing revealed differences of OS regarding stage (p = 0.000), prognostic groups (p = 0.001), and cyclin A expression in blastemal component (p = 0.025). After uni…
bibliographic citation: Radojević-Škodrić et al. (2019) Immunohistochemical analysis of cyclin A expression in Wilms tumor. PeerJ 6:e6212 https://doi.org/10.7717/peerj.6212
date submitted: 2018-06-19
date accepted: 2018-12-03
issued: 2019-01-11
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Radojević-Škodrić
  given name: Sanja
author list: Agent
  family name: Brašanac
  given name: Dimitrije
author list: Agent
  family name: Đuričić
  given name: Slaviša M.
author list: Agent
  family name: Glumac
  given name: Sofija
author list: Agent
  family name: Lončar
  given name: Zlatibor
author list: Agent
  family name: Pavlović
  given name: Ivan
author list: Agent
  family name: Todorović
  given name: Ana
author list: Agent
  family name: Nikolić
  given name: Gorana
author list: Agent
  family name: Baralić
  given name: Ivana
author list: Agent
  family name: Pejić
  given name: Snežana
doi: 10.7717/peerj.6212
volume: 6
issn: 2167-8359
publication name: PeerJ
publication date: 2019-01-11
copyright: © 2019 Radojević-Škodrić et al.
attribution name: Radojević-Škodrić et al.

Detection and variability analyses of CRISPR-like loci in the H. pylori genome
type: item
type: AcademicArticle
description: Helicobacter pylori is a human pathogenic bacterium with a high genomic plasticity. Although the functional CRISPR-Cas system has not been found in its genome, CRISPR-like loci have been recently identified. In this work, 53 genomes from different geographical areas are analyzed for the search and analysis of variability of this type of structure. We confirm the presence of a locus that was previously described in the VlpC gene in al lgenomes, and we characterize new CRISPR-like loci in other genomic locations. By studying the variability and gene location of these loci, the evolution and the possible roles of these sequences are discussed. Additionally, the usefulness of this type of sequences as a phylogenetic marker has been demonstrated, associating the different strains by geographical area.
format: application/pdf
format: text/html
creator: Jerson Alexander García-Zea
creator: Roberto de la Herrán
creator: Francisca Robles Rodríguez
creator: Rafael Navajas-Pérez
creator: Carmelo Ruiz Rejón
subject: Bioinformatics
subject: Evolutionary Studies
subject: Genetics
subject: Genomics
description: doi:10.7717/peerj.6221
publisher: PeerJ Inc.
rights: © 2019 García-Zea et al.
abstract: Helicobacter pylori is a human pathogenic bacterium with a high genomic plasticity. Although the functional CRISPR-Cas system has not been found in its genome, CRISPR-like loci have been recently identified. In this work, 53 genomes from different geographical areas are analyzed for the search and analysis of variability of this type of structure. We confirm the presence of a locus that was previously described in the VlpC gene in al lgenomes, and we characterize new CRISPR-like loci in other genomic locations. By studying the variability and gene location of these loci, the evolution and the possible roles of these sequences are discussed. Additionally, the usefulness of this type of sequences as a phylogenetic marker has been demonstrated, associating the different strains by geographical area.
bibliographic citation: García-Zea et al. (2019) Detection and variability analyses of CRISPR-like loci in the H. pylori genome. PeerJ 7:e6221 https://doi.org/10.7717/peerj.6221
date submitted: 2018-09-10
date accepted: 2018-12-05
issued: 2019-01-11
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: García-Zea
  given name: Jerson Alexander
author list: Agent
  family name: de la Herrán
  given name: Roberto
author list: Agent
  family name: Robles Rodríguez
  given name: Francisca
author list: Agent
  family name: Navajas-Pérez
  given name: Rafael
author list: Agent
  family name: Ruiz Rejón
  given name: Carmelo
doi: 10.7717/peerj.6221
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-01-11
copyright: ©2019 García-Zea et al.
attribution name: García-Zea et al.

Grazing by large savanna herbivores indirectly alters ant diversity and promotes resource monopolisation
type: item
type: AcademicArticle
description: In savannas, grazing is an important disturbance that modifies the grass layer structure and composition. Habitat structural complexity influences species diversity and assemblage functioning. By using a combination of natural sites and manipulated experiments, we explored how habitat structure (grazing lawns and adjacent bunch grass) affects ant diversity and foraging behaviour, specifically the efficiency of resource acquisition, resource monopolisation and ant body size. We found that in the natural sites there was no difference in the amount of time ants took to locate resources, but in the manipulated experiments, ants were faster at locating resources and were more abundant in the simple treatments than in the more complex treatments. Ant body size was only affected by the manipulated experiments, with smaller ants found in the more complex treatments. In both the grazing lawn and bunch grass habitats there were differences in assemblage patterns of ants discovering resources and those dominating them. Seasonality, which was predicted to affect the speed at which ants discovered resources and the intensity of resource monopolisation, also played a role. We show that ants in winter monopolised more baits and discovered resources at a slower rate, but only at certain times within the experiment. Grazing in conjunction with season thus had a significant effect on ant diversity and foraging behaviour, with dominant ants promoted where habitat complexity was simplified when temperatures were low. Our results indicate that structural complexity plays a major role in determining ant assemblage structure and function in African savannas.
format: application/pdf
format: text/html
creator: Jean Purdon
creator: Catherine L. Parr
creator: Michael J. Somers
subject: Biodiversity
subject: Conservation Biology
subject: Ecology
subject: Entomology
subject: Zoology
description: doi:10.7717/peerj.6226
publisher: PeerJ Inc.
rights: © 2019 Purdon et al.
abstract: In savannas, grazing is an important disturbance that modifies the grass layer structure and composition. Habitat structural complexity influences species diversity and assemblage functioning. By using a combination of natural sites and manipulated experiments, we explored how habitat structure (grazing lawns and adjacent bunch grass) affects ant diversity and foraging behaviour, specifically the efficiency of resource acquisition, resource monopolisation and ant body size. We found that in the natural sites there was no difference in the amount of time ants took to locate resources, but in the manipulated experiments, ants were faster at locating resources and were more abundant in the simple treatments than in the more complex treatments. Ant body size was only affected by the manipulated experiments, with smaller ants found in the more complex treatments. In both the grazing lawn and bunch grass habitats there were differences in assemblage patterns of ants discovering resources and those dominating them. Seasonality, which was predicted to affect the speed at which ants discovered resources and the intensity of resource monopolisation, also played a role. We show that ants in winter monopolised more baits and discovered resources at a slower rate, but only at certain times within the experiment. Grazing in conjunction with season thus had a significant effect on ant diversity and foraging behaviour, with dominant ants promoted where habitat complexity was simplified when temperatures were low. Our results indicate that structural complexity plays a major role in determining ant assemblage structure and function in African savannas.
bibliographic citation: Purdon et al. (2019) Grazing by large savanna herbivores indirectly alters ant diversity and promotes resource monopolisation. PeerJ 7:e6226 https://doi.org/10.7717/peerj.6226
date submitted: 2018-03-10
date accepted: 2018-12-06
issued: 2019-01-11
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Purdon
  given name: Jean
author list: Agent
  family name: Parr
  given name: Catherine L.
author list: Agent
  family name: Somers
  given name: Michael J.
doi: 10.7717/peerj.6226
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-01-11
copyright: ©2019 Purdon et al.
attribution name: Purdon et al.

Individual tree crown delineation and tree species classification with hyperspectral and LiDAR data
type: item
type: AcademicArticle
description: An international data science challenge, called National Ecological Observatory Network—National Institute of Standards and Technology data science evaluation, was set up in autumn 2017 with the goal to improve the use of remote sensing data in ecological applications. The competition was divided into three tasks: (1) individual tree crown (ITC) delineation, for identifying the location and size of individual trees; (2) alignment between field surveyed trees and ITCs delineated on remote sensing data; and (3) tree species classification. In this paper, the methods and results of team Fondazione Edmund Mach (FEM) are presented. The ITC delineation (Task 1 of the challenge) was done using a region growing method applied to a near-infrared band of the hyperspectral images. The optimization of the parameters of the delineation algorithm was done in a supervised way on the basis of the Jaccard score using the training set provided by the organizers. The alignment (Task 2) between the delineated ITCs and the field surveyed trees was done using the Euclidean distance among the position, the height, and the crown radius of the ITCs and the field surveyed trees. The classification (Task 3) was performed using a support vector machine classifier applied to a selection of the hyperspectral bands and the canopy height model. The selection of the bands was done using the sequential forward floating selection method and the Jeffries Matusita distance. The results of the three tasks were very promising: team FEM ranked first in the data science competition in Task 1 and 2, and second in Task 3. The Jaccard score of the delineated crowns was 0.3402, and the results showed that the proposed approach delineated both small and large crowns. The alignment was correctly done for all the test samples. The classification results were good (overall accuracy of 88.1%, kappa accuracy of 75.7%, and mean class accuracy of 61.5%), although the accuracy was biased toward the most represented spe…
format: application/pdf
format: text/html
creator: Michele Dalponte
creator: Lorenzo Frizzera
creator: Damiano Gianelle
subject: Ecology
subject: Forestry
subject: Spatial and Geographic Information Science
description: doi:10.7717/peerj.6227
publisher: PeerJ Inc.
rights: © 2019 Dalponte et al.
abstract: An international data science challenge, called National Ecological Observatory Network—National Institute of Standards and Technology data science evaluation, was set up in autumn 2017 with the goal to improve the use of remote sensing data in ecological applications. The competition was divided into three tasks: (1) individual tree crown (ITC) delineation, for identifying the location and size of individual trees; (2) alignment between field surveyed trees and ITCs delineated on remote sensing data; and (3) tree species classification. In this paper, the methods and results of team Fondazione Edmund Mach (FEM) are presented. The ITC delineation (Task 1 of the challenge) was done using a region growing method applied to a near-infrared band of the hyperspectral images. The optimization of the parameters of the delineation algorithm was done in a supervised way on the basis of the Jaccard score using the training set provided by the organizers. The alignment (Task 2) between the delineated ITCs and the field surveyed trees was done using the Euclidean distance among the position, the height, and the crown radius of the ITCs and the field surveyed trees. The classification (Task 3) was performed using a support vector machine classifier applied to a selection of the hyperspectral bands and the canopy height model. The selection of the bands was done using the sequential forward floating selection method and the Jeffries Matusita distance. The results of the three tasks were very promising: team FEM ranked first in the data science competition in Task 1 and 2, and second in Task 3. The Jaccard score of the delineated crowns was 0.3402, and the results showed that the proposed approach delineated both small and large crowns. The alignment was correctly done for all the test samples. The classification results were good (overall accuracy of 88.1%, kappa accuracy of 75.7%, and mean class accuracy of 61.5%), although the accuracy was biased toward the most represented spe…
bibliographic citation: Dalponte et al. (2019) Individual tree crown delineation and tree species classification with hyperspectral and LiDAR data. PeerJ 6:e6227 https://doi.org/10.7717/peerj.6227
date submitted: 2018-06-01
date accepted: 2018-12-06
issued: 2019-01-11
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Dalponte
  given name: Michele
author list: Agent
  family name: Frizzera
  given name: Lorenzo
author list: Agent
  family name: Gianelle
  given name: Damiano
doi: 10.7717/peerj.6227
volume: 6
issn: 2167-8359
publication name: PeerJ
publication date: 2019-01-11
copyright: © 2019 Dalponte et al.
attribution name: Dalponte et al.

Label-free quantitative proteomic analysis reveals potential biomarkers for early healing in cutaneous leishmaniasis
type: item
type: AcademicArticle
description: Background Leishmaniasis is a parasitic disease caused by more than 20 species of the Leishmania genus. The disease is globally distributed and is endemic in 97 countries and three territories in the tropical and subtropical regions. The efficacy of the current treatments is becoming increasingly low either due to incomplete treatment or resistant parasites. Failure of treatment is frequent, and therefore, the search for early biomarkers of therapeutic response in cutaneous leishmaniasis (CL) is urgently needed. Objective The aim of this study was to compare the proteomic profiles in patients with CL before and after 7 days of treatment and identify early biomarkers of curative response. Methods Four patients with a parasitological diagnosis of leishmaniasis with confirmation of species by PCR-RFLP were recruited. All patients had a single lesion, and a protein from the middle of the ulcer was quantified by liquid chromatography and mass spectrometry. Results A total of 12 proteins showed differential expression in the comparative LC-electrospray ionization MS/MS (LC-ESI-MS/MS) triplicate analysis. Seven of them were up-regulated and five of them were down-regulated. Calcium binding proteins A2, A8, and A9 and hemoglobin subunits alpha-2 and delta showed high correlation with epidermis development and immune response. Conclusion We identified changes in the profiles of proteins that had a positive therapeutic response to the treatment. The proteins identified with differential expression are related to the reduction of inflammation and increased tissue repair. These proteins can be useful as biomarkers for early monitoring of therapeutic response in CL.
format: application/pdf
format: text/html
creator: Andrés Montoya
creator: Manuel Carlos López
creator: Ivan D. Vélez
creator: Sara M. Robledo
subject: Parasitology
subject: Infectious Diseases
description: doi:10.7717/peerj.6228
publisher: PeerJ Inc.
rights: © 2019 Montoya et al.
abstract: Background Leishmaniasis is a parasitic disease caused by more than 20 species of the Leishmania genus. The disease is globally distributed and is endemic in 97 countries and three territories in the tropical and subtropical regions. The efficacy of the current treatments is becoming increasingly low either due to incomplete treatment or resistant parasites. Failure of treatment is frequent, and therefore, the search for early biomarkers of therapeutic response in cutaneous leishmaniasis (CL) is urgently needed. Objective The aim of this study was to compare the proteomic profiles in patients with CL before and after 7 days of treatment and identify early biomarkers of curative response. Methods Four patients with a parasitological diagnosis of leishmaniasis with confirmation of species by PCR-RFLP were recruited. All patients had a single lesion, and a protein from the middle of the ulcer was quantified by liquid chromatography and mass spectrometry. Results A total of 12 proteins showed differential expression in the comparative LC-electrospray ionization MS/MS (LC-ESI-MS/MS) triplicate analysis. Seven of them were up-regulated and five of them were down-regulated. Calcium binding proteins A2, A8, and A9 and hemoglobin subunits alpha-2 and delta showed high correlation with epidermis development and immune response. Conclusion We identified changes in the profiles of proteins that had a positive therapeutic response to the treatment. The proteins identified with differential expression are related to the reduction of inflammation and increased tissue repair. These proteins can be useful as biomarkers for early monitoring of therapeutic response in CL.
bibliographic citation: Montoya et al. (2019) Label-free quantitative proteomic analysis reveals potential biomarkers for early healing in cutaneous leishmaniasis. PeerJ 6:e6228 https://doi.org/10.7717/peerj.6228
date submitted: 2018-09-27
date accepted: 2018-12-06
issued: 2019-01-11
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Montoya
  given name: Andrés
author list: Agent
  family name: López
  given name: Manuel Carlos
author list: Agent
  family name: Vélez
  given name: Ivan D.
author list: Agent
  family name: Robledo
  given name: Sara M.
doi: 10.7717/peerj.6228
volume: 6
issn: 2167-8359
publication name: PeerJ
publication date: 2019-01-11
copyright: © 2019 Montoya et al.
attribution name: Montoya et al.

Assigning confidence scores to homoeologs using fuzzy logic
type: item
type: AcademicArticle
description: In polyploid genomes, homoeologs are a specific subtype of homologs, and can be thought of as orthologs between subgenomes. In Orthologous MAtrix, we infer homoeologs in three polyploid plant species: upland cotton (Gossypium hirsutum), rapeseed (Brassica napus), and bread wheat (Triticum aestivum). While we can typically recognize the features of a “good” homoeolog prediction (a consistent evolutionary distance, high synteny, and a one-to-one relationship), none of them is a hard-fast criterion. We devised a novel fuzzy logic-based method to assign confidence scores to each pair of predicted homoeologs. We inferred homoeolog pairs and used the new and improved method to assign confidence scores, which ranged from 0 to 100. Most confidence scores were between 70 and 100, but the distribution varied between genomes. The new confidence scores show an improvement over our previous method and were manually evaluated using a subset from various confidence ranges.
format: application/pdf
format: text/html
creator: Natasha M. Glover
creator: Adrian Altenhoff
creator: Christophe Dessimoz
subject: Bioinformatics
subject: Computational Biology
subject: Genomics
description: doi:10.7717/peerj.6231
publisher: PeerJ Inc.
rights: © 2019 Glover et al.
abstract: In polyploid genomes, homoeologs are a specific subtype of homologs, and can be thought of as orthologs between subgenomes. In Orthologous MAtrix, we infer homoeologs in three polyploid plant species: upland cotton (Gossypium hirsutum), rapeseed (Brassica napus), and bread wheat (Triticum aestivum). While we can typically recognize the features of a “good” homoeolog prediction (a consistent evolutionary distance, high synteny, and a one-to-one relationship), none of them is a hard-fast criterion. We devised a novel fuzzy logic-based method to assign confidence scores to each pair of predicted homoeologs. We inferred homoeolog pairs and used the new and improved method to assign confidence scores, which ranged from 0 to 100. Most confidence scores were between 70 and 100, but the distribution varied between genomes. The new confidence scores show an improvement over our previous method and were manually evaluated using a subset from various confidence ranges.
bibliographic citation: Glover et al. (2019) Assigning confidence scores to homoeologs using fuzzy logic. PeerJ 6:e6231 https://doi.org/10.7717/peerj.6231
date submitted: 2018-07-11
date accepted: 2018-12-07
issued: 2019-01-11
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Glover
  given name: Natasha M.
author list: Agent
  family name: Altenhoff
  given name: Adrian
author list: Agent
  family name: Dessimoz
  given name: Christophe
doi: 10.7717/peerj.6231
volume: 6
issn: 2167-8359
publication name: PeerJ
publication date: 2019-01-11
copyright: © 2019 Glover et al.
attribution name: Glover et al.

Characterizing ecomorphological patterns in hyenids: a multivariate approach using postcanine dentition
type: item
type: AcademicArticle
description: We analyze the multivariate pattern of lower and upper cheek dentition for the family Hyaenidae along its evolutionary history. A total of 11,698 individual measurements of lengths and widths for the main postcanine teeth were collected for 54 extinct and three extant species of this family and analyzed by means of principal component analyses. Our results indicate that the functional aspects are better reflected by lower cheek dentition as a result of mosaic evolution. The multivariate structure captured by the three first principal components correspond to different adaptive strategies. The two first components characterize the main groups of ecomorphs, while hunting species separate from scavengers along the third axis. In the context of Hyaenidae, the post-canine cheek dentition of Parahyaena brunnea and Hyaena hyaena shows an extreme degree of specialization in scavenging.
format: application/pdf
format: text/html
creator: Carlos Coca-Ortega
creator: Juan Antonio Pérez-Claros
subject: Biodiversity
subject: Evolutionary Studies
subject: Zoology
description: doi:10.7717/peerj.6238
publisher: PeerJ Inc.
rights: © 2019 Coca-Ortega and Pérez-Claros
abstract: We analyze the multivariate pattern of lower and upper cheek dentition for the family Hyaenidae along its evolutionary history. A total of 11,698 individual measurements of lengths and widths for the main postcanine teeth were collected for 54 extinct and three extant species of this family and analyzed by means of principal component analyses. Our results indicate that the functional aspects are better reflected by lower cheek dentition as a result of mosaic evolution. The multivariate structure captured by the three first principal components correspond to different adaptive strategies. The two first components characterize the main groups of ecomorphs, while hunting species separate from scavengers along the third axis. In the context of Hyaenidae, the post-canine cheek dentition of Parahyaena brunnea and Hyaena hyaena shows an extreme degree of specialization in scavenging.
bibliographic citation: Coca-Ortega et al. (2019) Characterizing ecomorphological patterns in hyenids: a multivariate approach using postcanine dentition. PeerJ 6:e6238 https://doi.org/10.7717/peerj.6238
date submitted: 2018-09-13
date accepted: 2018-12-07
issued: 2019-01-11
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Coca-Ortega
  given name: Carlos
author list: Agent
  family name: Pérez-Claros
  given name: Juan Antonio
doi: 10.7717/peerj.6238
volume: 6
issn: 2167-8359
publication name: PeerJ
publication date: 2019-01-11
copyright: © 2019 Coca-Ortega and Pérez-Claros
attribution name: Coca-Ortega and Pérez-Claros

Use of a leaf chlorophyll content index to improve the prediction of above-ground biomass and productivity
type: item
type: AcademicArticle
description: Improving the accuracy of predicting plant productivity is a key element in planning nutrient management strategies to ensure a balance between nutrient supply and demand under climate change. A calculation based on intercepted photosynthetically active radiation is an effective and relatively reliable way to determine the climate impact on a crop above-ground biomass (AGB). This research shows that using variations in a chlorophyll content index (CCI) in a mathematical function could effectively obtain good statistical diagnostic results between simulated and observed crop biomass. In this study, the leaf CCI, which is used as a biochemical photosynthetic component and calibration parameter, increased simulation accuracy across the growing stages during 2016–2017. This calculation improves the accuracy of prediction and modelling of crops under specific agroecosystems, and it may also improve projections of AGB for a variety of other crops.
format: application/pdf
format: text/html
creator: Chuang Liu
creator: Yi Liu
creator: Yanhong Lu
creator: Yulin Liao
creator: Jun Nie
creator: Xiaoliang Yuan
creator: Fang Chen
subject: Agricultural Science
subject: Climate Change Biology
description: doi:10.7717/peerj.6240
publisher: PeerJ Inc.
rights: © 2019 Liu et al.
abstract: Improving the accuracy of predicting plant productivity is a key element in planning nutrient management strategies to ensure a balance between nutrient supply and demand under climate change. A calculation based on intercepted photosynthetically active radiation is an effective and relatively reliable way to determine the climate impact on a crop above-ground biomass (AGB). This research shows that using variations in a chlorophyll content index (CCI) in a mathematical function could effectively obtain good statistical diagnostic results between simulated and observed crop biomass. In this study, the leaf CCI, which is used as a biochemical photosynthetic component and calibration parameter, increased simulation accuracy across the growing stages during 2016–2017. This calculation improves the accuracy of prediction and modelling of crops under specific agroecosystems, and it may also improve projections of AGB for a variety of other crops.
bibliographic citation: Liu et al. (2019) Use of a leaf chlorophyll content index to improve the prediction of above-ground biomass and productivity. PeerJ 6:e6240 https://doi.org/10.7717/peerj.6240
date submitted: 2018-08-20
date accepted: 2018-12-07
issued: 2019-01-11
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Liu
  given name: Chuang
author list: Agent
  family name: Liu
  given name: Yi
author list: Agent
  family name: Lu
  given name: Yanhong
author list: Agent
  family name: Liao
  given name: Yulin
author list: Agent
  family name: Nie
  given name: Jun
author list: Agent
  family name: Yuan
  given name: Xiaoliang
author list: Agent
  family name: Chen
  given name: Fang
doi: 10.7717/peerj.6240
volume: 6
issn: 2167-8359
publication name: PeerJ
publication date: 2019-01-11
copyright: © 2019 Liu et al.
attribution name: Liu et al.

Genome-wide identification and expression analysis of the MYB transcription factor in moso bamboo (Phyllostachys edulis)
type: item
type: AcademicArticle
description: The MYB family, one of the largest transcription factor (TF) families in the plant kingdom, plays vital roles in cell formation, morphogenesis and signal transduction, as well as responses to biotic and abiotic stresses. However, the underlying function of bamboo MYB TFs remains unclear. To gain insight into the status of these proteins, a total of 85 PeMYBs, which were further divided into 11 subgroups, were identified in moso bamboo (Phyllostachys edulis) by using a genome-wide search strategy. Gene structure analysis showed that PeMYBs were significantly different, with exon numbers varying from 4 to 13. Phylogenetic analysis indicated that PeMYBs clustered into 27 clades, of which the function of 18 clades has been predicted. In addition, almost all of the PeMYBs were differently expressed in leaves, panicles, rhizomes and shoots based on RNA-seq data. Furthermore, qRT-PCR analysis showed that 12 PeMYBs related to the biosynthesis and deposition of the secondary cell wall (SCW) were constitutively expressed, and their transcript abundance levels have changed significantly with increasing height of the bamboo shoots, for which the degree of lignification continuously increased. This result indicated that these PeMYBs might play fundamental roles in SCW thickening and bamboo shoot lignification. The present comprehensive and systematic study on the members of the MYB family provided a reference and solid foundation for further functional analysis of MYB TFs in moso bamboo.
format: application/pdf
format: text/html
creator: Kebin Yang
creator: Ying Li
creator: Sining Wang
creator: Xiurong Xu
creator: Huayu Sun
creator: Hansheng Zhao
creator: Xueping Li
creator: Zhimin Gao
subject: Bioinformatics
subject: Genomics
subject: Molecular Biology
subject: Plant Science
description: doi:10.7717/peerj.6242
publisher: PeerJ Inc.
rights: © 2019 Yang et al.
abstract: The MYB family, one of the largest transcription factor (TF) families in the plant kingdom, plays vital roles in cell formation, morphogenesis and signal transduction, as well as responses to biotic and abiotic stresses. However, the underlying function of bamboo MYB TFs remains unclear. To gain insight into the status of these proteins, a total of 85 PeMYBs, which were further divided into 11 subgroups, were identified in moso bamboo (Phyllostachys edulis) by using a genome-wide search strategy. Gene structure analysis showed that PeMYBs were significantly different, with exon numbers varying from 4 to 13. Phylogenetic analysis indicated that PeMYBs clustered into 27 clades, of which the function of 18 clades has been predicted. In addition, almost all of the PeMYBs were differently expressed in leaves, panicles, rhizomes and shoots based on RNA-seq data. Furthermore, qRT-PCR analysis showed that 12 PeMYBs related to the biosynthesis and deposition of the secondary cell wall (SCW) were constitutively expressed, and their transcript abundance levels have changed significantly with increasing height of the bamboo shoots, for which the degree of lignification continuously increased. This result indicated that these PeMYBs might play fundamental roles in SCW thickening and bamboo shoot lignification. The present comprehensive and systematic study on the members of the MYB family provided a reference and solid foundation for further functional analysis of MYB TFs in moso bamboo.
bibliographic citation: Yang et al. (2019) Genome-wide identification and expression analysis of the MYB transcription factor in moso bamboo (Phyllostachys edulis). PeerJ 6:e6242 https://doi.org/10.7717/peerj.6242
date submitted: 2018-09-12
date accepted: 2018-12-08
issued: 2019-01-11
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Yang
  given name: Kebin
author list: Agent
  family name: Li
  given name: Ying
author list: Agent
  family name: Wang
  given name: Sining
author list: Agent
  family name: Xu
  given name: Xiurong
author list: Agent
  family name: Sun
  given name: Huayu
author list: Agent
  family name: Zhao
  given name: Hansheng
author list: Agent
  family name: Li
  given name: Xueping
author list: Agent
  family name: Gao
  given name: Zhimin
doi: 10.7717/peerj.6242
volume: 6
issn: 2167-8359
publication name: PeerJ
publication date: 2019-01-11
copyright: © 2019 Yang et al.
attribution name: Yang et al.

Differential expression of the glucose transporter gene glcH in response to glucose and light in marine picocyanobacteria
type: item
type: AcademicArticle
description: Background Our team discovered that Prochlorococcus can take up glucose, in a process that changes the transcriptional pattern of several genes involved in glucose metabolization. We have also shown that glcH encodes a very high affinity glucose transporter, and that glucose is taken up by natural Prochlorococcus populations. We demonstrated that the kinetic parameters of glucose uptake show significant diversity in different Prochlorococcus and Synechococcus strains. Here, we tested whether the transcriptional response of glcH to several glucose concentrations and light conditions was also different depending on the studied strain. Methods Cultures were grown in the light, supplemented with five different glucose concentrations or subjected to darkness, and cells harvested after 24 h of treatment. qRT-PCR was used to determine glcH expression in four Prochlorococcus and two Synechococcus strains. Results In all studied strains glcH was expressed in the absence of glucose, and it increased upon glucose addition to cultures. The changes differed depending on the strain, both in the magnitude and in the way cells responded to the tested glucose concentrations. Unlike the other strains, Synechococcus BL107 showed the maximum glucose uptake at 5 nM glucose. Darkness induced a strong decrease in glcH expression, especially remarkable in Prochlorococcus MIT9313. Discussion Our results suggest that marine picocyanobacteria are actively monitoring the availability of glucose, to upregulate glcH expression in order to exploit the presence of sugars in the environment. The diverse responses observed in different strains suggest that the transcriptional regulation of glucose uptake has been adjusted by evolutive selection. Darkness promotes a strong decrease in glcH expression in all studied strains, which fits with previous results on glucose uptake in Prochlorococcus. Overall, this work reinforces the importance of mixotrophy for marine picocyanobacteria.
format: application/pdf
format: text/html
creator: José Ángel Moreno-Cabezuelo
creator: Antonio López-Lozano
creator: Jesús Díez
creator: José Manuel García-Fernández
subject: Ecology
subject: Marine Biology
subject: Microbiology
subject: Molecular Biology
subject: Biological Oceanography
description: doi:10.7717/peerj.6248
publisher: PeerJ Inc.
rights: © 2019 Moreno-Cabezuelo et al.
abstract: Background Our team discovered that Prochlorococcus can take up glucose, in a process that changes the transcriptional pattern of several genes involved in glucose metabolization. We have also shown that glcH encodes a very high affinity glucose transporter, and that glucose is taken up by natural Prochlorococcus populations. We demonstrated that the kinetic parameters of glucose uptake show significant diversity in different Prochlorococcus and Synechococcus strains. Here, we tested whether the transcriptional response of glcH to several glucose concentrations and light conditions was also different depending on the studied strain. Methods Cultures were grown in the light, supplemented with five different glucose concentrations or subjected to darkness, and cells harvested after 24 h of treatment. qRT-PCR was used to determine glcH expression in four Prochlorococcus and two Synechococcus strains. Results In all studied strains glcH was expressed in the absence of glucose, and it increased upon glucose addition to cultures. The changes differed depending on the strain, both in the magnitude and in the way cells responded to the tested glucose concentrations. Unlike the other strains, Synechococcus BL107 showed the maximum glucose uptake at 5 nM glucose. Darkness induced a strong decrease in glcH expression, especially remarkable in Prochlorococcus MIT9313. Discussion Our results suggest that marine picocyanobacteria are actively monitoring the availability of glucose, to upregulate glcH expression in order to exploit the presence of sugars in the environment. The diverse responses observed in different strains suggest that the transcriptional regulation of glucose uptake has been adjusted by evolutive selection. Darkness promotes a strong decrease in glcH expression in all studied strains, which fits with previous results on glucose uptake in Prochlorococcus. Overall, this work reinforces the importance of mixotrophy for marine picocyanobacteria.
bibliographic citation: Moreno-Cabezuelo et al. (2019) Differential expression of the glucose transporter gene glcH in response to glucose and light in marine picocyanobacteria. PeerJ 6:e6248 https://doi.org/10.7717/peerj.6248
date submitted: 2018-10-24
date accepted: 2018-12-09
issued: 2019-01-11
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Moreno-Cabezuelo
  given name: José Ángel
author list: Agent
  family name: López-Lozano
  given name: Antonio
author list: Agent
  family name: Díez
  given name: Jesús
author list: Agent
  family name: García-Fernández
  given name: José Manuel
doi: 10.7717/peerj.6248
volume: 6
issn: 2167-8359
publication name: PeerJ
publication date: 2019-01-11
copyright: © 2019 Moreno-Cabezuelo et al.
attribution name: Moreno-Cabezuelo et al.

Different revegetation types alter soil physical-chemical characteristics and fungal community in the Baishilazi Nature Reserve
type: item
type: AcademicArticle
description: The effects of different revegetation types on soil physical–chemical characteristics and fungal community diversity and composition of soils sampled from five different revegetation types (JM, Juglans mandshurica; QM, Quercus mongolica; conifer-broadleaf forest (CB); LG, Larix gmelinii; PK, Pinus koraiensis) in the Baishilazi Nature Reserve were determined. Soil fungal communities were assessed employing ITS rRNA Illunima Miseq high-throughput sequencing. Responses of the soil fungi community to soil environmental factors were assessed through canonical correspondence analysis (CCA) and Pearson correlation analysis. The coniferous forests (L. gmelinii, P. koraiensis) and CB had reduced soil total carbon (C), total nitrogen (N), and available nitrogen (AN) values compared with the broadleaf forest (J. mandshurica, Q. mongolica). The average fungus diversity according to the Shannon, ACE, Chao1, and Simpson index were increased in the J. mandshurica site. Basidiomycota, Ascomycota, Zygomycota, and Rozellomycota were the dominant fungal taxa in this region. The phylum Basidiomycota was dominant in the Q. mongolica, CB, L. gmelinii, and P. koraiensis sites, while Ascomycota was the dominant phylum in the J. mandshurica site. The clear differentiation of fungal communities and the clustering in the heatmap and in non-metric multidimensional scaling plot showed that broadleaf forests, CB, and coniferous forests harbored different fungal communities. The results of the CCA showed that soil environmental factors, such as soil pH, total C, total N, AN, and available phosphorus (P) greatly influenced the fungal community structure. Based on our results, the different responses of the soil fungal communities to the different revegetation types largely dependent on different forest types and soil physicochemical characteristic in Baishilazi Nature Reserve.
format: application/pdf
format: text/html
creator: Jiaojiao Deng
creator: You Yin
creator: Jiyao Luo
creator: Wenxu Zhu
creator: Yongbin Zhou
subject: Ecology
subject: Mycology
subject: Soil Science
subject: Forestry
description: doi:10.7717/peerj.6251
publisher: PeerJ Inc.
rights: © 2018 Deng et al.
abstract: The effects of different revegetation types on soil physical–chemical characteristics and fungal community diversity and composition of soils sampled from five different revegetation types (JM, Juglans mandshurica; QM, Quercus mongolica; conifer-broadleaf forest (CB); LG, Larix gmelinii; PK, Pinus koraiensis) in the Baishilazi Nature Reserve were determined. Soil fungal communities were assessed employing ITS rRNA Illunima Miseq high-throughput sequencing. Responses of the soil fungi community to soil environmental factors were assessed through canonical correspondence analysis (CCA) and Pearson correlation analysis. The coniferous forests (L. gmelinii, P. koraiensis) and CB had reduced soil total carbon (C), total nitrogen (N), and available nitrogen (AN) values compared with the broadleaf forest (J. mandshurica, Q. mongolica). The average fungus diversity according to the Shannon, ACE, Chao1, and Simpson index were increased in the J. mandshurica site. Basidiomycota, Ascomycota, Zygomycota, and Rozellomycota were the dominant fungal taxa in this region. The phylum Basidiomycota was dominant in the Q. mongolica, CB, L. gmelinii, and P. koraiensis sites, while Ascomycota was the dominant phylum in the J. mandshurica site. The clear differentiation of fungal communities and the clustering in the heatmap and in non-metric multidimensional scaling plot showed that broadleaf forests, CB, and coniferous forests harbored different fungal communities. The results of the CCA showed that soil environmental factors, such as soil pH, total C, total N, AN, and available phosphorus (P) greatly influenced the fungal community structure. Based on our results, the different responses of the soil fungal communities to the different revegetation types largely dependent on different forest types and soil physicochemical characteristic in Baishilazi Nature Reserve.
bibliographic citation: Deng et al. (2019) Different revegetation types alter soil physical-chemical characteristics and fungal community in the Baishilazi Nature Reserve. PeerJ 6:e6251 https://doi.org/10.7717/peerj.6251
date submitted: 2018-08-30
date accepted: 2018-12-08
issued: 2019-01-11
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Deng
  given name: Jiaojiao
author list: Agent
  family name: Yin
  given name: You
author list: Agent
  family name: Luo
  given name: Jiyao
author list: Agent
  family name: Zhu
  given name: Wenxu
author list: Agent
  family name: Zhou
  given name: Yongbin
doi: 10.7717/peerj.6251
volume: 6
issn: 2167-8359
publication name: PeerJ
publication date: 2019-01-11
copyright: © 2018 Deng et al.
attribution name: Deng et al.

Network models of driver behavior
type: item
type: AcademicArticle
description: The way people behave in traffic is not always optimal from the road safety perspective: drivers exceed speed limits, misjudge speeds or distances, tailgate other road users or fail to perceive them. Such behaviors are commonly investigated using self-report-based latent variable models, and conceptualized as reflections of violation- and error-proneness. However, attributing dangerous behavior to stable properties of individuals may not be the optimal way of improving traffic safety, whereas investigating direct relationships between traffic behaviors offers a fruitful way forward. Network models of driver behavior and background factors influencing behavior were constructed using a large UK sample of novice drivers. The models show how individual violations, such as speeding, are related to and may contribute to individual errors such as tailgating and braking to avoid an accident. In addition, a network model of the background factors and driver behaviors was constructed. Finally, a model predicting crashes based on prior behavior was built and tested in separate datasets. This contribution helps to bridge a gap between experimental/theoretical studies and self-report-based studies in traffic research: the former have recognized the importance of focusing on relationships between individual driver behaviors, while network analysis offers a way to do so for self-report studies.
format: application/pdf
format: text/html
creator: Markus T. Mattsson
subject: Psychiatry and Psychology
subject: Statistics
description: doi:10.7717/peerj.6119
publisher: PeerJ Inc.
rights: © 2019 Mattsson
abstract: The way people behave in traffic is not always optimal from the road safety perspective: drivers exceed speed limits, misjudge speeds or distances, tailgate other road users or fail to perceive them. Such behaviors are commonly investigated using self-report-based latent variable models, and conceptualized as reflections of violation- and error-proneness. However, attributing dangerous behavior to stable properties of individuals may not be the optimal way of improving traffic safety, whereas investigating direct relationships between traffic behaviors offers a fruitful way forward. Network models of driver behavior and background factors influencing behavior were constructed using a large UK sample of novice drivers. The models show how individual violations, such as speeding, are related to and may contribute to individual errors such as tailgating and braking to avoid an accident. In addition, a network model of the background factors and driver behaviors was constructed. Finally, a model predicting crashes based on prior behavior was built and tested in separate datasets. This contribution helps to bridge a gap between experimental/theoretical studies and self-report-based studies in traffic research: the former have recognized the importance of focusing on relationships between individual driver behaviors, while network analysis offers a way to do so for self-report studies.
bibliographic citation: Mattsson (2019) Network models of driver behavior. PeerJ 6:e6119 https://doi.org/10.7717/peerj.6119
date submitted: 2018-07-03
date accepted: 2018-11-16
issued: 2019-01-10
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Mattsson
  given name: Markus T.
doi: 10.7717/peerj.6119
volume: 6
issn: 2167-8359
publication name: PeerJ
publication date: 2019-01-10
copyright: © 2019 Mattsson
attribution name: Mattsson

cRegions—a tool for detecting conserved cis-elements in multiple sequence alignment of diverged coding sequences
type: item
type: AcademicArticle
description: Identifying cis-acting elements and understanding regulatory mechanisms of a gene is crucial to fully understand the molecular biology of an organism. In general, it is difficult to identify previously uncharacterised cis-acting elements with an unknown consensus sequence. The task is especially problematic with viruses containing regions of limited or no similarity to other previously characterised sequences. Fortunately, the fast increase in the number of sequenced genomes allows us to detect some of these elusive cis-elements. In this work, we introduce a web-based tool called cRegions. It was developed to identify regions within a protein-coding sequence where the conservation in the amino acid sequence is caused by the conservation in the nucleotide sequence. The cRegion can be the first step in discovering novel cis-acting sequences from diverged protein-coding genes. The results can be used as a basis for future experimental analysis. We applied cRegions on the non-structural and structural polyproteins of alphaviruses as an example and successfully detected all known cis-acting elements. In this publication and in previous work, we have shown that cRegions is able to detect a wide variety of functional elements in DNA and RNA viruses. These functional elements include splice sites, stem-loops, overlapping reading frames, internal promoters, ribosome frameshifting signals and other embedded elements with yet unknown function. The cRegions web tool is available at http://bioinfo.ut.ee/cRegions/.
format: application/pdf
format: text/html
creator: Mikk Puustusmaa
creator: Aare Abroi
subject: Bioinformatics
subject: Evolutionary Studies
subject: Genetics
subject: Virology
subject: Data Science
description: doi:10.7717/peerj.6176
publisher: PeerJ Inc.
rights: © 2019 Puustusmaa and Abroi
abstract: Identifying cis-acting elements and understanding regulatory mechanisms of a gene is crucial to fully understand the molecular biology of an organism. In general, it is difficult to identify previously uncharacterised cis-acting elements with an unknown consensus sequence. The task is especially problematic with viruses containing regions of limited or no similarity to other previously characterised sequences. Fortunately, the fast increase in the number of sequenced genomes allows us to detect some of these elusive cis-elements. In this work, we introduce a web-based tool called cRegions. It was developed to identify regions within a protein-coding sequence where the conservation in the amino acid sequence is caused by the conservation in the nucleotide sequence. The cRegion can be the first step in discovering novel cis-acting sequences from diverged protein-coding genes. The results can be used as a basis for future experimental analysis. We applied cRegions on the non-structural and structural polyproteins of alphaviruses as an example and successfully detected all known cis-acting elements. In this publication and in previous work, we have shown that cRegions is able to detect a wide variety of functional elements in DNA and RNA viruses. These functional elements include splice sites, stem-loops, overlapping reading frames, internal promoters, ribosome frameshifting signals and other embedded elements with yet unknown function. The cRegions web tool is available at http://bioinfo.ut.ee/cRegions/.
bibliographic citation: Puustusmaa et al. (2019) cRegions—a tool for detecting conserved cis-elements in multiple sequence alignment of diverged coding sequences. PeerJ 6:e6176 https://doi.org/10.7717/peerj.6176
date submitted: 2018-07-18
date accepted: 2018-11-27
issued: 2019-01-10
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Puustusmaa
  given name: Mikk
author list: Agent
  family name: Abroi
  given name: Aare
doi: 10.7717/peerj.6176
volume: 6
issn: 2167-8359
publication name: PeerJ
publication date: 2019-01-10
copyright: © 2019 Puustusmaa and Abroi
attribution name: Puustusmaa and Abroi

Optimization of a pretreatment and hydrolysis process for the efficient recovery of recycled sugars and unknown compounds from agricultural sweet sorghum bagasse stem pith solid waste
type: item
type: AcademicArticle
description: Background Sweet sorghum bagasse (SSB), comprising both a dermal layer and pith, is a solid waste generated by agricultural activities. Open burning was previously used to treat agricultural solid waste but is harmful to the environment and human health. Recent reports showed that certain techniques can convert this agricultural waste into valuable products. While SSB has been considered an attractive raw material for sugar extraction and the production of value-added products, the pith root in the SSB can be difficult to process. Therefore, it is necessary to pretreat bagasse before conventional hydrolysis. Methods A thorough analysis and comparison of various pretreatment methods were conducted based on physicochemical and microscopic approaches. The responses of agricultural SSB stem pith with different particle sizes to pretreatment temperature, acid and alkali concentration and enzyme dosage were investigated to determine the optimal pretreatment. The integrated methods are beneficial to the utilization of carbohydrate-based and unknown compounds in agricultural solid waste. Results Acid (1.5−4.5%, v/v) and alkali (5−8%, w/v) reagents were used to collect cellulose from different meshes of pith at 25–100 °C. The results showed that the use of 100 mesh pith soaked in 8% (w/v) NaOH solution at 100 °C resulted in 32.47% ± 0.01% solid recovery. Follow-up fermentation with 3% (v/v) acid and 6.5% (w/v) alkali at 50 °C for enzymolysis was performed with the optimal enzyme ratio. An analysis of the surface topography and porosity before and after pretreatment showed that both the pore size of the pith and the amount of exposed cellulose increased as the mesh size increased. Interestingly, various compounds, including 42 compounds previously known to be present and 13 compounds not previously known to be present, were detected in the pretreatment liquid, while 10 types of monosaccharides, including D-glucose, D-xylose and D-arabinose, were found in the enzymatic solutio…
format: application/pdf
format: text/html
creator: Ting-Ting Jiang
creator: Yan Liang
creator: Xiang Zhou
creator: Zi-Wei Shi
creator: Zhi-Jun Xin
subject: Agricultural Science
subject: Food Science and Technology
subject: Plant Science
subject: Food, Water and Energy Nexus
subject: Green Chemistry
description: doi:10.7717/peerj.6186
publisher: PeerJ Inc.
rights: © 2019 Jiang et al.
abstract: Background Sweet sorghum bagasse (SSB), comprising both a dermal layer and pith, is a solid waste generated by agricultural activities. Open burning was previously used to treat agricultural solid waste but is harmful to the environment and human health. Recent reports showed that certain techniques can convert this agricultural waste into valuable products. While SSB has been considered an attractive raw material for sugar extraction and the production of value-added products, the pith root in the SSB can be difficult to process. Therefore, it is necessary to pretreat bagasse before conventional hydrolysis. Methods A thorough analysis and comparison of various pretreatment methods were conducted based on physicochemical and microscopic approaches. The responses of agricultural SSB stem pith with different particle sizes to pretreatment temperature, acid and alkali concentration and enzyme dosage were investigated to determine the optimal pretreatment. The integrated methods are beneficial to the utilization of carbohydrate-based and unknown compounds in agricultural solid waste. Results Acid (1.5−4.5%, v/v) and alkali (5−8%, w/v) reagents were used to collect cellulose from different meshes of pith at 25–100 °C. The results showed that the use of 100 mesh pith soaked in 8% (w/v) NaOH solution at 100 °C resulted in 32.47% ± 0.01% solid recovery. Follow-up fermentation with 3% (v/v) acid and 6.5% (w/v) alkali at 50 °C for enzymolysis was performed with the optimal enzyme ratio. An analysis of the surface topography and porosity before and after pretreatment showed that both the pore size of the pith and the amount of exposed cellulose increased as the mesh size increased. Interestingly, various compounds, including 42 compounds previously known to be present and 13 compounds not previously known to be present, were detected in the pretreatment liquid, while 10 types of monosaccharides, including D-glucose, D-xylose and D-arabinose, were found in the enzymatic solutio…
bibliographic citation: Jiang et al. (2019) Optimization of a pretreatment and hydrolysis process for the efficient recovery of recycled sugars and unknown compounds from agricultural sweet sorghum bagasse stem pith solid waste. PeerJ 6:e6186 https://doi.org/10.7717/peerj.6186
date submitted: 2018-09-05
date accepted: 2018-11-29
issued: 2019-01-10
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Jiang
  given name: Ting-Ting
author list: Agent
  family name: Liang
  given name: Yan
author list: Agent
  family name: Zhou
  given name: Xiang
author list: Agent
  family name: Shi
  given name: Zi-Wei
author list: Agent
  family name: Xin
  given name: Zhi-Jun
doi: 10.7717/peerj.6186
volume: 6
issn: 2167-8359
publication name: PeerJ
publication date: 2019-01-10
copyright: © 2019 Jiang et al.
attribution name: Jiang et al.

Checklist to the Elatostema (Urticaceae) of Vietnam including 19 new records, ten new combinations, two new names and four new synonyms
type: item
type: AcademicArticle
description: Elatostema (Urticaceae) comprises several hundred herbaceous species distributed in tropical and subtropical Africa, Asia, Australia and Oceania. The greatest species richness occurs on limestone karst in Southeast Asia. Taxonomic revisions of Elatostema are largely out of date and contradict each other with respect to the delimitation of Elatostema and Pellionia. Most herbaria in SE Asia and worldwide contain significant amounts of unidentified material. As part of a broader revision of Elatostema in SE Asia, we present an updated checklist for Vietnam based on field visits, a review of specimens in herbaria worldwide, a review of type material and nomenclature. We recognize 77 taxa (75 species and two infraspecific taxa) of Elatostema in Vietnam, 23 of which were previously ascribed to Pellionia. Nineteen of these are new records for the country, i.e., E. attenuatoides, E. austrosinense, E. backeri, E. brunneinerve, E. crassiusculum, E. crenatum, E. fengshanense, E. glochidioides, E. malacotrichum, E. nanchuanense, E. oblongifolium, E. obtusum, E. oppositum, E. pergameneum, E. prunifolium, E. pseudolongipes, E. pycnodontum, E. salvinioides and E. xichouense. We place E. baviensis in synonymy of E. platyphyllum, E. colaniae in synonymy of E. myrtillus, P. macroceras in synonymy of E. hookerianum, and P. tetramera in synonymy of E. dissectum for the first time. Fourteen taxa (18% of all the recognized taxa) are endemic to Vietnam, which makes Elatostema one of the richest genera for endemic species in this country; this level of endemism is comparable to levels observed in Orchidaceae. Our checklist suggests that the highest diversity and endemism of Elatostema occurs in northern Vietnam, and that there is the greatest floristic similarity of northern Vietnam to SW China. The relationship among floristic regions is also investigated. We could find no records of Elatostema for 33 out of 63 provincial units of Vietnam, including all the southernmost provinces. We prop…
format: application/pdf
format: text/html
creator: Long-Fei Fu
creator: Alex Monro
creator: Truong Van Do
creator: Maxim S. Nuraliev
creator: Leonid V. Averyanov
creator: Fang Wen
creator: Zi-Bing Xin
creator: Tatiana V. Maisak
creator: Andrey N. Kuznetsov
creator: Svetlana P. Kuznetsova
creator: Khang Sinh Nguyen
creator: Yi-Gang Wei
subject: Plant Science
subject: Taxonomy
description: doi:10.7717/peerj.6188
publisher: PeerJ Inc.
rights: © 2019 Fu et al.
abstract: Elatostema (Urticaceae) comprises several hundred herbaceous species distributed in tropical and subtropical Africa, Asia, Australia and Oceania. The greatest species richness occurs on limestone karst in Southeast Asia. Taxonomic revisions of Elatostema are largely out of date and contradict each other with respect to the delimitation of Elatostema and Pellionia. Most herbaria in SE Asia and worldwide contain significant amounts of unidentified material. As part of a broader revision of Elatostema in SE Asia, we present an updated checklist for Vietnam based on field visits, a review of specimens in herbaria worldwide, a review of type material and nomenclature. We recognize 77 taxa (75 species and two infraspecific taxa) of Elatostema in Vietnam, 23 of which were previously ascribed to Pellionia. Nineteen of these are new records for the country, i.e., E. attenuatoides, E. austrosinense, E. backeri, E. brunneinerve, E. crassiusculum, E. crenatum, E. fengshanense, E. glochidioides, E. malacotrichum, E. nanchuanense, E. oblongifolium, E. obtusum, E. oppositum, E. pergameneum, E. prunifolium, E. pseudolongipes, E. pycnodontum, E. salvinioides and E. xichouense. We place E. baviensis in synonymy of E. platyphyllum, E. colaniae in synonymy of E. myrtillus, P. macroceras in synonymy of E. hookerianum, and P. tetramera in synonymy of E. dissectum for the first time. Fourteen taxa (18% of all the recognized taxa) are endemic to Vietnam, which makes Elatostema one of the richest genera for endemic species in this country; this level of endemism is comparable to levels observed in Orchidaceae. Our checklist suggests that the highest diversity and endemism of Elatostema occurs in northern Vietnam, and that there is the greatest floristic similarity of northern Vietnam to SW China. The relationship among floristic regions is also investigated. We could find no records of Elatostema for 33 out of 63 provincial units of Vietnam, including all the southernmost provinces. We prop…
bibliographic citation: Fu et al. (2019) Checklist to the Elatostema (Urticaceae) of Vietnam including 19 new records, ten new combinations, two new names and four new synonyms. PeerJ 7:e6188 https://doi.org/10.7717/peerj.6188
date submitted: 2018-08-31
date accepted: 2018-11-30
issued: 2019-01-10
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Fu
  given name: Long-Fei
author list: Agent
  family name: Monro
  given name: Alex
author list: Agent
  family name: Do
  given name: Truong Van
author list: Agent
  family name: Nuraliev
  given name: Maxim S.
author list: Agent
  family name: Averyanov
  given name: Leonid V.
author list: Agent
  family name: Wen
  given name: Fang
author list: Agent
  family name: Xin
  given name: Zi-Bing
author list: Agent
  family name: Maisak
  given name: Tatiana V.
author list: Agent
  family name: Kuznetsov
  given name: Andrey N.
author list: Agent
  family name: Kuznetsova
  given name: Svetlana P.
author list: Agent
  family name: Nguyen
  given name: Khang Sinh
author list: Agent
  family name: Wei
  given name: Yi-Gang
doi: 10.7717/peerj.6188
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-01-10
copyright: ©2019 Fu et al.
attribution name: Fu et al.

Forest floor temperature and greenness link significantly to canopy attributes in South Africa’s fragmented coastal forests
type: item
type: AcademicArticle
description: Tropical landscapes are changing rapidly due to changes in land use and land management. Being able to predict and monitor land use change impacts on species for conservation or food security concerns requires the use of habitat quality metrics, that are consistent, can be mapped using above-ground sensor data and are relevant for species performance. Here, we focus on ground surface temperature (Thermalground) and ground vegetation greenness (NDVIdown) as potentially suitable metrics of habitat quality. Both have been linked to species demography and community structure in the literature. We test whether they can be measured consistently from the ground and whether they can be up-scaled indirectly using canopy structure maps (Leaf Area Index, LAI, and Fractional vegetation cover, FCover) developed from Landsat remote sensing data. We measured Thermalground and NDVIdown across habitats differing in tree cover (natural grassland to forest edges to forests and tree plantations) in the human-modified coastal forested landscapes of Kwa-Zulua Natal, South Africa. We show that both metrics decline significantly with increasing canopy closure and leaf area, implying a potential pathway for upscaling both metrics using canopy structure maps derived using earth observation. Specifically, our findings suggest that opening forest canopies by 20% or decreasing forest canopy LAI by one unit would result in increases of Thermalground by 1.2 °C across the range of observations studied. NDVIdown appears to decline by 0.1 in response to an increase in canopy LAI by 1 unit and declines nonlinearly with canopy closure. Accounting for micro-scale variation in temperature and resources is seen as essential to improve biodiversity impact predictions. Our study suggests that mapping ground surface temperature and ground vegetation greenness utilising remotely sensed canopy cover maps could provide a useful tool for mapping habitat quality metrics that matter to species. However, this appr…
format: application/pdf
format: text/html
creator: Marion Pfeifer
creator: Michael J.W. Boyle
creator: Stuart Dunning
creator: Pieter I. Olivier
subject: Ecosystem Science
subject: Climate Change Biology
subject: Forestry
subject: Spatial and Geographic Information Science
description: doi:10.7717/peerj.6190
publisher: PeerJ Inc.
rights: © 2019 Pfeifer et al.
abstract: Tropical landscapes are changing rapidly due to changes in land use and land management. Being able to predict and monitor land use change impacts on species for conservation or food security concerns requires the use of habitat quality metrics, that are consistent, can be mapped using above-ground sensor data and are relevant for species performance. Here, we focus on ground surface temperature (Thermalground) and ground vegetation greenness (NDVIdown) as potentially suitable metrics of habitat quality. Both have been linked to species demography and community structure in the literature. We test whether they can be measured consistently from the ground and whether they can be up-scaled indirectly using canopy structure maps (Leaf Area Index, LAI, and Fractional vegetation cover, FCover) developed from Landsat remote sensing data. We measured Thermalground and NDVIdown across habitats differing in tree cover (natural grassland to forest edges to forests and tree plantations) in the human-modified coastal forested landscapes of Kwa-Zulua Natal, South Africa. We show that both metrics decline significantly with increasing canopy closure and leaf area, implying a potential pathway for upscaling both metrics using canopy structure maps derived using earth observation. Specifically, our findings suggest that opening forest canopies by 20% or decreasing forest canopy LAI by one unit would result in increases of Thermalground by 1.2 °C across the range of observations studied. NDVIdown appears to decline by 0.1 in response to an increase in canopy LAI by 1 unit and declines nonlinearly with canopy closure. Accounting for micro-scale variation in temperature and resources is seen as essential to improve biodiversity impact predictions. Our study suggests that mapping ground surface temperature and ground vegetation greenness utilising remotely sensed canopy cover maps could provide a useful tool for mapping habitat quality metrics that matter to species. However, this appr…
bibliographic citation: Pfeifer et al. (2019) Forest floor temperature and greenness link significantly to canopy attributes in South Africa’s fragmented coastal forests. PeerJ 7:e6190 https://doi.org/10.7717/peerj.6190
date submitted: 2018-08-30
date accepted: 2018-11-30
issued: 2019-01-10
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Pfeifer
  given name: Marion
author list: Agent
  family name: Boyle
  given name: Michael J.W.
author list: Agent
  family name: Dunning
  given name: Stuart
author list: Agent
  family name: Olivier
  given name: Pieter I.
doi: 10.7717/peerj.6190
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-01-10
copyright: ©2019 Pfeifer et al.
attribution name: Pfeifer et al.

Native bluegill influence the foraging and aggressive behavior of invasive mosquitofish
type: item
type: AcademicArticle
description: Two fish species that are common invaders of aquatic ecosystems world-wide are Gambusia affinis and G. holbrooki, commonly known as mosquitofish. In North America, introduced G. affinis are thought to have contributed to the population decline of several native fish species. Sunfish (family Centrarchidae) naturally occur across much of North American, thus mosquitofish and sunfish are likely to come into contact and interact more frequently as mosquitofish spread. However, the nature of this interaction is not well known. We used a lab experiment to explore whether and how the aggressive and foraging behaviors of G. affinis might be influenced by a representative and ubiquitous native centrarchid (Lepomis macrochirus; bluegill sunfish), a species with juveniles that inhabit littoral habitats also preferred by mosquitofish. The experiment partnered an individual male or female mosquitofish (focal fish) with a juvenile bluegill, or a same- or opposite-sex conspecific, filmed these one-to-one interactions, and quantified foraging and aggressive actions for the focal mosquitofish. We found that juvenile bluegill affect foraging in male mosquitofish, resulting in lower percent of handling attempts and handling time in which the male consumed a food item. The presence of juvenile bluegill also led to a reduction in the number of aggressive acts by mosquitofish compared to aggression levels when focal mosquitofish were with conspecifics. In nature, when mosquitofish encounter juvenile bluegill in littoral habitats, our results suggest that the foraging and aggressive behaviors of mosquitofish will be modified, especially for males. This mechanism may influence the rate or geographic extent of the spread of mosquitofish into North American waterbodies.
format: application/pdf
format: text/html
creator: Jennifer H. Clemmer
creator: Jessica E. Rettig
subject: Animal Behavior
subject: Aquaculture, Fisheries and Fish Science
subject: Ecology
subject: Zoology
subject: Freshwater Biology
description: doi:10.7717/peerj.6203
publisher: PeerJ Inc.
rights: © 2019 Clemmer and Rettig
abstract: Two fish species that are common invaders of aquatic ecosystems world-wide are Gambusia affinis and G. holbrooki, commonly known as mosquitofish. In North America, introduced G. affinis are thought to have contributed to the population decline of several native fish species. Sunfish (family Centrarchidae) naturally occur across much of North American, thus mosquitofish and sunfish are likely to come into contact and interact more frequently as mosquitofish spread. However, the nature of this interaction is not well known. We used a lab experiment to explore whether and how the aggressive and foraging behaviors of G. affinis might be influenced by a representative and ubiquitous native centrarchid (Lepomis macrochirus; bluegill sunfish), a species with juveniles that inhabit littoral habitats also preferred by mosquitofish. The experiment partnered an individual male or female mosquitofish (focal fish) with a juvenile bluegill, or a same- or opposite-sex conspecific, filmed these one-to-one interactions, and quantified foraging and aggressive actions for the focal mosquitofish. We found that juvenile bluegill affect foraging in male mosquitofish, resulting in lower percent of handling attempts and handling time in which the male consumed a food item. The presence of juvenile bluegill also led to a reduction in the number of aggressive acts by mosquitofish compared to aggression levels when focal mosquitofish were with conspecifics. In nature, when mosquitofish encounter juvenile bluegill in littoral habitats, our results suggest that the foraging and aggressive behaviors of mosquitofish will be modified, especially for males. This mechanism may influence the rate or geographic extent of the spread of mosquitofish into North American waterbodies.
bibliographic citation: Clemmer et al. (2019) Native bluegill influence the foraging and aggressive behavior of invasive mosquitofish. PeerJ 7:e6203 https://doi.org/10.7717/peerj.6203
date submitted: 2018-09-14
date accepted: 2018-12-03
issued: 2019-01-10
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Clemmer
  given name: Jennifer H.
author list: Agent
  family name: Rettig
  given name: Jessica E.
doi: 10.7717/peerj.6203
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-01-10
copyright: ©2019 Clemmer and Rettig
attribution name: Clemmer and Rettig

Different ecological processes determined the alpha and beta components of taxonomic, functional, and phylogenetic diversity for plant communities in dryland regions of Northwest China
type: item
type: AcademicArticle
description: Drylands account for more than 30% of China’s terrestrial area, while the ecological drivers of taxonomic (TD), functional (FD) and phylogenetic (PD) diversity in dryland regions have not been explored simultaneously. Therefore, we selected 36 plots of desert and 32 plots of grassland (10 × 10 m) from a typical dryland region of northwest China. We calculated the alpha and beta components of TD, FD and PD for 68 dryland plant communities using Rao quadratic entropy index, which included 233 plant species. Redundancy analyses and variation partitioning analyses were used to explore the relative influence of environmental and spatial factors on the above three facets of diversity, at the alpha and beta scales. We found that soil, climate, topography and spatial structures (principal coordinates of neighbor matrices) were significantly correlated with TD, FD and PD at both alpha and beta scales, implying that these diversity patterns are shaped by contemporary environment and spatial processes together. However, we also found that alpha diversity was predominantly regulated by spatial structure, whereas beta diversity was largely determined by environmental variables. Among environmental factors, TD was most strongly correlated with climatic factors at the alpha scale, while with soil factors at the beta scale. FD was only significantly correlated with soil factors at the alpha scale, but with altitude, soil and climatic factors at the beta scale. In contrast, PD was more strongly correlated with altitude at the alpha scale, but with soil factors at the beta scale. Environment and space explained a smaller portion of variance in PD than in TD and FD. These results provide robust evidence that the ecological drivers of biodiversity differ among different scales and facets of diversity. Future research that focuses on the comparisons among TD, FD and PD would likely provide new insights into elucidating the underlying community assembly.
format: application/pdf
format: text/html
creator: Jianming Wang
creator: Chen Chen
creator: Jingwen Li
creator: Yiming Feng
creator: Qi Lu
subject: Biodiversity
subject: Biogeography
subject: Ecology
subject: Plant Science
subject: Forestry
description: doi:10.7717/peerj.6220
publisher: PeerJ Inc.
rights: © 2019 Wang et al.
abstract: Drylands account for more than 30% of China’s terrestrial area, while the ecological drivers of taxonomic (TD), functional (FD) and phylogenetic (PD) diversity in dryland regions have not been explored simultaneously. Therefore, we selected 36 plots of desert and 32 plots of grassland (10 × 10 m) from a typical dryland region of northwest China. We calculated the alpha and beta components of TD, FD and PD for 68 dryland plant communities using Rao quadratic entropy index, which included 233 plant species. Redundancy analyses and variation partitioning analyses were used to explore the relative influence of environmental and spatial factors on the above three facets of diversity, at the alpha and beta scales. We found that soil, climate, topography and spatial structures (principal coordinates of neighbor matrices) were significantly correlated with TD, FD and PD at both alpha and beta scales, implying that these diversity patterns are shaped by contemporary environment and spatial processes together. However, we also found that alpha diversity was predominantly regulated by spatial structure, whereas beta diversity was largely determined by environmental variables. Among environmental factors, TD was most strongly correlated with climatic factors at the alpha scale, while with soil factors at the beta scale. FD was only significantly correlated with soil factors at the alpha scale, but with altitude, soil and climatic factors at the beta scale. In contrast, PD was more strongly correlated with altitude at the alpha scale, but with soil factors at the beta scale. Environment and space explained a smaller portion of variance in PD than in TD and FD. These results provide robust evidence that the ecological drivers of biodiversity differ among different scales and facets of diversity. Future research that focuses on the comparisons among TD, FD and PD would likely provide new insights into elucidating the underlying community assembly.
bibliographic citation: Wang et al. (2019) Different ecological processes determined the alpha and beta components of taxonomic, functional, and phylogenetic diversity for plant communities in dryland regions of Northwest China. PeerJ 6:e6220 https://doi.org/10.7717/peerj.6220
date submitted: 2018-06-10
date accepted: 2018-12-05
issued: 2019-01-10
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Wang
  given name: Jianming
author list: Agent
  family name: Chen
  given name: Chen
author list: Agent
  family name: Li
  given name: Jingwen
author list: Agent
  family name: Feng
  given name: Yiming
author list: Agent
  family name: Lu
  given name: Qi
doi: 10.7717/peerj.6220
volume: 6
issn: 2167-8359
publication name: PeerJ
publication date: 2019-01-10
copyright: © 2019 Wang et al.
attribution name: Wang et al.

Aridity and land use negatively influence a dominant species' upper critical thermal limits
type: item
type: AcademicArticle
description: Understanding the physiological tolerances of ectotherms, such as thermal limits, is important in predicting biotic responses to climate change. However, it is even more important to examine these impacts alongside those from other landscape changes: such as the reduction of native vegetation cover, landscape fragmentation and changes in land use intensity (LUI). Here, we integrate the observed thermal limits of the dominant and ubiquitous meat ant Iridomyrmex purpureus across climate (aridity), land cover and land use gradients spanning 270 km in length and 840 m in altitude across northern New South Wales, Australia. Meat ants were chosen for study as they are ecosystem engineers and changes in their populations may result in a cascade of changes in the populations of other species. When we assessed critical thermal maximum temperatures (CTmax) of meat ants in relation to the environmental gradients we found little influence of climate (aridity) but that CTmax decreased as LUI increased. We found no overall correlation between CTmax and CTmin. We did however find that tolerance to warming was lower for ants sampled from more arid locations. Our findings suggest that as LUI and aridification increase, the physiological resilience of I. purpureus will decline. A reduction in physiological resilience may lead to a reduction in the ecosystem service provision that these populations provide throughout their distribution.
format: application/pdf
format: text/html
creator: Nigel R. Andrew
creator: Cara Miller
creator: Graham Hall
creator: Zac Hemmings
creator: Ian Oliver
subject: Ecology
subject: Entomology
subject: Zoology
subject: Climate Change Biology
description: doi:10.7717/peerj.6252
publisher: PeerJ Inc.
rights: © 2019 Andrew et al.
abstract: Understanding the physiological tolerances of ectotherms, such as thermal limits, is important in predicting biotic responses to climate change. However, it is even more important to examine these impacts alongside those from other landscape changes: such as the reduction of native vegetation cover, landscape fragmentation and changes in land use intensity (LUI). Here, we integrate the observed thermal limits of the dominant and ubiquitous meat ant Iridomyrmex purpureus across climate (aridity), land cover and land use gradients spanning 270 km in length and 840 m in altitude across northern New South Wales, Australia. Meat ants were chosen for study as they are ecosystem engineers and changes in their populations may result in a cascade of changes in the populations of other species. When we assessed critical thermal maximum temperatures (CTmax) of meat ants in relation to the environmental gradients we found little influence of climate (aridity) but that CTmax decreased as LUI increased. We found no overall correlation between CTmax and CTmin. We did however find that tolerance to warming was lower for ants sampled from more arid locations. Our findings suggest that as LUI and aridification increase, the physiological resilience of I. purpureus will decline. A reduction in physiological resilience may lead to a reduction in the ecosystem service provision that these populations provide throughout their distribution.
bibliographic citation: Andrew et al. (2019) Aridity and land use negatively influence a dominant species' upper critical thermal limits. PeerJ 6:e6252 https://doi.org/10.7717/peerj.6252
date submitted: 2018-04-11
date accepted: 2018-12-10
issued: 2019-01-10
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Andrew
  given name: Nigel R.
author list: Agent
  family name: Miller
  given name: Cara
author list: Agent
  family name: Hall
  given name: Graham
author list: Agent
  family name: Hemmings
  given name: Zac
author list: Agent
  family name: Oliver
  given name: Ian
doi: 10.7717/peerj.6252
volume: 6
issn: 2167-8359
publication name: PeerJ
publication date: 2019-01-10
copyright: © 2019 Andrew et al.
attribution name: Andrew et al.

MicroRNA-705 regulates the differentiation of mouse mandible bone marrow mesenchymal stem cells
type: item
type: AcademicArticle
description: The craniofacial skeleton is the foundation of most stomatological treatments, including prosthodontics and maxillofacial surgery. Although histologically similar to the appendicular skeleton, the craniofacial skeleton manifests many unique properties in response to external stimuli and signals. However, the mandibular or maxillary bone marrow mesenchyme, which is the intrinsic foundation of the functions of craniofacial skeleton, has not been well studied, and its homeostasis mechanism remains elusive. Osteoporosis is a systemic disease that affects all skeletons and is characterized by bone mass loss. Osteoporotic bone marrow mesenchymal stem cells (BMMSCs) exhibit disturbed homeostasis and distorted lineage commitment. Many reports have shown that microRNAs (miRNAs) play important roles in regulating MSCs homeostasis. Here, to obtain a better understanding of mandibular bone marrow MSCs homeostasis, we isolated and cultured mandible marrow MSCs from mouse mandibles. Using miR-705 mimics and an inhibitor, we demonstrated that miR-705 played a vital role in shifting the mandibular MSCs lineage commitment in vitro. Utilizing an osteoporosis mouse model, we demonstrated that MSCs from ovariectomized (OVX) mouse mandibular bone marrow exhibited impaired osteogenic and excessive adipogenic differentiation. miR-705 was found overexpressed in OVX mandibular MSCs. The knock down of miR-705 in vitro partially attenuated the differentiation disorder of the OVX mandibular MSCs by upregulating the expression of osteogenic marker genes but suppressing adipogenic genes. Taken together, our findings provide a better understanding of the homeostasis mechanism of mandibular BMMSCs and a novel potential therapeutic target for treating mandibular osteoporosis.
format: application/pdf
format: text/html
creator: Xiao Hong Yang
creator: Kun Yang
creator: Yu Lin An
creator: Li Bo Wang
creator: Guo Luo
creator: Xiao Hua Hu
subject: Cell Biology
subject: Genetics
subject: Molecular Biology
subject: Dentistry
description: doi:10.7717/peerj.6279
publisher: PeerJ Inc.
rights: © 2019 Yang et al.
abstract: The craniofacial skeleton is the foundation of most stomatological treatments, including prosthodontics and maxillofacial surgery. Although histologically similar to the appendicular skeleton, the craniofacial skeleton manifests many unique properties in response to external stimuli and signals. However, the mandibular or maxillary bone marrow mesenchyme, which is the intrinsic foundation of the functions of craniofacial skeleton, has not been well studied, and its homeostasis mechanism remains elusive. Osteoporosis is a systemic disease that affects all skeletons and is characterized by bone mass loss. Osteoporotic bone marrow mesenchymal stem cells (BMMSCs) exhibit disturbed homeostasis and distorted lineage commitment. Many reports have shown that microRNAs (miRNAs) play important roles in regulating MSCs homeostasis. Here, to obtain a better understanding of mandibular bone marrow MSCs homeostasis, we isolated and cultured mandible marrow MSCs from mouse mandibles. Using miR-705 mimics and an inhibitor, we demonstrated that miR-705 played a vital role in shifting the mandibular MSCs lineage commitment in vitro. Utilizing an osteoporosis mouse model, we demonstrated that MSCs from ovariectomized (OVX) mouse mandibular bone marrow exhibited impaired osteogenic and excessive adipogenic differentiation. miR-705 was found overexpressed in OVX mandibular MSCs. The knock down of miR-705 in vitro partially attenuated the differentiation disorder of the OVX mandibular MSCs by upregulating the expression of osteogenic marker genes but suppressing adipogenic genes. Taken together, our findings provide a better understanding of the homeostasis mechanism of mandibular BMMSCs and a novel potential therapeutic target for treating mandibular osteoporosis.
bibliographic citation: Yang et al. (2019) MicroRNA-705 regulates the differentiation of mouse mandible bone marrow mesenchymal stem cells. PeerJ 7:e6279 https://doi.org/10.7717/peerj.6279
date submitted: 2018-02-24
date accepted: 2018-11-12
issued: 2019-01-10
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Yang
  given name: Xiao Hong
author list: Agent
  family name: Yang
  given name: Kun
author list: Agent
  family name: An
  given name: Yu Lin
author list: Agent
  family name: Wang
  given name: Li Bo
author list: Agent
  family name: Luo
  given name: Guo
author list: Agent
  family name: Hu
  given name: Xiao Hua
doi: 10.7717/peerj.6279
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-01-10
copyright: ©2019 Yang et al.
attribution name: Yang et al.

Influence of substrate types and morphological traits on movement behavior in a toad and newt species
type: item
type: AcademicArticle
description: Background Inter-patch movements may lead to genetic mixing, decreasing both inbreeding and population extinction risks, and is hence a crucial aspect of amphibian meta-population dynamics. Traveling through heterogeneous landscapes might be particularly risky for amphibians. Understanding how these species perceive their environment and how they move in heterogeneous habitats is an essential step in explaining metapopulation dynamics and can be important for predicting species’ responses to climate change and for conservation policy and management. Methods Using an experimental approach, the present study focused on the movement behavior (crossing speed and number of stops) on different substrates mimicking landscape components (human-made and natural substrates) in two amphibian species contrasting in locomotion mode: the common toad (Bufo bufo), a hopping and burrowing anuran and the marbled newt (Triturus marmoratus), a walking salamander. We tested the hypothesis that species reaction to substrate is dependent on specific ecological requirements or locomotion modes because of morphological and behavioral differences. Results In both species, substrate type influenced individual crossing speed, with individuals moving faster on soil than on concrete substrate. We also demonstrated that long-legged individuals moved faster than individuals with short legs. In both species, the number of stops was higher in females than in males. In common toads, the number of stops did not vary between substrates tested, whereas in marbled newts the number of stops was higher on concrete than on soil substrate. Discussion We highlighted that concrete substrate (mimicking roads) negatively affect the crossing speed of both studied species, with an effect potentially higher in marbled newts. Our findings corroborate negative effects of such heterogeneous landscapes on movement behavior of two amphibian species, which may have implications for the dynamics of metapopulations.
format: application/pdf
format: text/html
creator: Audrey Trochet
creator: Hugo Le Chevalier
creator: Olivier Calvez
creator: Alexandre Ribéron
creator: Romain Bertrand
creator: Simon Blanchet
subject: Animal Behavior
subject: Biodiversity
subject: Conservation Biology
description: doi:10.7717/peerj.6053
publisher: PeerJ Inc.
rights: © 2019 Trochet et al.
abstract: Background Inter-patch movements may lead to genetic mixing, decreasing both inbreeding and population extinction risks, and is hence a crucial aspect of amphibian meta-population dynamics. Traveling through heterogeneous landscapes might be particularly risky for amphibians. Understanding how these species perceive their environment and how they move in heterogeneous habitats is an essential step in explaining metapopulation dynamics and can be important for predicting species’ responses to climate change and for conservation policy and management. Methods Using an experimental approach, the present study focused on the movement behavior (crossing speed and number of stops) on different substrates mimicking landscape components (human-made and natural substrates) in two amphibian species contrasting in locomotion mode: the common toad (Bufo bufo), a hopping and burrowing anuran and the marbled newt (Triturus marmoratus), a walking salamander. We tested the hypothesis that species reaction to substrate is dependent on specific ecological requirements or locomotion modes because of morphological and behavioral differences. Results In both species, substrate type influenced individual crossing speed, with individuals moving faster on soil than on concrete substrate. We also demonstrated that long-legged individuals moved faster than individuals with short legs. In both species, the number of stops was higher in females than in males. In common toads, the number of stops did not vary between substrates tested, whereas in marbled newts the number of stops was higher on concrete than on soil substrate. Discussion We highlighted that concrete substrate (mimicking roads) negatively affect the crossing speed of both studied species, with an effect potentially higher in marbled newts. Our findings corroborate negative effects of such heterogeneous landscapes on movement behavior of two amphibian species, which may have implications for the dynamics of metapopulations.
bibliographic citation: Trochet et al. (2019) Influence of substrate types and morphological traits on movement behavior in a toad and newt species. PeerJ 6:e6053 https://doi.org/10.7717/peerj.6053
date submitted: 2018-07-02
date accepted: 2018-10-29
issued: 2019-01-09
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Trochet
  given name: Audrey
author list: Agent
  family name: Le Chevalier
  given name: Hugo
author list: Agent
  family name: Calvez
  given name: Olivier
author list: Agent
  family name: Ribéron
  given name: Alexandre
author list: Agent
  family name: Bertrand
  given name: Romain
author list: Agent
  family name: Blanchet
  given name: Simon
doi: 10.7717/peerj.6053
volume: 6
issn: 2167-8359
publication name: PeerJ
publication date: 2019-01-09
copyright: © 2019 Trochet et al.
attribution name: Trochet et al.

Amelioration of drought effects in wheat and cucumber by the combined application of super absorbent polymer and potential biofertilizer
type: item
type: AcademicArticle
description: Biofertilizer is a good substitute for chemical fertilizer in sustainable agriculture, but its effects are often hindered by drought stress. Super absorbent polymer (SAP), showing good capacity of water absorption and retention, can increase soil moisture. However, limited information is available about the efficiency of biofertilizer amended with SAP. This study was conducted to investigate the effects of synergistic application of SAP and biofertilizers (Paenibacillus beijingensis BJ-18 and Bacillus sp. L-56) on plant growth, including wheat and cucumber. Potted soil was treated with different fertilizer combinations (SAP, BJ-18 biofertilizer, L-56 biofertilizer, BJ-18 + SAP, L-56 + SAP), and pot experiment was carried out to explore its effects on viability of inoculants, seed germination rate, plant physiological and biochemical parameters, and expression pattern of stress-related genes under drought condition. At day 29 after sowing, the highest viability of strain P. beijingensis BJ-18 (264 copies ng−1 gDNA) was observed in BJ-18 + SAP treatment group of wheat rhizosphere soil, while that of strain Bacillus sp. L-56 (331 copies ng−1 gDNA) was observed in the L-56 + SAP treatment group of cucumber rhizosphere soil. In addition, both biofertilizers amended with SAP could promote germination rate of seeds (wheat and cucumber), plant growth, soil fertility (urease, sucrose, and dehydrogenase activities). Quantitative real-time PCR analysis showed that biofertilizer + SAP significantly down-regulated the expression levels of genes involved in ROS scavenging (TaCAT, CsCAT, TaAPX, and CsAPX2), ethylene biosynthesis (TaACO2, CsACO1, and CsACS1), stress response (TaDHN3, TaLEA, and CsLEA11), salicylic acid (TaPR1-1a and CsPR1-1a), and transcription activation (TaNAC2D and CsNAC35) in plants under drought stress. These results suggest that SAP addition in biofertilizer is a good tactic for enhancing the efficiency of biofertilizer, which is beneficial for plants in resp…
format: application/pdf
format: text/html
creator: Yongbin Li
creator: Haowen Shi
creator: Haowei Zhang
creator: Sanfeng Chen
subject: Agricultural Science
subject: Biodiversity
subject: Microbiology
subject: Plant Science
subject: Soil Science
description: doi:10.7717/peerj.6073
publisher: PeerJ Inc.
rights: © 2019 Li et al.
abstract: Biofertilizer is a good substitute for chemical fertilizer in sustainable agriculture, but its effects are often hindered by drought stress. Super absorbent polymer (SAP), showing good capacity of water absorption and retention, can increase soil moisture. However, limited information is available about the efficiency of biofertilizer amended with SAP. This study was conducted to investigate the effects of synergistic application of SAP and biofertilizers (Paenibacillus beijingensis BJ-18 and Bacillus sp. L-56) on plant growth, including wheat and cucumber. Potted soil was treated with different fertilizer combinations (SAP, BJ-18 biofertilizer, L-56 biofertilizer, BJ-18 + SAP, L-56 + SAP), and pot experiment was carried out to explore its effects on viability of inoculants, seed germination rate, plant physiological and biochemical parameters, and expression pattern of stress-related genes under drought condition. At day 29 after sowing, the highest viability of strain P. beijingensis BJ-18 (264 copies ng−1 gDNA) was observed in BJ-18 + SAP treatment group of wheat rhizosphere soil, while that of strain Bacillus sp. L-56 (331 copies ng−1 gDNA) was observed in the L-56 + SAP treatment group of cucumber rhizosphere soil. In addition, both biofertilizers amended with SAP could promote germination rate of seeds (wheat and cucumber), plant growth, soil fertility (urease, sucrose, and dehydrogenase activities). Quantitative real-time PCR analysis showed that biofertilizer + SAP significantly down-regulated the expression levels of genes involved in ROS scavenging (TaCAT, CsCAT, TaAPX, and CsAPX2), ethylene biosynthesis (TaACO2, CsACO1, and CsACS1), stress response (TaDHN3, TaLEA, and CsLEA11), salicylic acid (TaPR1-1a and CsPR1-1a), and transcription activation (TaNAC2D and CsNAC35) in plants under drought stress. These results suggest that SAP addition in biofertilizer is a good tactic for enhancing the efficiency of biofertilizer, which is beneficial for plants in resp…
bibliographic citation: Li et al. (2019) Amelioration of drought effects in wheat and cucumber by the combined application of super absorbent polymer and potential biofertilizer. PeerJ 7:e6073 https://doi.org/10.7717/peerj.6073
date submitted: 2018-09-12
date accepted: 2018-11-06
issued: 2019-01-09
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Li
  given name: Yongbin
author list: Agent
  family name: Shi
  given name: Haowen
author list: Agent
  family name: Zhang
  given name: Haowei
author list: Agent
  family name: Chen
  given name: Sanfeng
doi: 10.7717/peerj.6073
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-01-09
copyright: ©2019 Li et al.
attribution name: Li et al.

Post-mortem detection of six human herpesviruses (HSV-1, HSV-2, VZV, EBV, CMV, HHV-6) in trigeminal and facial nerve ganglia by PCR
type: item
type: AcademicArticle
description: Background Among over 100 types of Herpesviridae viruses, eight can infect humans: herpes simplex viruses (HSV-1, HSV-2), varicella zoster virus (VZV), cytomegalovirus (CMV), Epstein-Barr virus (EBV), and human herpesviruses 6, 7, and 8 (HHV-6, HHV-7, HHV-8). After initial infection, the viruses remain latent for the lifetime of the host. The aim of this study was to determine the distribution of six different herpesviruses: HSV-1, HSV-2, VZV, EBV, CMV, and HHV-6 in trigeminal and facial nerve ganglia among a random group of Polish population. Methods The studied group consisted of 47 individuals (40 male, seven female); mean age of 47.4 ± 16.5 years) who died of independent causes (suicide, traffic accident, and poisoning, among others). Bilateral trigeminal and facial nerve ganglia of each cadaver were collected during the autopsy. Herpesviruses were detected using multiplex polymerase chain reaction technique. Results Herpesviruses were found in trigeminal and/or facial ganglia in 30/47 (63.8%) of cadavers. HHV-6 was the most prevalent of the herpesviruses and was found in nearly half of cadavers (n = 22; 46.8%), followed by HSV-1 (n = 7; 14.9%), VZV (n = 4; 8.5%), EBV (n = 4; 8.5%), HSV-2 (n = 2; 4.3%), and CMV (n = 1; 2.1%). Facial nerve ganglia (n = 23; 48.9%) were more often infected than trigeminal ganglia (n = 13; 27.7%). Discussion The results of this study have revealed a common presence of the herpesviruses in trigeminal and facial nerve ganglia among a random group of Polish population. Furthermore, the data also demonstrate simultaneous infection of the ganglia with different herpesviruses. This study has contributed to the knowledge of prevalence and localization of herpesviruses in different structures of the nervous system.
format: application/pdf
format: text/html
creator: Iwona Ptaszyńska-Sarosiek
creator: Justyna Dunaj
creator: Agata Zajkowska
creator: Anna Niemcunowicz-Janica
creator: Monika Król
creator: Sławomir Pancewicz
creator: Joanna Zajkowska
subject: Epidemiology
subject: Infectious Diseases
subject: Neurology
subject: Pathology
description: doi:10.7717/peerj.6095
publisher: PeerJ Inc.
rights: © 2019 Ptaszyńska-Sarosiek et al.
abstract: Background Among over 100 types of Herpesviridae viruses, eight can infect humans: herpes simplex viruses (HSV-1, HSV-2), varicella zoster virus (VZV), cytomegalovirus (CMV), Epstein-Barr virus (EBV), and human herpesviruses 6, 7, and 8 (HHV-6, HHV-7, HHV-8). After initial infection, the viruses remain latent for the lifetime of the host. The aim of this study was to determine the distribution of six different herpesviruses: HSV-1, HSV-2, VZV, EBV, CMV, and HHV-6 in trigeminal and facial nerve ganglia among a random group of Polish population. Methods The studied group consisted of 47 individuals (40 male, seven female); mean age of 47.4 ± 16.5 years) who died of independent causes (suicide, traffic accident, and poisoning, among others). Bilateral trigeminal and facial nerve ganglia of each cadaver were collected during the autopsy. Herpesviruses were detected using multiplex polymerase chain reaction technique. Results Herpesviruses were found in trigeminal and/or facial ganglia in 30/47 (63.8%) of cadavers. HHV-6 was the most prevalent of the herpesviruses and was found in nearly half of cadavers (n = 22; 46.8%), followed by HSV-1 (n = 7; 14.9%), VZV (n = 4; 8.5%), EBV (n = 4; 8.5%), HSV-2 (n = 2; 4.3%), and CMV (n = 1; 2.1%). Facial nerve ganglia (n = 23; 48.9%) were more often infected than trigeminal ganglia (n = 13; 27.7%). Discussion The results of this study have revealed a common presence of the herpesviruses in trigeminal and facial nerve ganglia among a random group of Polish population. Furthermore, the data also demonstrate simultaneous infection of the ganglia with different herpesviruses. This study has contributed to the knowledge of prevalence and localization of herpesviruses in different structures of the nervous system.
bibliographic citation: Ptaszyńska-Sarosiek et al. (2019) Post-mortem detection of six human herpesviruses (HSV-1, HSV-2, VZV, EBV, CMV, HHV-6) in trigeminal and facial nerve ganglia by PCR. PeerJ 6:e6095 https://doi.org/10.7717/peerj.6095
date submitted: 2018-07-13
date accepted: 2018-11-10
issued: 2019-01-09
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Ptaszyńska-Sarosiek
  given name: Iwona
author list: Agent
  family name: Dunaj
  given name: Justyna
author list: Agent
  family name: Zajkowska
  given name: Agata
author list: Agent
  family name: Niemcunowicz-Janica
  given name: Anna
author list: Agent
  family name: Król
  given name: Monika
author list: Agent
  family name: Pancewicz
  given name: Sławomir
author list: Agent
  family name: Zajkowska
  given name: Joanna
doi: 10.7717/peerj.6095
volume: 6
issn: 2167-8359
publication name: PeerJ
publication date: 2019-01-09
copyright: © 2019 Ptaszyńska-Sarosiek et al.
attribution name: Ptaszyńska-Sarosiek et al.

The gut microbiome correlates with conspecific aggression in a small population of rescued dogs (Canis familiaris)
type: item
type: AcademicArticle
description: Aggression is a serious behavioral disorder in domestic dogs that endangers both dogs and humans. The underlying causes of canine aggression are poorly resolved and require illumination to ensure effective therapy. Recent research links the compositional diversity of the gut microbiome to behavioral and psychological regulation in other mammals, such as mice and humans. Given these observations, we hypothesized that the composition of the canine gut microbiome could associate with aggression. We analyzed fecal microbiome samples collected from a small population of pit bull type dogs seized from a dogfighting organization. This population included 21 dogs that displayed conspecific aggressive behaviors and 10 that did not. Beta-diversity analyses support an association between gut microbiome structure and dog aggression. Additionally, we used a phylogenetic approach to resolve specific clades of gut bacteria that stratify aggressive and non-aggressive dogs, including clades within Lactobacillus, Dorea, Blautia, Turicibacter, and Bacteroides. Several of these taxa have been implicated in modulating mammalian behavior as well as gastrointestinal disease states. Although sample size limits this study, our findings indicate that gut microorganisms are linked to dog aggression and point to an aggression-associated physiological state that interacts with the gut microbiome. These results also indicate that the gut microbiome may be useful for diagnosing aggressive behaviors prior to their manifestation and potentially discerning cryptic etiologies of aggression.
format: application/pdf
format: text/html
creator: Nicole S. Kirchoff
creator: Monique A.R. Udell
creator: Thomas J. Sharpton
subject: Animal Behavior
subject: Bioinformatics
subject: Microbiology
description: doi:10.7717/peerj.6103
publisher: PeerJ Inc.
rights: © 2019 Kirchoff et al.
abstract: Aggression is a serious behavioral disorder in domestic dogs that endangers both dogs and humans. The underlying causes of canine aggression are poorly resolved and require illumination to ensure effective therapy. Recent research links the compositional diversity of the gut microbiome to behavioral and psychological regulation in other mammals, such as mice and humans. Given these observations, we hypothesized that the composition of the canine gut microbiome could associate with aggression. We analyzed fecal microbiome samples collected from a small population of pit bull type dogs seized from a dogfighting organization. This population included 21 dogs that displayed conspecific aggressive behaviors and 10 that did not. Beta-diversity analyses support an association between gut microbiome structure and dog aggression. Additionally, we used a phylogenetic approach to resolve specific clades of gut bacteria that stratify aggressive and non-aggressive dogs, including clades within Lactobacillus, Dorea, Blautia, Turicibacter, and Bacteroides. Several of these taxa have been implicated in modulating mammalian behavior as well as gastrointestinal disease states. Although sample size limits this study, our findings indicate that gut microorganisms are linked to dog aggression and point to an aggression-associated physiological state that interacts with the gut microbiome. These results also indicate that the gut microbiome may be useful for diagnosing aggressive behaviors prior to their manifestation and potentially discerning cryptic etiologies of aggression.
bibliographic citation: Kirchoff et al. (2019) The gut microbiome correlates with conspecific aggression in a small population of rescued dogs (Canis familiaris). PeerJ 7:e6103 https://doi.org/10.7717/peerj.6103
date submitted: 2018-06-12
date accepted: 2018-11-13
issued: 2019-01-09
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Kirchoff
  given name: Nicole S.
author list: Agent
  family name: Udell
  given name: Monique A.R.
author list: Agent
  family name: Sharpton
  given name: Thomas J.
doi: 10.7717/peerj.6103
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-01-09
copyright: ©2019 Kirchoff et al.
attribution name: Kirchoff et al.

Efficient generation of human primordial germ cell-like cells from pluripotent stem cells in a methylcellulose-based 3D system at large scale
type: item
type: AcademicArticle
description: Background The mechanisms underlying human germ cell development and infertility remain largely unknown due to bioethical issues and the shortage of experimental materials. Therefore, an effective in vitro induction system of human primordial germ-like cells (hPGCLCs) from human pluripotent stem cells (hPSC) is in high demand. The current strategies used for the generation of hPGCLCs are not only costly but also difficult to perform at a large scale, thereby posing barriers to further research. In this study, we attempted to solve these problems by providing a new 3D culture system for hPGCLC differentiation. Methods The efficiency and relative yield of a methylcellulose (MC)-based 3D hPGCLC induction system were first compared with that of a conventional U96 system. Then, we examined the gene expression of germ cell marker genes and the key epigenetic modifications of the EpCAM-/INTEGRINα6-high cells from the 3D MC induction system and the U96 system via quantitative PCR and immunofluorescence. Finally, the reliability of the MC-based 3D hPGCLC induction system was evaluated via the generation of induced pluripotent stem cells (iPSCs) from the testicular cells of one patient with obstructive azoospermia (OA) and followed by the subsequent differentiation of iPSCs into the germ cell lineage. Results In the present study, we demonstrated that the 3D MC induction system combined with low-cell attachment plates facilitated the generation of hPGCLCs at a large scale. We found that the hPGCLCs generated via the MC system shared similar characteristics to that via the U96 system in terms of the gene expression profiles, germ cell-specific markers, epigenetic modification states and cellular states. In addition, hPGCLCs from iPSCs derived from one OA patient were generated with high efficiency via the present 3D MC induction system. Discussion The in vitro induction of hPGCLCs from human embryonic stem cells (hESCs)/human induced pluripotent stem cells (hiPSCs) has signifi…
format: application/pdf
format: text/html
creator: Xiaoman Wang
creator: Tingting Liao
creator: Cong Wan
creator: Xiaoyu Yang
creator: Jiexiang Zhao
creator: Rui Fu
creator: Zhaokai Yao
creator: Yaping Huang
creator: Yujia Shi
creator: Gang Chang
creator: Yi Zheng
creator: Fang Luo
creator: Zhaoting Liu
creator: Yu Wang
creator: Xinliang Mao
creator: Xiao-Yang Zhao
subject: Cell Biology
subject: Developmental Biology
subject: Molecular Biology
description: doi:10.7717/peerj.6143
publisher: PeerJ Inc.
rights: © 2019 Wang et al.
abstract: Background The mechanisms underlying human germ cell development and infertility remain largely unknown due to bioethical issues and the shortage of experimental materials. Therefore, an effective in vitro induction system of human primordial germ-like cells (hPGCLCs) from human pluripotent stem cells (hPSC) is in high demand. The current strategies used for the generation of hPGCLCs are not only costly but also difficult to perform at a large scale, thereby posing barriers to further research. In this study, we attempted to solve these problems by providing a new 3D culture system for hPGCLC differentiation. Methods The efficiency and relative yield of a methylcellulose (MC)-based 3D hPGCLC induction system were first compared with that of a conventional U96 system. Then, we examined the gene expression of germ cell marker genes and the key epigenetic modifications of the EpCAM-/INTEGRINα6-high cells from the 3D MC induction system and the U96 system via quantitative PCR and immunofluorescence. Finally, the reliability of the MC-based 3D hPGCLC induction system was evaluated via the generation of induced pluripotent stem cells (iPSCs) from the testicular cells of one patient with obstructive azoospermia (OA) and followed by the subsequent differentiation of iPSCs into the germ cell lineage. Results In the present study, we demonstrated that the 3D MC induction system combined with low-cell attachment plates facilitated the generation of hPGCLCs at a large scale. We found that the hPGCLCs generated via the MC system shared similar characteristics to that via the U96 system in terms of the gene expression profiles, germ cell-specific markers, epigenetic modification states and cellular states. In addition, hPGCLCs from iPSCs derived from one OA patient were generated with high efficiency via the present 3D MC induction system. Discussion The in vitro induction of hPGCLCs from human embryonic stem cells (hESCs)/human induced pluripotent stem cells (hiPSCs) has signifi…
bibliographic citation: Wang et al. (2019) Efficient generation of human primordial germ cell-like cells from pluripotent stem cells in a methylcellulose-based 3D system at large scale. PeerJ 6:e6143 https://doi.org/10.7717/peerj.6143
date submitted: 2018-07-23
date accepted: 2018-11-20
issued: 2019-01-09
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Wang
  given name: Xiaoman
author list: Agent
  family name: Liao
  given name: Tingting
author list: Agent
  family name: Wan
  given name: Cong
author list: Agent
  family name: Yang
  given name: Xiaoyu
author list: Agent
  family name: Zhao
  given name: Jiexiang
author list: Agent
  family name: Fu
  given name: Rui
author list: Agent
  family name: Yao
  given name: Zhaokai
author list: Agent
  family name: Huang
  given name: Yaping
author list: Agent
  family name: Shi
  given name: Yujia
author list: Agent
  family name: Chang
  given name: Gang
author list: Agent
  family name: Zheng
  given name: Yi
author list: Agent
  family name: Luo
  given name: Fang
author list: Agent
  family name: Liu
  given name: Zhaoting
author list: Agent
  family name: Wang
  given name: Yu
author list: Agent
  family name: Mao
  given name: Xinliang
author list: Agent
  family name: Zhao
  given name: Xiao-Yang
doi: 10.7717/peerj.6143
volume: 6
issn: 2167-8359
publication name: PeerJ
publication date: 2019-01-09
copyright: © 2019 Wang et al.
attribution name: Wang et al.

Changes in bone density and bone quality caused by single fasting for 96 hours in rats
type: item
type: AcademicArticle
description: Background Young women occasionally engage in dietary restrictions accompanied by fasting for the purpose of losing weight, but such restrictions have various effects on body functions. The recent increase in the number of people suffering from osteoporosis has become a major social problem mainly in industrialized countries.Therefore, we think it is important to understand the effects of fasting on bone vulnerability, especially to bone quality. Methods Animals used male Wister rats weighing 130 g (6 weeks of age), and were divided into a control group (n = 5) and a fasting group (n = 6). The experimental period was 14 days, the control group had ad libitum food throughout the experimental period, the fasted group was fasted for 4 days, and than, had ad libitum food for 10 days. In this study, parameters related to bone fragility due to three-dimensional bone architecture were determined on Contrast enhanced micro-CT images of the lumbar spine and were used as a method for the evaluation of bone quality. In addition, a time-course observation of each individual was carried out during the fasting period and later upon resuming food intake. Cross-sectional images of all vertebrae were obtained from radiographic computed tomography and were analyzed by using Latheta software ver. 3.0 (Hitachi-Aloka Medical, Nagasaki, Japan). The region of interest that was misrecognized in each cross-sectional image was made consistent with the anatomical structure by carrying out corrections manually and by identifying the cortical bone areas and cancellous bone areas. Results Our findings showed that while single fasting for 96 h did not cause any major change in the macroscopic morphology of bone, it caused a marked decrease in bone density. In addition, the minimum cross-sectional moment, which indicated the “strength against bending” as well as the polar moment that indicated the “strength against torsion” were both lower than in non-fasted rats. Further, after resumption of feed…
format: application/pdf
format: text/html
creator: Yuko Hisatomi
creator: Kenji Kugino
subject: Nutrition
subject: Orthopedics
subject: Women’s Health
description: doi:10.7717/peerj.6161
publisher: PeerJ Inc.
rights: © 2019 Hisatomi and Kugino
abstract: Background Young women occasionally engage in dietary restrictions accompanied by fasting for the purpose of losing weight, but such restrictions have various effects on body functions. The recent increase in the number of people suffering from osteoporosis has become a major social problem mainly in industrialized countries.Therefore, we think it is important to understand the effects of fasting on bone vulnerability, especially to bone quality. Methods Animals used male Wister rats weighing 130 g (6 weeks of age), and were divided into a control group (n = 5) and a fasting group (n = 6). The experimental period was 14 days, the control group had ad libitum food throughout the experimental period, the fasted group was fasted for 4 days, and than, had ad libitum food for 10 days. In this study, parameters related to bone fragility due to three-dimensional bone architecture were determined on Contrast enhanced micro-CT images of the lumbar spine and were used as a method for the evaluation of bone quality. In addition, a time-course observation of each individual was carried out during the fasting period and later upon resuming food intake. Cross-sectional images of all vertebrae were obtained from radiographic computed tomography and were analyzed by using Latheta software ver. 3.0 (Hitachi-Aloka Medical, Nagasaki, Japan). The region of interest that was misrecognized in each cross-sectional image was made consistent with the anatomical structure by carrying out corrections manually and by identifying the cortical bone areas and cancellous bone areas. Results Our findings showed that while single fasting for 96 h did not cause any major change in the macroscopic morphology of bone, it caused a marked decrease in bone density. In addition, the minimum cross-sectional moment, which indicated the “strength against bending” as well as the polar moment that indicated the “strength against torsion” were both lower than in non-fasted rats. Further, after resumption of feed…
bibliographic citation: Hisatomi et al. (2019) Changes in bone density and bone quality caused by single fasting for 96 hours in rats. PeerJ 6:e6161 https://doi.org/10.7717/peerj.6161
date submitted: 2018-07-13
date accepted: 2018-11-22
issued: 2019-01-09
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Hisatomi
  given name: Yuko
author list: Agent
  family name: Kugino
  given name: Kenji
doi: 10.7717/peerj.6161
volume: 6
issn: 2167-8359
publication name: PeerJ
publication date: 2019-01-09
copyright: © 2019 Hisatomi and Kugino
attribution name: Hisatomi and Kugino

Microbiota variations in Culex nigripalpus disease vector mosquito of West Nile virus and Saint Louis Encephalitis from different geographic origins
type: item
type: AcademicArticle
description: Although mosquito microbiota are known to influence reproduction, nutrition, disease transmission, and pesticide resistance, the relationship between host-associated microbial community composition and geographical location is poorly understood. To begin addressing this knowledge gap, we characterized microbiota associated with adult females of Culex nigripalpus mosquito vectors of Saint Louis Encephalitis and West Nile viruses sampled from three locations in Florida (Vero Beach, Palmetto Inland, and Palmetto Coast). High-throughput sequencing of PCR-amplified 16S rRNA genes demonstrated significant differences among microbial communities of mosquitoes sampled from the three locations. Mosquitoes from Vero Beach (east coast Florida) were dominated by uncultivated Asaia sp. (Alphaproteobacteria), whereas microbiota associated with mosquitoes collected from two mosquito populations at Palmetto (west coast Florida) sites were dominated by uncultured Spironema culicis (Spirochaetes), Salinisphaera hydrothermalis (Gammaproteobacteria), Spiroplasma (Mollicutes), uncultured Enterobacteriaceae, Candidatus Megaira (Alphaproteobacteria; Rickettsiae), and Zymobacter (Gammaproteobacteria). The variation in taxonomic profiles of Cx. nigripalpus gut microbial communities, especially with respect to dominating taxa, is a potentially critical factor in understanding disease transmission and mosquito susceptibility to insecticides among different mosquito populations.
format: application/pdf
format: text/html
creator: Dagne Duguma
creator: Michael W. Hall
creator: Chelsea T. Smartt
creator: Mustapha Debboun
creator: Josh D. Neufeld
subject: Ecology
subject: Entomology
subject: Microbiology
subject: Infectious Diseases
subject: Public Health
description: doi:10.7717/peerj.6168
publisher: PeerJ Inc.
rights: © 2019 Duguma et al.
abstract: Although mosquito microbiota are known to influence reproduction, nutrition, disease transmission, and pesticide resistance, the relationship between host-associated microbial community composition and geographical location is poorly understood. To begin addressing this knowledge gap, we characterized microbiota associated with adult females of Culex nigripalpus mosquito vectors of Saint Louis Encephalitis and West Nile viruses sampled from three locations in Florida (Vero Beach, Palmetto Inland, and Palmetto Coast). High-throughput sequencing of PCR-amplified 16S rRNA genes demonstrated significant differences among microbial communities of mosquitoes sampled from the three locations. Mosquitoes from Vero Beach (east coast Florida) were dominated by uncultivated Asaia sp. (Alphaproteobacteria), whereas microbiota associated with mosquitoes collected from two mosquito populations at Palmetto (west coast Florida) sites were dominated by uncultured Spironema culicis (Spirochaetes), Salinisphaera hydrothermalis (Gammaproteobacteria), Spiroplasma (Mollicutes), uncultured Enterobacteriaceae, Candidatus Megaira (Alphaproteobacteria; Rickettsiae), and Zymobacter (Gammaproteobacteria). The variation in taxonomic profiles of Cx. nigripalpus gut microbial communities, especially with respect to dominating taxa, is a potentially critical factor in understanding disease transmission and mosquito susceptibility to insecticides among different mosquito populations.
bibliographic citation: Duguma et al. (2019) Microbiota variations in Culex nigripalpus disease vector mosquito of West Nile virus and Saint Louis Encephalitis from different geographic origins. PeerJ 6:e6168 https://doi.org/10.7717/peerj.6168
date submitted: 2018-05-04
date accepted: 2018-11-27
issued: 2019-01-09
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Duguma
  given name: Dagne
author list: Agent
  family name: Hall
  given name: Michael W.
author list: Agent
  family name: Smartt
  given name: Chelsea T.
author list: Agent
  family name: Debboun
  given name: Mustapha
author list: Agent
  family name: Neufeld
  given name: Josh D.
doi: 10.7717/peerj.6168
volume: 6
issn: 2167-8359
publication name: PeerJ
publication date: 2019-01-09
copyright: © 2019 Duguma et al.
attribution name: Duguma et al.

Whole-genome comparisons of Penicillium spp. reveals secondary metabolic gene clusters and candidate genes associated with fungal aggressiveness during apple fruit decay
type: item
type: AcademicArticle
description: Blue mold is a postharvest rot of pomaceous fruits caused by Penicillium expansum and a number of other Penicillium species. The genome of the highly aggressive P. expansum strain R19 was re-sequenced and analyzed together with the genome of the less aggressive P. solitum strain RS1. Whole genome scale similarities and differences were examined. A phylogenetic analysis of P. expansum, P. solitum, and several closely related Penicillium species revealed that the two pathogens isolated from decayed apple with blue mold symptoms are not each other’s closest relatives. Among a total of 10,560 and 10,672 protein coding sequences respectively, a comparative genomics analysis revealed 41 genes in P. expansum R19 and 43 genes in P. solitum RS1 that are unique to these two species. These genes may be associated with pome fruit–fungal interactions, subsequent decay processes, and mycotoxin accumulation. An intact patulin gene cluster consisting of 15 biosynthetic genes was identified in the patulin producing P. expansum strain R19, while only a remnant, seven-gene cluster was identified in the patulin-deficient P. solitum strain. However, P. solitum contained a large number of additional secondary metabolite gene clusters, indicating that this species has the potential capacity to produce an array of known as well as not-yet-identified products of possible toxicological or biotechnological interest.
format: application/pdf
format: text/html
creator: Guangxi Wu
creator: Wayne M. Jurick II
creator: Franz J. Lichtner
creator: Hui Peng
creator: Guohua Yin
creator: Verneta L. Gaskins
creator: Yanbin Yin
creator: Sui-Sheng Hua
creator: Kari A. Peter
creator: Joan W. Bennett
subject: Agricultural Science
subject: Genomics
subject: Mycology
subject: Plant Science
description: doi:10.7717/peerj.6170
publisher: PeerJ Inc.
rights: © 2019 Wu et al.
abstract: Blue mold is a postharvest rot of pomaceous fruits caused by Penicillium expansum and a number of other Penicillium species. The genome of the highly aggressive P. expansum strain R19 was re-sequenced and analyzed together with the genome of the less aggressive P. solitum strain RS1. Whole genome scale similarities and differences were examined. A phylogenetic analysis of P. expansum, P. solitum, and several closely related Penicillium species revealed that the two pathogens isolated from decayed apple with blue mold symptoms are not each other’s closest relatives. Among a total of 10,560 and 10,672 protein coding sequences respectively, a comparative genomics analysis revealed 41 genes in P. expansum R19 and 43 genes in P. solitum RS1 that are unique to these two species. These genes may be associated with pome fruit–fungal interactions, subsequent decay processes, and mycotoxin accumulation. An intact patulin gene cluster consisting of 15 biosynthetic genes was identified in the patulin producing P. expansum strain R19, while only a remnant, seven-gene cluster was identified in the patulin-deficient P. solitum strain. However, P. solitum contained a large number of additional secondary metabolite gene clusters, indicating that this species has the potential capacity to produce an array of known as well as not-yet-identified products of possible toxicological or biotechnological interest.
bibliographic citation: Wu et al. (2019) Whole-genome comparisons of Penicillium spp. reveals secondary metabolic gene clusters and candidate genes associated with fungal aggressiveness during apple fruit decay. PeerJ 7:e6170 https://doi.org/10.7717/peerj.6170
date submitted: 2018-07-11
date accepted: 2018-11-27
issued: 2019-01-09
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Wu
  given name: Guangxi
author list: Agent
  family name: Jurick II
  given name: Wayne M.
author list: Agent
  family name: Lichtner
  given name: Franz J.
author list: Agent
  family name: Peng
  given name: Hui
author list: Agent
  family name: Yin
  given name: Guohua
author list: Agent
  family name: Gaskins
  given name: Verneta L.
author list: Agent
  family name: Yin
  given name: Yanbin
author list: Agent
  family name: Hua
  given name: Sui-Sheng
author list: Agent
  family name: Peter
  given name: Kari A.
author list: Agent
  family name: Bennett
  given name: Joan W.
doi: 10.7717/peerj.6170
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-01-09
copyright: ©2019 Wu et al.
attribution name: Wu et al.

Social network analysis for the assessment of pig, cattle and buffalo movement in Xayabouli, Lao PDR
type: item
type: AcademicArticle
description: The aim of this study is to understand the role that the movement patterns of pigs, cattle and buffalo play in the spread of foot-and-mouth disease (FMD). A cross-sectional survey consisting of a questionnaire was used in a hotspot area for FMD: Xayabouli Province, Lao People’s Democratic Republic. A total of 189 respondents were interviewed. We found that the key players in this network were people who were involved with more than one species of animal or occupation (multipurpose occupational node), which represents the highest number of activities of animals moved off the holding (shown with the highest out-degree centrality) and a high likelihood of being an intermediary between others (shown with the highest betweenness centrality). Moreover, the results show that the animals moved to and away from each node had few connections. Some nodes (such as traders) always received animals from the same group of cattle owners at different times. The subgroup connection within this network has many weak components, which means a connection in this network shows that some people can be reached by others, but most people were not. In this way, the number of connections present in the network was low when we defined the proportion of observed connections with all possible connections (density). These findings indicate that the network might not be busy; only one type of node is dominant which enables increased control of disease spread. We recommend that the relevant authorities implement control measures regarding the key players, which is the best way to effectively control the spread of infectious diseases.
format: application/pdf
format: text/html
creator: Chaithep Poolkhet
creator: Suwicha Kasemsuwan
creator: Sithong Phiphakhavong
creator: Intha Phouangsouvanh
creator: Khamphouth Vongxay
creator: Man Sub Shin
creator: Wantanee Kalpravidh
creator: Jan Hinrichs
subject: Veterinary Medicine
subject: Epidemiology
description: doi:10.7717/peerj.6177
publisher: PeerJ Inc.
rights: © 2019 Poolkhet et al.
abstract: The aim of this study is to understand the role that the movement patterns of pigs, cattle and buffalo play in the spread of foot-and-mouth disease (FMD). A cross-sectional survey consisting of a questionnaire was used in a hotspot area for FMD: Xayabouli Province, Lao People’s Democratic Republic. A total of 189 respondents were interviewed. We found that the key players in this network were people who were involved with more than one species of animal or occupation (multipurpose occupational node), which represents the highest number of activities of animals moved off the holding (shown with the highest out-degree centrality) and a high likelihood of being an intermediary between others (shown with the highest betweenness centrality). Moreover, the results show that the animals moved to and away from each node had few connections. Some nodes (such as traders) always received animals from the same group of cattle owners at different times. The subgroup connection within this network has many weak components, which means a connection in this network shows that some people can be reached by others, but most people were not. In this way, the number of connections present in the network was low when we defined the proportion of observed connections with all possible connections (density). These findings indicate that the network might not be busy; only one type of node is dominant which enables increased control of disease spread. We recommend that the relevant authorities implement control measures regarding the key players, which is the best way to effectively control the spread of infectious diseases.
bibliographic citation: Poolkhet et al. (2019) Social network analysis for the assessment of pig, cattle and buffalo movement in Xayabouli, Lao PDR. PeerJ 6:e6177 https://doi.org/10.7717/peerj.6177
date submitted: 2018-08-28
date accepted: 2018-11-28
issued: 2019-01-09
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Poolkhet
  given name: Chaithep
author list: Agent
  family name: Kasemsuwan
  given name: Suwicha
author list: Agent
  family name: Phiphakhavong
  given name: Sithong
author list: Agent
  family name: Phouangsouvanh
  given name: Intha
author list: Agent
  family name: Vongxay
  given name: Khamphouth
author list: Agent
  family name: Shin
  given name: Man Sub
author list: Agent
  family name: Kalpravidh
  given name: Wantanee
author list: Agent
  family name: Hinrichs
  given name: Jan
doi: 10.7717/peerj.6177
volume: 6
issn: 2167-8359
publication name: PeerJ
publication date: 2019-01-09
copyright: © 2019 Poolkhet et al.
attribution name: Poolkhet et al.

A public database for the new MLST scheme for Treponema pallidum subsp. pallidum: surveillance and epidemiology of the causative agent of syphilis
type: item
type: AcademicArticle
description: Treponema pallidum subsp. pallidum is the causative agent of syphilis, a sexually transmitted disease with worldwide prevalence. Several different molecular typing schemes are currently available for this pathogen. To enable population biology studies of the syphilis agent and for epidemiological surveillance at the global scale, a harmonized typing tool needs to be introduced. Recently, we published a new multi-locus sequence typing (MLST) with the potential to significantly enhance the epidemiological data in several aspects (e.g., distinguishing genetically different clades of syphilis, subtyping inside these clades, and finally, distinguishing different subspecies of non-cultivable pathogenic treponemes). In this short report, we introduce the PubMLST database for treponemal DNA data storage and for assignments of allelic profiles and sequencing types. Moreover, we have summarized epidemiological data of all treponemal strains (n = 358) with available DNA sequences in typing loci and found several association between genetic groups and characteristics of patients. This study proposes the establishment of a single MLST of T. p. pallidum and encourages researchers and public health communities to use this PubMLST database as a universal tool for molecular typing studies of the syphilis pathogen.
format: application/pdf
format: text/html
creator: Linda Grillova
creator: Keith Jolley
creator: David Šmajs
creator: Mathieu Picardeau
subject: Microbiology
subject: Epidemiology
subject: Infectious Diseases
description: doi:10.7717/peerj.6182
publisher: PeerJ Inc.
rights: © 2019 Grillova et al.
abstract: Treponema pallidum subsp. pallidum is the causative agent of syphilis, a sexually transmitted disease with worldwide prevalence. Several different molecular typing schemes are currently available for this pathogen. To enable population biology studies of the syphilis agent and for epidemiological surveillance at the global scale, a harmonized typing tool needs to be introduced. Recently, we published a new multi-locus sequence typing (MLST) with the potential to significantly enhance the epidemiological data in several aspects (e.g., distinguishing genetically different clades of syphilis, subtyping inside these clades, and finally, distinguishing different subspecies of non-cultivable pathogenic treponemes). In this short report, we introduce the PubMLST database for treponemal DNA data storage and for assignments of allelic profiles and sequencing types. Moreover, we have summarized epidemiological data of all treponemal strains (n = 358) with available DNA sequences in typing loci and found several association between genetic groups and characteristics of patients. This study proposes the establishment of a single MLST of T. p. pallidum and encourages researchers and public health communities to use this PubMLST database as a universal tool for molecular typing studies of the syphilis pathogen.
bibliographic citation: Grillova et al. (2019) A public database for the new MLST scheme for Treponema pallidum subsp. pallidum: surveillance and epidemiology of the causative agent of syphilis. PeerJ 6:e6182 https://doi.org/10.7717/peerj.6182
date submitted: 2018-10-10
date accepted: 2018-11-29
issued: 2019-01-09
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Grillova
  given name: Linda
author list: Agent
  family name: Jolley
  given name: Keith
author list: Agent
  family name: Šmajs
  given name: David
author list: Agent
  family name: Picardeau
  given name: Mathieu
doi: 10.7717/peerj.6182
volume: 6
issn: 2167-8359
publication name: PeerJ
publication date: 2019-01-09
copyright: © 2019 Grillova et al.
attribution name: Grillova et al.

MLPA is a practical and complementary alternative to CMA for diagnostic testing in patients with autism spectrum disorders and identifying new candidate CNVs associated with autism
type: item
type: AcademicArticle
description: Background Autism spectrum disorder (ASD) is a complex heterogeneous developmental disease with a significant genetic background that is frequently caused by rare copy number variants (CNVs). Microarray-based whole-genome approaches for CNV detection are widely accepted. However, the clinical significance of most CNV is poorly understood, so results obtained using such methods are sometimes ambiguous. We therefore evaluated a targeted approach based on multiplex ligation-dependent probe amplification (MLPA) using selected probemixes to detect clinically relevant variants for diagnostic testing of ASD patients. We compare the reliability and efficiency of this test to those of chromosomal microarray analysis (CMA) and other tests available to our laboratory. In addition, we identify new candidate genes for ASD identified in a cohort of ASD-diagnosed patients. Method We describe the use of MLPA, CMA, and karyotyping to detect CNV in 92 ASD patients and evaluate their clinical significance. Result Pathogenic and likely pathogenic mutations were identified by CMA in eight (8.07% of the studied cohort) and 12 (13.04%) ASD patients, respectively, and in eight (8.07%) and four (4.35%) patients, respectively, by MLPA. The detected mutations include the 22q13.3 deletion, which was attributed to ring chromosome 22 formation based on karyotyping. CMA revealed a total of 91 rare CNV in 55 patients: eight pathogenic, 15 designated variants of unknown significance (VOUS)—likely pathogenic, 10 VOUS—uncertain, and 58 VOUS—likely benign or benign. MLPA revealed 18 CNV in 18 individuals: eight pathogenic, four designated as VOUS—likely pathogenic, and six designated as VOUS—likely benign/benign. Rare CNVs were detected in 17 (58.62%) out of 29 females and 38 (60.32%) out of 63 males in the cohort. Two genes, DOCK8 and PARK2, were found to be overlapped by CNV designated pathogenic, VOUS—likely pathogenic, or VOUS—uncertain in multiple patients. Moreover, the studied ASD cohort exhibi…
format: application/pdf
format: text/html
creator: Pavlina Capkova
creator: Josef Srovnal
creator: Zuzana Capkova
creator: Katerina Staffova
creator: Vera Becvarova
creator: Marie Trkova
creator: Katerina Adamova
creator: Alena Santava
creator: Vaclava Curtisova
creator: Marian Hajduch
creator: Martin Prochazka
subject: Pediatrics
subject: Translational Medicine
subject: Medical Genetics
description: doi:10.7717/peerj.6183
publisher: PeerJ Inc.
rights: © 2019 Capkova et al.
abstract: Background Autism spectrum disorder (ASD) is a complex heterogeneous developmental disease with a significant genetic background that is frequently caused by rare copy number variants (CNVs). Microarray-based whole-genome approaches for CNV detection are widely accepted. However, the clinical significance of most CNV is poorly understood, so results obtained using such methods are sometimes ambiguous. We therefore evaluated a targeted approach based on multiplex ligation-dependent probe amplification (MLPA) using selected probemixes to detect clinically relevant variants for diagnostic testing of ASD patients. We compare the reliability and efficiency of this test to those of chromosomal microarray analysis (CMA) and other tests available to our laboratory. In addition, we identify new candidate genes for ASD identified in a cohort of ASD-diagnosed patients. Method We describe the use of MLPA, CMA, and karyotyping to detect CNV in 92 ASD patients and evaluate their clinical significance. Result Pathogenic and likely pathogenic mutations were identified by CMA in eight (8.07% of the studied cohort) and 12 (13.04%) ASD patients, respectively, and in eight (8.07%) and four (4.35%) patients, respectively, by MLPA. The detected mutations include the 22q13.3 deletion, which was attributed to ring chromosome 22 formation based on karyotyping. CMA revealed a total of 91 rare CNV in 55 patients: eight pathogenic, 15 designated variants of unknown significance (VOUS)—likely pathogenic, 10 VOUS—uncertain, and 58 VOUS—likely benign or benign. MLPA revealed 18 CNV in 18 individuals: eight pathogenic, four designated as VOUS—likely pathogenic, and six designated as VOUS—likely benign/benign. Rare CNVs were detected in 17 (58.62%) out of 29 females and 38 (60.32%) out of 63 males in the cohort. Two genes, DOCK8 and PARK2, were found to be overlapped by CNV designated pathogenic, VOUS—likely pathogenic, or VOUS—uncertain in multiple patients. Moreover, the studied ASD cohort exhibi…
bibliographic citation: Capkova et al. (2019) MLPA is a practical and complementary alternative to CMA for diagnostic testing in patients with autism spectrum disorders and identifying new candidate CNVs associated with autism. PeerJ 6:e6183 https://doi.org/10.7717/peerj.6183
date submitted: 2018-06-10
date accepted: 2018-11-28
issued: 2019-01-09
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Capkova
  given name: Pavlina
author list: Agent
  family name: Srovnal
  given name: Josef
author list: Agent
  family name: Capkova
  given name: Zuzana
author list: Agent
  family name: Staffova
  given name: Katerina
author list: Agent
  family name: Becvarova
  given name: Vera
author list: Agent
  family name: Trkova
  given name: Marie
author list: Agent
  family name: Adamova
  given name: Katerina
author list: Agent
  family name: Santava
  given name: Alena
author list: Agent
  family name: Curtisova
  given name: Vaclava
author list: Agent
  family name: Hajduch
  given name: Marian
author list: Agent
  family name: Prochazka
  given name: Martin
doi: 10.7717/peerj.6183
volume: 6
issn: 2167-8359
publication name: PeerJ
publication date: 2019-01-09
copyright: © 2019 Capkova et al.
attribution name: Capkova et al.

First record of Phyllorhiza sp. (Cnidaria: Scyphozoa) in a Chinese coastal aquaculture pond
type: item
type: AcademicArticle
description: Background It has been suggested that aquaculture ponds on the Chinese coast could act as breeding grounds for scyphozoans. Here, we present the first record of the scyphomedusa Phyllorhiza sp. in an aquaculture pond on the coast of the southern Yellow Sea, based on a combination of morphological characteristics and mitochondrial 16S DNA sequence data. Methods A field survey was performed on June 29, 2017 in a pond used for culturing the shrimp Penaeus japonicus, located in the southern Yellow Sea, China. Jellyfish specimens were collected for morphological and genetic analysis. The morphological characters of the jellyfish specimens were compared to taxonomic literature. Additionally, phylogenetic analysis of the mitochondrial 16S fragments of these specimens were also conducted. Results These specimens had the following morphological characters: hemispherical umbrella without scapulets; J-shaped oral arms; a single larger terminal club on each arm; bluish colored with a slightly expanded white tip; and mouthlets present only in the lower half to one-third of each arm. These morphological features of the medusae indicated that the specimens found in the shrimp culture ponds belong to the genus Phyllorhiza Agassiz, 1862, but did not match with the description of any of the known species of the genus Phyllorhiza. Phylogenetic analyses of the mtDNA 16S regions revealed that these specimens, together with Phyllorhiza sp. from Malaysian coastal waters, belong to a sister group of Phyllorhiza punctata. Juveniles and ephyrae of Phyllorhiza sp. were observed in the aquaculture pond. The mean density of Phyllorhiza sp. medusa in the surface water within the pond was estimated to be 0.05 individuals/m2. Discussion Based on our observations of the gross morphology and molecular data, we state that the specimens collected in the aquaculture pond can be identified as Phyllorhiza sp. This is the first record of Phyllorhiza sp. in Chinese seas. Large scale dispersal through balla…
format: application/pdf
format: text/html
creator: Zhijun Dong
creator: André C. Morandini
creator: Agustin Schiariti
creator: Lei Wang
creator: Tingting Sun
subject: Aquaculture, Fisheries and Fish Science
subject: Biodiversity
subject: Marine Biology
description: doi:10.7717/peerj.6191
publisher: PeerJ Inc.
rights: © 2019 Dong et al.
abstract: Background It has been suggested that aquaculture ponds on the Chinese coast could act as breeding grounds for scyphozoans. Here, we present the first record of the scyphomedusa Phyllorhiza sp. in an aquaculture pond on the coast of the southern Yellow Sea, based on a combination of morphological characteristics and mitochondrial 16S DNA sequence data. Methods A field survey was performed on June 29, 2017 in a pond used for culturing the shrimp Penaeus japonicus, located in the southern Yellow Sea, China. Jellyfish specimens were collected for morphological and genetic analysis. The morphological characters of the jellyfish specimens were compared to taxonomic literature. Additionally, phylogenetic analysis of the mitochondrial 16S fragments of these specimens were also conducted. Results These specimens had the following morphological characters: hemispherical umbrella without scapulets; J-shaped oral arms; a single larger terminal club on each arm; bluish colored with a slightly expanded white tip; and mouthlets present only in the lower half to one-third of each arm. These morphological features of the medusae indicated that the specimens found in the shrimp culture ponds belong to the genus Phyllorhiza Agassiz, 1862, but did not match with the description of any of the known species of the genus Phyllorhiza. Phylogenetic analyses of the mtDNA 16S regions revealed that these specimens, together with Phyllorhiza sp. from Malaysian coastal waters, belong to a sister group of Phyllorhiza punctata. Juveniles and ephyrae of Phyllorhiza sp. were observed in the aquaculture pond. The mean density of Phyllorhiza sp. medusa in the surface water within the pond was estimated to be 0.05 individuals/m2. Discussion Based on our observations of the gross morphology and molecular data, we state that the specimens collected in the aquaculture pond can be identified as Phyllorhiza sp. This is the first record of Phyllorhiza sp. in Chinese seas. Large scale dispersal through balla…
bibliographic citation: Dong et al. (2019) First record of Phyllorhiza sp. (Cnidaria: Scyphozoa) in a Chinese coastal aquaculture pond. PeerJ 7:e6191 https://doi.org/10.7717/peerj.6191
date submitted: 2018-07-24
date accepted: 2018-11-27
issued: 2019-01-09
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Dong
  given name: Zhijun
author list: Agent
  family name: Morandini
  given name: André C.
author list: Agent
  family name: Schiariti
  given name: Agustin
author list: Agent
  family name: Wang
  given name: Lei
author list: Agent
  family name: Sun
  given name: Tingting
doi: 10.7717/peerj.6191
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-01-09
copyright: ©2019 Dong et al.
attribution name: Dong et al.

Climatic niche evolution in the viviparous Sceloporus torquatus group (Squamata: Phrynosomatidae)
type: item
type: AcademicArticle
description: The cold-climate hypothesis maintains that viviparity arose as a means to prevent increased egg mortality in nests owing to low temperatures, and this hypothesis represents the primary and most strongly supported explanation for the evolution of viviparity in reptiles. In this regard, certain authors have stated that viviparous species will exhibit speciation via climatic niche conservatism, with similar climatic niches being observed in allopatric sister species. However, this prediction remains to be tested with bioclimatic variables relevant to each viviparous group. In the present study, we examined climatic niche evolution in a group of North American viviparous lizards to determine whether their diversification is linked to phylogenetic niche conservatism (PNC). We evaluated the phylogenetic signal and trait evolution of individual bioclimatic variables and principal component (PC) scores of a PC analysis, along with reconstructions of ancestral climate tolerances. The results suggest that diversification of the Sceloporus torquatus group species is associated with both niche differentiation and PNC. Furthermore, we did not observe PNC across nearly all bioclimatic variables and in PC2 and PC3. However, in Precipitation Seasonality (Bio15), in Precipitation of Coldest Quarter (Bio19) and in PC1 (weakly associated with variability of temperature), we did observe PNC. Additionally, variation of the scores along the phylogeny and Pagel’s delta (δ) >1 of PC3 suggests a fast, recent evolution to dry conditions in the clade that sustains S. serrifer.
format: application/pdf
format: text/html
creator: Norberto Martínez-Méndez
creator: Omar Mejía
creator: Jorge Ortega
creator: Fausto Méndez-de la Cruz
subject: Biogeography
subject: Ecology
subject: Evolutionary Studies
subject: Zoology
description: doi:10.7717/peerj.6192
publisher: PeerJ Inc.
rights: © 2019 Martínez-Méndez et al.
abstract: The cold-climate hypothesis maintains that viviparity arose as a means to prevent increased egg mortality in nests owing to low temperatures, and this hypothesis represents the primary and most strongly supported explanation for the evolution of viviparity in reptiles. In this regard, certain authors have stated that viviparous species will exhibit speciation via climatic niche conservatism, with similar climatic niches being observed in allopatric sister species. However, this prediction remains to be tested with bioclimatic variables relevant to each viviparous group. In the present study, we examined climatic niche evolution in a group of North American viviparous lizards to determine whether their diversification is linked to phylogenetic niche conservatism (PNC). We evaluated the phylogenetic signal and trait evolution of individual bioclimatic variables and principal component (PC) scores of a PC analysis, along with reconstructions of ancestral climate tolerances. The results suggest that diversification of the Sceloporus torquatus group species is associated with both niche differentiation and PNC. Furthermore, we did not observe PNC across nearly all bioclimatic variables and in PC2 and PC3. However, in Precipitation Seasonality (Bio15), in Precipitation of Coldest Quarter (Bio19) and in PC1 (weakly associated with variability of temperature), we did observe PNC. Additionally, variation of the scores along the phylogeny and Pagel’s delta (δ) >1 of PC3 suggests a fast, recent evolution to dry conditions in the clade that sustains S. serrifer.
bibliographic citation: Martínez-Méndez et al. (2019) Climatic niche evolution in the viviparous Sceloporus torquatus group (Squamata: Phrynosomatidae). PeerJ 6:e6192 https://doi.org/10.7717/peerj.6192
date submitted: 2017-12-22
date accepted: 2018-12-01
issued: 2019-01-09
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Martínez-Méndez
  given name: Norberto
author list: Agent
  family name: Mejía
  given name: Omar
author list: Agent
  family name: Ortega
  given name: Jorge
author list: Agent
  family name: Méndez-de la Cruz
  given name: Fausto
doi: 10.7717/peerj.6192
volume: 6
issn: 2167-8359
publication name: PeerJ
publication date: 2019-01-09
copyright: © 2019 Martínez-Méndez et al.
attribution name: Martínez-Méndez et al.

Carabid community structure in northern China grassland ecosystems: Effects of local habitat on species richness, species composition and functional diversity
type: item
type: AcademicArticle
description: Background Most carabid beetles are particularly sensitive to local habitat characteristics. Although in China grasslands account for more than 40% of the national land, their biodiversity is still poorly known. The aim of this paper is to identify the main environmental characteristics influencing carabid diversity in different types of grassland in northern China. Methods We investigated the influence of vegetation (plant biomass, cover, density, height and species richness), soil (bulk density, above ground litter, moisture and temperature) and climate (humidity, precipitation and temperature) on carabid community structure (species richness, species composition and functional diversity—measured as body size, movement and total diversity) in three types of grasslands: desert, typical and meadow steppes. We used Canonical correspondence analysis to investigate the role of habitat characteristics on species composition and eigenvector spatial filtering to investigate the responses of species richness and functional diversities. Results We found that carabid community structure was strongly influenced by local habitat characteristics and particularly by climatic factors. Carabids in the desert steppe showed the lowest richness and functional diversities. Climate predictors (temperature, precipitation and humidity) had positive effects on carabid species richness at both regional and ecosystem levels, with difference among ecosystems. Plant diversity had a positive influence on carabid richness at the regional level. Soil compaction and temperature were negatively related to species richness at regional level. Climatic factors positively influenced functional diversities, whereas soil temperature had negative effects. Soil moisture and temperature were the most important drivers of species composition at regional level, whereas the relative importance of the various environmental parameters varied among ecosystems. Discussion Carabid responses to environmental charac…
format: application/pdf
format: text/html
creator: Noelline Tsafack
creator: François Rebaudo
creator: Hui Wang
creator: Dávid D. Nagy
creator: Yingzhong Xie
creator: Xinpu Wang
creator: Simone Fattorini
subject: Conservation Biology
subject: Ecology
subject: Ecosystem Science
subject: Entomology
subject: Environmental Impacts
description: doi:10.7717/peerj.6197
publisher: PeerJ Inc.
rights: © 2019 Tsafack et al.
abstract: Background Most carabid beetles are particularly sensitive to local habitat characteristics. Although in China grasslands account for more than 40% of the national land, their biodiversity is still poorly known. The aim of this paper is to identify the main environmental characteristics influencing carabid diversity in different types of grassland in northern China. Methods We investigated the influence of vegetation (plant biomass, cover, density, height and species richness), soil (bulk density, above ground litter, moisture and temperature) and climate (humidity, precipitation and temperature) on carabid community structure (species richness, species composition and functional diversity—measured as body size, movement and total diversity) in three types of grasslands: desert, typical and meadow steppes. We used Canonical correspondence analysis to investigate the role of habitat characteristics on species composition and eigenvector spatial filtering to investigate the responses of species richness and functional diversities. Results We found that carabid community structure was strongly influenced by local habitat characteristics and particularly by climatic factors. Carabids in the desert steppe showed the lowest richness and functional diversities. Climate predictors (temperature, precipitation and humidity) had positive effects on carabid species richness at both regional and ecosystem levels, with difference among ecosystems. Plant diversity had a positive influence on carabid richness at the regional level. Soil compaction and temperature were negatively related to species richness at regional level. Climatic factors positively influenced functional diversities, whereas soil temperature had negative effects. Soil moisture and temperature were the most important drivers of species composition at regional level, whereas the relative importance of the various environmental parameters varied among ecosystems. Discussion Carabid responses to environmental charac…
bibliographic citation: Tsafack et al. (2019) Carabid community structure in northern China grassland ecosystems: Effects of local habitat on species richness, species composition and functional diversity. PeerJ 6:e6197 https://doi.org/10.7717/peerj.6197
date submitted: 2018-09-18
date accepted: 2018-12-02
issued: 2019-01-09
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Tsafack
  given name: Noelline
author list: Agent
  family name: Rebaudo
  given name: François
author list: Agent
  family name: Wang
  given name: Hui
author list: Agent
  family name: Nagy
  given name: Dávid D.
author list: Agent
  family name: Xie
  given name: Yingzhong
author list: Agent
  family name: Wang
  given name: Xinpu
author list: Agent
  family name: Fattorini
  given name: Simone
doi: 10.7717/peerj.6197
volume: 6
issn: 2167-8359
publication name: PeerJ
publication date: 2019-01-09
copyright: © 2019 Tsafack et al.
attribution name: Tsafack et al.

Fluoxetine-induced alteration of murine gut microbial community structure: evidence for a microbial endocrinology-based mechanism of action responsible for fluoxetine-induced side effects
type: item
type: AcademicArticle
description: Background Depression and major depressive disorder affect 25% of the population. First line treatment utilizing selective serotonin reuptake inhibitors (SSRIs) have met with limited success due to well-recognized negative side effects which include weight gain or loss. This inability to control unwanted side effects often result in patients stopping their antidepressant medications. The mechanisms underlying the failure of SSRIs are incompletely understood. Methods Male CF-1 mice (5 weeks of age, N = 10 per group) were per orally administered fluoxetine (20 mg per kg body weight) or diluent daily for 29 days. During this time fecal specimens were collected at three defined time points (0, 15 and 29 days). At the conclusion of the 29-day dosing regimen, animals were subjected to two behavioral assessments. For bacterial identification of the microbiota, 16S rRNA gene sequencing was performed on 60 fecal specimens (three specimens per mouse time course, N = 20 mice) using Illumina MiSeq. Analysis of community sequence data was done using mothur and LEfSe bioinformatic software packages. Results Daily per oral administration of fluoxetine for 29 days to male mice resulted in a significant, time dependent, alteration in microbial communities accompanying changes in body weight. The calculated species richness and diversity indicators of the murine fecal microbial communities were inconsistent and not significantly different between the groups. Among the phylotypes decreased in abundance due to fluoxetine administration were Lactobacillus johnsonii and Bacteroidales S24-7 which belong to phyla associated with regulation of body mass. The observed changes in body weight due to fluoxetine administration mimicked the dramatic shifts in weight gain/loss that has been observed in humans. Further, at the conclusion of the 29-day dosing regimen fluoxetine-dosed animals evidenced a mild anxiogenic-like behavior. Discussion We report that the most widely used antidepressant, flu…
format: application/pdf
format: text/html
creator: Mark Lyte
creator: Karrie M. Daniels
creator: Stephan Schmitz-Esser
subject: Microbiology
subject: Neuroscience
subject: Psychiatry and Psychology
description: doi:10.7717/peerj.6199
publisher: PeerJ Inc.
rights: © 2019 Lyte et al.
abstract: Background Depression and major depressive disorder affect 25% of the population. First line treatment utilizing selective serotonin reuptake inhibitors (SSRIs) have met with limited success due to well-recognized negative side effects which include weight gain or loss. This inability to control unwanted side effects often result in patients stopping their antidepressant medications. The mechanisms underlying the failure of SSRIs are incompletely understood. Methods Male CF-1 mice (5 weeks of age, N = 10 per group) were per orally administered fluoxetine (20 mg per kg body weight) or diluent daily for 29 days. During this time fecal specimens were collected at three defined time points (0, 15 and 29 days). At the conclusion of the 29-day dosing regimen, animals were subjected to two behavioral assessments. For bacterial identification of the microbiota, 16S rRNA gene sequencing was performed on 60 fecal specimens (three specimens per mouse time course, N = 20 mice) using Illumina MiSeq. Analysis of community sequence data was done using mothur and LEfSe bioinformatic software packages. Results Daily per oral administration of fluoxetine for 29 days to male mice resulted in a significant, time dependent, alteration in microbial communities accompanying changes in body weight. The calculated species richness and diversity indicators of the murine fecal microbial communities were inconsistent and not significantly different between the groups. Among the phylotypes decreased in abundance due to fluoxetine administration were Lactobacillus johnsonii and Bacteroidales S24-7 which belong to phyla associated with regulation of body mass. The observed changes in body weight due to fluoxetine administration mimicked the dramatic shifts in weight gain/loss that has been observed in humans. Further, at the conclusion of the 29-day dosing regimen fluoxetine-dosed animals evidenced a mild anxiogenic-like behavior. Discussion We report that the most widely used antidepressant, flu…
bibliographic citation: Lyte et al. (2019) Fluoxetine-induced alteration of murine gut microbial community structure: evidence for a microbial endocrinology-based mechanism of action responsible for fluoxetine-induced side effects. PeerJ 7:e6199 https://doi.org/10.7717/peerj.6199
date submitted: 2018-09-13
date accepted: 2018-12-02
issued: 2019-01-09
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Lyte
  given name: Mark
author list: Agent
  family name: Daniels
  given name: Karrie M.
author list: Agent
  family name: Schmitz-Esser
  given name: Stephan
doi: 10.7717/peerj.6199
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-01-09
copyright: ©2019 Lyte et al.
attribution name: Lyte et al.

https://peerj.com/articles/6215
type: item
type: AcademicArticle
title: Survival under anthropogenic impact: the response of dragonflies (Odonata), beetles (Coleoptera) and caddisflies (Trichoptera) to environmental disturbances in a two-way industrial canal system (central Poland)
description: Ecological metrics and assemblages of three orders of aquatic insects (Odonata, Coleoptera and Trichoptera—OCT) in an industrial canal system affected by dredging were studied. Five sites (a river as a control site and canals) along the Vistula River in Central Poland were sampled during six sampling periods (2011 and 2013). Canonical correspondence analyses (CCA) was used to assess the influence of environmental variables on the distribution of 54 insect species in the following system of habitats—a river feeding the canals, river-fed inlet canals and outlet canals with cooling waters. Additionally, before and after control impact (BACI) was used to test for the impact of canal dredging in 2011 on the insect response metrics. Non-metric multidimensional scaling analysis differentiated insect assemblages of the three habitats and similarity percentage (SIMPER) indicated the species most responsible for the faunistic dissimilarities. Temperature was found to be a key factor governing the presence of insects in the outlet canals with cooling water. CCAs revealed that electrolytic conductivity (EC) and salinity had the greatest influence on the OCT fauna in the river and the inlet canals, whilst it was the dissolved oxygen and the level of development of aquatic plants that proved most important in the outlet canals. Modified ANOVAs showed that dredging significantly affected the mean species richness and the dominance in the canals. The changes in OCT species composition were highly informative. The comparison between tolerance patterns of the OCT orders against the five parameters (temperature, EC, total dissolved solids (TDS), pH and current) revealed that caddisflies are the most sensitive group, followed by Coleoptera while Odonata proved the most resistant. Dragonflies have the greatest potential to serve as bioindicators of industrially heated waters. The OCT fauna responded specifically to different environmental factors and stressors, it is strongly recommende…
format: application/pdf
format: text/html
creator: Edyta Buczyńska
creator: Paweł Buczyński
subject: Biodiversity
subject: Entomology
subject: Freshwater Biology
subject: Environmental Impacts
description: doi:10.7717/peerj.6215
publisher: PeerJ Inc.
rights: © 2019 Buczyńska and Buczyński
abstract: Ecological metrics and assemblages of three orders of aquatic insects (Odonata, Coleoptera and Trichoptera—OCT) in an industrial canal system affected by dredging were studied. Five sites (a river as a control site and canals) along the Vistula River in Central Poland were sampled during six sampling periods (2011 and 2013). Canonical correspondence analyses (CCA) was used to assess the influence of environmental variables on the distribution of 54 insect species in the following system of habitats—a river feeding the canals, river-fed inlet canals and outlet canals with cooling waters. Additionally, before and after control impact (BACI) was used to test for the impact of canal dredging in 2011 on the insect response metrics. Non-metric multidimensional scaling analysis differentiated insect assemblages of the three habitats and similarity percentage (SIMPER) indicated the species most responsible for the faunistic dissimilarities. Temperature was found to be a key factor governing the presence of insects in the outlet canals with cooling water. CCAs revealed that electrolytic conductivity (EC) and salinity had the greatest influence on the OCT fauna in the river and the inlet canals, whilst it was the dissolved oxygen and the level of development of aquatic plants that proved most important in the outlet canals. Modified ANOVAs showed that dredging significantly affected the mean species richness and the dominance in the canals. The changes in OCT species composition were highly informative. The comparison between tolerance patterns of the OCT orders against the five parameters (temperature, EC, total dissolved solids (TDS), pH and current) revealed that caddisflies are the most sensitive group, followed by Coleoptera while Odonata proved the most resistant. Dragonflies have the greatest potential to serve as bioindicators of industrially heated waters. The OCT fauna responded specifically to different environmental factors and stressors, it is strongly recommende…
bibliographic citation: Buczyńska et al. (2019) Survival under anthropogenic impact: the response of dragonflies (Odonata), beetles (Coleoptera) and caddisflies (Trichoptera) to environmental disturbances in a two-way industrial canal system (central Poland). PeerJ 6:e6215 https://doi.org/10.7717/peerj.6215
date submitted: 2018-08-20
date accepted: 2018-12-03
issued: 2019-01-09
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Buczyńska
  given name: Edyta
author list: Agent
  family name: Buczyński
  given name: Paweł
doi: 10.7717/peerj.6215
volume: 6
issn: 2167-8359
publication name: PeerJ
publication date: 2019-01-09
copyright: © 2019 Buczyńska and Buczyński
attribution name: Buczyńska and Buczyński

Didymin improves UV irradiation resistance in C. elegans
type: item
type: AcademicArticle
description: Didymin, a type of flavono-o-glycoside compound naturally present in citrus fruits, has been reported to be an effective anticancer agent. However, its effects on stress resistance are unclear. In this study, we treated Caenorhabditis elegans with didymin at several concentrations. We found that didymin reduced the effects of UV stressor on nematodes by decreasing reactive oxygen species levels and increasing superoxide dismutase (SOD) activity. Furthermore, we found that specific didymin-treated mutant nematodes daf-16(mu86) & daf-2(e1370), daf-16(mu86), akt-1(ok525), akt-2(ok393), and age-1(hx546) were susceptible to UV irradiation, whereas daf-2(e1371) was resistant to UV irradiation. In addition, we found that didymin not only promoted DAF-16 to transfer from cytoplasm to nucleus, but also increased both protein and mRNA expression levels of SOD-3 and HSP-16.2 after UV irradiation. Our results show that didymin affects UV irradiation resistance and it may act on daf-2 to regulate downstream genes through the insulin/IGF-1-like signaling pathway.
format: application/pdf
format: text/html
creator: Lin Zhou
creator: Lu Wang
creator: Jialing Zhang
creator: Jiahe Li
creator: Shuju Bai
creator: Junfeng Ma
creator: Xueqi Fu
subject: Biochemistry
subject: Molecular Biology
description: doi:10.7717/peerj.6218
publisher: PeerJ Inc.
rights: © 2019 Zhou et al.
abstract: Didymin, a type of flavono-o-glycoside compound naturally present in citrus fruits, has been reported to be an effective anticancer agent. However, its effects on stress resistance are unclear. In this study, we treated Caenorhabditis elegans with didymin at several concentrations. We found that didymin reduced the effects of UV stressor on nematodes by decreasing reactive oxygen species levels and increasing superoxide dismutase (SOD) activity. Furthermore, we found that specific didymin-treated mutant nematodes daf-16(mu86) & daf-2(e1370), daf-16(mu86), akt-1(ok525), akt-2(ok393), and age-1(hx546) were susceptible to UV irradiation, whereas daf-2(e1371) was resistant to UV irradiation. In addition, we found that didymin not only promoted DAF-16 to transfer from cytoplasm to nucleus, but also increased both protein and mRNA expression levels of SOD-3 and HSP-16.2 after UV irradiation. Our results show that didymin affects UV irradiation resistance and it may act on daf-2 to regulate downstream genes through the insulin/IGF-1-like signaling pathway.
bibliographic citation: Zhou et al. (2019) Didymin improves UV irradiation resistance in C. elegans. PeerJ 6:e6218 https://doi.org/10.7717/peerj.6218
date submitted: 2018-10-22
date accepted: 2018-12-05
issued: 2019-01-09
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Zhou
  given name: Lin
author list: Agent
  family name: Wang
  given name: Lu
author list: Agent
  family name: Zhang
  given name: Jialing
author list: Agent
  family name: Li
  given name: Jiahe
author list: Agent
  family name: Bai
  given name: Shuju
author list: Agent
  family name: Ma
  given name: Junfeng
author list: Agent
  family name: Fu
  given name: Xueqi
doi: 10.7717/peerj.6218
volume: 6
issn: 2167-8359
publication name: PeerJ
publication date: 2019-01-09
copyright: © 2019 Zhou et al.
attribution name: Zhou et al.

Descriptive anatomy of the largest known specimen of Protoichthyosaurus prostaxalis (Reptilia: Ichthyosauria) including computed tomography and digital reconstruction of a three-dimensional skull
type: item
type: AcademicArticle
description: Ichthyosaur fossils are abundant in Lower Jurassic sediments with nine genera found in the UK. In this paper, we describe the partial skeleton of a large ichthyosaur from the Lower Jurassic (lower Sinemurian) of Warwickshire, England, which was conserved and rearticulated to form the centrepiece of a new permanent gallery at the Thinktank, Birmingham Science Museum in 2015. The unusual three-dimensional preservation of the specimen permitted computed tomography (CT) scanning of individual braincase elements as well as the entire reassembled skull. This represents one of the first times that medical imaging and three-dimensional reconstruction methods have been applied to a large skull of a marine reptile. Data from these scans provide new anatomical information, such as the presence of branching vascular canals within the premaxilla and dentary, and an undescribed dorsal (quadrate) wing of the pterygoid hidden within matrix. Scanning also revealed areas of the skull that had been modelled in wood, clay and other materials after the specimen’s initial discovery, highlighting the utility of applying advanced imaging techniques to historical specimens. Additionally, the CT data served as the basis for a new three-dimensional reconstruction of the skull, in which minor damage was repaired and the preserved bones digitally rearticulated. Thus, for the first time a digital reconstruction of the skull and mandible of a large marine reptile skull is available. Museum records show the specimen was originally identified as an example of Ichthyosaurus communis but we identify this specimen as Protoichthyosaurus prostaxalis. The specimen features a skull nearly twice as long as any previously described specimen of P. prostaxalis, representing an individual with an estimated total body length between 3.2 and 4 m.
format: application/pdf
format: text/html
creator: Dean R. Lomax
creator: Laura B. Porro
creator: Nigel R. Larkin
subject: Paleontology
subject: Taxonomy
description: doi:10.7717/peerj.6112
publisher: PeerJ Inc.
rights: © 2019 Lomax et al.
abstract: Ichthyosaur fossils are abundant in Lower Jurassic sediments with nine genera found in the UK. In this paper, we describe the partial skeleton of a large ichthyosaur from the Lower Jurassic (lower Sinemurian) of Warwickshire, England, which was conserved and rearticulated to form the centrepiece of a new permanent gallery at the Thinktank, Birmingham Science Museum in 2015. The unusual three-dimensional preservation of the specimen permitted computed tomography (CT) scanning of individual braincase elements as well as the entire reassembled skull. This represents one of the first times that medical imaging and three-dimensional reconstruction methods have been applied to a large skull of a marine reptile. Data from these scans provide new anatomical information, such as the presence of branching vascular canals within the premaxilla and dentary, and an undescribed dorsal (quadrate) wing of the pterygoid hidden within matrix. Scanning also revealed areas of the skull that had been modelled in wood, clay and other materials after the specimen’s initial discovery, highlighting the utility of applying advanced imaging techniques to historical specimens. Additionally, the CT data served as the basis for a new three-dimensional reconstruction of the skull, in which minor damage was repaired and the preserved bones digitally rearticulated. Thus, for the first time a digital reconstruction of the skull and mandible of a large marine reptile skull is available. Museum records show the specimen was originally identified as an example of Ichthyosaurus communis but we identify this specimen as Protoichthyosaurus prostaxalis. The specimen features a skull nearly twice as long as any previously described specimen of P. prostaxalis, representing an individual with an estimated total body length between 3.2 and 4 m.
bibliographic citation: Lomax et al. (2019) Descriptive anatomy of the largest known specimen of Protoichthyosaurus prostaxalis (Reptilia: Ichthyosauria) including computed tomography and digital reconstruction of a three-dimensional skull. PeerJ 7:e6112 https://doi.org/10.7717/peerj.6112
date submitted: 2018-08-09
date accepted: 2018-11-13
issued: 2019-01-08
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Lomax
  given name: Dean R.
author list: Agent
  family name: Porro
  given name: Laura B.
author list: Agent
  family name: Larkin
  given name: Nigel R.
doi: 10.7717/peerj.6112
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-01-08
copyright: © 2019 Lomax et al.
attribution name: Lomax et al.

Another choice for measuring tree photosynthesis in vitro
type: item
type: AcademicArticle
description: Background In the case of tall trees in the field or in rugged terrain where an instrument cannot be placed operationally, beveling is a popular method used to measure in vitro photosynthesis. However, some studies and our own research have shown that net photosynthesis values measured in vitro are generally significantly lower than values measured in situ. Methods To develop a more accurate and applicable method for in vitro determination of photosynthesis, we evaluated five different methods for preparing detached tree branches to measure photosynthesis and gas exchange in vitro (beveling, cracking, splitting, girdling, and immersion in salicylic acid solution). Ten common tree-species were used. Results By comparing light response curves and water-status data, we found that (1) it is possible, to some extent, to substitute in vitro measurement of photosynthetic characteristics of tree species for in situ measurement, provided a suitable treatment is employed; (2) the beveling method is likely to underestimate photosynthetic potential of some trees; (3) after cracking application, most detached branches effectively continued to absorb water; and (4) measurements obtained using detached tree-branches processed by the cracking method were closer to those obtained in situ in intact trees; (5) some tree species (Diospyros kaki, Eriobotrya japonica) appeared to be particularly sensitive to the cracking method, and their in-vitro maximum net photosynthesis rate (Pmax) was significantly less than the in-situ value (P < 0.05). Discussion Our findings provide a methodological support for comprehensive and accurate measurement of plant functional traits. The use of the cracking method contributes to feasibility and reliability of the measurement of photosynthetic parameters in tall trees, thus providing more accurate photosynthetic parameters for the analysis of trade-off strategies at the leaf level.
format: application/pdf
format: text/html
creator: Changjun Meng
creator: Xiao Liu
creator: Yongfu Chai
creator: Jinshi Xu
creator: Ming Yue
subject: Ecology
subject: Forestry
description: doi:10.7717/peerj.5933
publisher: PeerJ Inc.
rights: © 2019 Meng et al.
abstract: Background In the case of tall trees in the field or in rugged terrain where an instrument cannot be placed operationally, beveling is a popular method used to measure in vitro photosynthesis. However, some studies and our own research have shown that net photosynthesis values measured in vitro are generally significantly lower than values measured in situ. Methods To develop a more accurate and applicable method for in vitro determination of photosynthesis, we evaluated five different methods for preparing detached tree branches to measure photosynthesis and gas exchange in vitro (beveling, cracking, splitting, girdling, and immersion in salicylic acid solution). Ten common tree-species were used. Results By comparing light response curves and water-status data, we found that (1) it is possible, to some extent, to substitute in vitro measurement of photosynthetic characteristics of tree species for in situ measurement, provided a suitable treatment is employed; (2) the beveling method is likely to underestimate photosynthetic potential of some trees; (3) after cracking application, most detached branches effectively continued to absorb water; and (4) measurements obtained using detached tree-branches processed by the cracking method were closer to those obtained in situ in intact trees; (5) some tree species (Diospyros kaki, Eriobotrya japonica) appeared to be particularly sensitive to the cracking method, and their in-vitro maximum net photosynthesis rate (Pmax) was significantly less than the in-situ value (P < 0.05). Discussion Our findings provide a methodological support for comprehensive and accurate measurement of plant functional traits. The use of the cracking method contributes to feasibility and reliability of the measurement of photosynthetic parameters in tall trees, thus providing more accurate photosynthetic parameters for the analysis of trade-off strategies at the leaf level.
bibliographic citation: Meng et al. (2019) Another choice for measuring tree photosynthesis in vitro. PeerJ 7:e5933 https://doi.org/10.7717/peerj.5933
date submitted: 2018-07-12
date accepted: 2018-10-15
issued: 2019-01-08
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Meng
  given name: Changjun
author list: Agent
  family name: Liu
  given name: Xiao
author list: Agent
  family name: Chai
  given name: Yongfu
author list: Agent
  family name: Xu
  given name: Jinshi
author list: Agent
  family name: Yue
  given name: Ming
doi: 10.7717/peerj.5933
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-01-08
copyright: ©2019 Meng et al.
attribution name: Meng et al.

The effect of cycling hypoxia on MCF-7 cancer stem cells and the impact of their microenvironment on angiogenesis using human umbilical vein endothelial cells (HUVECs) as a model
type: item
type: AcademicArticle
description: Background Breast cancer is the most common type of cancer among females. Hypoxia mediates cancer hallmarks and results from reduced oxygen level due to irregularities in tumor vascularization or when the tumor size prevents oxygen diffusion and triggers angiogenesis to compensate for low oxygen. Cancer stem cells (CSCs) are a rare subpopulation, able to self-renew and to give rise to tumor-initiating cells. It is proposed that CSCs’ secretions help to recruit endothelial cells via angiogenic factors to establish tumor vascularization. In the tumor microenvironment, the effect of hypoxia on CSCs and the impact of their secretions on triggering angiogenesis and tumor vascularization remain questionable. In this study, three-dimensional (3D) CSCs derived from MCF-7 were directly exposed to repetitive long-term cycles of hypoxia to assess its effect on CSCs and then to evaluate the role of the hypoxic CSCs’ (CSCsHYP) secretions in angiogenesis using (HUVECs) as a model for tumor neovascularization response. Methods CSCs derived from MCF-7 cell-line were expanded under repetitive, strictly optimized, long-term/continuous and intermittent hypoxic shots for almost four months to assess hypoxic effect on CSCs, sorted based on CD44+/CD24− biomarkers. Hypoxic phenotype of CSCsHYP was evaluated by assessing the acquired chemoresistance using MTT assay and elevated stemness properties were assessed by flow cytometry. To evaluate the effect of the secretions from CSCsHYP on angiogenesis, HUVECs were exposed to CSCsHYP conditioned-medium (CdM)—in which CSCs had been previously grown—to mimic the tumor microenvironment and to assess the effect of the secretions from CSCsHYP on the HUVECs’ capability of tube formation, migration and wound healing. Additionally, co-culture of CSCsHYP with HUVECs was performed. Results CSCsHYP acquired higher chemoresistance, increased stemness properties and obtained greater propagation, migration, and wound healing capacities, when compared to CSC…
format: application/pdf
format: text/html
creator: Fuad M. Alhawarat
creator: Hana M. Hammad
creator: Majd S. Hijjawi
creator: Ahmad S. Sharab
creator: Duaa A. Abuarqoub
creator: Mohammad A. Al Shhab
creator: Malek A. Zihlif
subject: Cell Biology
subject: Oncology
subject: Pharmacology
description: doi:10.7717/peerj.5990
publisher: PeerJ Inc.
rights: © 2019 Alhawarat et al.
abstract: Background Breast cancer is the most common type of cancer among females. Hypoxia mediates cancer hallmarks and results from reduced oxygen level due to irregularities in tumor vascularization or when the tumor size prevents oxygen diffusion and triggers angiogenesis to compensate for low oxygen. Cancer stem cells (CSCs) are a rare subpopulation, able to self-renew and to give rise to tumor-initiating cells. It is proposed that CSCs’ secretions help to recruit endothelial cells via angiogenic factors to establish tumor vascularization. In the tumor microenvironment, the effect of hypoxia on CSCs and the impact of their secretions on triggering angiogenesis and tumor vascularization remain questionable. In this study, three-dimensional (3D) CSCs derived from MCF-7 were directly exposed to repetitive long-term cycles of hypoxia to assess its effect on CSCs and then to evaluate the role of the hypoxic CSCs’ (CSCsHYP) secretions in angiogenesis using (HUVECs) as a model for tumor neovascularization response. Methods CSCs derived from MCF-7 cell-line were expanded under repetitive, strictly optimized, long-term/continuous and intermittent hypoxic shots for almost four months to assess hypoxic effect on CSCs, sorted based on CD44+/CD24− biomarkers. Hypoxic phenotype of CSCsHYP was evaluated by assessing the acquired chemoresistance using MTT assay and elevated stemness properties were assessed by flow cytometry. To evaluate the effect of the secretions from CSCsHYP on angiogenesis, HUVECs were exposed to CSCsHYP conditioned-medium (CdM)—in which CSCs had been previously grown—to mimic the tumor microenvironment and to assess the effect of the secretions from CSCsHYP on the HUVECs’ capability of tube formation, migration and wound healing. Additionally, co-culture of CSCsHYP with HUVECs was performed. Results CSCsHYP acquired higher chemoresistance, increased stemness properties and obtained greater propagation, migration, and wound healing capacities, when compared to CSC…
bibliographic citation: Alhawarat et al. (2019) The effect of cycling hypoxia on MCF-7 cancer stem cells and the impact of their microenvironment on angiogenesis using human umbilical vein endothelial cells (HUVECs) as a model. PeerJ 7:e5990 https://doi.org/10.7717/peerj.5990
date submitted: 2018-06-07
date accepted: 2018-10-22
issued: 2019-01-08
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Alhawarat
  given name: Fuad M.
author list: Agent
  family name: Hammad
  given name: Hana M.
author list: Agent
  family name: Hijjawi
  given name: Majd S.
author list: Agent
  family name: Sharab
  given name: Ahmad S.
author list: Agent
  family name: Abuarqoub
  given name: Duaa A.
author list: Agent
  family name: Al Shhab
  given name: Mohammad A.
author list: Agent
  family name: Zihlif
  given name: Malek A.
doi: 10.7717/peerj.5990
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-01-08
copyright: ©2019 Alhawarat et al.
attribution name: Alhawarat et al.

Simultaneous rapid detection of Hantaan virus and Seoul virus using RT-LAMP in rats
type: item
type: AcademicArticle
description: Background Hemorrhagic fever with renal syndrome is in most cases caused by the Hantaan virus (HTNV) and Seoul virus (SEOV). To develop and apply reverse transcription loop-mediated isothermal amplification (RT-LAMP) to detect HTNV and SEOV simultaneously, which was faster, more cost effective, and easier to perform as the target gene amplified rapidly. In this article an assay based on LAMP is demonstrated, which only employs such apparatus as a water bath or a heat block. Methods A chromogenic method using the calcein/Mn2+ complex and real-time turbidity monitoring method were used to assess reaction progress of the reaction, and the specificity of the RT-LAMP-based assay was assessed by detecting cDNAs/cRNAs generated from Coxsackievirus A16, Influenza virus, lymphocytic choriomeningitis virus, mouse poxvirus, rotavirus, mouse hepatitis virus. In addition, 23 clinical specimens were used to determine the agreement between the RT-LAMP assay with reverse transcriptase polymerase chain reaction (RT-PCR) and immunofluorescence (IFT) method. Results The detection limit of RT-LAMP to HNTV and SEOV was as low as 10 copies/μL with optimized reaction conditions, which was much more sensitive than the RT-PCR method (100–1,000 copies/μL). At the same time, the detection results of 23 clinical specimens have also illustrated the agreement between this the RT-LAMP assay with RT-PCR and IFT. Discussion This RT-LAMP assay could be used to perform simultaneous and rapid detection of HTNV and SEOV to the clinical specimens.
format: application/pdf
format: text/html
creator: Xin Sui
creator: Xu Zhang
creator: Dongliang Fei
creator: Zhen Zhang
creator: Mingxiao Ma
subject: Microbiology
subject: Molecular Biology
subject: Veterinary Medicine
subject: Virology
description: doi:10.7717/peerj.6068
publisher: PeerJ Inc.
rights: © 2019 Sui et al.
abstract: Background Hemorrhagic fever with renal syndrome is in most cases caused by the Hantaan virus (HTNV) and Seoul virus (SEOV). To develop and apply reverse transcription loop-mediated isothermal amplification (RT-LAMP) to detect HTNV and SEOV simultaneously, which was faster, more cost effective, and easier to perform as the target gene amplified rapidly. In this article an assay based on LAMP is demonstrated, which only employs such apparatus as a water bath or a heat block. Methods A chromogenic method using the calcein/Mn2+ complex and real-time turbidity monitoring method were used to assess reaction progress of the reaction, and the specificity of the RT-LAMP-based assay was assessed by detecting cDNAs/cRNAs generated from Coxsackievirus A16, Influenza virus, lymphocytic choriomeningitis virus, mouse poxvirus, rotavirus, mouse hepatitis virus. In addition, 23 clinical specimens were used to determine the agreement between the RT-LAMP assay with reverse transcriptase polymerase chain reaction (RT-PCR) and immunofluorescence (IFT) method. Results The detection limit of RT-LAMP to HNTV and SEOV was as low as 10 copies/μL with optimized reaction conditions, which was much more sensitive than the RT-PCR method (100–1,000 copies/μL). At the same time, the detection results of 23 clinical specimens have also illustrated the agreement between this the RT-LAMP assay with RT-PCR and IFT. Discussion This RT-LAMP assay could be used to perform simultaneous and rapid detection of HTNV and SEOV to the clinical specimens.
bibliographic citation: Sui et al. (2019) Simultaneous rapid detection of Hantaan virus and Seoul virus using RT-LAMP in rats. PeerJ 6:e6068 https://doi.org/10.7717/peerj.6068
date submitted: 2018-06-09
date accepted: 2018-11-04
issued: 2019-01-08
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Sui
  given name: Xin
author list: Agent
  family name: Zhang
  given name: Xu
author list: Agent
  family name: Fei
  given name: Dongliang
author list: Agent
  family name: Zhang
  given name: Zhen
author list: Agent
  family name: Ma
  given name: Mingxiao
doi: 10.7717/peerj.6068
volume: 6
issn: 2167-8359
publication name: PeerJ
publication date: 2019-01-08
copyright: © 2019 Sui et al.
attribution name: Sui et al.

Advances in cultivation, wastewater treatment application, bioactive components of Caulerpa lentillifera and their biotechnological applications
type: item
type: AcademicArticle
description: The edible seaweed Caulerpa lentillifera, a powerful natural food source that is rich in protein, minerals, dietary fibers, vitamins, saturated fatty acids and unsaturated fatty acids, has been mass cultured in some Asian countries and has been the focus of researchers in recent years. Here, the operational conditions of its culture, application in wastewater treatment, and bioactive components are summarized and comparatively analyzed. Based on previous studies, salinity, nutrient concentrations, irradiance and temperature are stress factors for algal growth. Moreover, dried Caulerpa lentillifera seaweed is efficient in the biosorption of heavy metals and cationic dyes in wastewater, and fresh seaweed can be introduced as a biofilter in aquaculture system treatment. In addition, among the rich bioactive compounds in Caulerpa lentillifera, the phenolic compounds show the potential ability for regulating glucose metabolism in vivo. Polysaccharides and oligosaccharides exhibit anticoagulant, immunomodulatory effects and cancer-preventing activity. Siphonaxanthin is a compound with attractive novel functions in cancer-preventing activity and lipogenesis-inhibiting effects. Furthermore, the antioxidant activity of siphonaxanthin extracted from Caulerpa lentillifera could be stronger than that of astaxanthin. This review offers an overview of studies of Caulerpa lentillifera addressing various aspects including cultivation, wastewater treatment and biological active components which may provide valuable information for the cultivation and utilization of this green alga.
format: application/pdf
format: text/html
creator: Xiaolin Chen
creator: Yuhao Sun
creator: Hong Liu
creator: Song Liu
creator: Yukun Qin
creator: Pengcheng Li
subject: Natural Resource Management
subject: Environmental Contamination and Remediation
description: doi:10.7717/peerj.6118
publisher: PeerJ Inc.
rights: © 2019 Chen et al.
abstract: The edible seaweed Caulerpa lentillifera, a powerful natural food source that is rich in protein, minerals, dietary fibers, vitamins, saturated fatty acids and unsaturated fatty acids, has been mass cultured in some Asian countries and has been the focus of researchers in recent years. Here, the operational conditions of its culture, application in wastewater treatment, and bioactive components are summarized and comparatively analyzed. Based on previous studies, salinity, nutrient concentrations, irradiance and temperature are stress factors for algal growth. Moreover, dried Caulerpa lentillifera seaweed is efficient in the biosorption of heavy metals and cationic dyes in wastewater, and fresh seaweed can be introduced as a biofilter in aquaculture system treatment. In addition, among the rich bioactive compounds in Caulerpa lentillifera, the phenolic compounds show the potential ability for regulating glucose metabolism in vivo. Polysaccharides and oligosaccharides exhibit anticoagulant, immunomodulatory effects and cancer-preventing activity. Siphonaxanthin is a compound with attractive novel functions in cancer-preventing activity and lipogenesis-inhibiting effects. Furthermore, the antioxidant activity of siphonaxanthin extracted from Caulerpa lentillifera could be stronger than that of astaxanthin. This review offers an overview of studies of Caulerpa lentillifera addressing various aspects including cultivation, wastewater treatment and biological active components which may provide valuable information for the cultivation and utilization of this green alga.
bibliographic citation: Chen et al. (2019) Advances in cultivation, wastewater treatment application, bioactive components of Caulerpa lentillifera and their biotechnological applications. PeerJ 7:e6118 https://doi.org/10.7717/peerj.6118
date submitted: 2018-07-20
date accepted: 2018-11-12
issued: 2019-01-08
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Chen
  given name: Xiaolin
author list: Agent
  family name: Sun
  given name: Yuhao
author list: Agent
  family name: Liu
  given name: Hong
author list: Agent
  family name: Liu
  given name: Song
author list: Agent
  family name: Qin
  given name: Yukun
author list: Agent
  family name: Li
  given name: Pengcheng
doi: 10.7717/peerj.6118
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-01-08
copyright: ©2019 Chen et al.
attribution name: Chen et al.

Defensin-like peptides in wheat analyzed by whole-transcriptome sequencing: a focus on structural diversity and role in induced resistance
type: item
type: AcademicArticle
description: Antimicrobial peptides (AMPs) are the main components of the plant innate immune system. Defensins represent the most important AMP family involved in defense and non-defense functions. In this work, global RNA sequencing and de novo transcriptome assembly were performed to explore the diversity of defensin-like (DEFL) genes in the wheat Triticum kiharae and to study their role in induced resistance (IR) mediated by the elicitor metabolites of a non-pathogenic strain FS-94 of Fusarium sambucinum. Using a combination of two pipelines for DEFL mining in transcriptome data sets, as many as 143 DEFL genes were identified in T. kiharae, the vast majority of them represent novel genes. According to the number of cysteine residues and the cysteine motif, wheat DEFLs were classified into ten groups. Classical defensins with a characteristic 8-Cys motif assigned to group 1 DEFLs represent the most abundant group comprising 52 family members. DEFLs with a characteristic 4-Cys motif CX{3,5}CX{8,17}CX{4,6}C named group 4 DEFLs previously found only in legumes were discovered in wheat. Within DEFL groups, subgroups of similar sequences originated by duplication events were isolated. Variation among DEFLs within subgroups is due to amino acid substitutions and insertions/deletions of amino acid sequences. To identify IR-related DEFL genes, transcriptional changes in DEFL gene expression during elicitor-mediated IR were monitored. Transcriptional diversity of DEFL genes in wheat seedlings in response to the fungus Fusarium oxysporum, FS-94 elicitors, and the combination of both (elicitors + fungus) was demonstrated, with specific sets of up- and down-regulated DEFL genes. DEFL expression profiling allowed us to gain insight into the mode of action of the elicitors from F. sambucinum. We discovered that the elicitors up-regulated a set of 24 DEFL genes. After challenge inoculation with F. oxysporum, another set of 22 DEFLs showed enhanced expression in IR-displaying seedlings. Thes…
format: application/pdf
format: text/html
creator: Tatyana I. Odintsova
creator: Marina P. Slezina
creator: Ekaterina A. Istomina
creator: Tatyana V. Korostyleva
creator: Artem S. Kasianov
creator: Alexey S. Kovtun
creator: Vsevolod J. Makeev
creator: Larisa A. Shcherbakova
creator: Alexander M. Kudryavtsev
subject: Agricultural Science
subject: Biodiversity
subject: Bioinformatics
subject: Genomics
subject: Plant Science
description: doi:10.7717/peerj.6125
publisher: PeerJ Inc.
rights: © 2019 Odintsova et al.
abstract: Antimicrobial peptides (AMPs) are the main components of the plant innate immune system. Defensins represent the most important AMP family involved in defense and non-defense functions. In this work, global RNA sequencing and de novo transcriptome assembly were performed to explore the diversity of defensin-like (DEFL) genes in the wheat Triticum kiharae and to study their role in induced resistance (IR) mediated by the elicitor metabolites of a non-pathogenic strain FS-94 of Fusarium sambucinum. Using a combination of two pipelines for DEFL mining in transcriptome data sets, as many as 143 DEFL genes were identified in T. kiharae, the vast majority of them represent novel genes. According to the number of cysteine residues and the cysteine motif, wheat DEFLs were classified into ten groups. Classical defensins with a characteristic 8-Cys motif assigned to group 1 DEFLs represent the most abundant group comprising 52 family members. DEFLs with a characteristic 4-Cys motif CX{3,5}CX{8,17}CX{4,6}C named group 4 DEFLs previously found only in legumes were discovered in wheat. Within DEFL groups, subgroups of similar sequences originated by duplication events were isolated. Variation among DEFLs within subgroups is due to amino acid substitutions and insertions/deletions of amino acid sequences. To identify IR-related DEFL genes, transcriptional changes in DEFL gene expression during elicitor-mediated IR were monitored. Transcriptional diversity of DEFL genes in wheat seedlings in response to the fungus Fusarium oxysporum, FS-94 elicitors, and the combination of both (elicitors + fungus) was demonstrated, with specific sets of up- and down-regulated DEFL genes. DEFL expression profiling allowed us to gain insight into the mode of action of the elicitors from F. sambucinum. We discovered that the elicitors up-regulated a set of 24 DEFL genes. After challenge inoculation with F. oxysporum, another set of 22 DEFLs showed enhanced expression in IR-displaying seedlings. Thes…
bibliographic citation: Odintsova et al. (2019) Defensin-like peptides in wheat analyzed by whole-transcriptome sequencing: a focus on structural diversity and role in induced resistance. PeerJ 7:e6125 https://doi.org/10.7717/peerj.6125
date submitted: 2018-07-17
date accepted: 2018-11-18
issued: 2019-01-08
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Odintsova
  given name: Tatyana I.
author list: Agent
  family name: Slezina
  given name: Marina P.
author list: Agent
  family name: Istomina
  given name: Ekaterina A.
author list: Agent
  family name: Korostyleva
  given name: Tatyana V.
author list: Agent
  family name: Kasianov
  given name: Artem S.
author list: Agent
  family name: Kovtun
  given name: Alexey S.
author list: Agent
  family name: Makeev
  given name: Vsevolod J.
author list: Agent
  family name: Shcherbakova
  given name: Larisa A.
author list: Agent
  family name: Kudryavtsev
  given name: Alexander M.
doi: 10.7717/peerj.6125
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-01-08
copyright: ©2019 Odintsova et al.
attribution name: Odintsova et al.

Direct and indirect parental exposure to endocrine disruptors and elevated temperature influences gene expression across generations in a euryhaline model fish
type: item
type: AcademicArticle
description: Aquatic organisms inhabiting polluted waterways face numerous adverse effects, including physiological disruption by endocrine disrupting compounds (EDCs). Little is known about how the temperatures associated with global climate change may influence the response of organisms exposed to EDCs, and the effects that these combined stressors may have on molecular endpoints such as gene expression. We exposed Menidia beryllina (inland silversides) to environmentally relevant concentrations (1 ng/L) of two estrogenic EDCs (bifenthrin and 17α-ethinylestradiol; EE2) at 22 °C and 28 °C. We conducted this experiment over multiple generations to better understand the potential effects to chronically exposed populations in the wild. We exposed adult parental fish (F0) for 14 days prior to spawning of the next generation. F1 larvae were then exposed from fertilization until 21 days post hatch (dph) before being transferred to clean water tanks. F1 larvae were reared to adulthood, then spawned in clean water to test for further effects of parental exposure on offspring (F2 generation). Gene expression was quantified by performing qPCR on F0 and F1 gonads, as well as F1 and F2 larvae. We did not detect any significant differences in the expression of genes measured in the parental or F1 adult gonads. We found that the 28 °C EE2 treatment significantly decreased the expression of nearly all genes measured in the F1 larvae. This pattern was transferred to the F2 generation for expression of the follicle-stimulating hormone receptor (FSHR) gene. Expression of 17β-hydroxysteroid dehydrogenase (17β-HSD) and G protein-coupled receptor 30 (GPR30) revealed changes not measured in the previous generation. Effects of the bifenthrin treatments were not observed until the F2 generation, which were exposed to the chemicals indirectly as germ cells. Our results indicate that effects of EDCs and their interactions with abiotic factors, may not be adequately represented by singular generation tes…
format: application/pdf
format: text/html
creator: Bethany M. DeCourten
creator: Richard E. Connon
creator: Susanne M. Brander
subject: Genomics
subject: Toxicology
subject: Climate Change Biology
subject: Ecotoxicology
subject: Environmental Impacts
description: doi:10.7717/peerj.6156
publisher: PeerJ Inc.
rights: © 2019 DeCourten et al.
abstract: Aquatic organisms inhabiting polluted waterways face numerous adverse effects, including physiological disruption by endocrine disrupting compounds (EDCs). Little is known about how the temperatures associated with global climate change may influence the response of organisms exposed to EDCs, and the effects that these combined stressors may have on molecular endpoints such as gene expression. We exposed Menidia beryllina (inland silversides) to environmentally relevant concentrations (1 ng/L) of two estrogenic EDCs (bifenthrin and 17α-ethinylestradiol; EE2) at 22 °C and 28 °C. We conducted this experiment over multiple generations to better understand the potential effects to chronically exposed populations in the wild. We exposed adult parental fish (F0) for 14 days prior to spawning of the next generation. F1 larvae were then exposed from fertilization until 21 days post hatch (dph) before being transferred to clean water tanks. F1 larvae were reared to adulthood, then spawned in clean water to test for further effects of parental exposure on offspring (F2 generation). Gene expression was quantified by performing qPCR on F0 and F1 gonads, as well as F1 and F2 larvae. We did not detect any significant differences in the expression of genes measured in the parental or F1 adult gonads. We found that the 28 °C EE2 treatment significantly decreased the expression of nearly all genes measured in the F1 larvae. This pattern was transferred to the F2 generation for expression of the follicle-stimulating hormone receptor (FSHR) gene. Expression of 17β-hydroxysteroid dehydrogenase (17β-HSD) and G protein-coupled receptor 30 (GPR30) revealed changes not measured in the previous generation. Effects of the bifenthrin treatments were not observed until the F2 generation, which were exposed to the chemicals indirectly as germ cells. Our results indicate that effects of EDCs and their interactions with abiotic factors, may not be adequately represented by singular generation tes…
bibliographic citation: DeCourten et al. (2019) Direct and indirect parental exposure to endocrine disruptors and elevated temperature influences gene expression across generations in a euryhaline model fish. PeerJ 7:e6156 https://doi.org/10.7717/peerj.6156
date submitted: 2018-06-26
date accepted: 2018-11-24
issued: 2019-01-08
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: DeCourten
  given name: Bethany M.
author list: Agent
  family name: Connon
  given name: Richard E.
author list: Agent
  family name: Brander
  given name: Susanne M.
doi: 10.7717/peerj.6156
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-01-08
copyright: ©2019 DeCourten et al.
attribution name: DeCourten et al.

High tempo music prolongs high intensity exercise
type: item
type: AcademicArticle
description: Music has been shown to reduce rating of perceived exertion, increase exercise enjoyment and enhance exercise performance, mainly in low-moderate intensity exercises. However, the effects of music are less conclusive with high-intensity activities. The purpose of this with-participant design study was to compare the effects of high tempo music (130 bpm) to a no-music condition during repeated high intensity cycling bouts (80% of peak power output (PPO)) on the following measures: time to exercise end-point, rating of perceived exertion (RPE), heart rate (HR), breathing frequency, ventilatory kinetics and blood lactate (BL). Under the music condition, participants exercised 10.7% longer (p = 0.035; Effect size (ES) = 0.28) (increase of 1 min) and had higher HR (4%; p = 0.043; ES = 0.25), breathing frequency (11.6%; p < 0.001; ES = 0.57), and RER (7% at TTF; p = 0.021; ES = 1.1) during exercise, as measured at the exercise end-point. Trivial differences were observed between conditions in RPE and other ventilatory kinetics during exercise. Interestingly, 5 min post-exercise termination, HR recovery was 13.0% faster following the music condition (p < 0.05) despite that music was not played during this period. These results strengthen the notion that music can alter the association between central motor drive, central cardiovascular command and perceived exertion, and contribute to prolonged exercise durations at higher intensities along with a quicken HR recovery.
format: application/pdf
format: text/html
creator: Meaghan E. Maddigan
creator: Kathleen M. Sullivan
creator: Israel Halperin
creator: Fabien A. Basset
creator: David G. Behm
subject: Kinesiology
description: doi:10.7717/peerj.6164
publisher: PeerJ Inc.
rights: © 2019 Maddigan et al.
abstract: Music has been shown to reduce rating of perceived exertion, increase exercise enjoyment and enhance exercise performance, mainly in low-moderate intensity exercises. However, the effects of music are less conclusive with high-intensity activities. The purpose of this with-participant design study was to compare the effects of high tempo music (130 bpm) to a no-music condition during repeated high intensity cycling bouts (80% of peak power output (PPO)) on the following measures: time to exercise end-point, rating of perceived exertion (RPE), heart rate (HR), breathing frequency, ventilatory kinetics and blood lactate (BL). Under the music condition, participants exercised 10.7% longer (p = 0.035; Effect size (ES) = 0.28) (increase of 1 min) and had higher HR (4%; p = 0.043; ES = 0.25), breathing frequency (11.6%; p < 0.001; ES = 0.57), and RER (7% at TTF; p = 0.021; ES = 1.1) during exercise, as measured at the exercise end-point. Trivial differences were observed between conditions in RPE and other ventilatory kinetics during exercise. Interestingly, 5 min post-exercise termination, HR recovery was 13.0% faster following the music condition (p < 0.05) despite that music was not played during this period. These results strengthen the notion that music can alter the association between central motor drive, central cardiovascular command and perceived exertion, and contribute to prolonged exercise durations at higher intensities along with a quicken HR recovery.
bibliographic citation: Maddigan et al. (2019) High tempo music prolongs high intensity exercise. PeerJ 6:e6164 https://doi.org/10.7717/peerj.6164
date submitted: 2018-07-17
date accepted: 2018-11-27
issued: 2019-01-08
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Maddigan
  given name: Meaghan E.
author list: Agent
  family name: Sullivan
  given name: Kathleen M.
author list: Agent
  family name: Halperin
  given name: Israel
author list: Agent
  family name: Basset
  given name: Fabien A.
author list: Agent
  family name: Behm
  given name: David G.
doi: 10.7717/peerj.6164
volume: 6
issn: 2167-8359
publication name: PeerJ
publication date: 2019-01-08
copyright: © 2019 Maddigan et al.
attribution name: Maddigan et al.

hdac4 mediates perichondral ossification and pharyngeal skeleton development in the zebrafish
type: item
type: AcademicArticle
description: Background Histone deacetylases (HDACs) are epigenetic factors that function to repress gene transcription by removing acetyl groups from the N-terminal of histone lysines. Histone deacetylase 4 (HDAC4), a class IIa HDAC, has previously been shown to regulate the process of endochondral ossification in mice via repression of Myocyte enhancer factor 2c (MEF2C), a transcriptional activator of Runx2, which in turn promotes chondrocyte maturation and production of bone by osteoblasts. Methods & Materials In this study, we generated two zebrafish lines with mutations in hdac4 using CRISPR/Cas9 and analyzed mutants for skeletal phenotypes and expression of genes known to be affected by Hdac4 expression. Results Lines have insertions causing a frameshift in a proximal exon of hdac4 and a premature stop codon. Mutations are predicted to result in aberrant protein sequence and a truncated protein, eliminating the Mef2c binding domain and Hdac domain. Zygotic mutants from two separate lines show a significant increase in ossification of pharyngeal ceratohyal cartilages at 7 days post fertilization (dpf) (p < 0.01, p < 0.001). At 4 dpf, mutant larvae have a significant increase of expression of runx2a and runx2b in the ceratohyal cartilage (p < 0.05 and p < 0.01, respectively). A subset of maternal-zygotic (mz) mutant and heterozygote larvae (40%) have dramatically increased ossification at 7 dpf compared to zygotic mutants, including formation of a premature anguloarticular bone and mineralization of the first and second ceratobranchial cartilages and symplectic cartilages, which normally does not occur until fish are approximately 10 or 12 dpf. Some maternal-zygotic mutants and heterozygotes show loss of pharyngeal first arch elements (25.9% and 10.2%, respectively) and neurocranium defects (30.8% and 15.2%, respectively). Analysis of RNA-seq mRNA transcript levels and in situ hybridizations from zygotic stages to 75–90% epiboly indicates that hdac4 is highly expressed in ea…
format: application/pdf
format: text/html
creator: April DeLaurier
creator: Cynthia Lizzet Alvarez
creator: Kali J Wiggins
subject: Developmental Biology
subject: Molecular Biology
description: doi:10.7717/peerj.6167
publisher: PeerJ Inc.
rights: © 2019 DeLaurier et al.
abstract: Background Histone deacetylases (HDACs) are epigenetic factors that function to repress gene transcription by removing acetyl groups from the N-terminal of histone lysines. Histone deacetylase 4 (HDAC4), a class IIa HDAC, has previously been shown to regulate the process of endochondral ossification in mice via repression of Myocyte enhancer factor 2c (MEF2C), a transcriptional activator of Runx2, which in turn promotes chondrocyte maturation and production of bone by osteoblasts. Methods & Materials In this study, we generated two zebrafish lines with mutations in hdac4 using CRISPR/Cas9 and analyzed mutants for skeletal phenotypes and expression of genes known to be affected by Hdac4 expression. Results Lines have insertions causing a frameshift in a proximal exon of hdac4 and a premature stop codon. Mutations are predicted to result in aberrant protein sequence and a truncated protein, eliminating the Mef2c binding domain and Hdac domain. Zygotic mutants from two separate lines show a significant increase in ossification of pharyngeal ceratohyal cartilages at 7 days post fertilization (dpf) (p < 0.01, p < 0.001). At 4 dpf, mutant larvae have a significant increase of expression of runx2a and runx2b in the ceratohyal cartilage (p < 0.05 and p < 0.01, respectively). A subset of maternal-zygotic (mz) mutant and heterozygote larvae (40%) have dramatically increased ossification at 7 dpf compared to zygotic mutants, including formation of a premature anguloarticular bone and mineralization of the first and second ceratobranchial cartilages and symplectic cartilages, which normally does not occur until fish are approximately 10 or 12 dpf. Some maternal-zygotic mutants and heterozygotes show loss of pharyngeal first arch elements (25.9% and 10.2%, respectively) and neurocranium defects (30.8% and 15.2%, respectively). Analysis of RNA-seq mRNA transcript levels and in situ hybridizations from zygotic stages to 75–90% epiboly indicates that hdac4 is highly expressed in ea…
bibliographic citation: DeLaurier et al. (2019) hdac4 mediates perichondral ossification and pharyngeal skeleton development in the zebrafish. PeerJ 7:e6167 https://doi.org/10.7717/peerj.6167
date submitted: 2018-07-16
date accepted: 2018-11-27
issued: 2019-01-08
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: DeLaurier
  given name: April
author list: Agent
  family name: Alvarez
  given name: Cynthia Lizzet
author list: Agent
  family name: Wiggins
  given name: Kali J
doi: 10.7717/peerj.6167
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-01-08
copyright: ©2019 DeLaurier et al.
attribution name: DeLaurier et al.

The origin of exotic pet sugar gliders (Petaurus breviceps) kept in the United States of America
type: item
type: AcademicArticle
description: The demand for exotic non-domesticated animals kept as pets in the United States of America (USA) is increasing the exportation rates of these species from their native ranges. Often, illegal harvesting of these species is used to boost captive-bred numbers and meet this demand. One such species, the sugar glider (Petaurus breviceps), endemic to Australia and New Guinea is a popular domestic pet due to its small size and “cute” demeanour. Despite a legal avenue for trade existing in Indonesia, concerns have been raised that sugar gliders may be entering the USA from other parts of their native range where exportation is prohibited such as Australia, Papua New Guinea and the surrounding Indonesian islands. We compared previously published DNA sequences from across the native range of sugar gliders with samples collected from domestically kept sugar gliders within the USA to determine provenance and gene flow between source and introduced populations. Here we show that as predicted, the USA sugar glider population originates from West Papua, Indonesia with no illegal harvesting from other native areas such as Papua New Guinea or Australia evident in the samples tested within this study.
format: application/pdf
format: text/html
creator: Catriona D. Campbell
creator: Jill Pecon-Slattery
creator: Rebecca Pollak
creator: Leo Joseph
creator: Clare E. Holleley
subject: Biodiversity
subject: Conservation Biology
subject: Ecology
subject: Genetics
subject: Population Biology
description: doi:10.7717/peerj.6180
publisher: PeerJ Inc.
rights: © 2019 Campbell et al.
abstract: The demand for exotic non-domesticated animals kept as pets in the United States of America (USA) is increasing the exportation rates of these species from their native ranges. Often, illegal harvesting of these species is used to boost captive-bred numbers and meet this demand. One such species, the sugar glider (Petaurus breviceps), endemic to Australia and New Guinea is a popular domestic pet due to its small size and “cute” demeanour. Despite a legal avenue for trade existing in Indonesia, concerns have been raised that sugar gliders may be entering the USA from other parts of their native range where exportation is prohibited such as Australia, Papua New Guinea and the surrounding Indonesian islands. We compared previously published DNA sequences from across the native range of sugar gliders with samples collected from domestically kept sugar gliders within the USA to determine provenance and gene flow between source and introduced populations. Here we show that as predicted, the USA sugar glider population originates from West Papua, Indonesia with no illegal harvesting from other native areas such as Papua New Guinea or Australia evident in the samples tested within this study.
bibliographic citation: Campbell et al. (2019) The origin of exotic pet sugar gliders (Petaurus breviceps) kept in the United States of America. PeerJ 7:e6180 https://doi.org/10.7717/peerj.6180
date submitted: 2018-08-08
date accepted: 2018-11-29
issued: 2019-01-08
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Campbell
  given name: Catriona D.
author list: Agent
  family name: Pecon-Slattery
  given name: Jill
author list: Agent
  family name: Pollak
  given name: Rebecca
author list: Agent
  family name: Joseph
  given name: Leo
author list: Agent
  family name: Holleley
  given name: Clare E.
doi: 10.7717/peerj.6180
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-01-08
copyright: ©2019 Campbell et al.
attribution name: Campbell et al.

Hardly habitual: chimpanzees and gorillas show flexibility in their motor responses when presented with a causally-clear task
type: item
type: AcademicArticle
description: In contrast to reports of wild primates, studies of captive primates’ flexibility often reveal conservatism: individuals are unable to switch to new and more efficient strategies when task demands change. We propose that such conservatism might be a result of task design and hypothesize that conservatism might be linked to primates’ lack of causal understanding in relation to experimental apparatuses. We investigated if chimpanzees (Pan troglodytes) and western lowland gorillas (Gorilla gorilla gorilla) would show greater flexibility when presented with a causally-clear task. We presented six chimpanzees and seven gorillas with a clear tube from which they had to remove straws to release a reward. To first evaluate the apes’ causal understanding, we recorded the efficiency with which the apes solved the task (i.e., whether they only removed straws below the reward, ignoring redundant ones above it). To further explore how they solved the task, we also recorded the order in which they removed the straws, which allowed us to determine if habitual action sequences emerged. All apes spontaneously solved the task in their first trial and across repeated trials the majority of their solutions were efficient (median = 90.9%), demonstrating their understanding of the puzzle. There was individual variation in the consistency of straw removal patterns exhibited by the apes, but no ape developed an exclusive habit in the order with which they removed the straws, further indicating their causal understanding of the task. Next, we presented the apes with a new configuration of the same task that required the apes to remove fewer straws to obtain the reward. All apes switched to a more efficient straw removal sequence even though their previously-successful, but now less-efficient, solution remained available. We theorize that because the apes understood the causality of the task, they did not form habits and were not conservative.
format: application/pdf
format: text/html
creator: Sarah L. Jacobson
creator: Lydia M. Hopper
subject: Animal Behaviour
subject: Zoology
subject: Psychiatry and Psychology
description: doi:10.7717/peerj.6195
publisher: PeerJ Inc.
rights: © 2019 Jacobson and Hopper
abstract: In contrast to reports of wild primates, studies of captive primates’ flexibility often reveal conservatism: individuals are unable to switch to new and more efficient strategies when task demands change. We propose that such conservatism might be a result of task design and hypothesize that conservatism might be linked to primates’ lack of causal understanding in relation to experimental apparatuses. We investigated if chimpanzees (Pan troglodytes) and western lowland gorillas (Gorilla gorilla gorilla) would show greater flexibility when presented with a causally-clear task. We presented six chimpanzees and seven gorillas with a clear tube from which they had to remove straws to release a reward. To first evaluate the apes’ causal understanding, we recorded the efficiency with which the apes solved the task (i.e., whether they only removed straws below the reward, ignoring redundant ones above it). To further explore how they solved the task, we also recorded the order in which they removed the straws, which allowed us to determine if habitual action sequences emerged. All apes spontaneously solved the task in their first trial and across repeated trials the majority of their solutions were efficient (median = 90.9%), demonstrating their understanding of the puzzle. There was individual variation in the consistency of straw removal patterns exhibited by the apes, but no ape developed an exclusive habit in the order with which they removed the straws, further indicating their causal understanding of the task. Next, we presented the apes with a new configuration of the same task that required the apes to remove fewer straws to obtain the reward. All apes switched to a more efficient straw removal sequence even though their previously-successful, but now less-efficient, solution remained available. We theorize that because the apes understood the causality of the task, they did not form habits and were not conservative.
bibliographic citation: Jacobson et al. (2019) Hardly habitual: chimpanzees and gorillas show flexibility in their motor responses when presented with a causally-clear task. PeerJ 7:e6195 https://doi.org/10.7717/peerj.6195
date submitted: 2018-09-21
date accepted: 2018-12-01
issued: 2019-01-08
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Jacobson
  given name: Sarah L.
author list: Agent
  family name: Hopper
  given name: Lydia M.
doi: 10.7717/peerj.6195
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-01-08
copyright: ©2019 Jacobson and Hopper
attribution name: Jacobson and Hopper

Inhibition of MEK1/2 and GSK3 (2i system) affects blastocyst quality and early differentiation of porcine parthenotes
type: item
type: AcademicArticle
description: Inhibition of both MEK1/2 and glycogen synthase kinase-3 (GSK3; 2i system) facilitates the maintenance of naïve stemness for embryonic stem cells in various mammalian species. However, the effect of the inhibition of the 2i system on porcine early embryogenesis is unknown. We investigated the effect of the 2i system on early embryo development, expression of pluripotency-related genes, and epigenetic modifications. Inhibition of MEK1/2 (by PD0325901) and/or GSK3 (by CHIR99021) did not alter the developmental potential of porcine parthenogenetic embryos, but improved blastocyst quality, as judged by the blastocyst cell number, diameter, and reduction in the number of apoptotic cells. The expression levels of octamer-binding transcription factor 4 and SOX2, the primary transcription factors that maintain embryonic pluripotency, were significantly increased by 2i treatments. Epigenetic modification-related gene expression was altered upon 2i treatment. The collective results indicate that the 2i system in porcine embryos improved embryo developmental potential and blastocyst quality by regulating epigenetic modifications and pluripotency-related gene expression.
format: application/pdf
format: text/html
creator: Jeongwoo Kwon
creator: Ying-Hua Li
creator: Yu-Jin Jo
creator: YoungJin Oh
creator: Suk Namgoong
creator: Nam-Hyung Kim
subject: Cell Biology
subject: Developmental Biology
subject: Zoology
description: doi:10.7717/peerj.5840
publisher: PeerJ Inc.
rights: © 2019 Kwon et al.
abstract: Inhibition of both MEK1/2 and glycogen synthase kinase-3 (GSK3; 2i system) facilitates the maintenance of naïve stemness for embryonic stem cells in various mammalian species. However, the effect of the inhibition of the 2i system on porcine early embryogenesis is unknown. We investigated the effect of the 2i system on early embryo development, expression of pluripotency-related genes, and epigenetic modifications. Inhibition of MEK1/2 (by PD0325901) and/or GSK3 (by CHIR99021) did not alter the developmental potential of porcine parthenogenetic embryos, but improved blastocyst quality, as judged by the blastocyst cell number, diameter, and reduction in the number of apoptotic cells. The expression levels of octamer-binding transcription factor 4 and SOX2, the primary transcription factors that maintain embryonic pluripotency, were significantly increased by 2i treatments. Epigenetic modification-related gene expression was altered upon 2i treatment. The collective results indicate that the 2i system in porcine embryos improved embryo developmental potential and blastocyst quality by regulating epigenetic modifications and pluripotency-related gene expression.
bibliographic citation: Kwon et al. (2019) Inhibition of MEK1/2 and GSK3 (2i system) affects blastocyst quality and early differentiation of porcine parthenotes. PeerJ 6:e5840 https://doi.org/10.7717/peerj.5840
date submitted: 2018-07-02
date accepted: 2018-09-28
issued: 2019-01-07
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Kwon
  given name: Jeongwoo
author list: Agent
  family name: Li
  given name: Ying-Hua
author list: Agent
  family name: Jo
  given name: Yu-Jin
author list: Agent
  family name: Oh
  given name: YoungJin
author list: Agent
  family name: Namgoong
  given name: Suk
author list: Agent
  family name: Kim
  given name: Nam-Hyung
doi: 10.7717/peerj.5840
volume: 6
issn: 2167-8359
publication name: PeerJ
publication date: 2019-01-07
copyright: © 2019 Kwon et al.
attribution name: Kwon et al.

Ocean acidification alters morphology of all otolith types in Clark’s anemonefish (Amphiprion clarkii)
type: item
type: AcademicArticle
description: Ocean acidification, the ongoing decline of surface ocean pH and [CO ${}_{3}^{2-}$ 3 2 − ] due to absorption of surplus atmospheric CO2, has far-reaching consequences for marine biota, especially calcifiers. Among these are teleost fishes, which internally calcify otoliths, critical elements of the inner ear and vestibular system. There is evidence in the literature that ocean acidification increases otolith size and alters shape, perhaps impacting otic mechanics and thus sensory perception. Here, larval Clark’s anemonefish, Amphiprion clarkii (Bennett, 1830), were reared in various seawater pCO2/pH treatments analogous to future ocean scenarios. At the onset of metamorphosis, all otoliths were removed from each individual fish and analyzed for treatment effects on morphometrics including area, perimeter, and circularity; scanning electron microscopy was used to screen for evidence of treatment effects on lateral development, surface roughness, and vaterite replacement. The results corroborate those of other experiments with other taxa that observed otolith growth with elevated pCO2, and provide evidence that lateral development and surface roughness increased as well. Both sagittae exhibited increasing area, perimeter, lateral development, and roughness; left lapilli exhibited increasing area and perimeter while right lapilli exhibited increasing lateral development and roughness; and left asterisci exhibited increasing perimeter, roughness, and ellipticity with increasing pCO2. Right lapilli and left asterisci were only impacted by the most extreme pCO2 treatment, suggesting they are resilient to any conditions short of aragonite undersaturation, while all other impacted otoliths responded to lower concentrations. Finally, fish settlement competency at 10 dph was dramatically reduced, and fish standard length marginally reduced with increasing pCO2. Increasing abnormality and asymmetry of otoliths may impact inner ear function by altering otolith-maculae interacti…
format: application/pdf
format: text/html
creator: Robert J. Holmberg
creator: Eric Wilcox-Freeburg
creator: Andrew L. Rhyne
creator: Michael F. Tlusty
creator: Alan Stebbins
creator: Steven W. Nye Jr.
creator: Aaron Honig
creator: Amy E. Johnston
creator: Christine M. San Antonio
creator: Bradford Bourque
creator: Robyn E. Hannigan
subject: Aquaculture, Fisheries and Fish Science
subject: Marine Biology
subject: Climate Change Biology
description: doi:10.7717/peerj.6152
publisher: PeerJ Inc.
rights: © 2019 Holmberg et al.
abstract: Ocean acidification, the ongoing decline of surface ocean pH and [CO ${}_{3}^{2-}$ 3 2 − ] due to absorption of surplus atmospheric CO2, has far-reaching consequences for marine biota, especially calcifiers. Among these are teleost fishes, which internally calcify otoliths, critical elements of the inner ear and vestibular system. There is evidence in the literature that ocean acidification increases otolith size and alters shape, perhaps impacting otic mechanics and thus sensory perception. Here, larval Clark’s anemonefish, Amphiprion clarkii (Bennett, 1830), were reared in various seawater pCO2/pH treatments analogous to future ocean scenarios. At the onset of metamorphosis, all otoliths were removed from each individual fish and analyzed for treatment effects on morphometrics including area, perimeter, and circularity; scanning electron microscopy was used to screen for evidence of treatment effects on lateral development, surface roughness, and vaterite replacement. The results corroborate those of other experiments with other taxa that observed otolith growth with elevated pCO2, and provide evidence that lateral development and surface roughness increased as well. Both sagittae exhibited increasing area, perimeter, lateral development, and roughness; left lapilli exhibited increasing area and perimeter while right lapilli exhibited increasing lateral development and roughness; and left asterisci exhibited increasing perimeter, roughness, and ellipticity with increasing pCO2. Right lapilli and left asterisci were only impacted by the most extreme pCO2 treatment, suggesting they are resilient to any conditions short of aragonite undersaturation, while all other impacted otoliths responded to lower concentrations. Finally, fish settlement competency at 10 dph was dramatically reduced, and fish standard length marginally reduced with increasing pCO2. Increasing abnormality and asymmetry of otoliths may impact inner ear function by altering otolith-maculae interacti…
bibliographic citation: Holmberg et al. (2019) Ocean acidification alters morphology of all otolith types in Clark’s anemonefish (Amphiprion clarkii). PeerJ 7:e6152 https://doi.org/10.7717/peerj.6152
date submitted: 2018-07-16
date accepted: 2018-11-23
issued: 2019-01-07
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Holmberg
  given name: Robert J.
author list: Agent
  family name: Wilcox-Freeburg
  given name: Eric
author list: Agent
  family name: Rhyne
  given name: Andrew L.
author list: Agent
  family name: Tlusty
  given name: Michael F.
author list: Agent
  family name: Stebbins
  given name: Alan
author list: Agent
  family name: Nye Jr.
  given name: Steven W.
author list: Agent
  family name: Honig
  given name: Aaron
author list: Agent
  family name: Johnston
  given name: Amy E.
author list: Agent
  family name: San Antonio
  given name: Christine M.
author list: Agent
  family name: Bourque
  given name: Bradford
author list: Agent
  family name: Hannigan
  given name: Robyn E.
doi: 10.7717/peerj.6152
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-01-07
copyright: ©2019 Holmberg et al.
attribution name: Holmberg et al.

Relationship between physical and cognitive performance in community dwelling, ethnically diverse older adults: a cross-sectional study
type: item
type: AcademicArticle
description: Background Regular exercise training stimulates physiological adaptations to improve physical performance, reduce chronic disease risk, and slow age-related cognitive decline. Since the physiological mechanisms responsible for aging-associated cognitive decline are not yet fully understood, and training-induced physiological adaptations responsible for performance measure improvements are specific to the type (aerobic vs. strength) and intensity of training, studies are needed to assess the relationships between physical performance measures and cognitive performance in older adults. These results could be used to guide exercise prescriptions with the goal of improving age-related cognitive performance. The purpose of this study was to investigate the relationship between physical performance measures and cognitive performance in a population of community dwelling, ethnically diverse older adults. Methods The cognitive performance of ninety independent, community dwelling participants (69 female, 21 male), aged 75 ± 9.5 years (mean ± SD) was measured with the Modified Mini-Mental State Test (3MS), Trailmaking Tests A and B (TMT A & B), and the Animal Naming test. Sociodemographic (age, sex, ethnicity, medication use, years of education) and anthropometric data were collected, physical activity was assessed with the Physical Activity Scale for the Elderly (PASE), peak hand-grip strength, distance walked in the 6MWT, and heart rate pre-, during, and up to 5 min. post- 6MWT were measured. Forward stepwise multiple regression analyses were performed with each cognitive measure as a dependent variable. Results and Discussion Controlling for sociodemographic covariates, peak heart rate during the 6MWT (6MWT HRPEAK) was positively correlated with performance in the 3MS (p < 0.017), and TMT A (p < 0.001) and B (p < 0.029). Controlling for sociodemographic covariates, PASE was positively (p = 0.001), and β-blocker use negatively (p = 0.035), correlated with performance on th…
format: application/pdf
format: text/html
creator: Jennifer J. Sherwood
creator: Cathy Inouye
creator: Shannon L. Webb
creator: Ange Zhou
creator: Erik A. Anderson
creator: Nicole S. Spink
subject: Geriatrics
subject: Kinesiology
description: doi:10.7717/peerj.6159
publisher: PeerJ Inc.
rights: © 2019 Sherwood et al.
abstract: Background Regular exercise training stimulates physiological adaptations to improve physical performance, reduce chronic disease risk, and slow age-related cognitive decline. Since the physiological mechanisms responsible for aging-associated cognitive decline are not yet fully understood, and training-induced physiological adaptations responsible for performance measure improvements are specific to the type (aerobic vs. strength) and intensity of training, studies are needed to assess the relationships between physical performance measures and cognitive performance in older adults. These results could be used to guide exercise prescriptions with the goal of improving age-related cognitive performance. The purpose of this study was to investigate the relationship between physical performance measures and cognitive performance in a population of community dwelling, ethnically diverse older adults. Methods The cognitive performance of ninety independent, community dwelling participants (69 female, 21 male), aged 75 ± 9.5 years (mean ± SD) was measured with the Modified Mini-Mental State Test (3MS), Trailmaking Tests A and B (TMT A & B), and the Animal Naming test. Sociodemographic (age, sex, ethnicity, medication use, years of education) and anthropometric data were collected, physical activity was assessed with the Physical Activity Scale for the Elderly (PASE), peak hand-grip strength, distance walked in the 6MWT, and heart rate pre-, during, and up to 5 min. post- 6MWT were measured. Forward stepwise multiple regression analyses were performed with each cognitive measure as a dependent variable. Results and Discussion Controlling for sociodemographic covariates, peak heart rate during the 6MWT (6MWT HRPEAK) was positively correlated with performance in the 3MS (p < 0.017), and TMT A (p < 0.001) and B (p < 0.029). Controlling for sociodemographic covariates, PASE was positively (p = 0.001), and β-blocker use negatively (p = 0.035), correlated with performance on th…
bibliographic citation: Sherwood et al. (2019) Relationship between physical and cognitive performance in community dwelling, ethnically diverse older adults: a cross-sectional study. PeerJ 7:e6159 https://doi.org/10.7717/peerj.6159
date submitted: 2018-07-25
date accepted: 2018-11-26
issued: 2019-01-07
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Sherwood
  given name: Jennifer J.
author list: Agent
  family name: Inouye
  given name: Cathy
author list: Agent
  family name: Webb
  given name: Shannon L.
author list: Agent
  family name: Zhou
  given name: Ange
author list: Agent
  family name: Anderson
  given name: Erik A.
author list: Agent
  family name: Spink
  given name: Nicole S.
doi: 10.7717/peerj.6159
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-01-07
copyright: ©2019 Sherwood et al.
attribution name: Sherwood et al.

Diversity analysis of the rhizospheric and endophytic bacterial communities of Senecio vulgaris L. (Asteraceae) in an invasive range
type: item
type: AcademicArticle
description: Increasing evidence has confirmed the importance of plant-associated bacteria for plant growth and productivity, and thus it is hypothesized that interactions between bacteria and alien plants might play an important role in plant invasions. However, the diversity of the bacterial communities associated with invasive plants is poorly understood. We therefore investigated the diversity of rhizospheric and endophytic bacteria associated with the invasive annual plant Senecio vulgaris L. (Asteraceae) based on 16S rRNA gene data obtained from 57 samples of four Senecio vulgaris populations in a subtropical mountainous area in central China. Significant differences in diversity were observed between plant compartments. Specifically, the rhizosphere harbored many more bacterial operational taxonomic units and showed higher alpha diversity than the leaf and root endospheres. The relative abundance profiles of the bacterial community composition differed substantially between the compartments and populations, especially at the phylum and family levels. However, the top five phyla (Proteobacteria, Firmicutes, Bacteroidetes, Actinobacteria, and Acidobacteria) accounted for more than 90% of all the bacterial communities. Moreover, similar endophytic communities with a shared core set of bacteria were observed from different Senecio vulgaris populations. Heavy-metal-resistant, phosphate-solubilizing bacteria (Brevundimonas diminuta), nitrogen-fixing bacteria (Rhizobium leguminosarum), and cold-resistant bacteria (Exiguobacterium sibiricum) were present in the endosphere at relatively high abundance. This study, which reveals the structure of bacterial communities and their putative function in invasive Senecio vulgaris plants, is the first step in investigating the role of plant–bacteria interactions in the invasion of this species in China.
format: application/pdf
format: text/html
creator: Dandan Cheng
creator: Zhongsai Tian
creator: Liang Feng
creator: Lin Xu
creator: Hongmei Wang
subject: Biodiversity
subject: Ecology
subject: Microbiology
subject: Plant Science
description: doi:10.7717/peerj.6162
publisher: PeerJ Inc.
rights: © 2019 Cheng et al.
abstract: Increasing evidence has confirmed the importance of plant-associated bacteria for plant growth and productivity, and thus it is hypothesized that interactions between bacteria and alien plants might play an important role in plant invasions. However, the diversity of the bacterial communities associated with invasive plants is poorly understood. We therefore investigated the diversity of rhizospheric and endophytic bacteria associated with the invasive annual plant Senecio vulgaris L. (Asteraceae) based on 16S rRNA gene data obtained from 57 samples of four Senecio vulgaris populations in a subtropical mountainous area in central China. Significant differences in diversity were observed between plant compartments. Specifically, the rhizosphere harbored many more bacterial operational taxonomic units and showed higher alpha diversity than the leaf and root endospheres. The relative abundance profiles of the bacterial community composition differed substantially between the compartments and populations, especially at the phylum and family levels. However, the top five phyla (Proteobacteria, Firmicutes, Bacteroidetes, Actinobacteria, and Acidobacteria) accounted for more than 90% of all the bacterial communities. Moreover, similar endophytic communities with a shared core set of bacteria were observed from different Senecio vulgaris populations. Heavy-metal-resistant, phosphate-solubilizing bacteria (Brevundimonas diminuta), nitrogen-fixing bacteria (Rhizobium leguminosarum), and cold-resistant bacteria (Exiguobacterium sibiricum) were present in the endosphere at relatively high abundance. This study, which reveals the structure of bacterial communities and their putative function in invasive Senecio vulgaris plants, is the first step in investigating the role of plant–bacteria interactions in the invasion of this species in China.
bibliographic citation: Cheng et al. (2019) Diversity analysis of the rhizospheric and endophytic bacterial communities of Senecio vulgaris L. (Asteraceae) in an invasive range. PeerJ 6:e6162 https://doi.org/10.7717/peerj.6162
date submitted: 2018-03-13
date accepted: 2018-11-25
issued: 2019-01-07
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Cheng
  given name: Dandan
author list: Agent
  family name: Tian
  given name: Zhongsai
author list: Agent
  family name: Feng
  given name: Liang
author list: Agent
  family name: Xu
  given name: Lin
author list: Agent
  family name: Wang
  given name: Hongmei
doi: 10.7717/peerj.6162
volume: 6
issn: 2167-8359
publication name: PeerJ
publication date: 2019-01-07
copyright: © 2019 Cheng et al.
attribution name: Cheng et al.

Intestinal parasitic infection alters bacterial gut microbiota in children
type: item
type: AcademicArticle
description: The study of the burden that parasites can exert upon the bacterial gut microbiota was restricted by the available technologies and their costs. Currently, next-generation sequencing coupled with traditional methodologies allows the study of eukaryotic parasites (protozoa and helminths) and its effects on the human bacterial gut microbiota diversity. This diversity can be altered by a variety of factors such as age, diet, genetics and parasitic infections among others. The disturbances of the gut microbiota have been associated with a variety of illnesses. Children population in developing countries, are especially susceptible to parasitic infections because of the lack of proper sanitation and undernutrition, allowing both, the thriving of intestinal parasites and profound alteration of the gut microbiota. In this work, we have sampled the stool of 23 children from four different children’s care-centers in Medellin, Colombia, and we have identified the eukaryotic parasites by traditional and molecular methodologies coupled with microbial profiling using 16S rDNA sequencing. This mixed methodology approach has allowed us to establish an interesting relationship between Giardia intestinalis and helminth infection, having both effects upon the bacterial gut microbiota enterotypes, causing a switch from a type I to a type II enterotype upon infection.
format: application/pdf
format: text/html
creator: Miguel A. Toro-Londono
creator: Katherine Bedoya-Urrego
creator: Gisela M. Garcia-Montoya
creator: Ana L. Galvan-Diaz
creator: Juan F. Alzate
subject: Bioinformatics
subject: Microbiology
subject: Parasitology
subject: Infectious Diseases
subject: Pediatrics
description: doi:10.7717/peerj.6200
publisher: PeerJ Inc.
rights: © 2019 Toro-Londono et al.
abstract: The study of the burden that parasites can exert upon the bacterial gut microbiota was restricted by the available technologies and their costs. Currently, next-generation sequencing coupled with traditional methodologies allows the study of eukaryotic parasites (protozoa and helminths) and its effects on the human bacterial gut microbiota diversity. This diversity can be altered by a variety of factors such as age, diet, genetics and parasitic infections among others. The disturbances of the gut microbiota have been associated with a variety of illnesses. Children population in developing countries, are especially susceptible to parasitic infections because of the lack of proper sanitation and undernutrition, allowing both, the thriving of intestinal parasites and profound alteration of the gut microbiota. In this work, we have sampled the stool of 23 children from four different children’s care-centers in Medellin, Colombia, and we have identified the eukaryotic parasites by traditional and molecular methodologies coupled with microbial profiling using 16S rDNA sequencing. This mixed methodology approach has allowed us to establish an interesting relationship between Giardia intestinalis and helminth infection, having both effects upon the bacterial gut microbiota enterotypes, causing a switch from a type I to a type II enterotype upon infection.
bibliographic citation: Toro-Londono et al. (2019) Intestinal parasitic infection alters bacterial gut microbiota in children. PeerJ 7:e6200 https://doi.org/10.7717/peerj.6200
date submitted: 2018-08-26
date accepted: 2018-12-03
issued: 2019-01-07
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Toro-Londono
  given name: Miguel A.
author list: Agent
  family name: Bedoya-Urrego
  given name: Katherine
author list: Agent
  family name: Garcia-Montoya
  given name: Gisela M.
author list: Agent
  family name: Galvan-Diaz
  given name: Ana L.
author list: Agent
  family name: Alzate
  given name: Juan F.
doi: 10.7717/peerj.6200
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-01-07
copyright: ©2019 Toro-Londono et al.
attribution name: Toro-Londono et al.

Phylogeny of Paleozoic limbed vertebrates reassessed through revision and expansion of the largest published relevant data matrix
type: item
type: AcademicArticle
description: The largest published phylogenetic analysis of early limbed vertebrates (Ruta M, Coates MI. 2007. Journal of Systematic Palaeontology 5:69–122) recovered, for example, Seymouriamorpha, Diadectomorpha and (in some trees) Caudata as paraphyletic and found the “temnospondyl hypothesis” on the origin of Lissamphibia (TH) to be more parsimonious than the “lepospondyl hypothesis” (LH)—though only, as we show, by one step. We report 4,200 misscored cells, over half of them due to typographic and similar accidental errors. Further, some characters were duplicated; some had only one described state; for one, most taxa were scored after presumed relatives. Even potentially continuous characters were unordered, the effects of ontogeny were not sufficiently taken into account, and data published after 2001 were mostly excluded. After these issues are improved—we document and justify all changes to the matrix—but no characters are added, we find (Analysis R1) much longer trees with, for example, monophyletic Caudata, Diadectomorpha and (in some trees) Seymouriamorpha; Ichthyostega either crownward or rootward of Acanthostega; and Anthracosauria either crownward or rootward of Temnospondyli. The LH is nine steps shorter than the TH (R2; constrained) and 12 steps shorter than the “polyphyly hypothesis” (PH—R3; constrained). Brachydectes (Lysorophia) is not found next to Lissamphibia; instead, a large clade that includes the adelogyrinids, urocordylid “nectrideans” and aïstopods occupies that position. As expected from the taxon/character ratio, most bootstrap values are low. Adding 56 terminal taxa to the original 102 increases the resolution (and decreases most bootstrap values). The added taxa range in completeness from complete articulated skeletons to an incomplete lower jaw. Even though the lissamphibian-like temnospondyls Gerobatrachus, Micropholis and Tungussogyrinus and the extremely peramorphic salamander Chelotriton are added, the difference between LH (R4; unconstrained…
format: application/pdf
format: text/html
creator: David Marjanović
creator: Michel Laurin
subject: Biodiversity
subject: Ecology
subject: Evolutionary Studies
subject: Paleontology
subject: Zoology
description: doi:10.7717/peerj.5565
publisher: PeerJ Inc.
rights: © 2019 Marjanović and Laurin
abstract: The largest published phylogenetic analysis of early limbed vertebrates (Ruta M, Coates MI. 2007. Journal of Systematic Palaeontology 5:69–122) recovered, for example, Seymouriamorpha, Diadectomorpha and (in some trees) Caudata as paraphyletic and found the “temnospondyl hypothesis” on the origin of Lissamphibia (TH) to be more parsimonious than the “lepospondyl hypothesis” (LH)—though only, as we show, by one step. We report 4,200 misscored cells, over half of them due to typographic and similar accidental errors. Further, some characters were duplicated; some had only one described state; for one, most taxa were scored after presumed relatives. Even potentially continuous characters were unordered, the effects of ontogeny were not sufficiently taken into account, and data published after 2001 were mostly excluded. After these issues are improved—we document and justify all changes to the matrix—but no characters are added, we find (Analysis R1) much longer trees with, for example, monophyletic Caudata, Diadectomorpha and (in some trees) Seymouriamorpha; Ichthyostega either crownward or rootward of Acanthostega; and Anthracosauria either crownward or rootward of Temnospondyli. The LH is nine steps shorter than the TH (R2; constrained) and 12 steps shorter than the “polyphyly hypothesis” (PH—R3; constrained). Brachydectes (Lysorophia) is not found next to Lissamphibia; instead, a large clade that includes the adelogyrinids, urocordylid “nectrideans” and aïstopods occupies that position. As expected from the taxon/character ratio, most bootstrap values are low. Adding 56 terminal taxa to the original 102 increases the resolution (and decreases most bootstrap values). The added taxa range in completeness from complete articulated skeletons to an incomplete lower jaw. Even though the lissamphibian-like temnospondyls Gerobatrachus, Micropholis and Tungussogyrinus and the extremely peramorphic salamander Chelotriton are added, the difference between LH (R4; unconstrained…
bibliographic citation: Marjanović et al. (2019) Phylogeny of Paleozoic limbed vertebrates reassessed through revision and expansion of the largest published relevant data matrix. PeerJ 6:e5565 https://doi.org/10.7717/peerj.5565
date submitted: 2016-01-16
date accepted: 2018-08-12
issued: 2019-01-04
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Marjanović
  given name: David
author list: Agent
  family name: Laurin
  given name: Michel
doi: 10.7717/peerj.5565
volume: 6
issn: 2167-8359
publication name: PeerJ
publication date: 2019-01-04
copyright: © 2019 Marjanović and Laurin
attribution name: Marjanović and Laurin

Changes in interleukin-27 levels in patients with acute coronary syndrome and their clinical significance
type: item
type: AcademicArticle
description: Background This study evaluated changes in interleukin (IL)-27 levels in patients with acute coronary syndrome (ACS) and their influence on Th1, Th2, and Th17 cells. Methods Serum levels of IL-27, IL-4, IL-17, and interferon (IFN)-γ in healthy subjects as well as patients with ACS, including stable angina pectoris (SA), unstable angina pectoris (UA), and acute myocardial infarction (AMI), were determined using an enzyme-linked immunosorbent assay. The proportions of Th1, Th2, and Th17 cells among peripheral blood mononuclear cells (PBMCs), were measured using flow cytometry, after incubation with phorbol myristate acetate (PMA) for 4 h. The proportions of Th1 and Th17 cells among PBMCs in AMI and UA were detected after stimulation with IL-27 or PMA + IL-27 for 4, 8, and 12 h. Results Serum levels of IL-27 in patients with AMI and UA were significantly lower than those in SA and control groups, while serum levels of IL-17 and IFN-γ in AMI and UA groups were dramatically increased compared to those in SA and healthy control groups. However, there were no statistically significant differences in serum IL-4. The proportions of Th1 and Th17 cells among PBMCs were statistically significantly higher in the AMI and UA groups than those in the SA and control groups, while there was no statistically significant difference in the proportion of Th2 cells among different groups. For patients with AMI and UA, the effect of co-stimulation of PBMCs with PMA and IL-27 was not significantly different from that of PMA single stimulation, while PMA + IL-27 co-stimulation lowered the Th17 cell proportion significantly compared to PMA single stimulation. Discussion Compared to SA patients and healthy controls, patients with ACS (AMI + UA) had lower serum levels of IL-27 and higher proportions of PBMC Th1 and Th17 cells, which could be attributed to the inhibitory effects of IL-27 on the proliferation of Th17 cells. These results indicated that IL-27 could be a novel therapeutic target in…
format: application/pdf
format: text/html
creator: Lin Zhang
creator: Junfeng Zhang
creator: Shaohong Su
creator: Suyan Luo
subject: Cardiology
description: doi:10.7717/peerj.5652
publisher: PeerJ Inc.
rights: © 2019 Zhang et al.
abstract: Background This study evaluated changes in interleukin (IL)-27 levels in patients with acute coronary syndrome (ACS) and their influence on Th1, Th2, and Th17 cells. Methods Serum levels of IL-27, IL-4, IL-17, and interferon (IFN)-γ in healthy subjects as well as patients with ACS, including stable angina pectoris (SA), unstable angina pectoris (UA), and acute myocardial infarction (AMI), were determined using an enzyme-linked immunosorbent assay. The proportions of Th1, Th2, and Th17 cells among peripheral blood mononuclear cells (PBMCs), were measured using flow cytometry, after incubation with phorbol myristate acetate (PMA) for 4 h. The proportions of Th1 and Th17 cells among PBMCs in AMI and UA were detected after stimulation with IL-27 or PMA + IL-27 for 4, 8, and 12 h. Results Serum levels of IL-27 in patients with AMI and UA were significantly lower than those in SA and control groups, while serum levels of IL-17 and IFN-γ in AMI and UA groups were dramatically increased compared to those in SA and healthy control groups. However, there were no statistically significant differences in serum IL-4. The proportions of Th1 and Th17 cells among PBMCs were statistically significantly higher in the AMI and UA groups than those in the SA and control groups, while there was no statistically significant difference in the proportion of Th2 cells among different groups. For patients with AMI and UA, the effect of co-stimulation of PBMCs with PMA and IL-27 was not significantly different from that of PMA single stimulation, while PMA + IL-27 co-stimulation lowered the Th17 cell proportion significantly compared to PMA single stimulation. Discussion Compared to SA patients and healthy controls, patients with ACS (AMI + UA) had lower serum levels of IL-27 and higher proportions of PBMC Th1 and Th17 cells, which could be attributed to the inhibitory effects of IL-27 on the proliferation of Th17 cells. These results indicated that IL-27 could be a novel therapeutic target in…
bibliographic citation: Zhang et al. (2019) Changes in interleukin-27 levels in patients with acute coronary syndrome and their clinical significance. PeerJ 7:e5652 https://doi.org/10.7717/peerj.5652
date submitted: 2018-05-30
date accepted: 2018-08-28
issued: 2019-01-04
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Zhang
  given name: Lin
author list: Agent
  family name: Zhang
  given name: Junfeng
author list: Agent
  family name: Su
  given name: Shaohong
author list: Agent
  family name: Luo
  given name: Suyan
doi: 10.7717/peerj.5652
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-01-04
copyright: ©2019 Zhang et al.
attribution name: Zhang et al.

Spiculous skeleton formation in the freshwater sponge Ephydatia fluviatilis under hypergravity conditions
type: item
type: AcademicArticle
description: Successful dispersal of freshwater sponges depends on the formation of dormant sponge bodies (gemmules) under adverse conditions. Gemmule formation allows the sponge to overcome critical environmental conditions, for example, desiccation or freezing, and to re-establish as a fully developed sponge when conditions are more favorable. A key process in sponge development from hatched gemmules is the construction of the silica skeleton. Silica spicules form the structural support for the three-dimensional filtration system the sponge uses to filter food particles from ambient water. We studied the effect of different hypergravity forces (1, 2.5, 5, 10, and 20 × g for 48 h)—as measure for environmental stress—on the ability of developing sponges to set-up their spiculous skeleton. Additionally, we assessed whether the addition of nutrients (i.e., dissolved 13C- and 15N-labeled amino acids) compensates for this stress. Our results show that freshwater sponges can withstand prolonged periods of hypergravity exposure and successfully set-up their skeleton, even after 48 h under 20 × g. Developing sponges were found to take up and assimilate dissolved food before forming a functional filtering system. However, fed and non-fed sponges showed no differences in skeleton formation and relative surface area growth, suggesting that the gemmules’ intrinsic energy fulfills the processes of skeleton construction. Additionally, non-fed sponges formed oscula significantly more often than fed sponges, especially under higher g-forces. This suggests that the eventual formation of a filtration system might be stimulated by food deprivation and environmentally stressful conditions. These findings indicate that the process of spiculous skeleton formation is energy-efficient and highly resilient. The uptake of dissolved food substances by freshwater sponges may contribute to the cycling of dissolved organic matter in freshwater ecosystems where sponges are abundant.
format: application/pdf
format: text/html
creator: Martijn C. Bart
creator: Sebastiaan J. de Vet
creator: Didier M. de Bakker
creator: Brittany E. Alexander
creator: Dick van Oevelen
creator: E. Emiel van Loon
creator: Jack J.W.A. van Loon
creator: Jasper M. de Goeij
subject: Ecology
subject: Freshwater Biology
description: doi:10.7717/peerj.6055
publisher: PeerJ Inc.
rights: © 2019 Bart et al.
abstract: Successful dispersal of freshwater sponges depends on the formation of dormant sponge bodies (gemmules) under adverse conditions. Gemmule formation allows the sponge to overcome critical environmental conditions, for example, desiccation or freezing, and to re-establish as a fully developed sponge when conditions are more favorable. A key process in sponge development from hatched gemmules is the construction of the silica skeleton. Silica spicules form the structural support for the three-dimensional filtration system the sponge uses to filter food particles from ambient water. We studied the effect of different hypergravity forces (1, 2.5, 5, 10, and 20 × g for 48 h)—as measure for environmental stress—on the ability of developing sponges to set-up their spiculous skeleton. Additionally, we assessed whether the addition of nutrients (i.e., dissolved 13C- and 15N-labeled amino acids) compensates for this stress. Our results show that freshwater sponges can withstand prolonged periods of hypergravity exposure and successfully set-up their skeleton, even after 48 h under 20 × g. Developing sponges were found to take up and assimilate dissolved food before forming a functional filtering system. However, fed and non-fed sponges showed no differences in skeleton formation and relative surface area growth, suggesting that the gemmules’ intrinsic energy fulfills the processes of skeleton construction. Additionally, non-fed sponges formed oscula significantly more often than fed sponges, especially under higher g-forces. This suggests that the eventual formation of a filtration system might be stimulated by food deprivation and environmentally stressful conditions. These findings indicate that the process of spiculous skeleton formation is energy-efficient and highly resilient. The uptake of dissolved food substances by freshwater sponges may contribute to the cycling of dissolved organic matter in freshwater ecosystems where sponges are abundant.
bibliographic citation: Bart et al. (2019) Spiculous skeleton formation in the freshwater sponge Ephydatia fluviatilis under hypergravity conditions. PeerJ 6:e6055 https://doi.org/10.7717/peerj.6055
date submitted: 2018-08-30
date accepted: 2018-10-30
issued: 2019-01-04
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Bart
  given name: Martijn C.
author list: Agent
  family name: de Vet
  given name: Sebastiaan J.
author list: Agent
  family name: de Bakker
  given name: Didier M.
author list: Agent
  family name: Alexander
  given name: Brittany E.
author list: Agent
  family name: van Oevelen
  given name: Dick
author list: Agent
  family name: van Loon
  given name: E. Emiel
author list: Agent
  family name: van Loon
  given name: Jack J.W.A.
author list: Agent
  family name: de Goeij
  given name: Jasper M.
doi: 10.7717/peerj.6055
volume: 6
issn: 2167-8359
publication name: PeerJ
publication date: 2019-01-04
copyright: © 2019 Bart et al.
attribution name: Bart et al.

Temperature-mediated feeding between spring-associated and riverine-associated congeners, with implications for community segregation
type: item
type: AcademicArticle
description: Freshwater fish communities segregate along water temperature gradients attributed in part to temperature-mediated physiological processes that affect species fitness. In spring complexes of southwest USA, spring complexes with narrow range of water temperatures are dominated by a community of fishes (i.e., spring-associated fishes), whereas riverine habitats with wide-range of water temperatures are dominated by a different community of fishes (i.e., riverine-associated fishes). The purpose of this study was to test a prediction of the concept that temperature-mediated species performance is a mechanism in maintaining community segregation. We predicted that a spring-associated fish (Largespring Gambusia Gambusia geiseri) would feed first and more often in a pairing with a riverine-associated fish (Western Mosquitofish G. affinis) at an average spring temperature (23 °C) and that the riverine-associated fish would feed first and more often in a pairing with the spring-associated fish at a warm riverine temperature (30 °C). Among four trails consisting of 30 pairings, at the spring complex temperature (23 °C), Largespring Gambusia had a greater number of first feeds (mean ± 1 SD, 5.0 ± 0.82) than Western Mosquitofish (2.5 ± 1.73) and had greater mean number of total feeds (1.9 ± 0.31) than Western Mosquitofish (0.81 ± 0.70). At the riverine environment temperature (30 °C), Western Mosquitofish had a greater number of first feeds (5.25 ± 1.71) than Largespring Gambusia (2.5 ± 1.73) and had greater mean number of total feeds (2.78 ± 1.05) than Largespring Gambusia (0.94 ± 0.68). Our findings suggest that temperature-mediated species performance could be maintaining segregation between the two fish communities. This study benefits our understanding of distributional patterns and improves threat assessments of stenothermal aquatic organisms.
format: application/pdf
format: text/html
creator: Cody A. Craig
creator: Jeremy D. Maikoetter
creator: Timothy H. Bonner
subject: Animal Behavior
subject: Aquaculture, Fisheries and Fish Science
subject: Ecology
subject: Freshwater Biology
description: doi:10.7717/peerj.6144
publisher: PeerJ Inc.
rights: © 2019 Craig et al.
abstract: Freshwater fish communities segregate along water temperature gradients attributed in part to temperature-mediated physiological processes that affect species fitness. In spring complexes of southwest USA, spring complexes with narrow range of water temperatures are dominated by a community of fishes (i.e., spring-associated fishes), whereas riverine habitats with wide-range of water temperatures are dominated by a different community of fishes (i.e., riverine-associated fishes). The purpose of this study was to test a prediction of the concept that temperature-mediated species performance is a mechanism in maintaining community segregation. We predicted that a spring-associated fish (Largespring Gambusia Gambusia geiseri) would feed first and more often in a pairing with a riverine-associated fish (Western Mosquitofish G. affinis) at an average spring temperature (23 °C) and that the riverine-associated fish would feed first and more often in a pairing with the spring-associated fish at a warm riverine temperature (30 °C). Among four trails consisting of 30 pairings, at the spring complex temperature (23 °C), Largespring Gambusia had a greater number of first feeds (mean ± 1 SD, 5.0 ± 0.82) than Western Mosquitofish (2.5 ± 1.73) and had greater mean number of total feeds (1.9 ± 0.31) than Western Mosquitofish (0.81 ± 0.70). At the riverine environment temperature (30 °C), Western Mosquitofish had a greater number of first feeds (5.25 ± 1.71) than Largespring Gambusia (2.5 ± 1.73) and had greater mean number of total feeds (2.78 ± 1.05) than Largespring Gambusia (0.94 ± 0.68). Our findings suggest that temperature-mediated species performance could be maintaining segregation between the two fish communities. This study benefits our understanding of distributional patterns and improves threat assessments of stenothermal aquatic organisms.
bibliographic citation: Craig et al. (2019) Temperature-mediated feeding between spring-associated and riverine-associated congeners, with implications for community segregation. PeerJ 6:e6144 https://doi.org/10.7717/peerj.6144
date submitted: 2018-08-13
date accepted: 2018-11-20
issued: 2019-01-04
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Craig
  given name: Cody A.
author list: Agent
  family name: Maikoetter
  given name: Jeremy D.
author list: Agent
  family name: Bonner
  given name: Timothy H.
doi: 10.7717/peerj.6144
volume: 6
issn: 2167-8359
publication name: PeerJ
publication date: 2019-01-04
copyright: © 2019 Craig et al.
attribution name: Craig et al.

Using the wax moth larva Galleria mellonella infection model to detect emerging bacterial pathogens
type: item
type: AcademicArticle
description: Climate change, changing farming practices, social and demographic changes and rising levels of antibiotic resistance are likely to lead to future increases in opportunistic bacterial infections that are more difficult to treat. Uncovering the prevalence and identity of pathogenic bacteria in the environment is key to assessing transmission risks. We describe the first use of the Wax moth larva Galleria mellonella, a well-established model for the mammalian innate immune system, to selectively enrich and characterize pathogens from coastal environments in the South West of the UK. Whole-genome sequencing of highly virulent isolates revealed amongst others a Proteus mirabilis strain carrying the Salmonella SGI1 genomic island not reported from the UK before and the recently described species Vibrio injenensis hitherto only reported from human patients in Korea. Our novel method has the power to detect bacterial pathogens in the environment that potentially pose a serious risk to public health.
format: application/pdf
format: text/html
creator: Rafael J. Hernandez
creator: Elze Hesse
creator: Andrea J. Dowling
creator: Nicola M. Coyle
creator: Edward J. Feil
creator: Will H. Gaze
creator: Michiel Vos
subject: Microbiology
subject: Infectious Diseases
subject: Environmental Contamination and Remediation
subject: Environmental Impacts
description: doi:10.7717/peerj.6150
publisher: PeerJ Inc.
rights: © 2019 Hernandez et al.
abstract: Climate change, changing farming practices, social and demographic changes and rising levels of antibiotic resistance are likely to lead to future increases in opportunistic bacterial infections that are more difficult to treat. Uncovering the prevalence and identity of pathogenic bacteria in the environment is key to assessing transmission risks. We describe the first use of the Wax moth larva Galleria mellonella, a well-established model for the mammalian innate immune system, to selectively enrich and characterize pathogens from coastal environments in the South West of the UK. Whole-genome sequencing of highly virulent isolates revealed amongst others a Proteus mirabilis strain carrying the Salmonella SGI1 genomic island not reported from the UK before and the recently described species Vibrio injenensis hitherto only reported from human patients in Korea. Our novel method has the power to detect bacterial pathogens in the environment that potentially pose a serious risk to public health.
bibliographic citation: Hernandez et al. (2019) Using the wax moth larva Galleria mellonella infection model to detect emerging bacterial pathogens. PeerJ 6:e6150 https://doi.org/10.7717/peerj.6150
date submitted: 2018-10-19
date accepted: 2018-11-23
issued: 2019-01-04
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Hernandez
  given name: Rafael J.
author list: Agent
  family name: Hesse
  given name: Elze
author list: Agent
  family name: Dowling
  given name: Andrea J.
author list: Agent
  family name: Coyle
  given name: Nicola M.
author list: Agent
  family name: Feil
  given name: Edward J.
author list: Agent
  family name: Gaze
  given name: Will H.
author list: Agent
  family name: Vos
  given name: Michiel
doi: 10.7717/peerj.6150
volume: 6
issn: 2167-8359
publication name: PeerJ
publication date: 2019-01-04
copyright: © 2019 Hernandez et al.
attribution name: Hernandez et al.

Role of the larval feeding morphology and digestive enzyme activity in the early development of the polychaete Boccardia wellingtonensis
type: item
type: AcademicArticle
description: In marine invertebrates, the modes of development at early stages are related to the type and capacity of larval feeding to achieve growth. Therefore, studying the factors that determine larval feeding strategies can help to understand the diversity of life histories and evolution of marine invertebrates. The polychaete Boccardia wellingtonensis is a poecilogonous species that encapsulates and incubates its offspring. This species produces two types of larvae: (1) larvae that do not feed within the capsule and hatch as planktotrophic larvae (indirect development), and (2) adelphophagic larvae that feed on nurse eggs and other larvae inside the capsule to hatch as advanced larvae or juveniles (direct development). Otherwise, the larval types are indistinguishable at the same stage of development. The non-apparent morphological differences between both types of larvae suggest that other factors are influencing their feeding behavior. This work studied the potential role of the activity of 19 digestive enzymes on the different feeding capacities of planktotrophic and adelphophagic larvae of B. wellingtonensis. Also, differences in larval feeding structures and the larval capacity to feed from intracapsular fluid were evaluated by electron and fluorescence microscopy. Results showed that both types of larvae present similar feeding structures and had the capacity to ingest intracapsular fluid protein. Adelphophagic larvae showed overall the highest activities of digestive enzymes. Significant differences between larval types were observed in nine enzymes related to the use of internal and external nutritional sources. Given that larval feeding is closely related to larval development in species with encapsulation, this work supports that the study of the digestive enzymatic machinery of larvae may contribute to understanding the evolution of developmental modes.
format: application/pdf
format: text/html
creator: Daniel Doherty-Weason
creator: Fernanda X. Oyarzun
creator: Luciano Vera
creator: Miguel Bascur
creator: Fabián Guzmán
creator: Francisco Silva
creator: Ángel Urzúa
creator: Antonio Brante
subject: Evolutionary Studies
subject: Marine Biology
description: doi:10.7717/peerj.6151
publisher: PeerJ Inc.
rights: © 2019 Doherty-Weason et al.
abstract: In marine invertebrates, the modes of development at early stages are related to the type and capacity of larval feeding to achieve growth. Therefore, studying the factors that determine larval feeding strategies can help to understand the diversity of life histories and evolution of marine invertebrates. The polychaete Boccardia wellingtonensis is a poecilogonous species that encapsulates and incubates its offspring. This species produces two types of larvae: (1) larvae that do not feed within the capsule and hatch as planktotrophic larvae (indirect development), and (2) adelphophagic larvae that feed on nurse eggs and other larvae inside the capsule to hatch as advanced larvae or juveniles (direct development). Otherwise, the larval types are indistinguishable at the same stage of development. The non-apparent morphological differences between both types of larvae suggest that other factors are influencing their feeding behavior. This work studied the potential role of the activity of 19 digestive enzymes on the different feeding capacities of planktotrophic and adelphophagic larvae of B. wellingtonensis. Also, differences in larval feeding structures and the larval capacity to feed from intracapsular fluid were evaluated by electron and fluorescence microscopy. Results showed that both types of larvae present similar feeding structures and had the capacity to ingest intracapsular fluid protein. Adelphophagic larvae showed overall the highest activities of digestive enzymes. Significant differences between larval types were observed in nine enzymes related to the use of internal and external nutritional sources. Given that larval feeding is closely related to larval development in species with encapsulation, this work supports that the study of the digestive enzymatic machinery of larvae may contribute to understanding the evolution of developmental modes.
bibliographic citation: Doherty-Weason et al. (2019) Role of the larval feeding morphology and digestive enzyme activity in the early development of the polychaete Boccardia wellingtonensis. PeerJ 7:e6151 https://doi.org/10.7717/peerj.6151
date submitted: 2018-08-13
date accepted: 2018-11-22
issued: 2019-01-04
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Doherty-Weason
  given name: Daniel
author list: Agent
  family name: Oyarzun
  given name: Fernanda X.
author list: Agent
  family name: Vera
  given name: Luciano
author list: Agent
  family name: Bascur
  given name: Miguel
author list: Agent
  family name: Guzmán
  given name: Fabián
author list: Agent
  family name: Silva
  given name: Francisco
author list: Agent
  family name: Urzúa
  given name: Ángel
author list: Agent
  family name: Brante
  given name: Antonio
doi: 10.7717/peerj.6151
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-01-04
copyright: ©2019 Doherty-Weason et al.
attribution name: Doherty-Weason et al.

Secreted Frizzled-related protein 4 inhibits the regeneration of hair follicles
type: item
type: AcademicArticle
description: Secreted Frizzled-related Protein 4 (sFRP4) belongs to Wnt inhibitors. Previously, we reported that sFRP4 inhibited the differentiation of melanocyte. Here, by using of immunostaining, we showed that sFRP4 is expressed in both human and mouse hair follicles, especially in the outer root sheath and inner root sheath. To reveal the role of sFRP4 in hair follicle growth and hair cycle, we induced synchronized hair cycle in the dorsal skin of mice by depilation, and injected sFRP4 intradermally into the skin. By hematoxylin and eosin staining, we found that the regeneration of hair follicles was inhibited by sFRP4. However, the structure of hair follicles remained complete. Compared with phosphate buffer saline-treated hair follicles, the sFRP4-treated hair follicles still had the same expression pattern of keratins. Our findings reveal that sFRP4 inhibits but not blocks the regeneration of hair follicles, and supply a potential therapeutic application to treat hair follicle regeneration disorders.
format: application/pdf
format: text/html
creator: Haiying Guo
creator: Yizhan Xing
creator: Fang Deng
creator: Ke Yang
creator: Yuhong Li
subject: Cell Biology
subject: Dermatology
description: doi:10.7717/peerj.6153
publisher: PeerJ Inc.
rights: © 2019 Guo et al.
abstract: Secreted Frizzled-related Protein 4 (sFRP4) belongs to Wnt inhibitors. Previously, we reported that sFRP4 inhibited the differentiation of melanocyte. Here, by using of immunostaining, we showed that sFRP4 is expressed in both human and mouse hair follicles, especially in the outer root sheath and inner root sheath. To reveal the role of sFRP4 in hair follicle growth and hair cycle, we induced synchronized hair cycle in the dorsal skin of mice by depilation, and injected sFRP4 intradermally into the skin. By hematoxylin and eosin staining, we found that the regeneration of hair follicles was inhibited by sFRP4. However, the structure of hair follicles remained complete. Compared with phosphate buffer saline-treated hair follicles, the sFRP4-treated hair follicles still had the same expression pattern of keratins. Our findings reveal that sFRP4 inhibits but not blocks the regeneration of hair follicles, and supply a potential therapeutic application to treat hair follicle regeneration disorders.
bibliographic citation: Guo et al. (2019) Secreted Frizzled-related protein 4 inhibits the regeneration of hair follicles. PeerJ 6:e6153 https://doi.org/10.7717/peerj.6153
date submitted: 2018-08-28
date accepted: 2018-11-24
issued: 2019-01-04
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Guo
  given name: Haiying
author list: Agent
  family name: Xing
  given name: Yizhan
author list: Agent
  family name: Deng
  given name: Fang
author list: Agent
  family name: Yang
  given name: Ke
author list: Agent
  family name: Li
  given name: Yuhong
doi: 10.7717/peerj.6153
volume: 6
issn: 2167-8359
publication name: PeerJ
publication date: 2019-01-04
copyright: © 2019 Guo et al.
attribution name: Guo et al.

Primulina anisocymosa (Gesneriaceae), a new species with a unique inflorescence structure from Guangdong, China
type: item
type: AcademicArticle
description: A new Primulina species from Guangdong, China with an unusual inflorescence is described here. Primulina anisocymosa is vegetatively most similar to P. bobaiensis. It can be distinguished from all species within Primulina morphologically by its unique zigzag monochasial cyme and infructescence. To confirm the phylogenetic relationships and generic placement of this species, not only morphological anatomical features but also chromosome and DNA sequence data were examined and analysed here. Two samples from different populations identified as Primulina anisocymosa are monophyletic and were nested in a monophyletic clade within Primulina with high branch support. The somatic chromosome number of the new species is also reported (2n = 36), supporting its placement in the genus.
format: application/pdf
format: text/html
creator: Xin Hong
creator: Jeremy Keene
creator: Zhi-Jing Qiu
creator: Fang Wen
subject: Plant Science
subject: Taxonomy
description: doi:10.7717/peerj.6157
publisher: PeerJ Inc.
rights: © 2019 Hong et al.
abstract: A new Primulina species from Guangdong, China with an unusual inflorescence is described here. Primulina anisocymosa is vegetatively most similar to P. bobaiensis. It can be distinguished from all species within Primulina morphologically by its unique zigzag monochasial cyme and infructescence. To confirm the phylogenetic relationships and generic placement of this species, not only morphological anatomical features but also chromosome and DNA sequence data were examined and analysed here. Two samples from different populations identified as Primulina anisocymosa are monophyletic and were nested in a monophyletic clade within Primulina with high branch support. The somatic chromosome number of the new species is also reported (2n = 36), supporting its placement in the genus.
bibliographic citation: Hong et al. (2019) Primulina anisocymosa (Gesneriaceae), a new species with a unique inflorescence structure from Guangdong, China. PeerJ 7:e6157 https://doi.org/10.7717/peerj.6157
date submitted: 2018-08-01
date accepted: 2018-11-25
issued: 2019-01-04
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Hong
  given name: Xin
author list: Agent
  family name: Keene
  given name: Jeremy
author list: Agent
  family name: Qiu
  given name: Zhi-Jing
author list: Agent
  family name: Wen
  given name: Fang
doi: 10.7717/peerj.6157
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-01-04
copyright: ©2019 Hong et al.
attribution name: Hong et al.

Identifying accurate metagenome and amplicon software via a meta-analysis of sequence to taxonomy benchmarking studies
type: item
type: AcademicArticle
description: Metagenomic and meta-barcode DNA sequencing has rapidly become a widely-used technique for investigating a range of questions, particularly related to health and environmental monitoring. There has also been a proliferation of bioinformatic tools for analysing metagenomic and amplicon datasets, which makes selecting adequate tools a significant challenge. A number of benchmark studies have been undertaken; however, these can present conflicting results. In order to address this issue we have applied a robust Z-score ranking procedure and a network meta-analysis method to identify software tools that are consistently accurate for mapping DNA sequences to taxonomic hierarchies. Based upon these results we have identified some tools and computational strategies that produce robust predictions.
format: application/pdf
format: text/html
creator: Paul P. Gardner
creator: Renee J. Watson
creator: Xochitl C. Morgan
creator: Jenny L. Draper
creator: Robert D. Finn
creator: Sergio E. Morales
creator: Matthew B. Stott
subject: Bioinformatics
subject: Computational Biology
description: doi:10.7717/peerj.6160
publisher: PeerJ Inc.
rights: © 2019 Gardner et al.
abstract: Metagenomic and meta-barcode DNA sequencing has rapidly become a widely-used technique for investigating a range of questions, particularly related to health and environmental monitoring. There has also been a proliferation of bioinformatic tools for analysing metagenomic and amplicon datasets, which makes selecting adequate tools a significant challenge. A number of benchmark studies have been undertaken; however, these can present conflicting results. In order to address this issue we have applied a robust Z-score ranking procedure and a network meta-analysis method to identify software tools that are consistently accurate for mapping DNA sequences to taxonomic hierarchies. Based upon these results we have identified some tools and computational strategies that produce robust predictions.
bibliographic citation: Gardner et al. (2019) Identifying accurate metagenome and amplicon software via a meta-analysis of sequence to taxonomy benchmarking studies. PeerJ 7:e6160 https://doi.org/10.7717/peerj.6160
date submitted: 2017-11-08
date accepted: 2018-11-14
issued: 2019-01-04
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Gardner
  given name: Paul P.
author list: Agent
  family name: Watson
  given name: Renee J.
author list: Agent
  family name: Morgan
  given name: Xochitl C.
author list: Agent
  family name: Draper
  given name: Jenny L.
author list: Agent
  family name: Finn
  given name: Robert D.
author list: Agent
  family name: Morales
  given name: Sergio E.
author list: Agent
  family name: Stott
  given name: Matthew B.
doi: 10.7717/peerj.6160
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-01-04
copyright: ©2019 Gardner et al.
attribution name: Gardner et al.

Long-term effects of straw and straw-derived biochar on soil aggregation and fungal community in a rice–wheat rotation system
type: item
type: AcademicArticle
description: Background Soil aggregation is fundamental for soil functioning and agricultural productivity. Aggregate formation depends on microbial activity influencing the production of exudates and hyphae, which in turn act as binding materials. Fungi are also important for improving soil quality and promoting plant growth in a symbiotic manner. There is a scarcity of findings comparing the long-term impacts of different yearly double-crop straw return modes (e.g., straw return to the field and straw-derived biochar return to the field) on soil aggregation and fungal community structure in rice–wheat rotation systems. Methods The effects of 6-year continuous straw and straw-derived biochar amendment on soil physicochemical properties and the fungal community were evaluated in an intensively managed crop rotation system (rice–wheat). Soil samples of different aggregates (macroaggregates, microaggregates, and silt clay) from four different fertilization regimes (control, CK; traditional inorganic fertilization, CF; straw returned to field, CS; straw-derived biochar addition, CB) were obtained, and Illumina MiSeq sequencing analysis of the fungal internal transcribed spacer gene was performed. Results Compared to CF, CS and CB enhanced soil organic carbon, total nitrogen, and aggregation in 0–20 and 20–40 cm soil, with CB exhibiting a stronger effect. Additionally, agrowaste addition increased the mean weight diameter and the geometric diameter and decreased the fractal dimension (p < 0.05). Principal coordinates analysis indicated that fertilization management affected fungal community structure and aggregation distribution. In addition, CS increased fungal community richness and diversity, compared to CK, CB decreased these aspects. Ascomycota, unclassified_k_Fungi, and Basidiomycota were the dominant phyla in all soil samples. At the genus level, CB clearly increased fungi decomposing biosolids (Articulospora in macroaggregates in 0–20 cm soil and Neurospora in macroaggregate…
format: application/pdf
format: text/html
creator: Naling Bai
creator: Hanlin Zhang
creator: Shuangxi Li
creator: Xianqing Zheng
creator: Juanqin Zhang
creator: Haiyun Zhang
creator: Sheng Zhou
creator: Huifeng Sun
creator: Weiguang Lv
subject: Ecology
subject: Microbiology
description: doi:10.7717/peerj.6171
publisher: PeerJ Inc.
rights: © 2019 Bai et al.
abstract: Background Soil aggregation is fundamental for soil functioning and agricultural productivity. Aggregate formation depends on microbial activity influencing the production of exudates and hyphae, which in turn act as binding materials. Fungi are also important for improving soil quality and promoting plant growth in a symbiotic manner. There is a scarcity of findings comparing the long-term impacts of different yearly double-crop straw return modes (e.g., straw return to the field and straw-derived biochar return to the field) on soil aggregation and fungal community structure in rice–wheat rotation systems. Methods The effects of 6-year continuous straw and straw-derived biochar amendment on soil physicochemical properties and the fungal community were evaluated in an intensively managed crop rotation system (rice–wheat). Soil samples of different aggregates (macroaggregates, microaggregates, and silt clay) from four different fertilization regimes (control, CK; traditional inorganic fertilization, CF; straw returned to field, CS; straw-derived biochar addition, CB) were obtained, and Illumina MiSeq sequencing analysis of the fungal internal transcribed spacer gene was performed. Results Compared to CF, CS and CB enhanced soil organic carbon, total nitrogen, and aggregation in 0–20 and 20–40 cm soil, with CB exhibiting a stronger effect. Additionally, agrowaste addition increased the mean weight diameter and the geometric diameter and decreased the fractal dimension (p < 0.05). Principal coordinates analysis indicated that fertilization management affected fungal community structure and aggregation distribution. In addition, CS increased fungal community richness and diversity, compared to CK, CB decreased these aspects. Ascomycota, unclassified_k_Fungi, and Basidiomycota were the dominant phyla in all soil samples. At the genus level, CB clearly increased fungi decomposing biosolids (Articulospora in macroaggregates in 0–20 cm soil and Neurospora in macroaggregate…
bibliographic citation: Bai et al. (2019) Long-term effects of straw and straw-derived biochar on soil aggregation and fungal community in a rice–wheat rotation system. PeerJ 6:e6171 https://doi.org/10.7717/peerj.6171
date submitted: 2018-10-14
date accepted: 2018-11-27
issued: 2019-01-04
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Bai
  given name: Naling
author list: Agent
  family name: Zhang
  given name: Hanlin
author list: Agent
  family name: Li
  given name: Shuangxi
author list: Agent
  family name: Zheng
  given name: Xianqing
author list: Agent
  family name: Zhang
  given name: Juanqin
author list: Agent
  family name: Zhang
  given name: Haiyun
author list: Agent
  family name: Zhou
  given name: Sheng
author list: Agent
  family name: Sun
  given name: Huifeng
author list: Agent
  family name: Lv
  given name: Weiguang
doi: 10.7717/peerj.6171
volume: 6
issn: 2167-8359
publication name: PeerJ
publication date: 2019-01-04
copyright: © 2019 Bai et al.
attribution name: Bai et al.

Functional polymorphisms of the APOA1/C3/A4/A5-ZPR1-BUD13 gene cluster are associated with dyslipidemia in a sex-specific pattern
type: item
type: AcademicArticle
description: Background Dyslipidemia contributes to the risk of many diseases, including stroke, cardiovascular disease and metabolic-related diseases. Previous studies have indicated that single nucleotide polymorphisms (SNPs) are associated with different levels of serum lipid. Therefore, this study explored the relationship between the APOA1/C3/A4/A5-ZPR1-BUD13 gene cluster gene polymorphisms and dyslipidemia in the total sample population and stratified by genders in a northeast Chinese population. Methods A total of 3,850 participants from Jilin Province, China, were enrolled in our study, and their serum lipid levels were measured. Six functional SNPs (APOA1 rs5072, APOC3 rs5128, APOA4 rs5104, APOA5 rs651821, ZPR1 rs2075294 and BUD13 rs10488698) were genotyped using polymerase chain reaction and MALDI-TOF-MS. Logistic regression analysis was performed to explore the relationship of APOA1/C3/A4/A5-ZPR1-BUD13 gene cluster gene polymorphisms with dyslipidemia. Linkage disequilibrium and haplotype analyses were performed with the SNPStats program and Haploview software. Results All SNPs conformed to Hardy–Weinberg equilibrium. Logistic regression analysis revealed that rs5072, rs5128 and rs651821 were associated with hypertriglyceridemia, rs5104 and rs651821 were associated with low-HDL cholesterolemia in overall group. rs651821 was associated with hypertriglyceridemia and low-HDL cholesterolemia in both the male and female group. However, among females, rs5072 was observed to be associated with hypertriglyceridemia. Haplotype analysis showed that haplotypes TGCCGC and CAGCGC were associated with dyslipidemia in the overall, male and female groups. Conclusion SNPs in the APOA1/C3/A4/A5-ZPR1-BUD13 gene cluster were associated with dyslipidemia. Furthermore, the association of APOA1 rs5072 in this gene cluster with dyslipidemia differed between genders; thus, additional studies are needed to confirm this conclusion, and the mechanisms underlying these results warrant further exp…
format: application/pdf
format: text/html
creator: Wei Bai
creator: Changgui Kou
creator: Lili Zhang
creator: Yueyue You
creator: Weiying Yu
creator: Wanqing Hua
creator: Yuanyuan Li
creator: Yaqin Yu
creator: Tiancheng Zhao
creator: Yanhua Wu
subject: Biochemistry
subject: Genetics
subject: Epidemiology
subject: Public Health
description: doi:10.7717/peerj.6175
publisher: PeerJ Inc.
rights: © 2019 Bai et al.
abstract: Background Dyslipidemia contributes to the risk of many diseases, including stroke, cardiovascular disease and metabolic-related diseases. Previous studies have indicated that single nucleotide polymorphisms (SNPs) are associated with different levels of serum lipid. Therefore, this study explored the relationship between the APOA1/C3/A4/A5-ZPR1-BUD13 gene cluster gene polymorphisms and dyslipidemia in the total sample population and stratified by genders in a northeast Chinese population. Methods A total of 3,850 participants from Jilin Province, China, were enrolled in our study, and their serum lipid levels were measured. Six functional SNPs (APOA1 rs5072, APOC3 rs5128, APOA4 rs5104, APOA5 rs651821, ZPR1 rs2075294 and BUD13 rs10488698) were genotyped using polymerase chain reaction and MALDI-TOF-MS. Logistic regression analysis was performed to explore the relationship of APOA1/C3/A4/A5-ZPR1-BUD13 gene cluster gene polymorphisms with dyslipidemia. Linkage disequilibrium and haplotype analyses were performed with the SNPStats program and Haploview software. Results All SNPs conformed to Hardy–Weinberg equilibrium. Logistic regression analysis revealed that rs5072, rs5128 and rs651821 were associated with hypertriglyceridemia, rs5104 and rs651821 were associated with low-HDL cholesterolemia in overall group. rs651821 was associated with hypertriglyceridemia and low-HDL cholesterolemia in both the male and female group. However, among females, rs5072 was observed to be associated with hypertriglyceridemia. Haplotype analysis showed that haplotypes TGCCGC and CAGCGC were associated with dyslipidemia in the overall, male and female groups. Conclusion SNPs in the APOA1/C3/A4/A5-ZPR1-BUD13 gene cluster were associated with dyslipidemia. Furthermore, the association of APOA1 rs5072 in this gene cluster with dyslipidemia differed between genders; thus, additional studies are needed to confirm this conclusion, and the mechanisms underlying these results warrant further exp…
bibliographic citation: Bai et al. (2019) Functional polymorphisms of the APOA1/C3/A4/A5-ZPR1-BUD13 gene cluster are associated with dyslipidemia in a sex-specific pattern. PeerJ 6:e6175 https://doi.org/10.7717/peerj.6175
date submitted: 2018-05-29
date accepted: 2018-11-26
issued: 2019-01-04
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Bai
  given name: Wei
author list: Agent
  family name: Kou
  given name: Changgui
author list: Agent
  family name: Zhang
  given name: Lili
author list: Agent
  family name: You
  given name: Yueyue
author list: Agent
  family name: Yu
  given name: Weiying
author list: Agent
  family name: Hua
  given name: Wanqing
author list: Agent
  family name: Li
  given name: Yuanyuan
author list: Agent
  family name: Yu
  given name: Yaqin
author list: Agent
  family name: Zhao
  given name: Tiancheng
author list: Agent
  family name: Wu
  given name: Yanhua
doi: 10.7717/peerj.6175
volume: 6
issn: 2167-8359
publication name: PeerJ
publication date: 2019-01-04
copyright: © 2019 Bai et al.
attribution name: Bai et al.

A Tournaisian (earliest Carboniferous) conglomerate-preserved non-marine faunal assemblage and its environmental and sedimentological context
type: item
type: AcademicArticle
description: A conglomerate bed from the Tournaisian Ballagan Formation of Scotland preserves a rich array of vertebrate and other nonmarine fossils providing an insight into the wider ecosystem and paleoenvironment that existed during this pivotal stage of Earth history. It challenges hypotheses of a long-lasting post-extinction trough following the end-Devonian extinction event. The fauna recovered includes a wide size range of tetrapods, rhizodonts, and dipnoans, from tiny juveniles or small-bodied taxa up to large adults, and more than one taxon of each group is likely. Some fauna, such as actinopterygians and chondrichthyans, are rare as macrofauna but are better represented in the microfossil assemblage. The fauna provides evidence of the largest Carboniferous lungfish ever found. The specimens are preserved in a localized, poorly-sorted conglomerate which was deposited in the deepest part of a river channel, the youngest of a group of channels. In addition to the fossils (micro- and macro-), the conglomerate includes locally-derived clasts of paleosols and other distinctive elements of the surrounding floodplains. Charcoal fragments represent small woody axes and possible larger trunk tissue from arborescent pteridosperms. Preservation of the fossils indicates some aerial exposure prior to transport, with abrasion from rolling. The findings presented here contrast with other published trends in vertebrate size that are used to interpret a reduction in maximum sizes during the Tournaisian. The richness of the fauna runs counter to the assumption of a depauperate nonmarine fauna following the end-Devonian Hangenberg event, and charcoal content highlights the occurrence of fire, with the requisite levels of atmospheric oxygen during that stage.
format: application/pdf
format: text/html
creator: Jennifer A. Clack
creator: Carys E. Bennett
creator: Sarah J. Davies
creator: Andrew C. Scott
creator: Janet E. Sherwin
creator: Timothy R. Smithson
subject: Evolutionary Studies
subject: Paleontology
description: doi:10.7717/peerj.5972
publisher: PeerJ Inc.
rights: © 2019 Clack et al.
abstract: A conglomerate bed from the Tournaisian Ballagan Formation of Scotland preserves a rich array of vertebrate and other nonmarine fossils providing an insight into the wider ecosystem and paleoenvironment that existed during this pivotal stage of Earth history. It challenges hypotheses of a long-lasting post-extinction trough following the end-Devonian extinction event. The fauna recovered includes a wide size range of tetrapods, rhizodonts, and dipnoans, from tiny juveniles or small-bodied taxa up to large adults, and more than one taxon of each group is likely. Some fauna, such as actinopterygians and chondrichthyans, are rare as macrofauna but are better represented in the microfossil assemblage. The fauna provides evidence of the largest Carboniferous lungfish ever found. The specimens are preserved in a localized, poorly-sorted conglomerate which was deposited in the deepest part of a river channel, the youngest of a group of channels. In addition to the fossils (micro- and macro-), the conglomerate includes locally-derived clasts of paleosols and other distinctive elements of the surrounding floodplains. Charcoal fragments represent small woody axes and possible larger trunk tissue from arborescent pteridosperms. Preservation of the fossils indicates some aerial exposure prior to transport, with abrasion from rolling. The findings presented here contrast with other published trends in vertebrate size that are used to interpret a reduction in maximum sizes during the Tournaisian. The richness of the fauna runs counter to the assumption of a depauperate nonmarine fauna following the end-Devonian Hangenberg event, and charcoal content highlights the occurrence of fire, with the requisite levels of atmospheric oxygen during that stage.
bibliographic citation: Clack et al. (2019) A Tournaisian (earliest Carboniferous) conglomerate-preserved non-marine faunal assemblage and its environmental and sedimentological context. PeerJ 6:e5972 https://doi.org/10.7717/peerj.5972
date submitted: 2018-08-06
date accepted: 2018-10-19
issued: 2019-01-03
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Clack
  given name: Jennifer A.
author list: Agent
  family name: Bennett
  given name: Carys E.
author list: Agent
  family name: Davies
  given name: Sarah J.
author list: Agent
  family name: Scott
  given name: Andrew C.
author list: Agent
  family name: Sherwin
  given name: Janet E.
author list: Agent
  family name: Smithson
  given name: Timothy R.
doi: 10.7717/peerj.5972
volume: 6
issn: 2167-8359
publication name: PeerJ
publication date: 2019-01-03
copyright: © 2019 Clack et al.
attribution name: Clack et al.

Steroidal glycoalkaloids from Solanum nigrum target cytoskeletal proteins: an in silico analysis
type: item
type: AcademicArticle
description: Background Solanum nigrum (black nightshade; S. nigrum), a member of family Solanaceae, has been endowed with a heterogeneous array of secondary metabolites of which the steroidal glycoalkaloids (SGAs) and steroidal saponins (SS) have vast potential to serve as anticancer agents. Since there has been much controversy regarding safety of use of glycoalkaloids as anticancer agents, this area has remained more or less unexplored. Cytoskeletal proteins like actin play an important role in maintaining cell shape, synchronizing cell division, cell motility, etc. and along with their accessory proteins may also serve as important therapeutic targets for potential anticancer candidates. In the present study, glycoalkaloids and saponins from S. nigrum were screened for their interaction and binding affinity to cytoskeletal proteins, using molecular docking. Methods Bioactivity score and Prediction of Activity Spectra for Substances (PASS) analysis were performed using softwares Molinspiration and Osiris Data Explorer respectively, to assess the feasibility of selected phytoconstituents as potential drug candidates. The results were compared with two standard reference drugs doxorubicin hydrochloride (anticancer) and tetracycline (antibiotic). Multivariate data obtained were analyzed using principal component analysis (PCA). Results Docking analysis revealed that the binding affinities of the phytoconstituents towards the target cytoskeletal proteins decreased in the order coronin>villin>ezrin>vimentin>gelsolin>thymosin>cofilin. Glycoalkaloid solasonine displayed the greatest binding affinity towards the target proteins followed by alpha-solanine whereas amongst the saponins, nigrumnin-I showed maximum binding affinity. PASS Analysis of the selected phytoconstituents revealed 1 to 3 violations of Lipinski’s parameters indicating the need for modification of their structure-activity relationship (SAR) for improvement of their bioactivity and bioavailability. Glycoalkaloids and…
format: application/pdf
format: text/html
creator: Rumana Ahmad
subject: Biochemistry
subject: Bioinformatics
subject: Cell Biology
subject: Computational Biology
subject: Plant Science
description: doi:10.7717/peerj.6012
publisher: PeerJ Inc.
rights: © 2019 Ahmad
abstract: Background Solanum nigrum (black nightshade; S. nigrum), a member of family Solanaceae, has been endowed with a heterogeneous array of secondary metabolites of which the steroidal glycoalkaloids (SGAs) and steroidal saponins (SS) have vast potential to serve as anticancer agents. Since there has been much controversy regarding safety of use of glycoalkaloids as anticancer agents, this area has remained more or less unexplored. Cytoskeletal proteins like actin play an important role in maintaining cell shape, synchronizing cell division, cell motility, etc. and along with their accessory proteins may also serve as important therapeutic targets for potential anticancer candidates. In the present study, glycoalkaloids and saponins from S. nigrum were screened for their interaction and binding affinity to cytoskeletal proteins, using molecular docking. Methods Bioactivity score and Prediction of Activity Spectra for Substances (PASS) analysis were performed using softwares Molinspiration and Osiris Data Explorer respectively, to assess the feasibility of selected phytoconstituents as potential drug candidates. The results were compared with two standard reference drugs doxorubicin hydrochloride (anticancer) and tetracycline (antibiotic). Multivariate data obtained were analyzed using principal component analysis (PCA). Results Docking analysis revealed that the binding affinities of the phytoconstituents towards the target cytoskeletal proteins decreased in the order coronin>villin>ezrin>vimentin>gelsolin>thymosin>cofilin. Glycoalkaloid solasonine displayed the greatest binding affinity towards the target proteins followed by alpha-solanine whereas amongst the saponins, nigrumnin-I showed maximum binding affinity. PASS Analysis of the selected phytoconstituents revealed 1 to 3 violations of Lipinski’s parameters indicating the need for modification of their structure-activity relationship (SAR) for improvement of their bioactivity and bioavailability. Glycoalkaloids and…
bibliographic citation: Ahmad (2019) Steroidal glycoalkaloids from Solanum nigrum target cytoskeletal proteins: an in silico analysis. PeerJ 7:e6012 https://doi.org/10.7717/peerj.6012
date submitted: 2018-03-05
date accepted: 2018-10-26
issued: 2019-01-03
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Ahmad
  given name: Rumana
doi: 10.7717/peerj.6012
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-01-03
copyright: ©2019 Ahmad
attribution name: Ahmad

The existence and evolution of morphotypes in Anolis lizards: coexistence patterns, not adaptive radiations, distinguish mainland and island faunas
type: item
type: AcademicArticle
description: The evolution of distinct ecologies and correlated morphologies (“ecomorphs,” in combination) among similar species allows sympatric occupation of diverse microhabitats. Particular ecomorphs may evolve repeatedly, that is, convergently, as separate lineages arrive at similar solutions. Caribbean Anolis lizards (anoles) are a classic ecomorph system, particularly well-studied for the diverse morphotypes resulting from adaptive radiations. But few studies have analyzed the equally species-diverse mainland Anolis. Here, we use clustering analyses of nine traits for 336 species of Anolis to objectively identify morphological groups (morphotypes). We analyze the presence of recovered morphotypes on mainland and islands in general and relative to the composition of 76 mainland and 91 island anole assemblages. We test for evolutionary convergence of morphotypes within and between mainland and island environments by mapping our recovered morphotypes onto recent phylogenetic estimates and by analyzing four of our measured traits using program SURFACE. We find that particular morphotypes tend to be restricted to either mainland or island environments. Morphotype diversity and convergence are not concentrated within either island or mainland environments. Morphotype content of assemblages differs between mainland and island areas, with island assemblages displaying greater numbers of morphotypes than mainland assemblages. Taken with recent research, these results suggest a restructuring of one of the classic adaptive radiation stories and a reconsideration of research concerning island–mainland faunal differences. Island radiations of anoles are unexceptional relative to mainland radiations with regard to species count, rates of speciation and phenotypic evolution, morphotype diversity, and rates of convergence. But local island assemblage appear to be more diverse than mainland assemblages. The explanation for this assemblage disparity may reside in one of the classic hypothe…
format: application/pdf
format: text/html
creator: Steven Poe
creator: Christopher G. Anderson
subject: Biodiversity
subject: Ecology
subject: Evolutionary Studies
description: doi:10.7717/peerj.6040
publisher: PeerJ Inc.
rights: © 2019 Poe and Anderson
abstract: The evolution of distinct ecologies and correlated morphologies (“ecomorphs,” in combination) among similar species allows sympatric occupation of diverse microhabitats. Particular ecomorphs may evolve repeatedly, that is, convergently, as separate lineages arrive at similar solutions. Caribbean Anolis lizards (anoles) are a classic ecomorph system, particularly well-studied for the diverse morphotypes resulting from adaptive radiations. But few studies have analyzed the equally species-diverse mainland Anolis. Here, we use clustering analyses of nine traits for 336 species of Anolis to objectively identify morphological groups (morphotypes). We analyze the presence of recovered morphotypes on mainland and islands in general and relative to the composition of 76 mainland and 91 island anole assemblages. We test for evolutionary convergence of morphotypes within and between mainland and island environments by mapping our recovered morphotypes onto recent phylogenetic estimates and by analyzing four of our measured traits using program SURFACE. We find that particular morphotypes tend to be restricted to either mainland or island environments. Morphotype diversity and convergence are not concentrated within either island or mainland environments. Morphotype content of assemblages differs between mainland and island areas, with island assemblages displaying greater numbers of morphotypes than mainland assemblages. Taken with recent research, these results suggest a restructuring of one of the classic adaptive radiation stories and a reconsideration of research concerning island–mainland faunal differences. Island radiations of anoles are unexceptional relative to mainland radiations with regard to species count, rates of speciation and phenotypic evolution, morphotype diversity, and rates of convergence. But local island assemblage appear to be more diverse than mainland assemblages. The explanation for this assemblage disparity may reside in one of the classic hypothe…
bibliographic citation: Poe et al. (2019) The existence and evolution of morphotypes in Anolis lizards: coexistence patterns, not adaptive radiations, distinguish mainland and island faunas. PeerJ 6:e6040 https://doi.org/10.7717/peerj.6040
date submitted: 2017-11-21
date accepted: 2018-10-30
issued: 2019-01-03
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Poe
  given name: Steven
author list: Agent
  family name: Anderson
  given name: Christopher G.
doi: 10.7717/peerj.6040
volume: 6
issn: 2167-8359
publication name: PeerJ
publication date: 2019-01-03
copyright: © 2019 Poe and Anderson
attribution name: Poe and Anderson

Isolation and identification of marine strains of Stenotrophomona maltophilia with high chitinolytic activity
type: item
type: AcademicArticle
description: Chitin is the second most abundant organic compound in nature and represents a rich carbon and nitrogen source that is primarily transformed by bacterial communities. Bacteria capable of gradually hydrolyzing chitin into N-acetylglucosamine monomers can have applications in the transformation of residues from shrimp and other crustaceans. The objective of the present study was to isolate, characterize and identify microorganisms with high chitinolytic activity. These microorganisms were isolated and characterized based on macro- and microscopic morphological traits. Strains were selected on colloidal chitin agar medium primarily based on a hydrolysis halo larger than 2 mm and a growing phase no longer than 6 days. Secondary selection consisted of semi-quantitative evaluation of chitinolytic activity with a drop dilution assay. From the above, ten strains were selected. Then, strain-specific activity was evaluated. The B4 strain showed the highest specific activity, which was 6,677.07 U/mg protein. Molecular identification indicated that the isolated strains belong to the species Stenotrophomonas maltophilia.
format: application/pdf
format: text/html
creator: Roger Salas-Ovilla
creator: Didiana Gálvez-López
creator: Alfredo Vázquez-Ovando
creator: Miguel Salvador-Figueroa
creator: Raymundo Rosas-Quijano
subject: Microbiology
subject: Molecular Biology
description: doi:10.7717/peerj.6102
publisher: PeerJ Inc.
rights: © 2019 Salas-Ovilla et al.
abstract: Chitin is the second most abundant organic compound in nature and represents a rich carbon and nitrogen source that is primarily transformed by bacterial communities. Bacteria capable of gradually hydrolyzing chitin into N-acetylglucosamine monomers can have applications in the transformation of residues from shrimp and other crustaceans. The objective of the present study was to isolate, characterize and identify microorganisms with high chitinolytic activity. These microorganisms were isolated and characterized based on macro- and microscopic morphological traits. Strains were selected on colloidal chitin agar medium primarily based on a hydrolysis halo larger than 2 mm and a growing phase no longer than 6 days. Secondary selection consisted of semi-quantitative evaluation of chitinolytic activity with a drop dilution assay. From the above, ten strains were selected. Then, strain-specific activity was evaluated. The B4 strain showed the highest specific activity, which was 6,677.07 U/mg protein. Molecular identification indicated that the isolated strains belong to the species Stenotrophomonas maltophilia.
bibliographic citation: Salas-Ovilla et al. (2019) Isolation and identification of marine strains of Stenotrophomona maltophilia with high chitinolytic activity. PeerJ 7:e6102 https://doi.org/10.7717/peerj.6102
date submitted: 2018-08-27
date accepted: 2018-11-06
issued: 2019-01-03
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Salas-Ovilla
  given name: Roger
author list: Agent
  family name: Gálvez-López
  given name: Didiana
author list: Agent
  family name: Vázquez-Ovando
  given name: Alfredo
author list: Agent
  family name: Salvador-Figueroa
  given name: Miguel
author list: Agent
  family name: Rosas-Quijano
  given name: Raymundo
doi: 10.7717/peerj.6102
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-01-03
copyright: ©2019 Salas-Ovilla et al.
attribution name: Salas-Ovilla et al.

The role of Central American barriers in shaping the evolutionary history of the northernmost glassfrog, Hyalinobatrachium fleischmanni (Anura: Centrolenidae)
type: item
type: AcademicArticle
description: The complex geological history of Central America has been useful for understanding the processes influencing the distribution and diversity of multiple groups of organisms. Anurans are an excellent choice for such studies because they typically exhibit site fidelity and reduced movement. The objective of this work was to identify the impact of recognized geographic barriers on the genetic structure, phylogeographic patterns and divergence times of a wide-ranging amphibian species, Hyalinobatrachium fleischmanni. We amplified three mitochondrial regions, two coding (COI and ND1) and one ribosomal (16S), in samples collected from the coasts of Veracruz and Guerrero in Mexico to the humid forests of Chocó in Ecuador. We examined the biogeographic history of the species through spatial clustering analyses (Geneland and sPCA), Bayesian and maximum likelihood reconstructions, and spatiotemporal diffusion analysis. Our data suggest a Central American origin of H. fleischmanni and two posterior independent dispersals towards North and South American regions. The first clade comprises individuals from Colombia, Ecuador, Panama and the sister species Hyalinobatrachium tatayoi; this clade shows little structure, despite the presence of the Andes mountain range and the long distances between sampling sites. The second clade consists of individuals from Costa Rica, Nicaragua, and eastern Honduras with no apparent structure. The third clade includes individuals from western Honduras, Guatemala, and Mexico and displays deep population structure. Herein, we synthesize the impact of known geographic areas that act as barriers to glassfrog dispersal and demonstrated their effect of differentiating H. fleischmanni into three markedly isolated clades. The observed genetic structure is associated with an initial dispersal event from Central America followed by vicariance that likely occurred during the Pliocene. The southern samples are characterized by a very recent population expansi…
format: application/pdf
format: text/html
creator: Angela M. Mendoza
creator: Wilmar Bolívar-García
creator: Ella Vázquez-Domínguez
creator: Roberto Ibáñez
creator: Gabriela Parra Olea
subject: Biogeography
subject: Zoology
description: doi:10.7717/peerj.6115
publisher: PeerJ Inc.
rights: © 2019 Mendoza et al.
abstract: The complex geological history of Central America has been useful for understanding the processes influencing the distribution and diversity of multiple groups of organisms. Anurans are an excellent choice for such studies because they typically exhibit site fidelity and reduced movement. The objective of this work was to identify the impact of recognized geographic barriers on the genetic structure, phylogeographic patterns and divergence times of a wide-ranging amphibian species, Hyalinobatrachium fleischmanni. We amplified three mitochondrial regions, two coding (COI and ND1) and one ribosomal (16S), in samples collected from the coasts of Veracruz and Guerrero in Mexico to the humid forests of Chocó in Ecuador. We examined the biogeographic history of the species through spatial clustering analyses (Geneland and sPCA), Bayesian and maximum likelihood reconstructions, and spatiotemporal diffusion analysis. Our data suggest a Central American origin of H. fleischmanni and two posterior independent dispersals towards North and South American regions. The first clade comprises individuals from Colombia, Ecuador, Panama and the sister species Hyalinobatrachium tatayoi; this clade shows little structure, despite the presence of the Andes mountain range and the long distances between sampling sites. The second clade consists of individuals from Costa Rica, Nicaragua, and eastern Honduras with no apparent structure. The third clade includes individuals from western Honduras, Guatemala, and Mexico and displays deep population structure. Herein, we synthesize the impact of known geographic areas that act as barriers to glassfrog dispersal and demonstrated their effect of differentiating H. fleischmanni into three markedly isolated clades. The observed genetic structure is associated with an initial dispersal event from Central America followed by vicariance that likely occurred during the Pliocene. The southern samples are characterized by a very recent population expansi…
bibliographic citation: Mendoza et al. (2019) The role of Central American barriers in shaping the evolutionary history of the northernmost glassfrog, Hyalinobatrachium fleischmanni (Anura: Centrolenidae). PeerJ 7:e6115 https://doi.org/10.7717/peerj.6115
date submitted: 2018-07-31
date accepted: 2018-11-15
issued: 2019-01-03
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Mendoza
  given name: Angela M.
author list: Agent
  family name: Bolívar-García
  given name: Wilmar
author list: Agent
  family name: Vázquez-Domínguez
  given name: Ella
author list: Agent
  family name: Ibáñez
  given name: Roberto
author list: Agent
  family name: Parra Olea
  given name: Gabriela
doi: 10.7717/peerj.6115
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-01-03
copyright: ©2019 Mendoza et al.
attribution name: Mendoza et al.

Comparison of non-magnetic and magnetic beads multiplex assay for assessment of Plasmodium falciparum antibodies
type: item
type: AcademicArticle
description: Background New reagents have emerged allowing researchers to assess a growing number of vaccine-associated immune parameters. Multiplex immunoassay(s) are emerging as efficient high-throughput assays in malaria serology. Currently, commercial vendors market several bead reagents for cytometric bead assays (CBA) but relative performances are not well published. We have compared two types of bead-based multiplex assays to measure relative antibody levels to malarial antigens. Methods Assays for the measurement of antibodies to five Plasmodium falciparum vaccine candidates using non-magnetic and magnetic fluorescent microspheres were compared for their performances with a Bio-Plex200 instrument. Mean fluorescence intensity (MFI) was determined from individuals from western Kenya and compared to known positive and negative control plasma samples. Results P. falciparum recombinant antigens were successfully coupled to both non-magnetic and magnetic beads in multiplex assays. MFIs between the two bead types were comparable for all antigens tested. Bead recovery was superior with magnetic beads for all antigens. MFI values of stored non-magnetic coupled beads did not differ from freshly coupled beads, though they showed higher levels of bead aggregation. Discussion Magnetic and non-magnetic beads performed similarly in P. falciparum antibody assays. Magnetic beads were more expensive, but had higher bead recovery, were more convenient to use, and provided rapid and easy protocol manipulation. Magnetic beads are a suitable alternative to non-magnetic beads in malarial antibody serology.
format: application/pdf
format: text/html
creator: Bartholomew N. Ondigo
creator: Gregory S. Park
creator: Cyrus Ayieko
creator: Donald D. Nyangahu
creator: Ronald Wasswa
creator: Chandy C. John
subject: Global Health
subject: Immunology
subject: Infectious Diseases
subject: Translational Medicine
description: doi:10.7717/peerj.6120
publisher: PeerJ Inc.
rights: © 2019 Ondigo et al.
abstract: Background New reagents have emerged allowing researchers to assess a growing number of vaccine-associated immune parameters. Multiplex immunoassay(s) are emerging as efficient high-throughput assays in malaria serology. Currently, commercial vendors market several bead reagents for cytometric bead assays (CBA) but relative performances are not well published. We have compared two types of bead-based multiplex assays to measure relative antibody levels to malarial antigens. Methods Assays for the measurement of antibodies to five Plasmodium falciparum vaccine candidates using non-magnetic and magnetic fluorescent microspheres were compared for their performances with a Bio-Plex200 instrument. Mean fluorescence intensity (MFI) was determined from individuals from western Kenya and compared to known positive and negative control plasma samples. Results P. falciparum recombinant antigens were successfully coupled to both non-magnetic and magnetic beads in multiplex assays. MFIs between the two bead types were comparable for all antigens tested. Bead recovery was superior with magnetic beads for all antigens. MFI values of stored non-magnetic coupled beads did not differ from freshly coupled beads, though they showed higher levels of bead aggregation. Discussion Magnetic and non-magnetic beads performed similarly in P. falciparum antibody assays. Magnetic beads were more expensive, but had higher bead recovery, were more convenient to use, and provided rapid and easy protocol manipulation. Magnetic beads are a suitable alternative to non-magnetic beads in malarial antibody serology.
bibliographic citation: Ondigo et al. (2019) Comparison of non-magnetic and magnetic beads multiplex assay for assessment of Plasmodium falciparum antibodies. PeerJ 7:e6120 https://doi.org/10.7717/peerj.6120
date submitted: 2018-04-26
date accepted: 2018-11-16
issued: 2019-01-03
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Ondigo
  given name: Bartholomew N.
author list: Agent
  family name: Park
  given name: Gregory S.
author list: Agent
  family name: Ayieko
  given name: Cyrus
author list: Agent
  family name: Nyangahu
  given name: Donald D.
author list: Agent
  family name: Wasswa
  given name: Ronald
author list: Agent
  family name: John
  given name: Chandy C.
doi: 10.7717/peerj.6120
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-01-03
copyright: ©2019 Ondigo et al.
attribution name: Ondigo et al.

Analysis of the complete genome sequence of a marine-derived strain Streptomyces sp. S063 CGMCC 14582 reveals its biosynthetic potential to produce novel anti-complement agents and peptides
type: item
type: AcademicArticle
description: Genome sequences of marine streptomycetes are valuable for the discovery of useful enzymes and bioactive compounds by genome mining. However, publicly available complete genome sequences of marine streptomycetes are still limited. Here, we present the complete genome sequence of a marine streptomycete Streptomyces sp. S063 CGMCC 14582. Species delineation based on the pairwise digital DNA-DNA hybridization and genome comparison ANI (average nucleotide identity) value showed that Streptomyces sp. S063 CGMCC 14582 possesses a unique genome that is clearly different from all of the other available genomes. Bioactivity tests showed that Streptomyces sp. S063 CGMCC 14582 produces metabolites with anti-complement activities, which are useful for treatment of numerous diseases that arise from inappropriate activation of the human complement system. Analysis of the genome reveals no biosynthetic gene cluster (BGC) which shows even low similarity to that of the known anti-complement agents was detected in the genome, indicating that Streptomyces sp. S063 CGMCC 14582 may produce novel anti-complement agents of microbial origin. Four BGCs which are potentially involved in biosynthesis of non-ribosomal peptides were disrupted, but no decrease of anti-complement activities was observed, suggesting that these four BGCs are not involved in biosynthesis of the anti-complement agents. In addition, LC-MS/MS analysis and subsequent alignment through the Global Natural Products Social Molecular Networking (GNPS) platform led to the detection of novel peptides produced by the strain. Streptomyces sp. S063 CGMCC 14582 grows rapidly and is salt tolerant, which benefits efficient secondary metabolite production via seawater-based fermentation. Our results indicate that Streptomyces sp. S063 has great potential to produce novel bioactive compounds, and also is a good host for heterologous production of useful secondary metabolites for drug discovery.
format: application/pdf
format: text/html
creator: Liang-Yu Chen
creator: Hao-Tian Cui
creator: Chun Su
creator: Feng-Wu Bai
creator: Xin-Qing Zhao
subject: Biochemistry
subject: Genomics
subject: Microbiology
description: doi:10.7717/peerj.6122
publisher: PeerJ Inc.
rights: © 2019 Chen et al.
abstract: Genome sequences of marine streptomycetes are valuable for the discovery of useful enzymes and bioactive compounds by genome mining. However, publicly available complete genome sequences of marine streptomycetes are still limited. Here, we present the complete genome sequence of a marine streptomycete Streptomyces sp. S063 CGMCC 14582. Species delineation based on the pairwise digital DNA-DNA hybridization and genome comparison ANI (average nucleotide identity) value showed that Streptomyces sp. S063 CGMCC 14582 possesses a unique genome that is clearly different from all of the other available genomes. Bioactivity tests showed that Streptomyces sp. S063 CGMCC 14582 produces metabolites with anti-complement activities, which are useful for treatment of numerous diseases that arise from inappropriate activation of the human complement system. Analysis of the genome reveals no biosynthetic gene cluster (BGC) which shows even low similarity to that of the known anti-complement agents was detected in the genome, indicating that Streptomyces sp. S063 CGMCC 14582 may produce novel anti-complement agents of microbial origin. Four BGCs which are potentially involved in biosynthesis of non-ribosomal peptides were disrupted, but no decrease of anti-complement activities was observed, suggesting that these four BGCs are not involved in biosynthesis of the anti-complement agents. In addition, LC-MS/MS analysis and subsequent alignment through the Global Natural Products Social Molecular Networking (GNPS) platform led to the detection of novel peptides produced by the strain. Streptomyces sp. S063 CGMCC 14582 grows rapidly and is salt tolerant, which benefits efficient secondary metabolite production via seawater-based fermentation. Our results indicate that Streptomyces sp. S063 has great potential to produce novel bioactive compounds, and also is a good host for heterologous production of useful secondary metabolites for drug discovery.
bibliographic citation: Chen et al. (2019) Analysis of the complete genome sequence of a marine-derived strain Streptomyces sp. S063 CGMCC 14582 reveals its biosynthetic potential to produce novel anti-complement agents and peptides. PeerJ 7:e6122 https://doi.org/10.7717/peerj.6122
date submitted: 2018-08-07
date accepted: 2018-11-12
issued: 2019-01-03
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Chen
  given name: Liang-Yu
author list: Agent
  family name: Cui
  given name: Hao-Tian
author list: Agent
  family name: Su
  given name: Chun
author list: Agent
  family name: Bai
  given name: Feng-Wu
author list: Agent
  family name: Zhao
  given name: Xin-Qing
doi: 10.7717/peerj.6122
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-01-03
copyright: ©2019 Chen et al.
attribution name: Chen et al.

Toxicity of TiO2, SiO2, ZnO, CuO, Au and Ag engineered nanoparticles on hatching and early nauplii of Artemia sp.
type: item
type: AcademicArticle
description: The potential of environmental release enhances with increased commercial applications of the nanomaterials. In this work, a simple and efficient test to estimate the acute toxicity of nanoparticles is carried out on Artemia species and their hatching rates. We have tested six different engineered nanoparticles (silver, gold, copper oxide, zinc oxide, TiO2 and SiO2 nanoparticles) and three soluble salts (CuSO4, ZnSO4 and AgNO3) on Artemia sp. The physicochemical properties of the nanoparticles involved in this study were analyzed in normal water and marine water. Hydrated and bleached Artemia cysts were allowed to hatch in continuously aerated, filtered sterile salt water containing nanoparticles; hatching of viable nauplii and total hatchlings have been recorded. In parallel, standard Artemia toxicity test was conducted on the nauplii monitoring the viability. In hatching experiments, a reduction in hatching rate was observed along with mortality of newly hatched nauplii. The results of the hatching experiment and of the standard Artemia test showed a good correlation. The toxicity of the nanoparticles was compared and the order of toxicity was estimated as Ag>CuO>ZnO>Au>TiO2>SiO2. The study thus suggests that the hatching test itself is a reliable assay for determining the toxicity of nanomaterials.
format: application/pdf
format: text/html
creator: Rohit Rekulapally
creator: Lakshmi Narsimha Murthy Chavali
creator: Mohammed M. Idris
creator: Shashi Singh
subject: Toxicology
subject: Ecotoxicology
description: doi:10.7717/peerj.6138
publisher: PeerJ Inc.
rights: © 2019 Rekulapally et al.
abstract: The potential of environmental release enhances with increased commercial applications of the nanomaterials. In this work, a simple and efficient test to estimate the acute toxicity of nanoparticles is carried out on Artemia species and their hatching rates. We have tested six different engineered nanoparticles (silver, gold, copper oxide, zinc oxide, TiO2 and SiO2 nanoparticles) and three soluble salts (CuSO4, ZnSO4 and AgNO3) on Artemia sp. The physicochemical properties of the nanoparticles involved in this study were analyzed in normal water and marine water. Hydrated and bleached Artemia cysts were allowed to hatch in continuously aerated, filtered sterile salt water containing nanoparticles; hatching of viable nauplii and total hatchlings have been recorded. In parallel, standard Artemia toxicity test was conducted on the nauplii monitoring the viability. In hatching experiments, a reduction in hatching rate was observed along with mortality of newly hatched nauplii. The results of the hatching experiment and of the standard Artemia test showed a good correlation. The toxicity of the nanoparticles was compared and the order of toxicity was estimated as Ag>CuO>ZnO>Au>TiO2>SiO2. The study thus suggests that the hatching test itself is a reliable assay for determining the toxicity of nanomaterials.
bibliographic citation: Rekulapally et al. (2019) Toxicity of TiO2, SiO2, ZnO, CuO, Au and Ag engineered nanoparticles on hatching and early nauplii of Artemia sp.. PeerJ 6:e6138 https://doi.org/10.7717/peerj.6138
date submitted: 2018-07-18
date accepted: 2018-11-20
issued: 2019-01-03
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Rekulapally
  given name: Rohit
author list: Agent
  family name: Murthy Chavali
  given name: Lakshmi Narsimha
author list: Agent
  family name: Idris
  given name: Mohammed M.
author list: Agent
  family name: Singh
  given name: Shashi
doi: 10.7717/peerj.6138
volume: 6
issn: 2167-8359
publication name: PeerJ
publication date: 2019-01-03
copyright: © 2019 Rekulapally et al.
attribution name: Rekulapally et al.

Fully automated sequence alignment methods are comparable to, and much faster than, traditional methods in large data sets: an example with hepatitis B virus
type: item
type: AcademicArticle
description: Aligning sequences for phylogenetic analysis (multiple sequence alignment; MSA) is an important, but increasingly computationally expensive step with the recent surge in DNA sequence data. Much of this sequence data is publicly available, but can be extremely fragmentary (i.e., a combination of full genomes and genomic fragments), which can compound the computational issues related to MSA. Traditionally, alignments are produced with automated algorithms and then checked and/or corrected “by eye” prior to phylogenetic inference. However, this manual curation is inefficient at the data scales required of modern phylogenetics and results in alignments that are not reproducible. Recently, methods have been developed for fully automating alignments of large data sets, but it is unclear if these methods produce alignments that result in compatible phylogenies when compared to more traditional alignment approaches that combined automated and manual methods. Here we use approximately 33,000 publicly available sequences from the hepatitis B virus (HBV), a globally distributed and rapidly evolving virus, to compare different alignment approaches. Using one data set comprised exclusively of whole genomes and a second that also included sequence fragments, we compared three MSA methods: (1) a purely automated approach using traditional software, (2) an automated approach including by eye manual editing, and (3) more recent fully automated approaches. To understand how these methods affect phylogenetic results, we compared resulting tree topologies based on these different alignment methods using multiple metrics. We further determined if the monophyly of existing HBV genotypes was supported in phylogenies estimated from each alignment type and under different statistical support thresholds. Traditional and fully automated alignments produced similar HBV phylogenies. Although there was variability between branch support thresholds, allowing lower support thresholds tended to res…
format: application/pdf
format: text/html
creator: Therese A. Catanach
creator: Andrew D. Sweet
creator: Nam-phuong D. Nguyen
creator: Rhiannon M. Peery
creator: Andrew H. Debevec
creator: Andrea K. Thomer
creator: Amanda C. Owings
creator: Bret M. Boyd
creator: Aron D. Katz
creator: Felipe N. Soto-Adames
creator: Julie M. Allen
subject: Bioinformatics
subject: Computational Biology
subject: Data Mining and Machine Learning
description: doi:10.7717/peerj.6142
publisher: PeerJ Inc.
rights: © 2019 Catanach et al.
abstract: Aligning sequences for phylogenetic analysis (multiple sequence alignment; MSA) is an important, but increasingly computationally expensive step with the recent surge in DNA sequence data. Much of this sequence data is publicly available, but can be extremely fragmentary (i.e., a combination of full genomes and genomic fragments), which can compound the computational issues related to MSA. Traditionally, alignments are produced with automated algorithms and then checked and/or corrected “by eye” prior to phylogenetic inference. However, this manual curation is inefficient at the data scales required of modern phylogenetics and results in alignments that are not reproducible. Recently, methods have been developed for fully automating alignments of large data sets, but it is unclear if these methods produce alignments that result in compatible phylogenies when compared to more traditional alignment approaches that combined automated and manual methods. Here we use approximately 33,000 publicly available sequences from the hepatitis B virus (HBV), a globally distributed and rapidly evolving virus, to compare different alignment approaches. Using one data set comprised exclusively of whole genomes and a second that also included sequence fragments, we compared three MSA methods: (1) a purely automated approach using traditional software, (2) an automated approach including by eye manual editing, and (3) more recent fully automated approaches. To understand how these methods affect phylogenetic results, we compared resulting tree topologies based on these different alignment methods using multiple metrics. We further determined if the monophyly of existing HBV genotypes was supported in phylogenies estimated from each alignment type and under different statistical support thresholds. Traditional and fully automated alignments produced similar HBV phylogenies. Although there was variability between branch support thresholds, allowing lower support thresholds tended to res…
bibliographic citation: Catanach et al. (2019) Fully automated sequence alignment methods are comparable to, and much faster than, traditional methods in large data sets: an example with hepatitis B virus. PeerJ 7:e6142 https://doi.org/10.7717/peerj.6142
date submitted: 2018-02-07
date accepted: 2018-11-14
issued: 2019-01-03
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Catanach
  given name: Therese A.
author list: Agent
  family name: Sweet
  given name: Andrew D.
author list: Agent
  family name: Nguyen
  given name: Nam-phuong D.
author list: Agent
  family name: Peery
  given name: Rhiannon M.
author list: Agent
  family name: Debevec
  given name: Andrew H.
author list: Agent
  family name: Thomer
  given name: Andrea K.
author list: Agent
  family name: Owings
  given name: Amanda C.
author list: Agent
  family name: Boyd
  given name: Bret M.
author list: Agent
  family name: Katz
  given name: Aron D.
author list: Agent
  family name: Soto-Adames
  given name: Felipe N.
author list: Agent
  family name: Allen
  given name: Julie M.
doi: 10.7717/peerj.6142
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-01-03
copyright: ©2019 Catanach et al.
attribution name: Catanach et al.

Otolith microchemistry and diadromy in Patagonian river fishes
type: item
type: AcademicArticle
description: Coastal habitats in Chile are hypothesized to support a number of diadromous fish species. The objective of this study was to document migratory life histories of native galaxiids and introduced salmonids from a wide latitudinal range in Chilean Patagonia (39–48°S). Otolith microchemistry data were analysed using a recursive partitioning approach to test for diadromy. Based on annular analysis of Sr:Ca ratios, a diadromous life history was suggested for populations of native Aplochiton taeniatus, A. marinus, and Galaxias maculatus. Lifetime residency in freshwater was suggested for populations of A. zebra and G. platei. Among introduced salmonids, populations of Oncorhynchus tshawytscha and O. kisutch exhibited patterns consistent with anadromy, whereas the screened population of O. mykiss appeared restricted to freshwater. Salmo trutta exhibited variable patterns suggesting freshwater residency and possibly anadromy in one case. The capacity and geographic scope of hydropower development is increasing and may disrupt migratory routes of diadromous fishes. Identification of diadromous species is a critical first step for preventing their loss due to hydropower development.
format: application/pdf
format: text/html
creator: Dominique Alò
creator: Cristian Correa
creator: Horacio Samaniego
creator: Corey A. Krabbenhoft
creator: Thomas F. Turner
subject: Aquaculture, Fisheries and Fish Science
subject: Ecology
subject: Freshwater Biology
description: doi:10.7717/peerj.6149
publisher: PeerJ Inc.
rights: © 2019 Alò et al.
abstract: Coastal habitats in Chile are hypothesized to support a number of diadromous fish species. The objective of this study was to document migratory life histories of native galaxiids and introduced salmonids from a wide latitudinal range in Chilean Patagonia (39–48°S). Otolith microchemistry data were analysed using a recursive partitioning approach to test for diadromy. Based on annular analysis of Sr:Ca ratios, a diadromous life history was suggested for populations of native Aplochiton taeniatus, A. marinus, and Galaxias maculatus. Lifetime residency in freshwater was suggested for populations of A. zebra and G. platei. Among introduced salmonids, populations of Oncorhynchus tshawytscha and O. kisutch exhibited patterns consistent with anadromy, whereas the screened population of O. mykiss appeared restricted to freshwater. Salmo trutta exhibited variable patterns suggesting freshwater residency and possibly anadromy in one case. The capacity and geographic scope of hydropower development is increasing and may disrupt migratory routes of diadromous fishes. Identification of diadromous species is a critical first step for preventing their loss due to hydropower development.
bibliographic citation: Alò et al. (2019) Otolith microchemistry and diadromy in Patagonian river fishes. PeerJ 7:e6149 https://doi.org/10.7717/peerj.6149
date submitted: 2018-06-01
date accepted: 2018-11-21
issued: 2019-01-03
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Alò
  given name: Dominique
author list: Agent
  family name: Correa
  given name: Cristian
author list: Agent
  family name: Samaniego
  given name: Horacio
author list: Agent
  family name: Krabbenhoft
  given name: Corey A.
author list: Agent
  family name: Turner
  given name: Thomas F.
doi: 10.7717/peerj.6149
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-01-03
copyright: ©2019 Alò et al.
attribution name: Alò et al.

Polyphasic evaluation of key cyanobacteria in biocrusts from the most arid region in Europe
type: item
type: AcademicArticle
description: Cyanobacteria are key microbes in topsoil communities that have important roles in preventing soil erosion, carbon and nitrogen fixation, and influencing soil hydrology. However, little is known regarding the identity and distribution of the microbial components in the photosynthetic assemblages that form a cohesive biological soil crust (biocrust) in drylands of Europe. In this study, we investigated the cyanobacterial species colonizing biocrusts in three representative dryland ecosystems from the most arid region in Europe (SE Spain) that are characterized by different soil conditions. Isolated cyanobacterial cultures were identified by a polyphasic approach, including 16S rRNA gene sequencing, phylogenetic relationship determination, and morphological and ecological habitat assessments. Three well-differentiated groups were identified: heterocystous-cyanobacteria (Nostoc commune, Nostoc calcicola, Tolypothrix distorta and Scytonema hyalinum), which play an important role in N and C cycling in soil; nonheterocystous bundle-forming cyanobacteria (Microcoleus steenstrupii, Trichocoleus desertorum, and Schizothrix cf. calcicola); and narrow filamentous cyanobacteria (Leptolyngbya frigida and Oculatella kazantipica), all of which are essential genera for initial biocrust formation. The results of this study contribute to our understanding of cyanobacterial species composition in biocrusts from important and understudied European habitats, such as the Mediterranean Basin, a hotspot of biodiversity, where these species are keystone pioneer organisms.
format: application/pdf
format: text/html
creator: Beatriz Roncero-Ramos
creator: M. Ángeles Muñoz-Martín
creator: Sonia Chamizo
creator: Lara Fernández-Valbuena
creator: Diego Mendoza
creator: Elvira Perona
creator: Yolanda Cantón
creator: Pilar Mateo
subject: Biodiversity
subject: Microbiology
subject: Soil Science
description: doi:10.7717/peerj.6169
publisher: PeerJ Inc.
rights: © 2019 Roncero-Ramos et al.
abstract: Cyanobacteria are key microbes in topsoil communities that have important roles in preventing soil erosion, carbon and nitrogen fixation, and influencing soil hydrology. However, little is known regarding the identity and distribution of the microbial components in the photosynthetic assemblages that form a cohesive biological soil crust (biocrust) in drylands of Europe. In this study, we investigated the cyanobacterial species colonizing biocrusts in three representative dryland ecosystems from the most arid region in Europe (SE Spain) that are characterized by different soil conditions. Isolated cyanobacterial cultures were identified by a polyphasic approach, including 16S rRNA gene sequencing, phylogenetic relationship determination, and morphological and ecological habitat assessments. Three well-differentiated groups were identified: heterocystous-cyanobacteria (Nostoc commune, Nostoc calcicola, Tolypothrix distorta and Scytonema hyalinum), which play an important role in N and C cycling in soil; nonheterocystous bundle-forming cyanobacteria (Microcoleus steenstrupii, Trichocoleus desertorum, and Schizothrix cf. calcicola); and narrow filamentous cyanobacteria (Leptolyngbya frigida and Oculatella kazantipica), all of which are essential genera for initial biocrust formation. The results of this study contribute to our understanding of cyanobacterial species composition in biocrusts from important and understudied European habitats, such as the Mediterranean Basin, a hotspot of biodiversity, where these species are keystone pioneer organisms.
bibliographic citation: Roncero-Ramos et al. (2019) Polyphasic evaluation of key cyanobacteria in biocrusts from the most arid region in Europe. PeerJ 7:e6169 https://doi.org/10.7717/peerj.6169
date submitted: 2018-07-11
date accepted: 2018-11-27
issued: 2019-01-03
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Roncero-Ramos
  given name: Beatriz
author list: Agent
  family name: Muñoz-Martín
  given name: M. Ángeles
author list: Agent
  family name: Chamizo
  given name: Sonia
author list: Agent
  family name: Fernández-Valbuena
  given name: Lara
author list: Agent
  family name: Mendoza
  given name: Diego
author list: Agent
  family name: Perona
  given name: Elvira
author list: Agent
  family name: Cantón
  given name: Yolanda
author list: Agent
  family name: Mateo
  given name: Pilar
doi: 10.7717/peerj.6169
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-01-03
copyright: ©2019 Roncero-Ramos et al.
attribution name: Roncero-Ramos et al.

PeerJ
type: Periodical
uri: PeerJ
issn: 2167-8359