PeerJ
type: channel
link: https://peerj.com/articles/
description: Articles published in PeerJ
publisher: PeerJ Inc.
publication name: PeerJ
issn: 2167-8359
items: A set of novel SNP loci for differentiating continental populations and three Chinese populations
items: Understanding the experience of psychopathology after intimate partner violence: the role of personality
items: Using road patrol data to identify factors associated with carnivore roadkill counts
items: IOCBIO Sparks detection and analysis software
items: Comparative analysis and characterization of the gut microbiota of four farmed snakes from southern China
items: Music-performance regulates microRNAs in professional musicians
items: Green potential of Pleurotus spp. in biotechnology
items: Transcriptional factor regulation network and competitive endogenous RNA (ceRNA) network determining response of esophageal squamous cell carcinomas to neoadjuvant chemoradiotherapy
items: Using opportunistic sightings to infer differential spatio-temporal use of western Mediterranean waters by the fin whale
items: Up-regulation of Grb2-associated binder 1 promotes hepatocyte growth factor-induced endothelial progenitor cell proliferation and migration
items: Factors that influence response classifications in chemotherapy treated patient-derived xenografts (PDX)
items: Evaluation of a toxoid fusion protein vaccine produced in plants to protect poultry against necrotic enteritis
items: Underwater sound production varies within not between species in sympatric newts
items: Comparison of the fecal microbiota of two free-ranging Chinese subspecies of the leopard (Panthera pardus) using high-throughput sequencing
items: Mammut pacificus sp. nov., a newly recognized species of mastodon from the Pleistocene of western North America
items: Old wild wolves: ancient DNA survey unveils population dynamics in Late Pleistocene and Holocene Italian remains
items: Clinicopathological characteristics, treatment and survival of pulmonary large cell neuroendocrine carcinoma: a SEER population-based study
items: Associated bacteria of Botryococcus braunii (Chlorophyta)
items: Evaluating the effects of a temporary fostering program on shelter dog welfare
items: Pixel: a content management platform for quantitative omics data
items: Biodegradation of thiocyanate by a native groundwater microbial consortium
items: Development of polymorphic EST-SSR markers and characterization of the autotetraploid genome of sainfoin (Onobrychis viciifolia)
items: Proteomics alterations in chicken jejunum caused by 24 h fasting
items: Comparative genomic analysis of the IDD genes in five Rosaceae species and expression analysis in Chinese white pear (Pyrus bretschneideri)
items: Isolation of cancer stem cells by selection for miR-302 expressing cells
items: Robust and automatic definition of microbiome states
items: Comparative analysis of the complete mitochondrial genomes of five Achilidae species (Hemiptera: Fulgoroidea) and other Fulgoroidea reveals conserved mitochondrial genome organization
items: Pharmacokinetic comparison of quercetin, isoquercitrin, and quercetin-3-O-β-D-glucuronide in rats by HPLC-MS
items: The relationship between serum uric acid within the normal range and β-cell function in Chinese patients with type 2 diabetes: differences by body mass index and gender
items: Loancorhynchus catrillancai gen. et sp. nov., a new swordfish (Xiphioidei, Blochiidae) from the Middle Eocene of central Chile
items: Translating the hemodynamic response: why focused interdisciplinary integration should matter for the future of functional neuroimaging
items: Dual effects of biochar and hyperaccumulator Solanum nigrum L. on the remediation of Cd-contaminated soil
items: Capacity for heat absorption by the wings of the butterfly Tirumala limniace (Cramer)
items: Evidence of cryptic lineages within a small South American crocodilian: the Schneider’s dwarf caiman Paleosuchus trigonatus (Alligatoridae: Caimaninae)
items: Pain neuroscience education on YouTube
items: The transcriptomic response to a short day to long day shift in leaves of the reference legume Medicago truncatula
items: Identification of key genes, pathways and potential therapeutic agents for liver fibrosis using an integrated bioinformatics analysis
items: Relative abundance and molecular evolution of Lake Sinai Virus (Sinaivirus) clades
items: Oceanographic moorings as year-round laboratories for investigating growth performance and settlement dynamics in the Antarctic scallop Adamussium colbecki (E. A. Smith, 1902)
items: Human gut resistome can be country-specific
items: Comparative analysis of the liver transcriptome in the red-eared slider Trachemys scripta elegans under chronic salinity stress
items: Association between herd management practices and antimicrobial resistance in Salmonella spp. from cull dairy cattle in Central California
items: Sea stars of the genus Henricia Gray, 1840 (Echinodermata, Asteroidea) from Vostok Bay, Sea of Japan
items: Spatial near future modeling of land use and land cover changes in the temperate forests of Mexico
items: Improvement of hydrogen production from Chlorella sp. biomass by acid-thermal pretreatment
items: The chemical composition of a new “mica sandwich” foraminiferal species from the East Coast of Korea: Capsammina crassa sp. nov.
items: Dose-dependent and strain-dependent anti-obesity effects of Lactobacillus sakei in a diet induced obese murine model
items: Maintenance of dominant populations in heavily grazed grassland: Inference from a Stipa breviflora seed germination experiment
items: Minimum inhibitory concentration of nano-silver bactericides for beneficial microbes and its effect on Ralstonia solanacearum and seed germination of Japanese Cucumber (Cucumis sativus)
items: Identification of an eight-gene signature for survival prediction for patients with hepatocellular carcinoma based on integrated bioinformatics analysis
items: Effects of handling and short-term captivity: a multi-behaviour approach using red sea urchins, Mesocentrotus franciscanus
items: High virulence gene diversity in Streptococcus pyogenes isolated in Central Italy
items: Evolution of host plant use and diversification in a species complex of parasitic weevils (Coleoptera: Curculionidae)
items: Transcriptome sequencing of olfactory-related genes in olfactory transduction of large yellow croaker (Larimichthy crocea) in response to bile salts
items: Low genetic diversity in captive populations of the critically endangered Blue-crowned Laughingthrush (Garrulax courtoisi) revealed by a panel of novel microsatellites
items: Fine-scale substrate heterogeneity does not affect arthropod communities on green roofs
items: Large carnivore habitat suitability modelling for Romania and associated predictions for protected areas
items: Identification of gene-phenotype connectivity associated with flavanone naringenin by functional network analysis
items: Increased risk of thyroid disease in patients with Sjogren's syndrome: a systematic review and meta-analysis
items: Integrated bioinformatics analysis of As, Au, Cd, Pb and Cu heavy metal responsive marker genes through Arabidopsis thaliana GEO datasets
items: Long-term high physical activity modulates event-related potential indices of inhibitory control in postmenopausal women
items: Estimating probabilistic context-free grammars for proteins using contact map constraints
items: Impact of El Niño-Southern Oscillation 2015-2016 on the soluble proteomic profile and cytolytic activity of Millepora alcicornis (“fire coral”) from the Mexican Caribbean
items: Genome-wide characterization of endogenous retroviruses in snub-nosed monkeys
items: Phytobiomes are compositionally nested from the ground up
items: A metagenomic study of DNA viruses from samples of local varieties of common bean in Kenya
items: Vocal recognition of a nest-predator in black grouse
items: Phylogenetic signal analysis in the basicranium of Ursidae (Carnivora, Mammalia)
items: Predicting electrocardiogram interpretation performance in Advanced Cardiovascular Life Support simulation: comparing knowledge tests and simulation performance among Mexican medical students
items: Genome-wide analysis of the Catalpa bungei caffeic acid O-methyltransferase (COMT) gene family: identification and expression profiles in normal, tension, and opposite wood
items: Identification of four hub genes associated with adrenocortical carcinoma progression by WGCNA
items: Acute toxicity and responses of antioxidant systems to dibutyl phthalate in neonate and adult Daphnia magna

A set of novel SNP loci for differentiating continental populations and three Chinese populations
type: item
type: AcademicArticle
description: In recent years, forensic geneticists have begun to develop some ancestry informative marker (AIM) panels for ancestry analysis of regional populations. In this study, we chose 48 single nucleotide polymorphisms (SNPs) from SPSmart database to infer ancestry origins of continental populations and Chinese subpopulations. Based on the genetic data of four continental populations (African, American, East Asian and European) from the CEPH-HGDP database, the power of these SNPs for differentiating continental populations was assessed. Population genetic structure revealed that distinct ancestry components among these continental populations could be discerned by these SNPs. Another novel population set from 1000 Genomes Phase 3 was treated as testing populations to further validate the efficiency of the selected SNPs. Twenty-two populations from CEPH-HGDP database were classified into three known populations (African, East Asian, and European) based on their biogeographical regions. Principal component analysis and Bayes analysis of testing populations and three known populations indicated these testing populations could be correctly assigned to their corresponding biogeographical origins. For three Chinese populations (Han, Mongolian, and Uygur), multinomial logistic regression analyses indicated that these 48 SNPs could be used to estimate ancestry origins of these populations. Therefore, these SNPs possessed the promising potency in ancestry analysis among continental populations and some Chinese populations, and they could be used in population genetics and forensic research.
format: application/pdf
format: text/html
creator: Xiao-Ye Jin
creator: Yuan-Yuan Wei
creator: Qiong Lan
creator: Wei Cui
creator: Chong Chen
creator: Yu-Xin Guo
creator: Ya-Ting Fang
creator: Bo-Feng Zhu
subject: Bioinformatics
subject: Genetics
subject: Data Science
subject: Population Biology
description: doi:10.7717/peerj.6508
publisher: PeerJ Inc.
rights: © 2019 Jin et al.
abstract: In recent years, forensic geneticists have begun to develop some ancestry informative marker (AIM) panels for ancestry analysis of regional populations. In this study, we chose 48 single nucleotide polymorphisms (SNPs) from SPSmart database to infer ancestry origins of continental populations and Chinese subpopulations. Based on the genetic data of four continental populations (African, American, East Asian and European) from the CEPH-HGDP database, the power of these SNPs for differentiating continental populations was assessed. Population genetic structure revealed that distinct ancestry components among these continental populations could be discerned by these SNPs. Another novel population set from 1000 Genomes Phase 3 was treated as testing populations to further validate the efficiency of the selected SNPs. Twenty-two populations from CEPH-HGDP database were classified into three known populations (African, East Asian, and European) based on their biogeographical regions. Principal component analysis and Bayes analysis of testing populations and three known populations indicated these testing populations could be correctly assigned to their corresponding biogeographical origins. For three Chinese populations (Han, Mongolian, and Uygur), multinomial logistic regression analyses indicated that these 48 SNPs could be used to estimate ancestry origins of these populations. Therefore, these SNPs possessed the promising potency in ancestry analysis among continental populations and some Chinese populations, and they could be used in population genetics and forensic research.
bibliographic citation: Jin et al. (2019) A set of novel SNP loci for differentiating continental populations and three Chinese populations. PeerJ 7:e6508 https://doi.org/10.7717/peerj.6508
date submitted: 2018-10-02
date accepted: 2019-01-22
issued: 2019-03-29
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Jin
  given name: Xiao-Ye
author list: Agent
  family name: Wei
  given name: Yuan-Yuan
author list: Agent
  family name: Lan
  given name: Qiong
author list: Agent
  family name: Cui
  given name: Wei
author list: Agent
  family name: Chen
  given name: Chong
author list: Agent
  family name: Guo
  given name: Yu-Xin
author list: Agent
  family name: Fang
  given name: Ya-Ting
author list: Agent
  family name: Zhu
  given name: Bo-Feng
doi: 10.7717/peerj.6508
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-03-29
copyright: ©2019 Jin et al.
attribution name: Jin et al.

Understanding the experience of psychopathology after intimate partner violence: the role of personality
type: item
type: AcademicArticle
description: Objective(s) To fully understand the dynamics of Intimate Partner Violence (IPV) it is necessary to understand the role of personality. The current understanding of which personality characteristics are associated with IPV victimization is, however, far from comprehensive. Given this gap in the literature, our objective was to examine the associations between the dimensions of the psychobiological model of personality and psychopathological symptoms in women who had experienced IPV. Methods Using a case-control design, a group of women who had experienced IPV and who were living in shelters (n = 50) were compared to a group of control women who had not experienced IPV (n = 50). All women completed the Temperament and Character Inventory–Revised and the Brief Symptom Inventory. Results Victims of IPV showed significantly higher levels of Harm Avoidance and Self-Transcendence, and lower levels of Reward Dependence and Self-Directedness, than the non-IPV control group. Victims of IPV also reported elevated levels of psychopathological symptoms. Personality dimensions showed a broadly consistent pattern of associations across different psychopathological symptoms. A regression analysis indicated that Novelty Seeking was negatively associated with psychopathological symptoms in victims of IPV, but not significantly associated in non-victims. Conclusions The study highlights the important role of Harm Avoidance and Self-Directedness for understanding psychopathological symptoms. Novelty Seeking appears to play an important role in the expression of individuals’ experiences of IPV. These results have important implications for research and practice, particularly the development and implementation of interventions.
format: application/pdf
format: text/html
creator: Paulo A.S. Moreira
creator: Márcia Pinto
creator: C. Robert Cloninger
creator: Daniela Rodrigues
creator: Carlos Fernandes da Silva
subject: Psychiatry and Psychology
subject: Women’s Health
description: doi:10.7717/peerj.6647
publisher: PeerJ Inc.
rights: © 2019 Moreira et al.
abstract: Objective(s) To fully understand the dynamics of Intimate Partner Violence (IPV) it is necessary to understand the role of personality. The current understanding of which personality characteristics are associated with IPV victimization is, however, far from comprehensive. Given this gap in the literature, our objective was to examine the associations between the dimensions of the psychobiological model of personality and psychopathological symptoms in women who had experienced IPV. Methods Using a case-control design, a group of women who had experienced IPV and who were living in shelters (n = 50) were compared to a group of control women who had not experienced IPV (n = 50). All women completed the Temperament and Character Inventory–Revised and the Brief Symptom Inventory. Results Victims of IPV showed significantly higher levels of Harm Avoidance and Self-Transcendence, and lower levels of Reward Dependence and Self-Directedness, than the non-IPV control group. Victims of IPV also reported elevated levels of psychopathological symptoms. Personality dimensions showed a broadly consistent pattern of associations across different psychopathological symptoms. A regression analysis indicated that Novelty Seeking was negatively associated with psychopathological symptoms in victims of IPV, but not significantly associated in non-victims. Conclusions The study highlights the important role of Harm Avoidance and Self-Directedness for understanding psychopathological symptoms. Novelty Seeking appears to play an important role in the expression of individuals’ experiences of IPV. These results have important implications for research and practice, particularly the development and implementation of interventions.
bibliographic citation: Moreira et al. (2019) Understanding the experience of psychopathology after intimate partner violence: the role of personality. PeerJ 7:e6647 https://doi.org/10.7717/peerj.6647
date submitted: 2018-12-13
date accepted: 2019-02-20
issued: 2019-03-29
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Moreira
  given name: Paulo A.S.
author list: Agent
  family name: Pinto
  given name: Márcia
author list: Agent
  family name: Cloninger
  given name: C. Robert
author list: Agent
  family name: Rodrigues
  given name: Daniela
author list: Agent
  family name: da Silva
  given name: Carlos Fernandes
doi: 10.7717/peerj.6647
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-03-29
copyright: ©2019 Moreira et al.
attribution name: Moreira et al.

Using road patrol data to identify factors associated with carnivore roadkill counts
type: item
type: AcademicArticle
description: As the global road network expands, roads pose an emerging threat to wildlife populations. One way in which roads can affect wildlife is wildlife-vehicle collisions, which can be a significant cause of mortality through roadkill. In order to successfully mitigate these problems, it is vital to understand the factors that can explain the distribution of roadkill. Collecting the data required to enable this can be expensive and time consuming, but there is significant potential in partnering with organisations that conduct existing road patrols to obtain the necessary data. We assessed the feasibility of using roadkill data collected daily between 2014 and 2017 by road patrol staff from a private road agency on a 410 km length of the N3 road in South Africa. We modelled the relationship between a set of environmental and anthropogenic variables on the number of roadkill carcasses, using serval (Leptailurus serval) as a model species. We recorded 5.24 serval roadkill carcasses/100 km/year. The number of carcasses was related to season, the amount of wetland, and NDVI, but was not related to any of the anthropogenic variables we included. This suggests that roadkill patterns may differ greatly depending on the ecology of species of interest, but targeting mitigation measures where roads pass through wetlands may help to reduce serval roadkill. Partnering with road agencies for data collection offers powerful opportunities to identify factors related to roadkill distribution and reduce the threats posed by roads to wildlife.
format: application/pdf
format: text/html
creator: Samual T. Williams
creator: Wendy Collinson
creator: Claire Patterson-Abrolat
creator: David G. Marneweck
creator: Lourens H. Swanepoel
subject: Conservation Biology
subject: Ecology
subject: Zoology
description: doi:10.7717/peerj.6650
publisher: PeerJ Inc.
rights: © 2019 Williams et al.
abstract: As the global road network expands, roads pose an emerging threat to wildlife populations. One way in which roads can affect wildlife is wildlife-vehicle collisions, which can be a significant cause of mortality through roadkill. In order to successfully mitigate these problems, it is vital to understand the factors that can explain the distribution of roadkill. Collecting the data required to enable this can be expensive and time consuming, but there is significant potential in partnering with organisations that conduct existing road patrols to obtain the necessary data. We assessed the feasibility of using roadkill data collected daily between 2014 and 2017 by road patrol staff from a private road agency on a 410 km length of the N3 road in South Africa. We modelled the relationship between a set of environmental and anthropogenic variables on the number of roadkill carcasses, using serval (Leptailurus serval) as a model species. We recorded 5.24 serval roadkill carcasses/100 km/year. The number of carcasses was related to season, the amount of wetland, and NDVI, but was not related to any of the anthropogenic variables we included. This suggests that roadkill patterns may differ greatly depending on the ecology of species of interest, but targeting mitigation measures where roads pass through wetlands may help to reduce serval roadkill. Partnering with road agencies for data collection offers powerful opportunities to identify factors related to roadkill distribution and reduce the threats posed by roads to wildlife.
bibliographic citation: Williams et al. (2019) Using road patrol data to identify factors associated with carnivore roadkill counts. PeerJ 7:e6650 https://doi.org/10.7717/peerj.6650
date submitted: 2019-01-07
date accepted: 2019-02-15
issued: 2019-03-29
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Williams
  given name: Samual T.
author list: Agent
  family name: Collinson
  given name: Wendy
author list: Agent
  family name: Patterson-Abrolat
  given name: Claire
author list: Agent
  family name: Marneweck
  given name: David G.
author list: Agent
  family name: Swanepoel
  given name: Lourens H.
doi: 10.7717/peerj.6650
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-03-29
copyright: ©2019 Williams et al.
attribution name: Williams et al.

IOCBIO Sparks detection and analysis software
type: item
type: AcademicArticle
description: Analysis of calcium sparks in cardiomyocytes can provide valuable information about functional changes of calcium handling in health and disease. As a part of the calcium sparks analysis, sparks detection and characterization is necessary. Here, we describe a new open-source platform for automatic calcium sparks detection from line scan confocal images. The developed software is tailored for detecting only calcium sparks, allowing us to design a graphical user interface specifically for this task. The software enables detecting sparks automatically as well as adding, removing, or adjusting regions of interest marking each spark. The results of the analysis are stored in an SQL database, allowing simple integration with statistical tools. We have analyzed the performance of the algorithm using a large set of synthetic images with varying spark sizes and noise levels and also compared the analysis results with results obtained by software established in the field. The use of our software is illustrated by an analysis of the effect of isoprenaline (ISO) on spark frequency, amplitude, and spatial and temporal characteristics. For that, cardiomyocytes from C57BL/6 mice were used. We demonstrated an increase in spark frequency, tendency of having larger spark amplitudes, sparks with a longer duration, and occurrence of multiple sparks from the same site in the presence of ISO. We also show that the duration and the width of sparks with the same amplitude were similar in the absence and presence of ISO. The software was released as an open source repository and is available for free use and collaborative development.
format: application/pdf
format: text/html
creator: Martin Laasmaa
creator: Niina Karro
creator: Rikke Birkedal
creator: Marko Vendelin
subject: Bioinformatics
subject: Biophysics
subject: Cell Biology
subject: Computational Biology
subject: Cardiology
description: doi:10.7717/peerj.6652
publisher: PeerJ Inc.
rights: © 2019 Laasmaa et al.
abstract: Analysis of calcium sparks in cardiomyocytes can provide valuable information about functional changes of calcium handling in health and disease. As a part of the calcium sparks analysis, sparks detection and characterization is necessary. Here, we describe a new open-source platform for automatic calcium sparks detection from line scan confocal images. The developed software is tailored for detecting only calcium sparks, allowing us to design a graphical user interface specifically for this task. The software enables detecting sparks automatically as well as adding, removing, or adjusting regions of interest marking each spark. The results of the analysis are stored in an SQL database, allowing simple integration with statistical tools. We have analyzed the performance of the algorithm using a large set of synthetic images with varying spark sizes and noise levels and also compared the analysis results with results obtained by software established in the field. The use of our software is illustrated by an analysis of the effect of isoprenaline (ISO) on spark frequency, amplitude, and spatial and temporal characteristics. For that, cardiomyocytes from C57BL/6 mice were used. We demonstrated an increase in spark frequency, tendency of having larger spark amplitudes, sparks with a longer duration, and occurrence of multiple sparks from the same site in the presence of ISO. We also show that the duration and the width of sparks with the same amplitude were similar in the absence and presence of ISO. The software was released as an open source repository and is available for free use and collaborative development.
bibliographic citation: Laasmaa et al. (2019) IOCBIO Sparks detection and analysis software. PeerJ 7:e6652 https://doi.org/10.7717/peerj.6652
date submitted: 2019-01-07
date accepted: 2019-02-19
issued: 2019-03-29
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Laasmaa
  given name: Martin
author list: Agent
  family name: Karro
  given name: Niina
author list: Agent
  family name: Birkedal
  given name: Rikke
author list: Agent
  family name: Vendelin
  given name: Marko
doi: 10.7717/peerj.6652
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-03-29
copyright: © 2019 Laasmaa et al.
attribution name: Laasmaa et al.

Comparative analysis and characterization of the gut microbiota of four farmed snakes from southern China
type: item
type: AcademicArticle
description: Background The gut microbiota plays an important role in host immunity and metabolic homeostasis. Although analyses of gut microbiotas have been used to assess host health and foster disease prevention and treatment, no comparative comprehensive study, assessing gut microbiotas among several species of farmed snake, is yet available. In this study, we characterized and compared the gut microbiotas of four species of farmed snakes (Naja atra, Ptyas mucosa, Elaphe carinata, and Deinagkistrodon acutus) using high-throughput sequencing of the 16S rDNA gene in southern China and tested whether there was a relationship between gut microbiotal composition and host species. Results A total of 629 operational taxonomic units across 22 samples were detected. The five most abundant phyla were Bacteroidetes, Proteobacteria, Firmicutes, Fusobacteria, and Actinobacteria, while the five most abundant genera were Bacteroides, Cetobacterium, Clostridium, Plesiomonas, and Paeniclostridium. This was the first report of the dominance of Fusobacteria and Cetobacterium in the snake gut. Our phylogenetic analysis recovered a relatively close relationship between Fusobacteria and Bacteroidetes. Alpha diversity analysis indicated that species richness and diversity were highest in the gut microbiota of D. acutus and lowest in that of E. carinata. Significant differences in alpha diversity were detected among the four farmed snake species. The gut microbiotas of conspecifics were more similar to each other than to those of heterospecifics. Conclusion This study provides the first comparative study of gut microbiotas among several species of farmed snakes, and provides valuable data for the management of farmed snakes. In farmed snakes, host species affected the species composition and diversity of the gut microbiota.
format: application/pdf
format: text/html
creator: Bing Zhang
creator: Jing Ren
creator: Daode Yang
creator: Shuoran Liu
creator: Xinguo Gong
subject: Bioinformatics
subject: Microbiology
subject: Veterinary Medicine
subject: Zoology
description: doi:10.7717/peerj.6658
publisher: PeerJ Inc.
rights: © 2019 Zhang et al.
abstract: Background The gut microbiota plays an important role in host immunity and metabolic homeostasis. Although analyses of gut microbiotas have been used to assess host health and foster disease prevention and treatment, no comparative comprehensive study, assessing gut microbiotas among several species of farmed snake, is yet available. In this study, we characterized and compared the gut microbiotas of four species of farmed snakes (Naja atra, Ptyas mucosa, Elaphe carinata, and Deinagkistrodon acutus) using high-throughput sequencing of the 16S rDNA gene in southern China and tested whether there was a relationship between gut microbiotal composition and host species. Results A total of 629 operational taxonomic units across 22 samples were detected. The five most abundant phyla were Bacteroidetes, Proteobacteria, Firmicutes, Fusobacteria, and Actinobacteria, while the five most abundant genera were Bacteroides, Cetobacterium, Clostridium, Plesiomonas, and Paeniclostridium. This was the first report of the dominance of Fusobacteria and Cetobacterium in the snake gut. Our phylogenetic analysis recovered a relatively close relationship between Fusobacteria and Bacteroidetes. Alpha diversity analysis indicated that species richness and diversity were highest in the gut microbiota of D. acutus and lowest in that of E. carinata. Significant differences in alpha diversity were detected among the four farmed snake species. The gut microbiotas of conspecifics were more similar to each other than to those of heterospecifics. Conclusion This study provides the first comparative study of gut microbiotas among several species of farmed snakes, and provides valuable data for the management of farmed snakes. In farmed snakes, host species affected the species composition and diversity of the gut microbiota.
bibliographic citation: Zhang et al. (2019) Comparative analysis and characterization of the gut microbiota of four farmed snakes from southern China. PeerJ 7:e6658 https://doi.org/10.7717/peerj.6658
date submitted: 2018-09-11
date accepted: 2019-02-22
issued: 2019-03-29
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Zhang
  given name: Bing
author list: Agent
  family name: Ren
  given name: Jing
author list: Agent
  family name: Yang
  given name: Daode
author list: Agent
  family name: Liu
  given name: Shuoran
author list: Agent
  family name: Gong
  given name: Xinguo
doi: 10.7717/peerj.6658
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-03-29
copyright: © 2019 Zhang et al.
attribution name: Zhang et al.

Music-performance regulates microRNAs in professional musicians
type: item
type: AcademicArticle
description: Musical training and performance require precise integration of multisensory and motor centres of the human brain and can be regarded as an epigenetic modifier of brain functions. Numerous studies have identified structural and functional differences between the brains of musicians and non-musicians and superior cognitive functions in musicians. Recently, music-listening and performance has also been shown to affect the regulation of several genes, many of which were identified in songbird singing. MicroRNAs affect gene regulation and studying their expression may give new insights into the epigenetic effect of music. Here, we studied the effect of 2 hours of classical music-performance on the peripheral blood microRNA expressions in professional musicians with respect to a control activity without music for the same duration. As detecting transcriptomic changes in the functional human brain remains a challenge for geneticists, we used peripheral blood to study music-performance induced microRNA changes and interpreted the results in terms of potential effects on brain function, based on the current knowledge about the microRNA function in blood and brain. We identified significant (FDR <0.05) up-regulation of five microRNAs; hsa-miR-3909, hsa-miR-30d-5p, hsa-miR-92a-3p, hsa-miR-222-3p and hsa-miR-30a-5p; and down-regulation of two microRNAs; hsa-miR-6803-3p and hsa-miR-1249-3p. hsa-miR-222-3p and hsa-miR-92a-3p putatively target FOXP2, which was found down-regulated by microRNA regulation in songbird singing. miR-30d and miR-222 corroborate microRNA response observed in zebra finch song-listening/learning. miR-222 is induced by ERK cascade, which is important for memory formation, motor neuron functions and neuronal plasticity. miR-222 is also activated by FOSL1, an immediate early gene from the FOS family of transcriptional regulators which are activated by auditory-motor stimuli. miR-222 and miR-92 promote neurite outgrowth by negatively regulating the neuronal g…
format: application/pdf
format: text/html
creator: Preethy Sasidharan Nair
creator: Tuire Kuusi
creator: Minna Ahvenainen
creator: Anju K. Philips
creator: Irma Järvelä
subject: Genetics
subject: Genomics
subject: Neuroscience
description: doi:10.7717/peerj.6660
publisher: PeerJ Inc.
rights: © 2019 Nair et al.
abstract: Musical training and performance require precise integration of multisensory and motor centres of the human brain and can be regarded as an epigenetic modifier of brain functions. Numerous studies have identified structural and functional differences between the brains of musicians and non-musicians and superior cognitive functions in musicians. Recently, music-listening and performance has also been shown to affect the regulation of several genes, many of which were identified in songbird singing. MicroRNAs affect gene regulation and studying their expression may give new insights into the epigenetic effect of music. Here, we studied the effect of 2 hours of classical music-performance on the peripheral blood microRNA expressions in professional musicians with respect to a control activity without music for the same duration. As detecting transcriptomic changes in the functional human brain remains a challenge for geneticists, we used peripheral blood to study music-performance induced microRNA changes and interpreted the results in terms of potential effects on brain function, based on the current knowledge about the microRNA function in blood and brain. We identified significant (FDR <0.05) up-regulation of five microRNAs; hsa-miR-3909, hsa-miR-30d-5p, hsa-miR-92a-3p, hsa-miR-222-3p and hsa-miR-30a-5p; and down-regulation of two microRNAs; hsa-miR-6803-3p and hsa-miR-1249-3p. hsa-miR-222-3p and hsa-miR-92a-3p putatively target FOXP2, which was found down-regulated by microRNA regulation in songbird singing. miR-30d and miR-222 corroborate microRNA response observed in zebra finch song-listening/learning. miR-222 is induced by ERK cascade, which is important for memory formation, motor neuron functions and neuronal plasticity. miR-222 is also activated by FOSL1, an immediate early gene from the FOS family of transcriptional regulators which are activated by auditory-motor stimuli. miR-222 and miR-92 promote neurite outgrowth by negatively regulating the neuronal g…
bibliographic citation: Nair et al. (2019) Music-performance regulates microRNAs in professional musicians. PeerJ 7:e6660 https://doi.org/10.7717/peerj.6660
date submitted: 2018-06-13
date accepted: 2019-02-19
issued: 2019-03-29
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Nair
  given name: Preethy Sasidharan
author list: Agent
  family name: Kuusi
  given name: Tuire
author list: Agent
  family name: Ahvenainen
  given name: Minna
author list: Agent
  family name: Philips
  given name: Anju K.
author list: Agent
  family name: Järvelä
  given name: Irma
doi: 10.7717/peerj.6660
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-03-29
copyright: © 2019 Nair et al.
attribution name: Nair et al.

Green potential of Pleurotus spp. in biotechnology
type: item
type: AcademicArticle
description: Background The genus Pleurotus is most exploitable xylotrophic fungi, with valuable biotechnological, medical, and nutritional properties. The relevant features of the representatives of this genus to provide attractive low-cost industrial tools have been reported in numerous studies to resolve the pressure of ecological issues. Additionally, a number of Pleurotus species are highly adaptive, do not require any special conditions for growth, and possess specific resistance to contaminating diseases and pests. The unique properties of Pleurotus species widely used in many environmental technologies, such as organic solid waste recycling, chemical pollutant degradation, and bioethanol production. Methodology The literature study encompasses peer-reviewed journals identified by systematic searches of electronic databases such as Google Scholar, NCBI, Springer, ResearchGate, ScienceDirect, and ISI Web of Knowledge. The search scheme was divided into several steps, as described below. Results In this review, we describe studies examining the biotechnological feasibility of Pleurotus spp. to elucidate the importance of this genus for use in green technology. Here, we review areas of application of the genus Pleurotus as a prospective biotechnological tool. Conclusion The incomplete description of some fungal biochemical pathways emphasises the future research goals for this fungal culture.
format: application/pdf
format: text/html
creator: Alona S. Sekan
creator: Olena S. Myronycheva
creator: Olov Karlsson
creator: Andrii P. Gryganskyi
creator: Yaroslav Blume
subject: Agricultural Science
subject: Biotechnology
subject: Molecular Biology
subject: Mycology
subject: Environmental Contamination and Remediation
description: doi:10.7717/peerj.6664
publisher: PeerJ Inc.
rights: © 2019 Sekan et al.
abstract: Background The genus Pleurotus is most exploitable xylotrophic fungi, with valuable biotechnological, medical, and nutritional properties. The relevant features of the representatives of this genus to provide attractive low-cost industrial tools have been reported in numerous studies to resolve the pressure of ecological issues. Additionally, a number of Pleurotus species are highly adaptive, do not require any special conditions for growth, and possess specific resistance to contaminating diseases and pests. The unique properties of Pleurotus species widely used in many environmental technologies, such as organic solid waste recycling, chemical pollutant degradation, and bioethanol production. Methodology The literature study encompasses peer-reviewed journals identified by systematic searches of electronic databases such as Google Scholar, NCBI, Springer, ResearchGate, ScienceDirect, and ISI Web of Knowledge. The search scheme was divided into several steps, as described below. Results In this review, we describe studies examining the biotechnological feasibility of Pleurotus spp. to elucidate the importance of this genus for use in green technology. Here, we review areas of application of the genus Pleurotus as a prospective biotechnological tool. Conclusion The incomplete description of some fungal biochemical pathways emphasises the future research goals for this fungal culture.
bibliographic citation: Sekan et al. (2019) Green potential of Pleurotus spp. in biotechnology. PeerJ 7:e6664 https://doi.org/10.7717/peerj.6664
date submitted: 2018-09-07
date accepted: 2019-02-22
issued: 2019-03-29
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Sekan
  given name: Alona S.
author list: Agent
  family name: Myronycheva
  given name: Olena S.
author list: Agent
  family name: Karlsson
  given name: Olov
author list: Agent
  family name: Gryganskyi
  given name: Andrii P.
author list: Agent
  family name: Blume
  given name: Yaroslav
doi: 10.7717/peerj.6664
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-03-29
copyright: © 2019 Sekan et al.
attribution name: Sekan et al.

Transcriptional factor regulation network and competitive endogenous RNA (ceRNA) network determining response of esophageal squamous cell carcinomas to neoadjuvant chemoradiotherapy
type: item
type: AcademicArticle
description: Background Neoadjuvant chemoradiotherapy (nCRT) followed by surgery benefits survival for patients with esophageal squamous cell carcinomas (ESCC) compared with surgery alone, but the clinical outcomes of nCRT are heterogeneous. This study aimed to elucidate transcriptional factor (TF) regulation network and competitive endogenous RNA (ceRNA) network determining response of ESCC to nCRT. Materials and Methods RNA microarray data of GSE59974 and GSE45670 were analyzed to investigate the significant changes of lincRNAs, miRNAs, mRNAs in responders and non-responders of nCRT in ESCC. Functional and enrichment analyses were conducted by clusterProfiler. The target lincRNAs and mRNAs of miRNAs were predicted by miRWalk. The ceRNA and TF regulatory networks were constructed using Cytoscape. Results Differentially expressed genes between responders and non-responders mainly enriched in biological process including Wnt signaling pathway and regulation of cell development and morphogenesis involved in differentiation. Besides, these genes showed enrichment in molecular function of glycosaminoglycan binding, metalloendopeptidase inhibitor and growth factor activity. KEGG analysis enriched these genes in pathways of neurotrophin signaling pathway, cell adhesion molecules and Wnt signaling pathway. We also constructed ceRNA network and TF network regulating response of ESCC to nCRT. Core regulatory miRNAs were miR-520a, miR-548am, miR-3184, miR-548d, miR-4725, miR-148a, miR-4659a and key regulatory TFs included MBNL1, SLC26A3, BMP4, ZIC1 and ANKRD7. Conclusion We identified significantly altered lincRNAs, miRNAs and mRNAs involved in the nCRT response of ESCC. In addition, the ceRNA regulatory network of lincRNA-miRNA-mRNA and TF regulatory network were constructed, which would elucidate novel molecular mechanisms determining nCRT response of ESCC, thus providing promising clues for clinical therapy.
format: application/pdf
format: text/html
creator: Mingrui Shao
creator: Wenya Li
subject: Oncology
subject: Data Mining and Machine Learning
description: doi:10.7717/peerj.6668
publisher: PeerJ Inc.
rights: © 2019 Shao and Li
abstract: Background Neoadjuvant chemoradiotherapy (nCRT) followed by surgery benefits survival for patients with esophageal squamous cell carcinomas (ESCC) compared with surgery alone, but the clinical outcomes of nCRT are heterogeneous. This study aimed to elucidate transcriptional factor (TF) regulation network and competitive endogenous RNA (ceRNA) network determining response of ESCC to nCRT. Materials and Methods RNA microarray data of GSE59974 and GSE45670 were analyzed to investigate the significant changes of lincRNAs, miRNAs, mRNAs in responders and non-responders of nCRT in ESCC. Functional and enrichment analyses were conducted by clusterProfiler. The target lincRNAs and mRNAs of miRNAs were predicted by miRWalk. The ceRNA and TF regulatory networks were constructed using Cytoscape. Results Differentially expressed genes between responders and non-responders mainly enriched in biological process including Wnt signaling pathway and regulation of cell development and morphogenesis involved in differentiation. Besides, these genes showed enrichment in molecular function of glycosaminoglycan binding, metalloendopeptidase inhibitor and growth factor activity. KEGG analysis enriched these genes in pathways of neurotrophin signaling pathway, cell adhesion molecules and Wnt signaling pathway. We also constructed ceRNA network and TF network regulating response of ESCC to nCRT. Core regulatory miRNAs were miR-520a, miR-548am, miR-3184, miR-548d, miR-4725, miR-148a, miR-4659a and key regulatory TFs included MBNL1, SLC26A3, BMP4, ZIC1 and ANKRD7. Conclusion We identified significantly altered lincRNAs, miRNAs and mRNAs involved in the nCRT response of ESCC. In addition, the ceRNA regulatory network of lincRNA-miRNA-mRNA and TF regulatory network were constructed, which would elucidate novel molecular mechanisms determining nCRT response of ESCC, thus providing promising clues for clinical therapy.
bibliographic citation: Shao et al. (2019) Transcriptional factor regulation network and competitive endogenous RNA (ceRNA) network determining response of esophageal squamous cell carcinomas to neoadjuvant chemoradiotherapy. PeerJ 7:e6668 https://doi.org/10.7717/peerj.6668
date submitted: 2018-10-17
date accepted: 2019-02-21
issued: 2019-03-29
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Shao
  given name: Mingrui
author list: Agent
  family name: Li
  given name: Wenya
doi: 10.7717/peerj.6668
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-03-29
copyright: ©2019 Shao and Li
attribution name: Shao and Li

Using opportunistic sightings to infer differential spatio-temporal use of western Mediterranean waters by the fin whale
type: item
type: AcademicArticle
description: The fin whale (Balaenoptera physalus) is a cosmopolitan species with a resident population in the Mediterranean Sea. Due to its habitat, open seas often far from ports and airfields, and its long-distance migratory behaviour, studying and monitoring its distribution is costly. Currently, many opportunistic sightings (OS) reports are available, which provide a source of potentially useful, low-cost information about the spatio-temporal distribution of this species. Since 1993, the Spanish Institute of Oceanography has compiled a dataset comprising 874 records of OS of nine species of cetaceans in the western Mediterranean Sea and adjacent waters. The aim of this study was to use this dataset to investigate the differential use of these waters by the fin whale when compared with other cetaceans. We compared the presence of fin whales with the presence of any other cetacean species in the dataset. Binary logistic regression was then used to model these occurrences according to several spatio-temporal variables expected to reflect their habitat use. Several significant models reveal that fin whales are more prone than other cetaceans to use the waters over the slope of the Gulf of Lion in summer. This finding confirms that the Gulf of Lion is an area of importance for this species and suggests that the slope of the continental shelf could be particularly important. Our study shows how OS can be a source of useful information when appropriately analyzed.
format: application/pdf
format: text/html
creator: Estefanía Torreblanca
creator: Juan Antonio Camiñas
creator: David Macías
creator: Salvador García-Barcelona
creator: Raimundo Real
creator: José Carlos Báez
subject: Biogeography
subject: Conservation Biology
subject: Ecology
subject: Marine Biology
description: doi:10.7717/peerj.6673
publisher: PeerJ Inc.
rights: © 2019 Torreblanca et al.
abstract: The fin whale (Balaenoptera physalus) is a cosmopolitan species with a resident population in the Mediterranean Sea. Due to its habitat, open seas often far from ports and airfields, and its long-distance migratory behaviour, studying and monitoring its distribution is costly. Currently, many opportunistic sightings (OS) reports are available, which provide a source of potentially useful, low-cost information about the spatio-temporal distribution of this species. Since 1993, the Spanish Institute of Oceanography has compiled a dataset comprising 874 records of OS of nine species of cetaceans in the western Mediterranean Sea and adjacent waters. The aim of this study was to use this dataset to investigate the differential use of these waters by the fin whale when compared with other cetaceans. We compared the presence of fin whales with the presence of any other cetacean species in the dataset. Binary logistic regression was then used to model these occurrences according to several spatio-temporal variables expected to reflect their habitat use. Several significant models reveal that fin whales are more prone than other cetaceans to use the waters over the slope of the Gulf of Lion in summer. This finding confirms that the Gulf of Lion is an area of importance for this species and suggests that the slope of the continental shelf could be particularly important. Our study shows how OS can be a source of useful information when appropriately analyzed.
bibliographic citation: Torreblanca et al. (2019) Using opportunistic sightings to infer differential spatio-temporal use of western Mediterranean waters by the fin whale. PeerJ 7:e6673 https://doi.org/10.7717/peerj.6673
date submitted: 2018-06-07
date accepted: 2019-02-23
issued: 2019-03-29
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Torreblanca
  given name: Estefanía
author list: Agent
  family name: Camiñas
  given name: Juan Antonio
author list: Agent
  family name: Macías
  given name: David
author list: Agent
  family name: García-Barcelona
  given name: Salvador
author list: Agent
  family name: Real
  given name: Raimundo
author list: Agent
  family name: Báez
  given name: José Carlos
doi: 10.7717/peerj.6673
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-03-29
copyright: © 2019 Torreblanca et al.
attribution name: Torreblanca et al.

Up-regulation of Grb2-associated binder 1 promotes hepatocyte growth factor-induced endothelial progenitor cell proliferation and migration
type: item
type: AcademicArticle
description: Objectives Grb2-associated binder 1 (Gab1), a scaffolding adaptor protein, plays an important role in transmitting key signals that control cell growth, migration, and function from multiple tyrosine kinase receptors. This study was designed to investigate the influence of upregulation of Gab1 in endothelial progenitor cells (EPCs) stimulated with hepatocyte growth factor (HGF), and the underlying molecular mechanisms. Materials and Methods Endothelial progenitor cells isolated from human umbilical cord blood were identified and divided into four groups. EPCs in the Control group were cultured normally; those in the Control+HGF group were treated with HGF stimulation; those in the AD-Gab1 group were transfected with adenovirus containing the Gab1 gene but not treated with HGF stimulation; and, those in the AD-Gab1+HGF group were treated with both HGF stimulation and transfection with adenovirus containing the Gab1 gene. Subsequently, Gab1 expression and proliferation and migration ability were compared for EPCs grown under different conditions. Furthermore, we measured phosphorylation levels of three key proteins Gab1, SHP2, and ERK1/2. Results The AD-Gab1+HGF group had the highest expression of Gab1 and higher proliferation and migration than the other three groups. Conclusions Upregulation of Gab1 promoted HGF-induced EPC proliferation and migration. Mechanistically, HGF stimulated Gab1 tyrosine phosphorylation in EPCs, thus leading to activation of extracellular regulated MAP kinase 1/2, which is involved in proliferation and migration signaling.
format: application/pdf
format: text/html
creator: Qing Fan
creator: Liyu Zhang
creator: Wenjie Zhu
creator: Sheng Xue
creator: Yisheng Song
creator: Qing Chang
subject: Cell Biology
subject: Molecular Biology
description: doi:10.7717/peerj.6675
publisher: PeerJ Inc.
rights: © 2019 Fan et al.
abstract: Objectives Grb2-associated binder 1 (Gab1), a scaffolding adaptor protein, plays an important role in transmitting key signals that control cell growth, migration, and function from multiple tyrosine kinase receptors. This study was designed to investigate the influence of upregulation of Gab1 in endothelial progenitor cells (EPCs) stimulated with hepatocyte growth factor (HGF), and the underlying molecular mechanisms. Materials and Methods Endothelial progenitor cells isolated from human umbilical cord blood were identified and divided into four groups. EPCs in the Control group were cultured normally; those in the Control+HGF group were treated with HGF stimulation; those in the AD-Gab1 group were transfected with adenovirus containing the Gab1 gene but not treated with HGF stimulation; and, those in the AD-Gab1+HGF group were treated with both HGF stimulation and transfection with adenovirus containing the Gab1 gene. Subsequently, Gab1 expression and proliferation and migration ability were compared for EPCs grown under different conditions. Furthermore, we measured phosphorylation levels of three key proteins Gab1, SHP2, and ERK1/2. Results The AD-Gab1+HGF group had the highest expression of Gab1 and higher proliferation and migration than the other three groups. Conclusions Upregulation of Gab1 promoted HGF-induced EPC proliferation and migration. Mechanistically, HGF stimulated Gab1 tyrosine phosphorylation in EPCs, thus leading to activation of extracellular regulated MAP kinase 1/2, which is involved in proliferation and migration signaling.
bibliographic citation: Fan et al. (2019) Up-regulation of Grb2-associated binder 1 promotes hepatocyte growth factor-induced endothelial progenitor cell proliferation and migration. PeerJ 7:e6675 https://doi.org/10.7717/peerj.6675
date submitted: 2018-11-21
date accepted: 2019-02-25
issued: 2019-03-29
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Fan
  given name: Qing
author list: Agent
  family name: Zhang
  given name: Liyu
author list: Agent
  family name: Zhu
  given name: Wenjie
author list: Agent
  family name: Xue
  given name: Sheng
author list: Agent
  family name: Song
  given name: Yisheng
author list: Agent
  family name: Chang
  given name: Qing
doi: 10.7717/peerj.6675
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-03-29
copyright: © 2019 Fan et al.
attribution name: Fan et al.

Factors that influence response classifications in chemotherapy treated patient-derived xenografts (PDX)
type: item
type: AcademicArticle
description: In this study, we investigated the impact of initial tumor volume, rate of tumor growth, cohort size, study duration, and data analysis method on chemotherapy treatment response classifications in patient-derived xenografts (PDXs). The analyses were conducted on cisplatin treatment response data for 70 PDX models representing ten cancer types with up to 28-day study duration and cohort sizes of 3–10 tumor-bearing mice. The results demonstrated that a 21-day dosing study using a cohort size of eight was necessary to reliably detect responsive models (i.e., tumor volume ratio of treated animals to control between 0.1 and 0.42)—independent of analysis method. A cohort of three tumor-bearing animals led to a reliable classification of models that were both highly responsive and highly nonresponsive to cisplatin (i.e., tumor volume ratio of treated animals to control animals less than 0.10). In our set of PDXs, we found that tumor growth rate in the control group impacted treatment response classification more than initial tumor volume. We repeated the study design factors using docetaxel treated PDXs with consistent results. Our results highlight the importance of defining endpoints for PDX dosing studies when deciding the size of cohorts to use in dosing studies and illustrate that response classifications for a study do not differ significantly across the commonly used analysis methods that are based on tumor volume changes in treatment versus control groups.
format: application/pdf
format: text/html
creator: Joan E. Malcolm
creator: Timothy M. Stearns
creator: Susan D. Airhart
creator: Joel H. Graber
creator: Carol J. Bult
subject: Bioengineering
subject: Drugs and Devices
subject: Oncology
subject: Translational Medicine
description: doi:10.7717/peerj.6586
publisher: PeerJ Inc.
rights: © 2019 Malcolm et al.
abstract: In this study, we investigated the impact of initial tumor volume, rate of tumor growth, cohort size, study duration, and data analysis method on chemotherapy treatment response classifications in patient-derived xenografts (PDXs). The analyses were conducted on cisplatin treatment response data for 70 PDX models representing ten cancer types with up to 28-day study duration and cohort sizes of 3–10 tumor-bearing mice. The results demonstrated that a 21-day dosing study using a cohort size of eight was necessary to reliably detect responsive models (i.e., tumor volume ratio of treated animals to control between 0.1 and 0.42)—independent of analysis method. A cohort of three tumor-bearing animals led to a reliable classification of models that were both highly responsive and highly nonresponsive to cisplatin (i.e., tumor volume ratio of treated animals to control animals less than 0.10). In our set of PDXs, we found that tumor growth rate in the control group impacted treatment response classification more than initial tumor volume. We repeated the study design factors using docetaxel treated PDXs with consistent results. Our results highlight the importance of defining endpoints for PDX dosing studies when deciding the size of cohorts to use in dosing studies and illustrate that response classifications for a study do not differ significantly across the commonly used analysis methods that are based on tumor volume changes in treatment versus control groups.
bibliographic citation: Malcolm et al. (2019) Factors that influence response classifications in chemotherapy treated patient-derived xenografts (PDX). PeerJ 7:e6586 https://doi.org/10.7717/peerj.6586
date submitted: 2018-09-12
date accepted: 2019-02-08
issued: 2019-03-28
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Malcolm
  given name: Joan E.
author list: Agent
  family name: Stearns
  given name: Timothy M.
author list: Agent
  family name: Airhart
  given name: Susan D.
author list: Agent
  family name: Graber
  given name: Joel H.
author list: Agent
  family name: Bult
  given name: Carol J.
doi: 10.7717/peerj.6586
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-03-28
copyright: ©2019 Malcolm et al.
attribution name: Malcolm et al.

Evaluation of a toxoid fusion protein vaccine produced in plants to protect poultry against necrotic enteritis
type: item
type: AcademicArticle
description: Background Necrotic enteritis (NE) is caused by type A strains of the bacterium Clostridium perfringens. Total global economic losses to the poultry industry due to NE is estimated to be over two billion dollars annually. Traditionally, NE has been effectively controlled by inclusion of antibiotics in the diet of poultry. However, recent concerns regarding the impact of this practice on increasing antibiotic resistance in human pathogens have led us to consider alternative approaches, such as vaccination, for controlling this disease. NE strains of C. perfringens produce two major toxins, a-toxin and NetB. Immune responses against either toxin can provide partial protection against NE. Methods We have developed a fusion protein combining a non-toxic carboxyl-terminal domain of a-toxin (PlcC) and an attenuated, mutant form of NetB (NetB-W262A) for use as a vaccine antigen to immunize poultry against NE. We utilized a DNA sequence that was codon-optimized for Nicotiana benthamiana to enable high levels of expression. The 6-His tagged PlcC-NetB fusion protein was synthesized in N. benthamiana using a geminiviral replicon transient expression system, purified by metal affinity chromatography, and used to immunize broiler birds. Results Immunized birds produced a strong serum IgY response against both the plant produced PlcC-NetB protein and against bacterially produced His-PlcC and His-NetB. Immunized birds were significantly protected against a subsequent in-feed challenge with virulent C. perfringens when treated with the fusion protein. These results indicate that a plant-produced PlcC-NetB toxoid is a promising vaccine candidate for controlling NE in poultry.
format: application/pdf
format: text/html
creator: Joseph G.L. Hunter
creator: Shyra Wilde
creator: Amanda M. Tafoya
creator: Jamie Horsman
creator: Miranda Yousif
creator: Andrew G. Diamos
creator: Kenneth L. Roland
creator: Hugh S. Mason
subject: Agricultural Science
subject: Biotechnology
subject: Microbiology
subject: Veterinary Medicine
description: doi:10.7717/peerj.6600
publisher: PeerJ Inc.
rights: © 2019 Hunter et al.
abstract: Background Necrotic enteritis (NE) is caused by type A strains of the bacterium Clostridium perfringens. Total global economic losses to the poultry industry due to NE is estimated to be over two billion dollars annually. Traditionally, NE has been effectively controlled by inclusion of antibiotics in the diet of poultry. However, recent concerns regarding the impact of this practice on increasing antibiotic resistance in human pathogens have led us to consider alternative approaches, such as vaccination, for controlling this disease. NE strains of C. perfringens produce two major toxins, a-toxin and NetB. Immune responses against either toxin can provide partial protection against NE. Methods We have developed a fusion protein combining a non-toxic carboxyl-terminal domain of a-toxin (PlcC) and an attenuated, mutant form of NetB (NetB-W262A) for use as a vaccine antigen to immunize poultry against NE. We utilized a DNA sequence that was codon-optimized for Nicotiana benthamiana to enable high levels of expression. The 6-His tagged PlcC-NetB fusion protein was synthesized in N. benthamiana using a geminiviral replicon transient expression system, purified by metal affinity chromatography, and used to immunize broiler birds. Results Immunized birds produced a strong serum IgY response against both the plant produced PlcC-NetB protein and against bacterially produced His-PlcC and His-NetB. Immunized birds were significantly protected against a subsequent in-feed challenge with virulent C. perfringens when treated with the fusion protein. These results indicate that a plant-produced PlcC-NetB toxoid is a promising vaccine candidate for controlling NE in poultry.
bibliographic citation: Hunter et al. (2019) Evaluation of a toxoid fusion protein vaccine produced in plants to protect poultry against necrotic enteritis. PeerJ 7:e6600 https://doi.org/10.7717/peerj.6600
date submitted: 2018-11-21
date accepted: 2019-02-08
issued: 2019-03-28
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Hunter
  given name: Joseph G.L.
author list: Agent
  family name: Wilde
  given name: Shyra
author list: Agent
  family name: Tafoya
  given name: Amanda M.
author list: Agent
  family name: Horsman
  given name: Jamie
author list: Agent
  family name: Yousif
  given name: Miranda
author list: Agent
  family name: Diamos
  given name: Andrew G.
author list: Agent
  family name: Roland
  given name: Kenneth L.
author list: Agent
  family name: Mason
  given name: Hugh S.
doi: 10.7717/peerj.6600
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-03-28
copyright: © 2019 Hunter et al.
attribution name: Hunter et al.

Underwater sound production varies within not between species in sympatric newts
type: item
type: AcademicArticle
description: Sound production is a widespread phenomenon among animals. Effective sound use for mate or species recognition requires some acoustic differentiation at an individual or species level. Several species of caudate amphibians produce underwater sounds, but information about intra- and interspecific variation in their acoustic production is missing. We examined individual, sex, and species variation in underwater sound production in adults of two sympatric newt taxa, Ichthyosaura alpestris and Lissotriton vulgaris. Individual newts produced simple low- (peak frequency = 7–8 kHz) and mid-high frequency (14–17 kHz) clicks, which greatly overlap between sexes and species. Individual differences explained about 40–50% of total variation in sound parameters. These results provide foundations for further studies on the mechanisms and eco-evolutionary consequences of underwater acoustics in newts.
format: application/pdf
format: text/html
creator: Jiří Hubáček
creator: Monika Šugerková
creator: Lumír Gvoždík
subject: Animal Behavior
subject: Zoology
subject: Freshwater Biology
description: doi:10.7717/peerj.6649
publisher: PeerJ Inc.
rights: © 2019 Hubáček et al.
abstract: Sound production is a widespread phenomenon among animals. Effective sound use for mate or species recognition requires some acoustic differentiation at an individual or species level. Several species of caudate amphibians produce underwater sounds, but information about intra- and interspecific variation in their acoustic production is missing. We examined individual, sex, and species variation in underwater sound production in adults of two sympatric newt taxa, Ichthyosaura alpestris and Lissotriton vulgaris. Individual newts produced simple low- (peak frequency = 7–8 kHz) and mid-high frequency (14–17 kHz) clicks, which greatly overlap between sexes and species. Individual differences explained about 40–50% of total variation in sound parameters. These results provide foundations for further studies on the mechanisms and eco-evolutionary consequences of underwater acoustics in newts.
bibliographic citation: Hubáček et al. (2019) Underwater sound production varies within not between species in sympatric newts. PeerJ 7:e6649 https://doi.org/10.7717/peerj.6649
date submitted: 2018-10-29
date accepted: 2019-02-20
issued: 2019-03-28
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Hubáček
  given name: Jiří
author list: Agent
  family name: Šugerková
  given name: Monika
author list: Agent
  family name: Gvoždík
  given name: Lumír
doi: 10.7717/peerj.6649
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-03-28
copyright: ©2019 Hubáček et al.
attribution name: Hubáček et al.

Comparison of the fecal microbiota of two free-ranging Chinese subspecies of the leopard (Panthera pardus) using high-throughput sequencing
type: item
type: AcademicArticle
description: The analysis of gut microbiota using fecal samples provides a non-invasive approach to understand the complex interactions between host species and their intestinal bacterial community. However, information on gut microbiota for wild endangered carnivores is scarce. The goal of this study was to describe the gut microbiota of two leopard subspecies, the Amur leopard (Panthera pardus orientalis) and North Chinese leopard (Panthera pardus japonensis). Fecal samples from the Amur leopard (n = 8) and North Chinese leopard (n = 13) were collected in Northeast Tiger and Leopard National Park and Shanxi Tieqiaoshan Provincial Nature Reserve in China, respectively. The gut microbiota of leopards was analyzed via high-throughput sequencing of the V3–V4 region of bacterial 16S rRNA gene using the Life Ion S5™ XL platform. A total of 1,413,825 clean reads representing 4,203 operational taxonomic units (OTUs) were detected. For Amur leopard samples, Firmicutes (78.4%) was the dominant phylum, followed by Proteobacteria (9.6%) and Actinobacteria (7.6%). And for the North Chinese leopard, Firmicutes (68.6%), Actinobacteria (11.6%) and Fusobacteria (6.4%) were the most predominant phyla. Clostridiales was the most diverse bacterial order with 37.9% for Amur leopard and 45.7% for North Chinese leopard. Based on the beta-diversity analysis, no significant difference was found in the bacterial community composition between the Amur leopard and North Chinese leopard samples. The current study provides the initial data about the composition and structure of the gut microbiota for wild Amur leopards and North Chinese leopards, and has laid the foundation for further investigations of the health, dietary preferences and physiological regulation of leopards.
format: application/pdf
format: text/html
creator: Siyu Han
creator: Yu Guan
creator: Hailong Dou
creator: Haitao Yang
creator: Meng Yao
creator: Jianping Ge
creator: Limin Feng
subject: Ecology
subject: Microbiology
subject: Molecular Biology
subject: Zoology
description: doi:10.7717/peerj.6684
publisher: PeerJ Inc.
rights: © 2019 Han et al.
abstract: The analysis of gut microbiota using fecal samples provides a non-invasive approach to understand the complex interactions between host species and their intestinal bacterial community. However, information on gut microbiota for wild endangered carnivores is scarce. The goal of this study was to describe the gut microbiota of two leopard subspecies, the Amur leopard (Panthera pardus orientalis) and North Chinese leopard (Panthera pardus japonensis). Fecal samples from the Amur leopard (n = 8) and North Chinese leopard (n = 13) were collected in Northeast Tiger and Leopard National Park and Shanxi Tieqiaoshan Provincial Nature Reserve in China, respectively. The gut microbiota of leopards was analyzed via high-throughput sequencing of the V3–V4 region of bacterial 16S rRNA gene using the Life Ion S5™ XL platform. A total of 1,413,825 clean reads representing 4,203 operational taxonomic units (OTUs) were detected. For Amur leopard samples, Firmicutes (78.4%) was the dominant phylum, followed by Proteobacteria (9.6%) and Actinobacteria (7.6%). And for the North Chinese leopard, Firmicutes (68.6%), Actinobacteria (11.6%) and Fusobacteria (6.4%) were the most predominant phyla. Clostridiales was the most diverse bacterial order with 37.9% for Amur leopard and 45.7% for North Chinese leopard. Based on the beta-diversity analysis, no significant difference was found in the bacterial community composition between the Amur leopard and North Chinese leopard samples. The current study provides the initial data about the composition and structure of the gut microbiota for wild Amur leopards and North Chinese leopards, and has laid the foundation for further investigations of the health, dietary preferences and physiological regulation of leopards.
bibliographic citation: Han et al. (2019) Comparison of the fecal microbiota of two free-ranging Chinese subspecies of the leopard (Panthera pardus) using high-throughput sequencing. PeerJ 7:e6684 https://doi.org/10.7717/peerj.6684
date submitted: 2018-08-14
date accepted: 2019-02-26
issued: 2019-03-28
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Han
  given name: Siyu
author list: Agent
  family name: Guan
  given name: Yu
author list: Agent
  family name: Dou
  given name: Hailong
author list: Agent
  family name: Yang
  given name: Haitao
author list: Agent
  family name: Yao
  given name: Meng
author list: Agent
  family name: Ge
  given name: Jianping
author list: Agent
  family name: Feng
  given name: Limin
doi: 10.7717/peerj.6684
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-03-28
copyright: ©2019 Han et al.
attribution name: Han et al.

Mammut pacificus sp. nov., a newly recognized species of mastodon from the Pleistocene of western North America
type: item
type: AcademicArticle
description: A new species of mastodon from the Pleistocene of western North America, Mammut pacificus sp. nov. is herein recognized, with specimens identified throughout California and from two localities in southern Idaho. This new taxon differs from the contemporaneous M. americanum in having narrower teeth, most prominently in M3/m3, as well as six sacral vertebrae, femur with a proportionally greater mid-shaft diameter, and no mandibular tusks at any growth stage. All known Pleistocene Mammut remains from California are consistent with our diagnosis of M. pacificus, which indicates that M. americanum was not present in California.
format: application/pdf
format: text/html
creator: Alton C. Dooley
creator: Eric Scott
creator: Jeremy Green
creator: Kathleen B. Springer
creator: Brett S. Dooley
creator: Gregory James Smith
subject: Paleontology
subject: Taxonomy
description: doi:10.7717/peerj.6614
publisher: PeerJ Inc.
rights: © 2019 Dooley et al.
abstract: A new species of mastodon from the Pleistocene of western North America, Mammut pacificus sp. nov. is herein recognized, with specimens identified throughout California and from two localities in southern Idaho. This new taxon differs from the contemporaneous M. americanum in having narrower teeth, most prominently in M3/m3, as well as six sacral vertebrae, femur with a proportionally greater mid-shaft diameter, and no mandibular tusks at any growth stage. All known Pleistocene Mammut remains from California are consistent with our diagnosis of M. pacificus, which indicates that M. americanum was not present in California.
bibliographic citation: Dooley et al. (2019) Mammut pacificus sp. nov., a newly recognized species of mastodon from the Pleistocene of western North America. PeerJ 7:e6614 https://doi.org/10.7717/peerj.6614
date submitted: 2018-10-16
date accepted: 2019-02-12
issued: 2019-03-27
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Dooley
  given name: Alton C.
author list: Agent
  family name: Scott
  given name: Eric
author list: Agent
  family name: Green
  given name: Jeremy
author list: Agent
  family name: Springer
  given name: Kathleen B.
author list: Agent
  family name: Dooley
  given name: Brett S.
author list: Agent
  family name: Smith
  given name: Gregory James
doi: 10.7717/peerj.6614
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-03-27
copyright: © 2019 Dooley et al.
attribution name: Dooley et al.

Old wild wolves: ancient DNA survey unveils population dynamics in Late Pleistocene and Holocene Italian remains
type: item
type: AcademicArticle
description: Background The contemporary Italian wolf (Canis lupus italicus) represents a case of morphological and genetic uniqueness. Today, Italian wolves are also the only documented population to fall exclusively within the mitochondrial haplogroup 2, which was the most diffused across Eurasian and North American wolves during the Late Pleistocene. However, the dynamics leading to such distinctiveness are still debated. Methods In order to shed light on the ancient genetic variability of this wolf population and on the origin of its current diversity, we collected 19 Late Pleistocene-Holocene samples from northern Italy, which we analyzed at a short portion of the hypervariable region 1 of the mitochondrial DNA, highly informative for wolf and dog phylogenetic analyses. Results Four out of the six detected haplotypes matched the ones found in ancient wolves from northern Europe and Beringia, or in modern European and Chinese wolves, and appeared closely related to the two haplotypes currently found in Italian wolves. The haplotype of two Late Pleistocene samples matched with primitive and contemporary dog sequences from the canine mitochondrial clade A. All these haplotypes belonged to haplogroup 2. The only exception was a Holocene sample dated 3,250 years ago, affiliated to haplogroup 1. Discussion In this study we describe the genetic variability of the most ancient wolf specimens from Italy analyzed so far, providing a preliminary overview of the genetic make-up of the population that inhabited this area from the last glacial maximum to the Middle Age period. Our results endorsed that the genetic diversity carried by the Pleistocene wolves here analyzed showed a strong continuity with other northern Eurasian wolf specimens from the same chronological period. Contrarily, the Holocene samples showed a greater similarity only with modern sequences from Europe and Asia, and the occurrence of an haplogroup 1 haplotype allowed to date back previous finding about its presence …
format: application/pdf
format: text/html
creator: Marta Maria Ciucani
creator: Davide Palumbo
creator: Marco Galaverni
creator: Patrizia Serventi
creator: Elena Fabbri
creator: Gloria Ravegnini
creator: Sabrina Angelini
creator: Elena Maini
creator: Davide Persico
creator: Romolo Caniglia
creator: Elisabetta Cilli
subject: Biodiversity
subject: Conservation Biology
subject: Evolutionary Studies
subject: Genetics
subject: Paleontology
description: doi:10.7717/peerj.6424
publisher: PeerJ Inc.
rights: © 2019 Ciucani et al.
abstract: Background The contemporary Italian wolf (Canis lupus italicus) represents a case of morphological and genetic uniqueness. Today, Italian wolves are also the only documented population to fall exclusively within the mitochondrial haplogroup 2, which was the most diffused across Eurasian and North American wolves during the Late Pleistocene. However, the dynamics leading to such distinctiveness are still debated. Methods In order to shed light on the ancient genetic variability of this wolf population and on the origin of its current diversity, we collected 19 Late Pleistocene-Holocene samples from northern Italy, which we analyzed at a short portion of the hypervariable region 1 of the mitochondrial DNA, highly informative for wolf and dog phylogenetic analyses. Results Four out of the six detected haplotypes matched the ones found in ancient wolves from northern Europe and Beringia, or in modern European and Chinese wolves, and appeared closely related to the two haplotypes currently found in Italian wolves. The haplotype of two Late Pleistocene samples matched with primitive and contemporary dog sequences from the canine mitochondrial clade A. All these haplotypes belonged to haplogroup 2. The only exception was a Holocene sample dated 3,250 years ago, affiliated to haplogroup 1. Discussion In this study we describe the genetic variability of the most ancient wolf specimens from Italy analyzed so far, providing a preliminary overview of the genetic make-up of the population that inhabited this area from the last glacial maximum to the Middle Age period. Our results endorsed that the genetic diversity carried by the Pleistocene wolves here analyzed showed a strong continuity with other northern Eurasian wolf specimens from the same chronological period. Contrarily, the Holocene samples showed a greater similarity only with modern sequences from Europe and Asia, and the occurrence of an haplogroup 1 haplotype allowed to date back previous finding about its presence …
bibliographic citation: Ciucani et al. (2019) Old wild wolves: ancient DNA survey unveils population dynamics in Late Pleistocene and Holocene Italian remains. PeerJ 7:e6424 https://doi.org/10.7717/peerj.6424
date submitted: 2018-03-26
date accepted: 2019-01-07
issued: 2019-03-27
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Ciucani
  given name: Marta Maria
author list: Agent
  family name: Palumbo
  given name: Davide
author list: Agent
  family name: Galaverni
  given name: Marco
author list: Agent
  family name: Serventi
  given name: Patrizia
author list: Agent
  family name: Fabbri
  given name: Elena
author list: Agent
  family name: Ravegnini
  given name: Gloria
author list: Agent
  family name: Angelini
  given name: Sabrina
author list: Agent
  family name: Maini
  given name: Elena
author list: Agent
  family name: Persico
  given name: Davide
author list: Agent
  family name: Caniglia
  given name: Romolo
author list: Agent
  family name: Cilli
  given name: Elisabetta
doi: 10.7717/peerj.6424
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-03-27
copyright: © 2019 Ciucani et al.
attribution name: Ciucani et al.

Clinicopathological characteristics, treatment and survival of pulmonary large cell neuroendocrine carcinoma: a SEER population-based study
type: item
type: AcademicArticle
description: Background This study was designed to investigate the clinicopathological characteristics, treatment and survival of patients with pulmonary large cell neuroendocrine carcinoma (LCNEC). Methods The Surveillance, Epidemiology and End Results database was utilized to identify patients diagnosed with pulmonary LCNEC between 2004 and 2013. Kaplan–Meier analysis was conducted to determine the overall survival (OS) and cancer-specific survival (CSS) rate. Univariate survival analysis along with log-rank test, and Cox proportional hazards model were employed to detect independent prognostic factors. Results Pulmonary LCNEC accounted for 0.58% (2972/510607) of the total number of lung and bronchus carcinoma. And a total of 1,530 eligible cases were identified, with the median follow-up time of 11 months. To be specific, the 3-, 5-year OS and CSS rates were 22.8%, 16.8% and 26.5%, 20.8% respectively. Generally, pulmonary LCNEC was commonly detected in the elderly (72.2%), males (55.9%), the upper lobe (62.0%) and advanced AJCC stage (65.5%). Multivariate analysis revealed that elderly [(≥60 and <80 years) HR:1.203, 95% CI [1.053–1.375], P = 0.007; (≥80 years) HR:1.530, 95% CI [1.238–1.891], P < 0.001] and advanced AJCC stage [(stage III) HR:2.606, 95% CI [2.083–3.260], P < 0.001; (stage IV) HR:4.881, 95% CI [3.923–6.072], P < 0.001] were independent unfavorable prognostic factors, and that female (HR:0.845, 95% CI [0.754–0.947], P = 0.004)), surgery [(Segmentectomy/wedge resection) HR:0.526, 95% CI [0.413–0.669], P < 0.001; (Lobectomy/Bilobectomy) HR:0.357, 95% CI [0.290–0.440], P < 0.001;(Pneumonectomy) HR:0.491, 95% CI [0.355–0.679], P < 0.001] , chemotherapy (HR:0.442, 95% CI [0.389–0.503], P < 0.001) and radiation (HR:0.837, 95% CI [0.738–0.949], P = 0.005) were independent favorable prognostic factors. Conclusion To sum up, age at diagnosis, sex, AJCC 8th edition stage, surgery, chemotherapy and radiation were significantly associated with OS of patients with pulmonary …
format: application/pdf
format: text/html
creator: Ling Cao
creator: Zhi-wen Li
creator: Min Wang
creator: Ting-ting Zhang
creator: Bo Bao
creator: Yun-peng Liu
subject: Epidemiology
subject: Oncology
subject: Public Health
description: doi:10.7717/peerj.6539
publisher: PeerJ Inc.
rights: © 2019 Cao et al.
abstract: Background This study was designed to investigate the clinicopathological characteristics, treatment and survival of patients with pulmonary large cell neuroendocrine carcinoma (LCNEC). Methods The Surveillance, Epidemiology and End Results database was utilized to identify patients diagnosed with pulmonary LCNEC between 2004 and 2013. Kaplan–Meier analysis was conducted to determine the overall survival (OS) and cancer-specific survival (CSS) rate. Univariate survival analysis along with log-rank test, and Cox proportional hazards model were employed to detect independent prognostic factors. Results Pulmonary LCNEC accounted for 0.58% (2972/510607) of the total number of lung and bronchus carcinoma. And a total of 1,530 eligible cases were identified, with the median follow-up time of 11 months. To be specific, the 3-, 5-year OS and CSS rates were 22.8%, 16.8% and 26.5%, 20.8% respectively. Generally, pulmonary LCNEC was commonly detected in the elderly (72.2%), males (55.9%), the upper lobe (62.0%) and advanced AJCC stage (65.5%). Multivariate analysis revealed that elderly [(≥60 and <80 years) HR:1.203, 95% CI [1.053–1.375], P = 0.007; (≥80 years) HR:1.530, 95% CI [1.238–1.891], P < 0.001] and advanced AJCC stage [(stage III) HR:2.606, 95% CI [2.083–3.260], P < 0.001; (stage IV) HR:4.881, 95% CI [3.923–6.072], P < 0.001] were independent unfavorable prognostic factors, and that female (HR:0.845, 95% CI [0.754–0.947], P = 0.004)), surgery [(Segmentectomy/wedge resection) HR:0.526, 95% CI [0.413–0.669], P < 0.001; (Lobectomy/Bilobectomy) HR:0.357, 95% CI [0.290–0.440], P < 0.001;(Pneumonectomy) HR:0.491, 95% CI [0.355–0.679], P < 0.001] , chemotherapy (HR:0.442, 95% CI [0.389–0.503], P < 0.001) and radiation (HR:0.837, 95% CI [0.738–0.949], P = 0.005) were independent favorable prognostic factors. Conclusion To sum up, age at diagnosis, sex, AJCC 8th edition stage, surgery, chemotherapy and radiation were significantly associated with OS of patients with pulmonary …
bibliographic citation: Cao et al. (2019) Clinicopathological characteristics, treatment and survival of pulmonary large cell neuroendocrine carcinoma: a SEER population-based study. PeerJ 7:e6539 https://doi.org/10.7717/peerj.6539
date submitted: 2018-09-13
date accepted: 2019-01-30
issued: 2019-03-27
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Cao
  given name: Ling
author list: Agent
  family name: Li
  given name: Zhi-wen
author list: Agent
  family name: Wang
  given name: Min
author list: Agent
  family name: Zhang
  given name: Ting-ting
author list: Agent
  family name: Bao
  given name: Bo
author list: Agent
  family name: Liu
  given name: Yun-peng
doi: 10.7717/peerj.6539
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-03-27
copyright: © 2019 Cao et al.
attribution name: Cao et al.

Associated bacteria of Botryococcus braunii (Chlorophyta)
type: item
type: AcademicArticle
description: Botryococcus braunii (Chlorophyta) is a green microalga known for producing hydrocarbons and exopolysaccharides (EPS). Improving the biomass productivity of B. braunii and hence, the productivity of the hydrocarbons and of the EPS, will make B. braunii more attractive for industries. Microalgae usually cohabit with bacteria which leads to the formation of species-specific communities with environmental and biological advantages. Bacteria have been found and identified with a few B. braunii strains, but little is known about the bacterial community across the different strains. A better knowledge of the bacterial community of B. braunii will help to optimize the biomass productivity, hydrocarbons, and EPS accumulation. To better understand the bacterial community diversity of B. braunii, we screened 12 strains from culture collections. Using 16S rRNA gene analysis by MiSeq we described the bacterial diversity across 12 B. braunii strains and identified possible shared communities. We found three bacterial families common to all strains: Rhizobiaceae, Bradyrhizobiaceae, and Comamonadaceae. Additionally, the results also suggest that each strain has its own specific bacteria that may be the result of long-term isolated culture.
format: application/pdf
format: text/html
creator: Joao D. Gouveia
creator: Jie Lian
creator: Georg Steinert
creator: Hauke Smidt
creator: Detmer Sipkema
creator: Rene H. Wijffels
creator: Maria J. Barbosa
subject: Microbiology
subject: Taxonomy
description: doi:10.7717/peerj.6610
publisher: PeerJ Inc.
rights: © 2019 Gouveia et al.
abstract: Botryococcus braunii (Chlorophyta) is a green microalga known for producing hydrocarbons and exopolysaccharides (EPS). Improving the biomass productivity of B. braunii and hence, the productivity of the hydrocarbons and of the EPS, will make B. braunii more attractive for industries. Microalgae usually cohabit with bacteria which leads to the formation of species-specific communities with environmental and biological advantages. Bacteria have been found and identified with a few B. braunii strains, but little is known about the bacterial community across the different strains. A better knowledge of the bacterial community of B. braunii will help to optimize the biomass productivity, hydrocarbons, and EPS accumulation. To better understand the bacterial community diversity of B. braunii, we screened 12 strains from culture collections. Using 16S rRNA gene analysis by MiSeq we described the bacterial diversity across 12 B. braunii strains and identified possible shared communities. We found three bacterial families common to all strains: Rhizobiaceae, Bradyrhizobiaceae, and Comamonadaceae. Additionally, the results also suggest that each strain has its own specific bacteria that may be the result of long-term isolated culture.
bibliographic citation: Gouveia et al. (2019) Associated bacteria of Botryococcus braunii (Chlorophyta). PeerJ 7:e6610 https://doi.org/10.7717/peerj.6610
date submitted: 2018-10-16
date accepted: 2019-02-12
issued: 2019-03-27
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Gouveia
  given name: Joao D.
author list: Agent
  family name: Lian
  given name: Jie
author list: Agent
  family name: Steinert
  given name: Georg
author list: Agent
  family name: Smidt
  given name: Hauke
author list: Agent
  family name: Sipkema
  given name: Detmer
author list: Agent
  family name: Wijffels
  given name: Rene H.
author list: Agent
  family name: Barbosa
  given name: Maria J.
doi: 10.7717/peerj.6610
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-03-27
copyright: © 2019 Gouveia et al.
attribution name: Gouveia et al.

Evaluating the effects of a temporary fostering program on shelter dog welfare
type: item
type: AcademicArticle
description: One of the greatest stressors for dogs living in animal shelters is social isolation. Many studies have demonstrated that human interaction reduces cortisol in shelter dogs, with the possibility that longer periods of interaction may yield greater effects. These types of interventions are contingent upon removing the dog from the kennel and any such reductions in cortisol are often lost when the dog returns to the kennel. More recently, animal shelters are utilizing short-term fostering programs to provide relief from the perceived stresses of kennel life; however the effects of these programs are not well understood. This study assessed the impacts of one- and two-night fostering programs on the urinary cortisol levels, resting pulse rates, longest bout of uninterrupted rest, and proportion of time spent resting of dogs awaiting adoption. Five animal shelters, open and limited-admission facilities, from across the United States participated in the study. During the study, dogs’ urine was collected in the morning before, during, and after fostering stays for cortisol: creatinine analysis. Non-invasive health monitors were worn by the dogs, which collected heart rates and activity levels, in the shelter and in foster homes. In total, 207 dogs participated in the study, and 1,076 cortisol values were used in our analysis. Across all shelters, we found that dogs’ cortisol: creatinine ratios dropped significantly during their fostering stay, but returned to baseline levels after return to the shelter. However, the observed reduction in cortisol varied in magnitude across shelters. We found that dogs of greater weight, age, and average resting pulse rate had higher cortisol levels; and dogs with longer bouts of uninterrupted rest had lower cortisol levels. Dogs had their longest bouts of rest during sleepovers, followed by in the shelter after their sleepovers. Lastly, significant differences were found when comparing in-shelter cortisol values at our five shelters, diff…
format: application/pdf
format: text/html
creator: Lisa M. Gunter
creator: Erica N. Feuerbacher
creator: Rachel J. Gilchrist
creator: Clive D.L. Wynne
subject: Animal Behavior
subject: Neuroscience
subject: Veterinary Medicine
description: doi:10.7717/peerj.6620
publisher: PeerJ Inc.
rights: © 2019 Gunter et al.
abstract: One of the greatest stressors for dogs living in animal shelters is social isolation. Many studies have demonstrated that human interaction reduces cortisol in shelter dogs, with the possibility that longer periods of interaction may yield greater effects. These types of interventions are contingent upon removing the dog from the kennel and any such reductions in cortisol are often lost when the dog returns to the kennel. More recently, animal shelters are utilizing short-term fostering programs to provide relief from the perceived stresses of kennel life; however the effects of these programs are not well understood. This study assessed the impacts of one- and two-night fostering programs on the urinary cortisol levels, resting pulse rates, longest bout of uninterrupted rest, and proportion of time spent resting of dogs awaiting adoption. Five animal shelters, open and limited-admission facilities, from across the United States participated in the study. During the study, dogs’ urine was collected in the morning before, during, and after fostering stays for cortisol: creatinine analysis. Non-invasive health monitors were worn by the dogs, which collected heart rates and activity levels, in the shelter and in foster homes. In total, 207 dogs participated in the study, and 1,076 cortisol values were used in our analysis. Across all shelters, we found that dogs’ cortisol: creatinine ratios dropped significantly during their fostering stay, but returned to baseline levels after return to the shelter. However, the observed reduction in cortisol varied in magnitude across shelters. We found that dogs of greater weight, age, and average resting pulse rate had higher cortisol levels; and dogs with longer bouts of uninterrupted rest had lower cortisol levels. Dogs had their longest bouts of rest during sleepovers, followed by in the shelter after their sleepovers. Lastly, significant differences were found when comparing in-shelter cortisol values at our five shelters, diff…
bibliographic citation: Gunter et al. (2019) Evaluating the effects of a temporary fostering program on shelter dog welfare. PeerJ 7:e6620 https://doi.org/10.7717/peerj.6620
date submitted: 2018-10-10
date accepted: 2019-02-14
issued: 2019-03-27
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Gunter
  given name: Lisa M.
author list: Agent
  family name: Feuerbacher
  given name: Erica N.
author list: Agent
  family name: Gilchrist
  given name: Rachel J.
author list: Agent
  family name: Wynne
  given name: Clive D.L.
doi: 10.7717/peerj.6620
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-03-27
copyright: ©2019 Gunter et al.
attribution name: Gunter et al.

Pixel: a content management platform for quantitative omics data
type: item
type: AcademicArticle
description: Background In biology, high-throughput experimental technologies, also referred as “omics” technologies, are increasingly used in research laboratories. Several thousands of gene expression measurements can be obtained in a single experiment. Researchers are routinely facing the challenge to annotate, store, explore and mine all the biological information they have at their disposal. We present here the Pixel web application (Pixel Web App), an original content management platform to help people involved in a multi-omics biological project. Methods The Pixel Web App is built with open source technologies and hosted on the collaborative development platform GitHub (https://github.com/Candihub/pixel). It is written in Python using the Django framework and stores all the data in a PostgreSQL database. It is developed in the open and licensed under the BSD 3-clause license. The Pixel Web App is also heavily tested with both unit and functional tests, a strong code coverage and continuous integration provided by CircleCI. To ease the development and the deployment of the Pixel Web App, Docker and Docker Compose are used to bundle the application as well as its dependencies. Results The Pixel Web App offers researchers an intuitive way to annotate, store, explore and mine their multi-omics results. It can be installed on a personal computer or on a server to fit the needs of many users. In addition, anyone can enhance the application to better suit their needs, either by contributing directly on GitHub (encouraged) or by extending Pixel on their own. The Pixel Web App does not provide any computational programs to analyze the data. Still, it helps to rapidly explore and mine existing results and holds a strategic position in the management of research data.
format: application/pdf
format: text/html
creator: Thomas Denecker
creator: William Durand
creator: Julien Maupetit
creator: Charles Hébert
creator: Jean-Michel Camadro
creator: Pierre Poulain
creator: Gaëlle Lelandais
subject: Computational Biology
subject: Genomics
subject: Data Science
description: doi:10.7717/peerj.6623
publisher: PeerJ Inc.
rights: © 2019 Denecker et al.
abstract: Background In biology, high-throughput experimental technologies, also referred as “omics” technologies, are increasingly used in research laboratories. Several thousands of gene expression measurements can be obtained in a single experiment. Researchers are routinely facing the challenge to annotate, store, explore and mine all the biological information they have at their disposal. We present here the Pixel web application (Pixel Web App), an original content management platform to help people involved in a multi-omics biological project. Methods The Pixel Web App is built with open source technologies and hosted on the collaborative development platform GitHub (https://github.com/Candihub/pixel). It is written in Python using the Django framework and stores all the data in a PostgreSQL database. It is developed in the open and licensed under the BSD 3-clause license. The Pixel Web App is also heavily tested with both unit and functional tests, a strong code coverage and continuous integration provided by CircleCI. To ease the development and the deployment of the Pixel Web App, Docker and Docker Compose are used to bundle the application as well as its dependencies. Results The Pixel Web App offers researchers an intuitive way to annotate, store, explore and mine their multi-omics results. It can be installed on a personal computer or on a server to fit the needs of many users. In addition, anyone can enhance the application to better suit their needs, either by contributing directly on GitHub (encouraged) or by extending Pixel on their own. The Pixel Web App does not provide any computational programs to analyze the data. Still, it helps to rapidly explore and mine existing results and holds a strategic position in the management of research data.
bibliographic citation: Denecker et al. (2019) Pixel: a content management platform for quantitative omics data. PeerJ 7:e6623 https://doi.org/10.7717/peerj.6623
date submitted: 2018-10-05
date accepted: 2019-02-14
issued: 2019-03-27
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Denecker
  given name: Thomas
author list: Agent
  family name: Durand
  given name: William
author list: Agent
  family name: Maupetit
  given name: Julien
author list: Agent
  family name: Hébert
  given name: Charles
author list: Agent
  family name: Camadro
  given name: Jean-Michel
author list: Agent
  family name: Poulain
  given name: Pierre
author list: Agent
  family name: Lelandais
  given name: Gaëlle
doi: 10.7717/peerj.6623
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-03-27
copyright: ©2019 Denecker et al.
attribution name: Denecker et al.

Biodegradation of thiocyanate by a native groundwater microbial consortium
type: item
type: AcademicArticle
description: Gold ore processing typically generates large amounts of thiocyanate (SCN−)-contaminated effluent. When this effluent is stored in unlined tailings dams, contamination of the underlying aquifer can occur. The potential for bioremediation of SCN−-contaminated groundwater, either in situ or ex situ, remains largely unexplored. This study aimed to enrich and characterise SCN−-degrading microorganisms from mining-contaminated groundwater under a range of culturing conditions. Mildly acidic and suboxic groundwater, containing ∼135 mg L−1 SCN−, was collected from an aquifer below an unlined tailings dam. An SCN−-degrading consortium was enriched from contaminated groundwater using combinatory amendments of air, glucose and phosphate. Biodegradation occurred in all oxic cultures, except with the sole addition of glucose, but was inhibited by NH4+ and did not occur under anoxic conditions. The SCN−-degrading consortium was characterised using 16S and 18S rRNA gene sequencing, identifying a variety of heterotrophic taxa in addition to sulphur-oxidising bacteria. Interestingly, few recognised SCN−-degrading taxa were identified in significant abundance. These results provide both proof-of-concept and the required conditions for biostimulation of SCN− degradation in groundwater by native aquifer microorganisms.
format: application/pdf
format: text/html
creator: Liam P. Spurr
creator: Mathew P. Watts
creator: Han M. Gan
creator: John W. Moreau
subject: Bioengineering
subject: Microbiology
subject: Environmental Contamination and Remediation
description: doi:10.7717/peerj.6498
publisher: PeerJ Inc.
rights: © 2019 Spurr et al.
abstract: Gold ore processing typically generates large amounts of thiocyanate (SCN−)-contaminated effluent. When this effluent is stored in unlined tailings dams, contamination of the underlying aquifer can occur. The potential for bioremediation of SCN−-contaminated groundwater, either in situ or ex situ, remains largely unexplored. This study aimed to enrich and characterise SCN−-degrading microorganisms from mining-contaminated groundwater under a range of culturing conditions. Mildly acidic and suboxic groundwater, containing ∼135 mg L−1 SCN−, was collected from an aquifer below an unlined tailings dam. An SCN−-degrading consortium was enriched from contaminated groundwater using combinatory amendments of air, glucose and phosphate. Biodegradation occurred in all oxic cultures, except with the sole addition of glucose, but was inhibited by NH4+ and did not occur under anoxic conditions. The SCN−-degrading consortium was characterised using 16S and 18S rRNA gene sequencing, identifying a variety of heterotrophic taxa in addition to sulphur-oxidising bacteria. Interestingly, few recognised SCN−-degrading taxa were identified in significant abundance. These results provide both proof-of-concept and the required conditions for biostimulation of SCN− degradation in groundwater by native aquifer microorganisms.
bibliographic citation: Spurr et al. (2019) Biodegradation of thiocyanate by a native groundwater microbial consortium. PeerJ 7:e6498 https://doi.org/10.7717/peerj.6498
date submitted: 2017-12-30
date accepted: 2019-01-20
issued: 2019-03-26
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Spurr
  given name: Liam P.
author list: Agent
  family name: Watts
  given name: Mathew P.
author list: Agent
  family name: Gan
  given name: Han M.
author list: Agent
  family name: Moreau
  given name: John W.
doi: 10.7717/peerj.6498
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-03-26
copyright: © 2019 Spurr et al.
attribution name: Spurr et al.

Development of polymorphic EST-SSR markers and characterization of the autotetraploid genome of sainfoin (Onobrychis viciifolia)
type: item
type: AcademicArticle
description: Background Sainfoin (Onobrychis viciifolia) is a highly nutritious, tannin-containing, and tetraploid forage legume. Due to the lack of detailed transcriptomic and genomic information on this species, genetic and breeding projects for sainfoin improvement have been significantly hindered. Methods In this study, a total of 24,630,711 clean reads were generated from 14 different sainfoin tissues using Illumina paired-end sequencing technology and deposited in the NCBI SRA database (SRX3763386). From these clean reads, 77,764 unigene sequences were obtained and 6,752 EST-SSRs were identified using de novo assembly. A total of 2,469 primer pairs were designed, and 200 primer pairs were randomly selected to analyze the polymorphism in five sainfoin wild accessions. Results Further analysis of 40 sainfoin individuals from the five wild populations using 61 EST-SSR loci showed that the number of alleles per locus ranged from 4 to 15, and the expected heterozygosity varied from 0.55 to 0.91. Additionally, by counting the EST-SSR band number and sequencing the three or four bands in one sainfoin individual, sainfoin was confirmed to be autotetraploid. This finding provides a high level of information about this plant. Discussion Through this study, 61 EST-SSR markers were successfully developed and shown to be useful for genetic studies and investigations of population genetic structures and variabilities among different sainfoin accessions.
format: application/pdf
format: text/html
creator: Shuheng Shen
creator: Xutian Chai
creator: Qiang Zhou
creator: Dong Luo
creator: Yanrong Wang
creator: Zhipeng Liu
subject: Agricultural Science
subject: Molecular Biology
subject: Plant Science
description: doi:10.7717/peerj.6542
publisher: PeerJ Inc.
rights: © 2019 Shen et al.
abstract: Background Sainfoin (Onobrychis viciifolia) is a highly nutritious, tannin-containing, and tetraploid forage legume. Due to the lack of detailed transcriptomic and genomic information on this species, genetic and breeding projects for sainfoin improvement have been significantly hindered. Methods In this study, a total of 24,630,711 clean reads were generated from 14 different sainfoin tissues using Illumina paired-end sequencing technology and deposited in the NCBI SRA database (SRX3763386). From these clean reads, 77,764 unigene sequences were obtained and 6,752 EST-SSRs were identified using de novo assembly. A total of 2,469 primer pairs were designed, and 200 primer pairs were randomly selected to analyze the polymorphism in five sainfoin wild accessions. Results Further analysis of 40 sainfoin individuals from the five wild populations using 61 EST-SSR loci showed that the number of alleles per locus ranged from 4 to 15, and the expected heterozygosity varied from 0.55 to 0.91. Additionally, by counting the EST-SSR band number and sequencing the three or four bands in one sainfoin individual, sainfoin was confirmed to be autotetraploid. This finding provides a high level of information about this plant. Discussion Through this study, 61 EST-SSR markers were successfully developed and shown to be useful for genetic studies and investigations of population genetic structures and variabilities among different sainfoin accessions.
bibliographic citation: Shen et al. (2019) Development of polymorphic EST-SSR markers and characterization of the autotetraploid genome of sainfoin (Onobrychis viciifolia). PeerJ 7:e6542 https://doi.org/10.7717/peerj.6542
date submitted: 2018-10-10
date accepted: 2019-01-30
issued: 2019-03-26
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Shen
  given name: Shuheng
author list: Agent
  family name: Chai
  given name: Xutian
author list: Agent
  family name: Zhou
  given name: Qiang
author list: Agent
  family name: Luo
  given name: Dong
author list: Agent
  family name: Wang
  given name: Yanrong
author list: Agent
  family name: Liu
  given name: Zhipeng
doi: 10.7717/peerj.6542
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-03-26
copyright: ©2019 Shen et al.
attribution name: Shen et al.

Proteomics alterations in chicken jejunum caused by 24 h fasting
type: item
type: AcademicArticle
description: The small intestine is the longest part of the chicken (Gallus gallus) gastrointestinal system that is specialized for nutrient absorption. It is known that decrease in intestinal villi area or height in early age can cause a reduction in essential nutrient intake, which may lead to delayed growth and consequently poorer performance of broiler chickens. The small intestinal absorptive surface is known to be affected by various factors, among others things the nutritional state. In our experiment, we aimed to investigate the possible protein expression alterations that lie behind the villus area and height decrease caused by feed deprivation. A total of 24 chickens were divided into three groups, namely ad libitum fed, fasted for 24 h, fasted for 24 h then refed for 2 h. The morphometric parameters were also measured in the duodenum, jejunum and ileum tissue sections using image analysis. Differential proteome analyses from jejunum samples were performed using two-dimensional difference gel electrophoresis followed by tryptic digestion and protein identification by matrix-assisted laser desorption/ionization mass spectrometry. Overall 541 protein spots were detected after 2D. Among them, eleven showed 1.5-fold or higher significant difference in expression and were successfully identified. In response to 24 h fasting, the expression of nine proteins was higher and that of two proteins was lower compared to the ad libitum fed group. The functions of the differentially expressed proteins indicate that the 24 h fasting mainly affects the expression of structural proteins, and proteins involved in lipid transport, general stress response, and intestinal defense.
format: application/pdf
format: text/html
creator: Ádám Simon
creator: Gabriella Gulyás
creator: Zoltán Mészár
creator: Mangesh Bhide
creator: János Oláh
creator: Péter Bai
creator: Éva Csősz
creator: András Jávor
creator: István Komlósi
creator: Judit Remenyik
creator: Levente Czeglédi
subject: Agricultural Science
subject: Genetics
subject: Molecular Biology
subject: Veterinary Medicine
subject: Zoology
description: doi:10.7717/peerj.6588
publisher: PeerJ Inc.
rights: © 2019 Simon et al.
abstract: The small intestine is the longest part of the chicken (Gallus gallus) gastrointestinal system that is specialized for nutrient absorption. It is known that decrease in intestinal villi area or height in early age can cause a reduction in essential nutrient intake, which may lead to delayed growth and consequently poorer performance of broiler chickens. The small intestinal absorptive surface is known to be affected by various factors, among others things the nutritional state. In our experiment, we aimed to investigate the possible protein expression alterations that lie behind the villus area and height decrease caused by feed deprivation. A total of 24 chickens were divided into three groups, namely ad libitum fed, fasted for 24 h, fasted for 24 h then refed for 2 h. The morphometric parameters were also measured in the duodenum, jejunum and ileum tissue sections using image analysis. Differential proteome analyses from jejunum samples were performed using two-dimensional difference gel electrophoresis followed by tryptic digestion and protein identification by matrix-assisted laser desorption/ionization mass spectrometry. Overall 541 protein spots were detected after 2D. Among them, eleven showed 1.5-fold or higher significant difference in expression and were successfully identified. In response to 24 h fasting, the expression of nine proteins was higher and that of two proteins was lower compared to the ad libitum fed group. The functions of the differentially expressed proteins indicate that the 24 h fasting mainly affects the expression of structural proteins, and proteins involved in lipid transport, general stress response, and intestinal defense.
bibliographic citation: Simon et al. (2019) Proteomics alterations in chicken jejunum caused by 24 h fasting. PeerJ 7:e6588 https://doi.org/10.7717/peerj.6588
date submitted: 2018-10-01
date accepted: 2019-02-09
issued: 2019-03-26
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Simon
  given name: Ádám
author list: Agent
  family name: Gulyás
  given name: Gabriella
author list: Agent
  family name: Mészár
  given name: Zoltán
author list: Agent
  family name: Bhide
  given name: Mangesh
author list: Agent
  family name: Oláh
  given name: János
author list: Agent
  family name: Bai
  given name: Péter
author list: Agent
  family name: Csősz
  given name: Éva
author list: Agent
  family name: Jávor
  given name: András
author list: Agent
  family name: Komlósi
  given name: István
author list: Agent
  family name: Remenyik
  given name: Judit
author list: Agent
  family name: Czeglédi
  given name: Levente
doi: 10.7717/peerj.6588
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-03-26
copyright: © 2019 Simon et al.
attribution name: Simon et al.

Comparative genomic analysis of the IDD genes in five Rosaceae species and expression analysis in Chinese white pear (Pyrus bretschneideri)
type: item
type: AcademicArticle
description: The INDETERMINATE DOMAIN (IDD) gene family encodes hybrid transcription factors with distinct zinc finger motifs and appears to be found in all higher plant genomes. IDD genes have been identified throughout the genomes of the model plants Arabidopsis thaliana and Oryza sativa, and the functions of many members of this gene family have been studied. However, few studies have investigated the IDD gene family in Rosaceae species (among these species, a genome-wide identification of the IDD gene family has only been completed in Malus domestica). This study focuses on a comparative genomic analysis of the IDD gene family in five Rosaceae species (Pyrus bretschneideri, Fragaria vesca, Prunus mume, Rubus occidentalis and Prunus avium). We identified a total of 68 IDD genes: 16 genes in Chinese white pear, 14 genes in F. vesca, 13 genes in Prunus mume, 14 genes in R. occidentalis and 11 genes in Prunus avium. The evolution of the IDD genes in these five Rosaceae species was revealed by constructing a phylogenetic tree, tracking gene duplication events, and performing a sliding window analysis and a conserved microsynteny analysis. The expression analysis of different organs showed that most of the pear IDD genes are found at a very high transcription level in fruits, flowers and buds. Based on our results with those obtained in previous research, we speculated that PbIDD2 and PbIDD8 might participate in flowering induction in pear. A temporal expression analysis showed that the expression patterns of PbIDD3 and PbIDD5 were completely opposite to the accumulation pattern of fruit lignin and the stone cell content. The results of the composite phylogenetic tree and expression pattern analysis indicated that PbIDD3 and PbIDD5 might be involved in the metabolism of lignin and secondary cell wall (SCW) formation. In summary, we provide basic information about the IDD genes in five Rosaceae species and thereby provide a theoretical basis for studying the function of these IDD g…
format: application/pdf
format: text/html
creator: Xueqiang Su
creator: Tiankai Meng
creator: Yu Zhao
creator: Guohui Li
creator: Xi Cheng
creator: Muhammad Abdullah
creator: Xu Sun
creator: Yongping Cai
creator: Yi Lin
subject: Agricultural Science
subject: Bioinformatics
subject: Genetics
subject: Genomics
description: doi:10.7717/peerj.6628
publisher: PeerJ Inc.
rights: © 2019 Su et al.
abstract: The INDETERMINATE DOMAIN (IDD) gene family encodes hybrid transcription factors with distinct zinc finger motifs and appears to be found in all higher plant genomes. IDD genes have been identified throughout the genomes of the model plants Arabidopsis thaliana and Oryza sativa, and the functions of many members of this gene family have been studied. However, few studies have investigated the IDD gene family in Rosaceae species (among these species, a genome-wide identification of the IDD gene family has only been completed in Malus domestica). This study focuses on a comparative genomic analysis of the IDD gene family in five Rosaceae species (Pyrus bretschneideri, Fragaria vesca, Prunus mume, Rubus occidentalis and Prunus avium). We identified a total of 68 IDD genes: 16 genes in Chinese white pear, 14 genes in F. vesca, 13 genes in Prunus mume, 14 genes in R. occidentalis and 11 genes in Prunus avium. The evolution of the IDD genes in these five Rosaceae species was revealed by constructing a phylogenetic tree, tracking gene duplication events, and performing a sliding window analysis and a conserved microsynteny analysis. The expression analysis of different organs showed that most of the pear IDD genes are found at a very high transcription level in fruits, flowers and buds. Based on our results with those obtained in previous research, we speculated that PbIDD2 and PbIDD8 might participate in flowering induction in pear. A temporal expression analysis showed that the expression patterns of PbIDD3 and PbIDD5 were completely opposite to the accumulation pattern of fruit lignin and the stone cell content. The results of the composite phylogenetic tree and expression pattern analysis indicated that PbIDD3 and PbIDD5 might be involved in the metabolism of lignin and secondary cell wall (SCW) formation. In summary, we provide basic information about the IDD genes in five Rosaceae species and thereby provide a theoretical basis for studying the function of these IDD g…
bibliographic citation: Su et al. (2019) Comparative genomic analysis of the IDD genes in five Rosaceae species and expression analysis in Chinese white pear (Pyrus bretschneideri). PeerJ 7:e6628 https://doi.org/10.7717/peerj.6628
date submitted: 2018-10-04
date accepted: 2019-02-15
issued: 2019-03-26
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Su
  given name: Xueqiang
author list: Agent
  family name: Meng
  given name: Tiankai
author list: Agent
  family name: Zhao
  given name: Yu
author list: Agent
  family name: Li
  given name: Guohui
author list: Agent
  family name: Cheng
  given name: Xi
author list: Agent
  family name: Abdullah
  given name: Muhammad
author list: Agent
  family name: Sun
  given name: Xu
author list: Agent
  family name: Cai
  given name: Yongping
author list: Agent
  family name: Lin
  given name: Yi
doi: 10.7717/peerj.6628
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-03-26
copyright: © 2019 Su et al.
attribution name: Su et al.

Isolation of cancer stem cells by selection for miR-302 expressing cells
type: item
type: AcademicArticle
description: Background Cancer stem cells are believed to be a major reason for long-term therapy failure because they are multi-drug resistant and able to rest mitotically inactive in the hypoxic center of tumors. Due to their variable number and their often low proliferation rate, cancer stem cells are difficult to purify in decent quantities and to grow in cell culture systems, where they are easily outcompeted by faster growing more ‘differentiated’, i.e., less stem cell-like tumor cells. Methods Here we present a proof of principle study based on the idea to select cancer stem cells by means of the expression of a stem cell-specific gene. A selectable egfp-neo coding sequence was inserted in the last exon of the non-coding murine miR-302 host gene. As a stem cell specific regulatory element, 2.1 kb of the genomic region immediately upstream of the miR-302 host gene transcription start site was used. Stable transgenic CJ7 embryonic stem cells were used to induce teratomas. Results After three weeks, tumors were removed for analysis and primary cultures were established. Stem cell-like cells were selected from these culture based on G418 selection. When the selection was removed, stem cell morphology and miR-302 expression were rapidly lost, indicating that it was not the original ES cells that had been isolated. Conclusions We show the possibility to use drug resistance expressed from a regulatory sequence of a stem cell-specific marker, to isolate and propagate cancer stem cells that otherwise might be hidden in the majority of tumor cells.
format: application/pdf
format: text/html
creator: Karim Rahimi
creator: Annette C. Füchtbauer
creator: Fardin Fathi
creator: Seyed J. Mowla
creator: Ernst-Martin Füchtbauer
subject: Cell Biology
subject: Developmental Biology
subject: Genetics
subject: Molecular Biology
subject: Oncology
description: doi:10.7717/peerj.6635
publisher: PeerJ Inc.
rights: © 2019 Rahimi et al.
abstract: Background Cancer stem cells are believed to be a major reason for long-term therapy failure because they are multi-drug resistant and able to rest mitotically inactive in the hypoxic center of tumors. Due to their variable number and their often low proliferation rate, cancer stem cells are difficult to purify in decent quantities and to grow in cell culture systems, where they are easily outcompeted by faster growing more ‘differentiated’, i.e., less stem cell-like tumor cells. Methods Here we present a proof of principle study based on the idea to select cancer stem cells by means of the expression of a stem cell-specific gene. A selectable egfp-neo coding sequence was inserted in the last exon of the non-coding murine miR-302 host gene. As a stem cell specific regulatory element, 2.1 kb of the genomic region immediately upstream of the miR-302 host gene transcription start site was used. Stable transgenic CJ7 embryonic stem cells were used to induce teratomas. Results After three weeks, tumors were removed for analysis and primary cultures were established. Stem cell-like cells were selected from these culture based on G418 selection. When the selection was removed, stem cell morphology and miR-302 expression were rapidly lost, indicating that it was not the original ES cells that had been isolated. Conclusions We show the possibility to use drug resistance expressed from a regulatory sequence of a stem cell-specific marker, to isolate and propagate cancer stem cells that otherwise might be hidden in the majority of tumor cells.
bibliographic citation: Rahimi et al. (2019) Isolation of cancer stem cells by selection for miR-302 expressing cells. PeerJ 7:e6635 https://doi.org/10.7717/peerj.6635
date submitted: 2018-10-10
date accepted: 2019-02-18
issued: 2019-03-26
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Rahimi
  given name: Karim
author list: Agent
  family name: Füchtbauer
  given name: Annette C.
author list: Agent
  family name: Fathi
  given name: Fardin
author list: Agent
  family name: Mowla
  given name: Seyed J.
author list: Agent
  family name: Füchtbauer
  given name: Ernst-Martin
doi: 10.7717/peerj.6635
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-03-26
copyright: ©2019 Rahimi et al.
attribution name: Rahimi et al.

Robust and automatic definition of microbiome states
type: item
type: AcademicArticle
description: Analysis of microbiome dynamics would allow elucidation of patterns within microbial community evolution under a variety of biologically or economically important circumstances; however, this is currently hampered in part by the lack of rigorous, formal, yet generally-applicable approaches to discerning distinct configurations of complex microbial populations. Clustering approaches to define microbiome “community state-types” at a population-scale are widely used, though not yet standardized. Similarly, distinct variations within a state-type are well documented, but there is no rigorous approach to discriminating these more subtle variations in community structure. Finally, intra-individual variations with even fewer differences will likely be found in, for example, longitudinal data, and will correlate with important features such as sickness versus health. We propose an automated, generic, objective, domain-independent, and internally-validating procedure to define statistically distinct microbiome states within datasets containing any degree of phylotypic diversity. Robustness of state identification is objectively established by a combination of diverse techniques for stable cluster verification. To demonstrate the efficacy of our approach in detecting discreet states even in datasets containing highly similar bacterial communities, and to demonstrate the broad applicability of our method, we reuse eight distinct longitudinal microbiome datasets from a variety of ecological niches and species. We also demonstrate our algorithm’s flexibility by providing it distinct taxa subsets as clustering input, demonstrating that it operates on filtered or unfiltered data, and at a range of different taxonomic levels. The final output is a set of robustly defined states which can then be used as general biomarkers for a wide variety of downstream purposes such as association with disease, monitoring response to intervention, or identifying optimally performant populations.
format: application/pdf
format: text/html
creator: Beatriz García-Jiménez
creator: Mark D. Wilkinson
subject: Bioinformatics
subject: Computational Biology
subject: Microbiology
subject: Data Mining and Machine Learning
description: doi:10.7717/peerj.6657
publisher: PeerJ Inc.
rights: © 2019 García-Jiménez and Wilkinson
abstract: Analysis of microbiome dynamics would allow elucidation of patterns within microbial community evolution under a variety of biologically or economically important circumstances; however, this is currently hampered in part by the lack of rigorous, formal, yet generally-applicable approaches to discerning distinct configurations of complex microbial populations. Clustering approaches to define microbiome “community state-types” at a population-scale are widely used, though not yet standardized. Similarly, distinct variations within a state-type are well documented, but there is no rigorous approach to discriminating these more subtle variations in community structure. Finally, intra-individual variations with even fewer differences will likely be found in, for example, longitudinal data, and will correlate with important features such as sickness versus health. We propose an automated, generic, objective, domain-independent, and internally-validating procedure to define statistically distinct microbiome states within datasets containing any degree of phylotypic diversity. Robustness of state identification is objectively established by a combination of diverse techniques for stable cluster verification. To demonstrate the efficacy of our approach in detecting discreet states even in datasets containing highly similar bacterial communities, and to demonstrate the broad applicability of our method, we reuse eight distinct longitudinal microbiome datasets from a variety of ecological niches and species. We also demonstrate our algorithm’s flexibility by providing it distinct taxa subsets as clustering input, demonstrating that it operates on filtered or unfiltered data, and at a range of different taxonomic levels. The final output is a set of robustly defined states which can then be used as general biomarkers for a wide variety of downstream purposes such as association with disease, monitoring response to intervention, or identifying optimally performant populations.
bibliographic citation: García-Jiménez et al. (2019) Robust and automatic definition of microbiome states. PeerJ 7:e6657 https://doi.org/10.7717/peerj.6657
date submitted: 2018-03-09
date accepted: 2019-02-22
issued: 2019-03-26
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: García-Jiménez
  given name: Beatriz
author list: Agent
  family name: Wilkinson
  given name: Mark D.
doi: 10.7717/peerj.6657
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-03-26
copyright: ©2019 García-Jiménez and Wilkinson
attribution name: García-Jiménez and Wilkinson

Comparative analysis of the complete mitochondrial genomes of five Achilidae species (Hemiptera: Fulgoroidea) and other Fulgoroidea reveals conserved mitochondrial genome organization
type: item
type: AcademicArticle
description: In the present study, the complete mitochondrial genomes (mitogenomes) of five Achilidae (Hemiptera: Fulgoroidea), Betatropis formosana, two new species (Magadhaideus luodiana sp. nov and Peltatavertexalis horizontalis sp. nov), Plectoderini sp. and Paracatonidia sp., were sequenced for the first time through next-generation sequencing. The five mitogenomes ranged from 15,214 to 16,216 bp in length, with the typical gene content and arrangement usually observed in Hexapods. The motif “ATGATAA” between atp8 and atp6 was found in all the analyzed species. An overlap “AAGCTTA” between trnW and trnC was observed in the mitogenomes of most Fulgoroidea. The structural and compositional analyses of 26 Fulgoroidea mitogenomes, including the gene rearrangement of five tRNAs (trnW, trnC and trnY; trnT and trnP), the A + T content and AT-skew of the whole mitogenomes, and the nuclear acid and amino acid compositions of the protein-coding genes (PCGs), revealed family-level differences between Delphacidae and other families (Achilidae, Flatidae, Fulgoridae, Issidae and Ricaniidae). Phylogenetic analyses of 13 protein-coding genes from 26 Fulgoroidea species by maximum likelihood and Bayesian Inference were consistent and well supported the basal position of Delphacidae, a close affinity among the families Flatidae, Issidae and Ricaniidae, and a close relationship between Achilidae and Fulgoridae.
format: application/pdf
format: text/html
creator: Shi-Yan Xu
creator: Jian-Kun Long
creator: Xiang-Sheng Chen
subject: Entomology
subject: Genomics
subject: Molecular Biology
subject: Taxonomy
description: doi:10.7717/peerj.6659
publisher: PeerJ Inc.
rights: © 2019 Xuet al.
abstract: In the present study, the complete mitochondrial genomes (mitogenomes) of five Achilidae (Hemiptera: Fulgoroidea), Betatropis formosana, two new species (Magadhaideus luodiana sp. nov and Peltatavertexalis horizontalis sp. nov), Plectoderini sp. and Paracatonidia sp., were sequenced for the first time through next-generation sequencing. The five mitogenomes ranged from 15,214 to 16,216 bp in length, with the typical gene content and arrangement usually observed in Hexapods. The motif “ATGATAA” between atp8 and atp6 was found in all the analyzed species. An overlap “AAGCTTA” between trnW and trnC was observed in the mitogenomes of most Fulgoroidea. The structural and compositional analyses of 26 Fulgoroidea mitogenomes, including the gene rearrangement of five tRNAs (trnW, trnC and trnY; trnT and trnP), the A + T content and AT-skew of the whole mitogenomes, and the nuclear acid and amino acid compositions of the protein-coding genes (PCGs), revealed family-level differences between Delphacidae and other families (Achilidae, Flatidae, Fulgoridae, Issidae and Ricaniidae). Phylogenetic analyses of 13 protein-coding genes from 26 Fulgoroidea species by maximum likelihood and Bayesian Inference were consistent and well supported the basal position of Delphacidae, a close affinity among the families Flatidae, Issidae and Ricaniidae, and a close relationship between Achilidae and Fulgoridae.
bibliographic citation: Xu et al. (2019) Comparative analysis of the complete mitochondrial genomes of five Achilidae species (Hemiptera: Fulgoroidea) and other Fulgoroidea reveals conserved mitochondrial genome organization. PeerJ 7:e6659 https://doi.org/10.7717/peerj.6659
date submitted: 2018-10-25
date accepted: 2019-02-19
issued: 2019-03-26
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Xu
  given name: Shi-Yan
author list: Agent
  family name: Long
  given name: Jian-Kun
author list: Agent
  family name: Chen
  given name: Xiang-Sheng
doi: 10.7717/peerj.6659
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-03-26
copyright: © 2019 Xu et al.
attribution name: Xuet al.

Pharmacokinetic comparison of quercetin, isoquercitrin, and quercetin-3-O-β-D-glucuronide in rats by HPLC-MS
type: item
type: AcademicArticle
description: Background Quercetin (Qr), isoquercitrin (IQ), and quercetin-3-O-β-D-glucuronide (QG) are powerful phytochemicals that have been shown to exhibit disease prevention and health promotion properties. However, there may exist transformations between Qr, IQ, and QG in vivo. And the pharmacokinetic profiles of Qr, IQ, and QG have not been systematically compared. The pharmacokinetics study would be helpful to better understand the pharmacological actions of them. Methods Herein, we developed a reliable HPLC-MS method to compare the pharmacokinetics of Qr, IQ, and QG after separate (50 mg/kg) oral administration of them in rats, using puerarin as internal standard. The detection was performed using negative selected ion monitoring. This method was validated in terms of selectivity, linearity, precision, accuracy, extraction recovery, matrix effect, and stability; and shows reliabilities in monitoring the pharmacokinetic behaviors of these three compounds. Results Our results showed that after separate oral administration of Qr, IQ, and QG, all of the compounds could be detected in plasma. In addition, QG could be detected in the Qr group; Qr and QG could be measured in the IQ group; and Qr could be found in rat plasma after 1.5 h of QG administration. Moreover, the AUC0−t of Qr in the; Qr group (2,590.5 ± 987.9 mg/L*min), IQ group (2,212.7 ± 914.1 mg/L*min), and QG group (3,505.7 ± 1,565.0 mg/L*min) was larger than the AUC0−t of QG in the; Qr group (1,550.0 ± 454.2 mg/L*min), IQ group (669.3 ± 188.3 mg/L*min), and QG group (962.7 ± 602.3 mg/L*min). The AUC0−t of IQ was the lowest among all groups. Discussion Quercetin, IQ, and QG can all be absorbed into plasma. A mutual transformation exists between Qr and QG, and IQ can be metabolized into Qr and QG in SD rats. These results would provide a meaningful basis for understanding the pharmacological actions of these three compounds.
format: application/pdf
format: text/html
creator: Hongli Yin
creator: Ji Ma
creator: Jichun Han
creator: Maoru Li
creator: Jing Shang
subject: Plant Science
subject: Drugs and Devices
subject: Pharmacology
subject: Metabolic Sciences
description: doi:10.7717/peerj.6665
publisher: PeerJ Inc.
rights: © 2019 Yin et al.
abstract: Background Quercetin (Qr), isoquercitrin (IQ), and quercetin-3-O-β-D-glucuronide (QG) are powerful phytochemicals that have been shown to exhibit disease prevention and health promotion properties. However, there may exist transformations between Qr, IQ, and QG in vivo. And the pharmacokinetic profiles of Qr, IQ, and QG have not been systematically compared. The pharmacokinetics study would be helpful to better understand the pharmacological actions of them. Methods Herein, we developed a reliable HPLC-MS method to compare the pharmacokinetics of Qr, IQ, and QG after separate (50 mg/kg) oral administration of them in rats, using puerarin as internal standard. The detection was performed using negative selected ion monitoring. This method was validated in terms of selectivity, linearity, precision, accuracy, extraction recovery, matrix effect, and stability; and shows reliabilities in monitoring the pharmacokinetic behaviors of these three compounds. Results Our results showed that after separate oral administration of Qr, IQ, and QG, all of the compounds could be detected in plasma. In addition, QG could be detected in the Qr group; Qr and QG could be measured in the IQ group; and Qr could be found in rat plasma after 1.5 h of QG administration. Moreover, the AUC0−t of Qr in the; Qr group (2,590.5 ± 987.9 mg/L*min), IQ group (2,212.7 ± 914.1 mg/L*min), and QG group (3,505.7 ± 1,565.0 mg/L*min) was larger than the AUC0−t of QG in the; Qr group (1,550.0 ± 454.2 mg/L*min), IQ group (669.3 ± 188.3 mg/L*min), and QG group (962.7 ± 602.3 mg/L*min). The AUC0−t of IQ was the lowest among all groups. Discussion Quercetin, IQ, and QG can all be absorbed into plasma. A mutual transformation exists between Qr and QG, and IQ can be metabolized into Qr and QG in SD rats. These results would provide a meaningful basis for understanding the pharmacological actions of these three compounds.
bibliographic citation: Yin et al. (2019) Pharmacokinetic comparison of quercetin, isoquercitrin, and quercetin-3-O-β-D-glucuronide in rats by HPLC-MS. PeerJ 7:e6665 https://doi.org/10.7717/peerj.6665
date submitted: 2018-10-29
date accepted: 2019-02-22
issued: 2019-03-26
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Yin
  given name: Hongli
author list: Agent
  family name: Ma
  given name: Ji
author list: Agent
  family name: Han
  given name: Jichun
author list: Agent
  family name: Li
  given name: Maoru
author list: Agent
  family name: Shang
  given name: Jing
doi: 10.7717/peerj.6665
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-03-26
copyright: © 2019 Yin et al.
attribution name: Yin et al.

The relationship between serum uric acid within the normal range and β-cell function in Chinese patients with type 2 diabetes: differences by body mass index and gender
type: item
type: AcademicArticle
description: Background Elevated serum uric acid (SUA) has a positive correlation with insulin secretion and insulin resistance indexes. However, whether weight- and gender-specific differences regarding the relationship between SUA within the normal range and β-cell function and insulin resistance exist is unknown in type 2 diabetes mellitus (T2DM) patients. Methods A total of 380 patients with type 2 diabetes were divided into two groups as overweight/obesity (n = 268) and normal weight (n = 112). Each group were again divided into low (LSUA) and high normal SUA (HSUA). The HbA1c, C-peptide, SUA, creatinine, and lipids profiles were measured. HOMA2IR and HOMA%2B were estimated using fasting glucose and C-peptide by homeostasis model assessment (HOMA). Pearson’s correlations and multiple linear regression analyses were conducted to assess the associations between SUA levels and islet function indexes. Results In overweight/obesity subgroup, the levels of body mass index, fasting C-peptide (FCP), P2hCP, fasting CPI (FCPI), postprandial CPI (PPCPI), ΔC-peptide, HOMA2%B, and HOMA2IR were higher in HSUA group than in LSUA group. In contrast, the HbA1c, FBS, and P2hBS were lower in HSUA than in LSUA. In normal weight subgroup, there were no differences between the HSUA than LSUA group in terms of clinical characteristics. Pearson’s correlations indicated that there were no significant correlations between SUA and insulin secretory capacity in normal weight group, but in overweight/obesity group, SUA had positive significant correlations with P2hCP, FCPI, PPCPI, ΔC-peptide, and HOMA2%B. In the female group, there were no significant correlations between SUA and insulin secretory capacity. However, in the male group, SUA had positive significant correlations with insulin secretory capacity include P2hCP, FCPI, PPCPI, ΔC-peptide, and HOMA2%B. Multiple linear regression showed that SUA was significantly associated with HOMA2%B, but not with HOMA2IR in overweight/obesity and male group. …
format: application/pdf
format: text/html
creator: Xing Zhong
creator: Deyuan Zhang
creator: Lina Yang
creator: Yijun Du
creator: Tianrong Pan
subject: Diabetes and Endocrinology
description: doi:10.7717/peerj.6666
publisher: PeerJ Inc.
rights: © 2019 Zhong et al.
abstract: Background Elevated serum uric acid (SUA) has a positive correlation with insulin secretion and insulin resistance indexes. However, whether weight- and gender-specific differences regarding the relationship between SUA within the normal range and β-cell function and insulin resistance exist is unknown in type 2 diabetes mellitus (T2DM) patients. Methods A total of 380 patients with type 2 diabetes were divided into two groups as overweight/obesity (n = 268) and normal weight (n = 112). Each group were again divided into low (LSUA) and high normal SUA (HSUA). The HbA1c, C-peptide, SUA, creatinine, and lipids profiles were measured. HOMA2IR and HOMA%2B were estimated using fasting glucose and C-peptide by homeostasis model assessment (HOMA). Pearson’s correlations and multiple linear regression analyses were conducted to assess the associations between SUA levels and islet function indexes. Results In overweight/obesity subgroup, the levels of body mass index, fasting C-peptide (FCP), P2hCP, fasting CPI (FCPI), postprandial CPI (PPCPI), ΔC-peptide, HOMA2%B, and HOMA2IR were higher in HSUA group than in LSUA group. In contrast, the HbA1c, FBS, and P2hBS were lower in HSUA than in LSUA. In normal weight subgroup, there were no differences between the HSUA than LSUA group in terms of clinical characteristics. Pearson’s correlations indicated that there were no significant correlations between SUA and insulin secretory capacity in normal weight group, but in overweight/obesity group, SUA had positive significant correlations with P2hCP, FCPI, PPCPI, ΔC-peptide, and HOMA2%B. In the female group, there were no significant correlations between SUA and insulin secretory capacity. However, in the male group, SUA had positive significant correlations with insulin secretory capacity include P2hCP, FCPI, PPCPI, ΔC-peptide, and HOMA2%B. Multiple linear regression showed that SUA was significantly associated with HOMA2%B, but not with HOMA2IR in overweight/obesity and male group. …
bibliographic citation: Zhong et al. (2019) The relationship between serum uric acid within the normal range and β-cell function in Chinese patients with type 2 diabetes: differences by body mass index and gender. PeerJ 7:e6666 https://doi.org/10.7717/peerj.6666
date submitted: 2018-11-21
date accepted: 2019-02-22
issued: 2019-03-26
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Zhong
  given name: Xing
author list: Agent
  family name: Zhang
  given name: Deyuan
author list: Agent
  family name: Yang
  given name: Lina
author list: Agent
  family name: Du
  given name: Yijun
author list: Agent
  family name: Pan
  given name: Tianrong
doi: 10.7717/peerj.6666
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-03-26
copyright: © 2019 Zhong et al.
attribution name: Zhong et al.

Loancorhynchus catrillancai gen. et sp. nov., a new swordfish (Xiphioidei, Blochiidae) from the Middle Eocene of central Chile
type: item
type: AcademicArticle
description: This contribution describes the skull remains of a swordfish (Perciformes, Xiphioidei), recovered from Middle Eocene beds of central Chile. Comparison with known fossil and extant xiphioids reveals derived traits only present in the Neogene swordfish Xiphias gladius (Xiphiidae, Xiphiinae), these being a elongated rostrum composed of premaxillaries and possible prenasals, a dorsoventrally high and slender hyomandibular-metapterygoid complex, and a rounded, convex operculum. Also, strong ridges and sulci are present in the dorsal part of the rostrum, a feature only present in the billfish genera Aglyptorhynchus and Xiphiorhynchus, and in the swordfish genus Blochius. In addition, the specimen also has villiform teeth in the rostrum and lower jaw, a feature previously documented only in the Paleocene genus Hemingwaya. Such a unique combination of characters in the specimen allows classifying it as a new genus and species, Loancorhynchus catrillancai. Phylogenetic analyses obtained Xiphiorhynchus outside the Xiphiidae, suggesting instead narrow relationships to the Paleocene-Eocene genera Hemingwaya + Palaeorhynchus + Homorhynchus. Loancorhynchus is obtained as an intermediate form between Xiphias and Blochius. The specimen represents the first Paleogene swordfish described in the southeastern Pacific.
format: application/pdf
format: text/html
creator: Rodrigo A. Otero
subject: Paleontology
subject: Taxonomy
subject: Zoology
description: doi:10.7717/peerj.6671
publisher: PeerJ Inc.
rights: © 2019 Otero
abstract: This contribution describes the skull remains of a swordfish (Perciformes, Xiphioidei), recovered from Middle Eocene beds of central Chile. Comparison with known fossil and extant xiphioids reveals derived traits only present in the Neogene swordfish Xiphias gladius (Xiphiidae, Xiphiinae), these being a elongated rostrum composed of premaxillaries and possible prenasals, a dorsoventrally high and slender hyomandibular-metapterygoid complex, and a rounded, convex operculum. Also, strong ridges and sulci are present in the dorsal part of the rostrum, a feature only present in the billfish genera Aglyptorhynchus and Xiphiorhynchus, and in the swordfish genus Blochius. In addition, the specimen also has villiform teeth in the rostrum and lower jaw, a feature previously documented only in the Paleocene genus Hemingwaya. Such a unique combination of characters in the specimen allows classifying it as a new genus and species, Loancorhynchus catrillancai. Phylogenetic analyses obtained Xiphiorhynchus outside the Xiphiidae, suggesting instead narrow relationships to the Paleocene-Eocene genera Hemingwaya + Palaeorhynchus + Homorhynchus. Loancorhynchus is obtained as an intermediate form between Xiphias and Blochius. The specimen represents the first Paleogene swordfish described in the southeastern Pacific.
bibliographic citation: Otero (2019) Loancorhynchus catrillancai gen. et sp. nov., a new swordfish (Xiphioidei, Blochiidae) from the Middle Eocene of central Chile. PeerJ 7:e6671 https://doi.org/10.7717/peerj.6671
date submitted: 2018-12-07
date accepted: 2019-02-22
issued: 2019-03-26
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Otero
  given name: Rodrigo A.
doi: 10.7717/peerj.6671
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-03-26
copyright: ©2019 Otero
attribution name: Otero

Translating the hemodynamic response: why focused interdisciplinary integration should matter for the future of functional neuroimaging
type: item
type: AcademicArticle
description: The amount of information acquired with functional neuroimaging techniques, particularly fNIRS and fMRI, is rapidly growing and has enormous potential for studying human brain functioning. Therefore, many scientists focus on solving computational neuroimaging and Big Data issues to advance the discipline. However, the main obstacle—the accurate translation of the hemodynamic response (HR) by the investigation of a physiological phenomenon called neurovascular coupling—is still not fully overcome and, more importantly, often overlooked in this context. This article provides a brief and critical overview of significant findings from cellular biology and in vivo brain physiology with a focus on advancing existing HR modelling paradigms. A brief historical timeline of these disciplines of neuroscience is presented for readers to grasp the concept better, and some possible solutions for further scientific discussion are provided.
format: application/pdf
format: text/html
creator: Sigita Cinciute
subject: Biophysics
subject: Cell Biology
subject: Molecular Biology
subject: Neuroscience
description: doi:10.7717/peerj.6621
publisher: PeerJ Inc.
rights: © 2019 Cinciute
abstract: The amount of information acquired with functional neuroimaging techniques, particularly fNIRS and fMRI, is rapidly growing and has enormous potential for studying human brain functioning. Therefore, many scientists focus on solving computational neuroimaging and Big Data issues to advance the discipline. However, the main obstacle—the accurate translation of the hemodynamic response (HR) by the investigation of a physiological phenomenon called neurovascular coupling—is still not fully overcome and, more importantly, often overlooked in this context. This article provides a brief and critical overview of significant findings from cellular biology and in vivo brain physiology with a focus on advancing existing HR modelling paradigms. A brief historical timeline of these disciplines of neuroscience is presented for readers to grasp the concept better, and some possible solutions for further scientific discussion are provided.
bibliographic citation: Cinciute (2019) Translating the hemodynamic response: why focused interdisciplinary integration should matter for the future of functional neuroimaging. PeerJ 7:e6621 https://doi.org/10.7717/peerj.6621
date submitted: 2018-10-11
date accepted: 2019-02-14
issued: 2019-03-25
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Cinciute
  given name: Sigita
doi: 10.7717/peerj.6621
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-03-25
copyright: © 2019 Cinciute
attribution name: Cinciute

Dual effects of biochar and hyperaccumulator Solanum nigrum L. on the remediation of Cd-contaminated soil
type: item
type: AcademicArticle
description: Biochar was widely developed for the soil amendment and remediation of heavy metal contaminated soil. The Cd hyperaccumulator, Solanum nigrum L., has been paid much more attention with the wide application of phytoremediation. The effects of biochar on the growth and accumulation capacity of Solanum nigrum L. in Cd contaminated soil have not been explored so far. The objectives of this study were to explore the dual effects of biochar addition on available Cd in the soil and hyperaccumulation of Cd in Solanum nigrum L. under different Cd contaminated levels. The correlations of soil physicochemical and biochemical properties and Cd absorption of Solanum nigrum L. were analyzed after a 60-day pot experiment under three biochar doses (0%, 1% and 5%) and four Cd concentrations (0, 25, 50 and 100 mg kg−1). The availability of Cd obtained by DTPA extraction significantly decreased after biochar application (P = 0.003, P = 0.0001, P = 0.0001 under 1% biochar addition for 25, 50, and 100 mg kg−1 Cd concentrations, P = 0.0001, P = 0.0001, P = 0.0001 under 5% biochar addition for 25, 50, and 100 mg kg−1 Cd concentrations, n ≥ 3). The 1% biochar dose significantly increased leaf dry weight (P = 0.039, P = 0.002 for the Cd concentrations of 50 and 100 mg kg−1, n ≥ 3) compared with the control in higher Cd concentrations (50 and 100 100 mg kg−1). In the presence of biochar, the bioconcentration factor (BCF) increased under the Cd concentrations of 50 and 100 mg kg−1. The translocation factors (TF) decreased with the biochar doses under the Cd concentration of 100 mg kg−1. The dose of 5% biochar significantly increased the urease activity by 41.18% compared to the 1% biochar addition in the Cd contaminated soil of 50 mg kg−1 concentration. The activities of acid phosphatase were inhibited by 1% biochar dose in all the Cd contaminated soils. The dry weight of the root of Solanum nigrum L. was significantly negatively correlated with acid phosphatase activity and BCF, respectively…
format: application/pdf
format: text/html
creator: Kang Li
creator: Baoshan Yang
creator: Hui Wang
creator: Xiaohan Xu
creator: Yongchao Gao
creator: Yidan Zhu
subject: Environmental Contamination and Remediation
subject: Environmental Impacts
description: doi:10.7717/peerj.6631
publisher: PeerJ Inc.
rights: © 2019 Li et al.
abstract: Biochar was widely developed for the soil amendment and remediation of heavy metal contaminated soil. The Cd hyperaccumulator, Solanum nigrum L., has been paid much more attention with the wide application of phytoremediation. The effects of biochar on the growth and accumulation capacity of Solanum nigrum L. in Cd contaminated soil have not been explored so far. The objectives of this study were to explore the dual effects of biochar addition on available Cd in the soil and hyperaccumulation of Cd in Solanum nigrum L. under different Cd contaminated levels. The correlations of soil physicochemical and biochemical properties and Cd absorption of Solanum nigrum L. were analyzed after a 60-day pot experiment under three biochar doses (0%, 1% and 5%) and four Cd concentrations (0, 25, 50 and 100 mg kg−1). The availability of Cd obtained by DTPA extraction significantly decreased after biochar application (P = 0.003, P = 0.0001, P = 0.0001 under 1% biochar addition for 25, 50, and 100 mg kg−1 Cd concentrations, P = 0.0001, P = 0.0001, P = 0.0001 under 5% biochar addition for 25, 50, and 100 mg kg−1 Cd concentrations, n ≥ 3). The 1% biochar dose significantly increased leaf dry weight (P = 0.039, P = 0.002 for the Cd concentrations of 50 and 100 mg kg−1, n ≥ 3) compared with the control in higher Cd concentrations (50 and 100 100 mg kg−1). In the presence of biochar, the bioconcentration factor (BCF) increased under the Cd concentrations of 50 and 100 mg kg−1. The translocation factors (TF) decreased with the biochar doses under the Cd concentration of 100 mg kg−1. The dose of 5% biochar significantly increased the urease activity by 41.18% compared to the 1% biochar addition in the Cd contaminated soil of 50 mg kg−1 concentration. The activities of acid phosphatase were inhibited by 1% biochar dose in all the Cd contaminated soils. The dry weight of the root of Solanum nigrum L. was significantly negatively correlated with acid phosphatase activity and BCF, respectively…
bibliographic citation: Li et al. (2019) Dual effects of biochar and hyperaccumulator Solanum nigrum L. on the remediation of Cd-contaminated soil. PeerJ 7:e6631 https://doi.org/10.7717/peerj.6631
date submitted: 2018-10-11
date accepted: 2019-02-17
issued: 2019-03-25
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Li
  given name: Kang
author list: Agent
  family name: Yang
  given name: Baoshan
author list: Agent
  family name: Wang
  given name: Hui
author list: Agent
  family name: Xu
  given name: Xiaohan
author list: Agent
  family name: Gao
  given name: Yongchao
author list: Agent
  family name: Zhu
  given name: Yidan
doi: 10.7717/peerj.6631
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-03-25
copyright: ©2019 Li et al.
attribution name: Li et al.

Capacity for heat absorption by the wings of the butterfly Tirumala limniace (Cramer)
type: item
type: AcademicArticle
description: Butterflies can directly absorb heat from the sun via their wings to facilitate autonomous flight. However, how is the heat absorbed by the butterfly from sunlight stored and transmitted in the wing? The answer to this scientific question remains unclear. The butterfly Tirumala limniace (Cramer) is a typical heat absorption insect, and its wing surface color is only composed of light and dark colors. Thus, in this study, we measured a number of wing traits relevant for heat absorption including the thoracic temperature at different light intensities and wing opening angles, the thoracic temperature of butterflies with only one right fore wing or one right hind wing; In addition, the spectral reflectance of the wing surfaces, the thoracic temperature of butterflies with the scales removed or present in light or dark areas, and the real-time changes in heat absorption by the wing surfaces with temperature were also measured. We found that high intensity light (600–60,000 lx) allowed the butterflies to absorb more heat and 60−90° was the optimal angle for heat absorption. The heat absorption capacity was stronger in the fore wings than the hind wings. Dark areas on the wing surfaces were heat absorption areas. The dark areas in the lower region of the fore wing surface and the inside region of the hind wing surface were heat storage areas. Heat was transferred from the heat storage areas to the wing base through the veins near the heat storage areas of the fore and hind wings.
format: application/pdf
format: text/html
creator: Huaijian Liao
creator: Ting Du
creator: Yuqi Zhang
creator: Lei Shi
creator: Xiyu Huai
creator: Chengli Zhou
creator: Jiang Deng
subject: Animal Behavior
subject: Biophysics
subject: Entomology
description: doi:10.7717/peerj.6648
publisher: PeerJ Inc.
rights: © 2019 Liao et al.
abstract: Butterflies can directly absorb heat from the sun via their wings to facilitate autonomous flight. However, how is the heat absorbed by the butterfly from sunlight stored and transmitted in the wing? The answer to this scientific question remains unclear. The butterfly Tirumala limniace (Cramer) is a typical heat absorption insect, and its wing surface color is only composed of light and dark colors. Thus, in this study, we measured a number of wing traits relevant for heat absorption including the thoracic temperature at different light intensities and wing opening angles, the thoracic temperature of butterflies with only one right fore wing or one right hind wing; In addition, the spectral reflectance of the wing surfaces, the thoracic temperature of butterflies with the scales removed or present in light or dark areas, and the real-time changes in heat absorption by the wing surfaces with temperature were also measured. We found that high intensity light (600–60,000 lx) allowed the butterflies to absorb more heat and 60−90° was the optimal angle for heat absorption. The heat absorption capacity was stronger in the fore wings than the hind wings. Dark areas on the wing surfaces were heat absorption areas. The dark areas in the lower region of the fore wing surface and the inside region of the hind wing surface were heat storage areas. Heat was transferred from the heat storage areas to the wing base through the veins near the heat storage areas of the fore and hind wings.
bibliographic citation: Liao et al. (2019) Capacity for heat absorption by the wings of the butterfly Tirumala limniace (Cramer). PeerJ 7:e6648 https://doi.org/10.7717/peerj.6648
date submitted: 2018-08-28
date accepted: 2019-02-20
issued: 2019-03-25
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Liao
  given name: Huaijian
author list: Agent
  family name: Du
  given name: Ting
author list: Agent
  family name: Zhang
  given name: Yuqi
author list: Agent
  family name: Shi
  given name: Lei
author list: Agent
  family name: Huai
  given name: Xiyu
author list: Agent
  family name: Zhou
  given name: Chengli
author list: Agent
  family name: Deng
  given name: Jiang
doi: 10.7717/peerj.6648
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-03-25
copyright: © 2019 Liao et al.
attribution name: Liao et al.

Evidence of cryptic lineages within a small South American crocodilian: the Schneider’s dwarf caiman Paleosuchus trigonatus (Alligatoridae: Caimaninae)
type: item
type: AcademicArticle
description: Schneider’s dwarf caiman Paleosuchus trigonatus is one of the smallest living crocodilians. Due to its broad distribution, cryptic behavior, and small home range, the species is well suited for the study of phylogeographic patterns on a continental scale. Additionally, this species is under threat due to habitat loss, trade and harvest, but is considered at low conservation risk by the IUCN. In the present study we test the hypothesis that P. trigonatus is comprised of geographically structured lineages. Phylogenetic reconstructions of the mitochondrial cytochrome b gene and single locus species discovery methods revealed the existence of two well-supported lineages within P. trigonatus—an Amazonian and Guianan lineage. Fossil calibrated divergence of these lineages was estimated to have occurred in the Late Miocene (7.5 Ma). The hypothesis that the Atlantic coast drainages might have been colonized from the southeast or central Amazon is supported by demographic metrics and relatively low genetic diversity of the Coastal and upper Branco populations when compared to the Amazon basin populations. The Amazon basin lineage is structured along an east-west gradient, with a sharp transition in haplotype frequencies to the east and west of the Negro and Madeira rivers. These lineages are already under anthropogenic threat and, therefore, are conservation dependent. Recognition of these lineages will foster discussion of conservation future of P. trigonatus and these lineages.
format: application/pdf
format: text/html
creator: Pedro Senna Bittencourt
creator: Zilca Campos
creator: Fábio de Lima Muniz
creator: Boris Marioni
creator: Bruno Campos Souza
creator: Ronis Da Silveira
creator: Benoit de Thoisy
creator: Tomas Hrbek
creator: Izeni Pires Farias
subject: Biodiversity
subject: Biogeography
subject: Evolutionary Studies
subject: Genetics
subject: Population Biology
description: doi:10.7717/peerj.6580
publisher: PeerJ Inc.
rights: © 2019 Bittencourt et al.
abstract: Schneider’s dwarf caiman Paleosuchus trigonatus is one of the smallest living crocodilians. Due to its broad distribution, cryptic behavior, and small home range, the species is well suited for the study of phylogeographic patterns on a continental scale. Additionally, this species is under threat due to habitat loss, trade and harvest, but is considered at low conservation risk by the IUCN. In the present study we test the hypothesis that P. trigonatus is comprised of geographically structured lineages. Phylogenetic reconstructions of the mitochondrial cytochrome b gene and single locus species discovery methods revealed the existence of two well-supported lineages within P. trigonatus—an Amazonian and Guianan lineage. Fossil calibrated divergence of these lineages was estimated to have occurred in the Late Miocene (7.5 Ma). The hypothesis that the Atlantic coast drainages might have been colonized from the southeast or central Amazon is supported by demographic metrics and relatively low genetic diversity of the Coastal and upper Branco populations when compared to the Amazon basin populations. The Amazon basin lineage is structured along an east-west gradient, with a sharp transition in haplotype frequencies to the east and west of the Negro and Madeira rivers. These lineages are already under anthropogenic threat and, therefore, are conservation dependent. Recognition of these lineages will foster discussion of conservation future of P. trigonatus and these lineages.
bibliographic citation: Bittencourt et al. (2019) Evidence of cryptic lineages within a small South American crocodilian: the Schneider’s dwarf caiman Paleosuchus trigonatus (Alligatoridae: Caimaninae). PeerJ 7:e6580 https://doi.org/10.7717/peerj.6580
date submitted: 2018-03-21
date accepted: 2019-02-01
issued: 2019-03-22
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Bittencourt
  given name: Pedro Senna
author list: Agent
  family name: Campos
  given name: Zilca
author list: Agent
  family name: Muniz
  given name: Fábio de Lima
author list: Agent
  family name: Marioni
  given name: Boris
author list: Agent
  family name: Souza
  given name: Bruno Campos
author list: Agent
  family name: Da Silveira
  given name: Ronis
author list: Agent
  family name: de Thoisy
  given name: Benoit
author list: Agent
  family name: Hrbek
  given name: Tomas
author list: Agent
  family name: Farias
  given name: Izeni Pires
doi: 10.7717/peerj.6580
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-03-22
copyright: ©2019 Bittencourt et al.
attribution name: Bittencourt et al.

Pain neuroscience education on YouTube
type: item
type: AcademicArticle
description: Objectives The Internet in general, and YouTube in particular, is now one of the most popular sources of health-related information. Pain neuroscience education has become a primary tool for managing persistent pain, based in part on the discovery that information about pain can change pain. Our objective was to examine the availability, characteristics, and content of YouTube videos that address the neuroscience of pain. Methods We conducted a systematic review of videos on YouTube using the search terms “pain education”, “what is pain”, and “pain brain” in January 2018. Videos were included if they were in English, were under 10 minutes long, and included information on the neuroscience of pain. Videos were coded for (i) descriptive characteristics (e.g., number of views, duration on YouTube), (ii) source and style, (iii) whether or not they addressed seven pre-determined target concepts of pain neuroscience education (e.g., ‘Pain is not an accurate marker of tissue state’), and (iv) how engaging they were. Results We found 106 unique videos that met the inclusion criteria. The videos ranged from having four views to over five million views (Mdn = 1,163 views), with the three most highly viewed videos accounting for 75% of the total views. Animated videos were much more highly viewed than non-animated videos. Only a small number of videos had been posted by a clearly-identifiable reputable source such as an academic or medical institution (10%), although a number of videos were posted by healthcare professionals and professional medical societies. For a small number of videos (7%), the source was unclear. We found 17 videos that addressed at least one target concept of pain neuroscience science education, only nine of which were considered to be at least somewhat engaging. The target concept ‘Pain is a brain output’ was considered to be well addressed by the most videos (N = 11), followed by ‘Pain is a protector’ (N = 10). We found only one video that adequately a…
format: application/pdf
format: text/html
creator: Lauren C. Heathcote
creator: Joshua W. Pate
creator: Anna L. Park
creator: Hayley B. Leake
creator: G. Lorimer Moseley
creator: Corey A. Kronman
creator: Molly Fischer
creator: Inge Timmers
creator: Laura E. Simons
subject: Neuroscience
subject: Anesthesiology and Pain Management
subject: Psychiatry and Psychology
subject: Science and Medical Education
description: doi:10.7717/peerj.6603
publisher: PeerJ Inc.
rights: © 2019 Heathcote et al.
abstract: Objectives The Internet in general, and YouTube in particular, is now one of the most popular sources of health-related information. Pain neuroscience education has become a primary tool for managing persistent pain, based in part on the discovery that information about pain can change pain. Our objective was to examine the availability, characteristics, and content of YouTube videos that address the neuroscience of pain. Methods We conducted a systematic review of videos on YouTube using the search terms “pain education”, “what is pain”, and “pain brain” in January 2018. Videos were included if they were in English, were under 10 minutes long, and included information on the neuroscience of pain. Videos were coded for (i) descriptive characteristics (e.g., number of views, duration on YouTube), (ii) source and style, (iii) whether or not they addressed seven pre-determined target concepts of pain neuroscience education (e.g., ‘Pain is not an accurate marker of tissue state’), and (iv) how engaging they were. Results We found 106 unique videos that met the inclusion criteria. The videos ranged from having four views to over five million views (Mdn = 1,163 views), with the three most highly viewed videos accounting for 75% of the total views. Animated videos were much more highly viewed than non-animated videos. Only a small number of videos had been posted by a clearly-identifiable reputable source such as an academic or medical institution (10%), although a number of videos were posted by healthcare professionals and professional medical societies. For a small number of videos (7%), the source was unclear. We found 17 videos that addressed at least one target concept of pain neuroscience science education, only nine of which were considered to be at least somewhat engaging. The target concept ‘Pain is a brain output’ was considered to be well addressed by the most videos (N = 11), followed by ‘Pain is a protector’ (N = 10). We found only one video that adequately a…
bibliographic citation: Heathcote et al. (2019) Pain neuroscience education on YouTube. PeerJ 7:e6603 https://doi.org/10.7717/peerj.6603
date submitted: 2018-12-12
date accepted: 2019-02-11
issued: 2019-03-22
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Heathcote
  given name: Lauren C.
author list: Agent
  family name: Pate
  given name: Joshua W.
author list: Agent
  family name: Park
  given name: Anna L.
author list: Agent
  family name: Leake
  given name: Hayley B.
author list: Agent
  family name: Moseley
  given name: G. Lorimer
author list: Agent
  family name: Kronman
  given name: Corey A.
author list: Agent
  family name: Fischer
  given name: Molly
author list: Agent
  family name: Timmers
  given name: Inge
author list: Agent
  family name: Simons
  given name: Laura E.
doi: 10.7717/peerj.6603
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-03-22
copyright: ©2019 Heathcote et al.
attribution name: Heathcote et al.

The transcriptomic response to a short day to long day shift in leaves of the reference legume Medicago truncatula
type: item
type: AcademicArticle
description: Photoperiodic flowering aligns plant reproduction to favourable seasons of the year to maximise successful production of seeds and grains. However understanding of this process in the temperate legumes of the Fabaceae family, which are important both agriculturally and ecologically, is incomplete. Previous work in the reference legume Medicago truncatula has shown that the FT-like gene MtFTa1 is a potent floral activator. While MtFTa1 is upregulated by long-day photoperiods (LD) and vernalisation, the molecular basis of this is unknown as functional homologues of key regulatory genes present in other species, notably CONSTANS in A. thaliana, have not been identified. In LD MtFTa1 maintains a near constant diurnal pattern of expression unlike its homologue FT in A. thaliana, which has a notable peak in expression at dusk. This suggests a different manner of regulation. Furthermore, M. truncatula possesses other FT-like genes such as two LD induced MtFTb genes which may also act in the regulation of flowering time. MtFTb genes have a diurnal pattern of expression with peaks at both four and sixteen hours after dawn. This study utilises RNA-Seq to analyse the transcriptome of M. truncatula leaves to identify genes which may regulate or be co-expressed with these FT-like genes following a shift from short-day photoperiods to inductive long-days. Specifically this study focuses on the first four hours of the day in the young leaves, which coincides with the first diurnal peak of the FTb genes. Following differential expression analysis at each timepoint, genes which alter their pattern of expression are distinguished from those which just alter their magnitude of expression (and those that do neither). It goes on to categorise these genes into groups with similar patterns of expression using c-means clustering and identifies a number of potential candidate photoperiod flowering time genes for future studies to consider.
format: application/pdf
format: text/html
creator: Geoffrey Thomson
creator: James Taylor
creator: Joanna Putterill
subject: Bioinformatics
subject: Genomics
subject: Molecular Biology
subject: Plant Science
description: doi:10.7717/peerj.6626
publisher: PeerJ Inc.
rights: © 2019 Thomson et al.
abstract: Photoperiodic flowering aligns plant reproduction to favourable seasons of the year to maximise successful production of seeds and grains. However understanding of this process in the temperate legumes of the Fabaceae family, which are important both agriculturally and ecologically, is incomplete. Previous work in the reference legume Medicago truncatula has shown that the FT-like gene MtFTa1 is a potent floral activator. While MtFTa1 is upregulated by long-day photoperiods (LD) and vernalisation, the molecular basis of this is unknown as functional homologues of key regulatory genes present in other species, notably CONSTANS in A. thaliana, have not been identified. In LD MtFTa1 maintains a near constant diurnal pattern of expression unlike its homologue FT in A. thaliana, which has a notable peak in expression at dusk. This suggests a different manner of regulation. Furthermore, M. truncatula possesses other FT-like genes such as two LD induced MtFTb genes which may also act in the regulation of flowering time. MtFTb genes have a diurnal pattern of expression with peaks at both four and sixteen hours after dawn. This study utilises RNA-Seq to analyse the transcriptome of M. truncatula leaves to identify genes which may regulate or be co-expressed with these FT-like genes following a shift from short-day photoperiods to inductive long-days. Specifically this study focuses on the first four hours of the day in the young leaves, which coincides with the first diurnal peak of the FTb genes. Following differential expression analysis at each timepoint, genes which alter their pattern of expression are distinguished from those which just alter their magnitude of expression (and those that do neither). It goes on to categorise these genes into groups with similar patterns of expression using c-means clustering and identifies a number of potential candidate photoperiod flowering time genes for future studies to consider.
bibliographic citation: Thomson et al. (2019) The transcriptomic response to a short day to long day shift in leaves of the reference legume Medicago truncatula. PeerJ 7:e6626 https://doi.org/10.7717/peerj.6626
date submitted: 2018-11-09
date accepted: 2019-02-15
issued: 2019-03-22
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Thomson
  given name: Geoffrey
author list: Agent
  family name: Taylor
  given name: James
author list: Agent
  family name: Putterill
  given name: Joanna
doi: 10.7717/peerj.6626
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-03-22
copyright: ©2019 Thomson et al.
attribution name: Thomson et al.

Identification of key genes, pathways and potential therapeutic agents for liver fibrosis using an integrated bioinformatics analysis
type: item
type: AcademicArticle
description: Background Liver fibrosis is often a consequence of chronic liver injury, and has the potential to progress to cirrhosis and liver cancer. Despite being an important human disease, there are currently no approved anti-fibrotic drugs. In this study, we aim to identify the key genes and pathways governing the pathophysiological processes of liver fibrosis, and to screen therapeutic anti-fibrotic agents. Methods Expression profiles were downloaded from the Gene Expression Omnibus (GEO), and differentially expressed genes (DEGs) were identified by R packages (Affy and limma). Gene functional enrichments of each dataset were performed on the DAVID database. Protein–protein interaction (PPI) network was constructed by STRING database and visualized in Cytoscape software. The hub genes were explored by the CytoHubba plugin app and validated in another GEO dataset and in a liver fibrosis cell model by quantitative real-time PCR assay. The Connectivity Map L1000 platform was used to identify potential anti-fibrotic agents. Results We integrated three fibrosis datasets of different disease etiologies, incorporating a total of 70 severe (F3–F4) and 116 mild (F0–F1) fibrotic tissue samples. Gene functional enrichment analyses revealed that cell cycle was a pathway uniquely enriched in a dataset from those patients infected by hepatitis B virus (HBV), while the immune-inflammatory response was enriched in both the HBV and hepatitis C virus (HCV) datasets, but not in the nonalcoholic fatty liver disease (NAFLD) dataset. There was overlap between these three datasets; 185 total shared DEGs that were enriched for pathways associated with extracellular matrix constitution, platelet-derived growth-factor binding, protein digestion and absorption, focal adhesion, and PI3K-Akt signaling. In the PPI network, 25 hub genes were extracted and deemed to be essential genes for fibrogenesis, and the expression trends were consistent with GSE14323 (an additional dataset) and liver fibrosis cel…
format: application/pdf
format: text/html
creator: Zhu Zhan
creator: Yuhe Chen
creator: Yuanqin Duan
creator: Lin Li
creator: Kenley Mew
creator: Peng Hu
creator: Hong Ren
creator: Mingli Peng
subject: Bioinformatics
subject: Gastroenterology and Hepatology
subject: Infectious Diseases
description: doi:10.7717/peerj.6645
publisher: PeerJ Inc.
rights: © 2019 Zhan et al.
abstract: Background Liver fibrosis is often a consequence of chronic liver injury, and has the potential to progress to cirrhosis and liver cancer. Despite being an important human disease, there are currently no approved anti-fibrotic drugs. In this study, we aim to identify the key genes and pathways governing the pathophysiological processes of liver fibrosis, and to screen therapeutic anti-fibrotic agents. Methods Expression profiles were downloaded from the Gene Expression Omnibus (GEO), and differentially expressed genes (DEGs) were identified by R packages (Affy and limma). Gene functional enrichments of each dataset were performed on the DAVID database. Protein–protein interaction (PPI) network was constructed by STRING database and visualized in Cytoscape software. The hub genes were explored by the CytoHubba plugin app and validated in another GEO dataset and in a liver fibrosis cell model by quantitative real-time PCR assay. The Connectivity Map L1000 platform was used to identify potential anti-fibrotic agents. Results We integrated three fibrosis datasets of different disease etiologies, incorporating a total of 70 severe (F3–F4) and 116 mild (F0–F1) fibrotic tissue samples. Gene functional enrichment analyses revealed that cell cycle was a pathway uniquely enriched in a dataset from those patients infected by hepatitis B virus (HBV), while the immune-inflammatory response was enriched in both the HBV and hepatitis C virus (HCV) datasets, but not in the nonalcoholic fatty liver disease (NAFLD) dataset. There was overlap between these three datasets; 185 total shared DEGs that were enriched for pathways associated with extracellular matrix constitution, platelet-derived growth-factor binding, protein digestion and absorption, focal adhesion, and PI3K-Akt signaling. In the PPI network, 25 hub genes were extracted and deemed to be essential genes for fibrogenesis, and the expression trends were consistent with GSE14323 (an additional dataset) and liver fibrosis cel…
bibliographic citation: Zhan et al. (2019) Identification of key genes, pathways and potential therapeutic agents for liver fibrosis using an integrated bioinformatics analysis. PeerJ 7:e6645 https://doi.org/10.7717/peerj.6645
date submitted: 2018-12-20
date accepted: 2019-02-17
issued: 2019-03-22
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Zhan
  given name: Zhu
author list: Agent
  family name: Chen
  given name: Yuhe
author list: Agent
  family name: Duan
  given name: Yuanqin
author list: Agent
  family name: Li
  given name: Lin
author list: Agent
  family name: Mew
  given name: Kenley
author list: Agent
  family name: Hu
  given name: Peng
author list: Agent
  family name: Ren
  given name: Hong
author list: Agent
  family name: Peng
  given name: Mingli
doi: 10.7717/peerj.6645
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-03-22
copyright: ©2019 Zhan et al.
attribution name: Zhan et al.

Relative abundance and molecular evolution of Lake Sinai Virus (Sinaivirus) clades
type: item
type: AcademicArticle
description: Lake Sinai Viruses (Sinaivirus) are commonly detected in honey bees (Apis mellifera) but no disease phenotypes or fitness consequences have yet been demonstrated. This viral group is genetically diverse, lacks obvious geographic structure, and multiple lineages can co-infect individual bees. While phylogenetic analyses have been performed, the molecular evolution of LSV has not been studied extensively. Here, I use LSV isolates from GenBank as well as contigs assembled from honey bee Sequence Read Archive (SRA) accessions to better understand the evolutionary history of these viruses. For each ORF, substitution rate variation, codon usage, and tests of positive selection were evaluated. Outlier regions of high or low diversity were sought with sliding window analysis and the role of recombination in creating LSV diversity was explored. Phylogenetic analysis consistently identified two large clusters of sequences that correspond to the current LSV1 and LSV2 nomenclature, however lineages sister to LSV1 were the most frequently detected in honey bee SRA accessions. Different expression levels among ORFs suggested the occurrence of subgenomic transcripts. ORF1 and RNA-dependent RNA polymerase had higher evolutionary rates than the capsid and ORF4. A hypervariable region of the ORF1 protein-coding sequence was identified that had reduced selective constraint, but a site-based model of positive selection was not significantly more likely than a neutral model for any ORF. The only significant recombination signals detected between LSV1 and LSV2 initiated within this hypervariable region, but assumptions of the test (single-frame coding and independence of substitution rate by site) were violated. LSV codon usage differed strikingly from that of honey bees and other common honey-bee viruses, suggesting LSV is not strongly co-evolved with that host. LSV codon usage was significantly correlated with that of Varroa destructor, however, despite the relatively weak codon bias e…
format: application/pdf
format: text/html
creator: Robert S. Cornman
subject: Agricultural Science
subject: Entomology
subject: Genomics
subject: Virology
description: doi:10.7717/peerj.6305
publisher: PeerJ Inc.
rights: © 2019 Cornman
abstract: Lake Sinai Viruses (Sinaivirus) are commonly detected in honey bees (Apis mellifera) but no disease phenotypes or fitness consequences have yet been demonstrated. This viral group is genetically diverse, lacks obvious geographic structure, and multiple lineages can co-infect individual bees. While phylogenetic analyses have been performed, the molecular evolution of LSV has not been studied extensively. Here, I use LSV isolates from GenBank as well as contigs assembled from honey bee Sequence Read Archive (SRA) accessions to better understand the evolutionary history of these viruses. For each ORF, substitution rate variation, codon usage, and tests of positive selection were evaluated. Outlier regions of high or low diversity were sought with sliding window analysis and the role of recombination in creating LSV diversity was explored. Phylogenetic analysis consistently identified two large clusters of sequences that correspond to the current LSV1 and LSV2 nomenclature, however lineages sister to LSV1 were the most frequently detected in honey bee SRA accessions. Different expression levels among ORFs suggested the occurrence of subgenomic transcripts. ORF1 and RNA-dependent RNA polymerase had higher evolutionary rates than the capsid and ORF4. A hypervariable region of the ORF1 protein-coding sequence was identified that had reduced selective constraint, but a site-based model of positive selection was not significantly more likely than a neutral model for any ORF. The only significant recombination signals detected between LSV1 and LSV2 initiated within this hypervariable region, but assumptions of the test (single-frame coding and independence of substitution rate by site) were violated. LSV codon usage differed strikingly from that of honey bees and other common honey-bee viruses, suggesting LSV is not strongly co-evolved with that host. LSV codon usage was significantly correlated with that of Varroa destructor, however, despite the relatively weak codon bias e…
bibliographic citation: Cornman (2019) Relative abundance and molecular evolution of Lake Sinai Virus (Sinaivirus) clades. PeerJ 7:e6305 https://doi.org/10.7717/peerj.6305
date submitted: 2018-10-22
date accepted: 2018-12-17
issued: 2019-03-21
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Cornman
  given name: Robert S.
doi: 10.7717/peerj.6305
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-03-21
copyright: © 2019 Cornman
attribution name: Cornman

Oceanographic moorings as year-round laboratories for investigating growth performance and settlement dynamics in the Antarctic scallop Adamussium colbecki (E. A. Smith, 1902)
type: item
type: AcademicArticle
description: Background Oceanographic moorings (OMs) are standard marine platforms composed of wires, buoys, weights and instruments, and are used as in situ observatories to record water column properties. However, OMs are also comprised of hard substrates on which a variety of invertebrates can settle when they encounter these structures along their dispersal routes. In this contribution, we studied the fouling communities found on two OMs deployed in the Ross Sea (Antarctica). Furthermore, a cage containing the Antarctic scallop Adamussium colbecki (E. A. Smith, 1902) was incorporated in the OM. The growth of the caged A. colbecki were evaluated after 1 year and their shells used as biological proxy for seawater temperature and salinity. Methods A variety of settlers were collected from two different OMs deployed in the Ross Sea (Antarctica) and species identified using a combination of morphological and genetic (mainly through DNA barcoding) characteristics. Caged scallops were individually marked with permanent tags and their growth studied in terms of size-increment data (SID). Cages were specifically designed to prevent damage to individuals due to water drag during OM deployment and retrieval. Growth parameters from the caged individuals were applied to the A. colbecki juveniles that had settled on the mooring, to trace the likely settlement period. Results The growth performance of caged A. colbecki was similar to that from previous growth studies of this species. The remarkable survival rate of caged specimens (96.6%) supports the feasibility of caging experiments, even for a species with a fragile shell such as the Antarctic scallop. Some of the new recruits found on the mooring were A. colbecki, the same species we put into special cages fixed to it. The settlement of the A. colbecki juveniles started during the Austral spring with a peak in summer months and, remarkably, coincided with seasonal changes in water temperature and flow direction, which were recorded by …
format: application/pdf
format: text/html
creator: Stefano Schiaparelli
creator: Stefano Aliani
subject: Ecology
subject: Marine Biology
subject: Zoology
subject: Biological Oceanography
description: doi:10.7717/peerj.6373
publisher: PeerJ Inc.
rights: © 2019 Schiaparelli and Aliani
abstract: Background Oceanographic moorings (OMs) are standard marine platforms composed of wires, buoys, weights and instruments, and are used as in situ observatories to record water column properties. However, OMs are also comprised of hard substrates on which a variety of invertebrates can settle when they encounter these structures along their dispersal routes. In this contribution, we studied the fouling communities found on two OMs deployed in the Ross Sea (Antarctica). Furthermore, a cage containing the Antarctic scallop Adamussium colbecki (E. A. Smith, 1902) was incorporated in the OM. The growth of the caged A. colbecki were evaluated after 1 year and their shells used as biological proxy for seawater temperature and salinity. Methods A variety of settlers were collected from two different OMs deployed in the Ross Sea (Antarctica) and species identified using a combination of morphological and genetic (mainly through DNA barcoding) characteristics. Caged scallops were individually marked with permanent tags and their growth studied in terms of size-increment data (SID). Cages were specifically designed to prevent damage to individuals due to water drag during OM deployment and retrieval. Growth parameters from the caged individuals were applied to the A. colbecki juveniles that had settled on the mooring, to trace the likely settlement period. Results The growth performance of caged A. colbecki was similar to that from previous growth studies of this species. The remarkable survival rate of caged specimens (96.6%) supports the feasibility of caging experiments, even for a species with a fragile shell such as the Antarctic scallop. Some of the new recruits found on the mooring were A. colbecki, the same species we put into special cages fixed to it. The settlement of the A. colbecki juveniles started during the Austral spring with a peak in summer months and, remarkably, coincided with seasonal changes in water temperature and flow direction, which were recorded by …
bibliographic citation: Schiaparelli et al. (2019) Oceanographic moorings as year-round laboratories for investigating growth performance and settlement dynamics in the Antarctic scallop Adamussium colbecki (E. A. Smith, 1902). PeerJ 7:e6373 https://doi.org/10.7717/peerj.6373
date submitted: 2018-03-19
date accepted: 2018-12-30
issued: 2019-03-21
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Schiaparelli
  given name: Stefano
author list: Agent
  family name: Aliani
  given name: Stefano
doi: 10.7717/peerj.6373
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-03-21
copyright: © 2019 Schiaparelli and Aliani
attribution name: Schiaparelli and Aliani

Human gut resistome can be country-specific
type: item
type: AcademicArticle
description: The emergence and spread of antibiotic resistance have become emerging threats to human health. The human gut is a large reservoir for antibiotic resistance genes. The gut resistome may be influenced by many factors, but the consumption of antibiotics at both individual and country level should be one of the most significant factors. Previous studies have suggested that the gut resistome of different populations may vary, but lack quantitative characterization supported with relatively large datasets. In this study, we filled the gap by analyzing a large gut resistome dataset of 1,267 human gut samples of America, China, Denmark, and Spain. We built a stacking machine-learning model to determine whether the gut resistome can act as the sole feature to identify the nationality of an individual reliably. It turned out that the machine learning method could successfully identify American, Chinese, Danish, and Spanish populations with F1 score of 0.964, 0.987, 0.971, and 0.986, respectively. Our finding does highlight the significant differences in the composition of the gut resistome among different nationalities. Our study should be valuable for policy-makers to look into the influences of country-specific factors of the human gut resistome.
format: application/pdf
format: text/html
creator: Yao Xia
creator: Yanshan Zhu
creator: Qier Li
creator: Jiahai Lu
subject: Bioinformatics
subject: Microbiology
subject: Epidemiology
subject: Global Health
subject: Data Mining and Machine Learning
description: doi:10.7717/peerj.6389
publisher: PeerJ Inc.
rights: © 2019 Xia et al.
abstract: The emergence and spread of antibiotic resistance have become emerging threats to human health. The human gut is a large reservoir for antibiotic resistance genes. The gut resistome may be influenced by many factors, but the consumption of antibiotics at both individual and country level should be one of the most significant factors. Previous studies have suggested that the gut resistome of different populations may vary, but lack quantitative characterization supported with relatively large datasets. In this study, we filled the gap by analyzing a large gut resistome dataset of 1,267 human gut samples of America, China, Denmark, and Spain. We built a stacking machine-learning model to determine whether the gut resistome can act as the sole feature to identify the nationality of an individual reliably. It turned out that the machine learning method could successfully identify American, Chinese, Danish, and Spanish populations with F1 score of 0.964, 0.987, 0.971, and 0.986, respectively. Our finding does highlight the significant differences in the composition of the gut resistome among different nationalities. Our study should be valuable for policy-makers to look into the influences of country-specific factors of the human gut resistome.
bibliographic citation: Xia et al. (2019) Human gut resistome can be country-specific. PeerJ 7:e6389 https://doi.org/10.7717/peerj.6389
date submitted: 2018-06-28
date accepted: 2019-01-04
issued: 2019-03-21
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Xia
  given name: Yao
author list: Agent
  family name: Zhu
  given name: Yanshan
author list: Agent
  family name: Li
  given name: Qier
author list: Agent
  family name: Lu
  given name: Jiahai
doi: 10.7717/peerj.6389
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-03-21
copyright: © 2019 Xia et al.
attribution name: Xia et al.

Comparative analysis of the liver transcriptome in the red-eared slider Trachemys scripta elegans under chronic salinity stress
type: item
type: AcademicArticle
description: The red-eared slider (Trachemys scripta elegans), identified as one of the 100 most invasive species in the world, is a freshwater turtle originally from the eastern United States and northeastern Mexico. Field investigations have shown that T. s. elegans can survive and lay eggs in saline habitats. In order to understand the molecular mechanisms of salinity adaptation, high-throughput RNA-Seq was utilized to identify the changes in gene expression profiles in the liver of T. s. elegans in response to elevated salinity. We exposed individuals to 0, 5, or 15 psu (practical salinity units) for 30 days. A total of 157.21 million reads were obtained and assembled into 205138 unigenes with an average length of 620 bp and N50 of 964 bp. Of these, 1019 DEGs (differentially expressed genes) were found in the comparison of 0 vs. 5 psu, 1194 DEGs in 0 vs. 15 psu and 1180 DEGs in 5 vs. 15 psu, which are mainly related to macromolecule metabolic process, ion transport, oxidoreductase activity and generation of precursor metabolites and energy by GO (Gene Ontology) enrichment analyses. T. s. elegans can adapt itself into salinity by balancing the entry of sodium and chloride ions via the up-regulation expression genes of ion transport (potassium voltage-gated channel subfamily H member 5, KCNH5; erine/threonine-protein kinase 32, STK32; salt-inducible kinase 1, SIK1; adiponectin, ACDC), and by accumulating plasma urea and free amino acid via the up-regulation expression genes of amino acid metabolism (ornithine decarboxylase antizyme 3, OAZ3; glutamine synthetase, GLUL; asparaginase-like protein 1b, ASRGL; L-amino-acid oxidase-like, LAAO; sodium-dependent neutral amino acid transporter B, SLC6A15s; amino acid permease, SLC7A9) in response to osmotic regulation. An investment of energy to maintain their homeostatic balance is required to salinity adaptation, therefore, the genes related to energy production and conversion (F-ATPase protein 6, ATP6; cytochrome c oxidase subunit I,…
format: application/pdf
format: text/html
creator: Meiling Hong
creator: Aiping Jiang
creator: Na Li
creator: Weihao Li
creator: Haitao Shi
creator: Kenneth B. Storey
creator: Li Ding
subject: Conservation Biology
subject: Ecology
subject: Genomics
subject: Molecular Biology
subject: Zoology
description: doi:10.7717/peerj.6538
publisher: PeerJ Inc.
rights: © 2019 Hong et al.
abstract: The red-eared slider (Trachemys scripta elegans), identified as one of the 100 most invasive species in the world, is a freshwater turtle originally from the eastern United States and northeastern Mexico. Field investigations have shown that T. s. elegans can survive and lay eggs in saline habitats. In order to understand the molecular mechanisms of salinity adaptation, high-throughput RNA-Seq was utilized to identify the changes in gene expression profiles in the liver of T. s. elegans in response to elevated salinity. We exposed individuals to 0, 5, or 15 psu (practical salinity units) for 30 days. A total of 157.21 million reads were obtained and assembled into 205138 unigenes with an average length of 620 bp and N50 of 964 bp. Of these, 1019 DEGs (differentially expressed genes) were found in the comparison of 0 vs. 5 psu, 1194 DEGs in 0 vs. 15 psu and 1180 DEGs in 5 vs. 15 psu, which are mainly related to macromolecule metabolic process, ion transport, oxidoreductase activity and generation of precursor metabolites and energy by GO (Gene Ontology) enrichment analyses. T. s. elegans can adapt itself into salinity by balancing the entry of sodium and chloride ions via the up-regulation expression genes of ion transport (potassium voltage-gated channel subfamily H member 5, KCNH5; erine/threonine-protein kinase 32, STK32; salt-inducible kinase 1, SIK1; adiponectin, ACDC), and by accumulating plasma urea and free amino acid via the up-regulation expression genes of amino acid metabolism (ornithine decarboxylase antizyme 3, OAZ3; glutamine synthetase, GLUL; asparaginase-like protein 1b, ASRGL; L-amino-acid oxidase-like, LAAO; sodium-dependent neutral amino acid transporter B, SLC6A15s; amino acid permease, SLC7A9) in response to osmotic regulation. An investment of energy to maintain their homeostatic balance is required to salinity adaptation, therefore, the genes related to energy production and conversion (F-ATPase protein 6, ATP6; cytochrome c oxidase subunit I,…
bibliographic citation: Hong et al. (2019) Comparative analysis of the liver transcriptome in the red-eared slider Trachemys scripta elegans under chronic salinity stress. PeerJ 7:e6538 https://doi.org/10.7717/peerj.6538
date submitted: 2018-09-21
date accepted: 2019-01-29
issued: 2019-03-21
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Hong
  given name: Meiling
author list: Agent
  family name: Jiang
  given name: Aiping
author list: Agent
  family name: Li
  given name: Na
author list: Agent
  family name: Li
  given name: Weihao
author list: Agent
  family name: Shi
  given name: Haitao
author list: Agent
  family name: Storey
  given name: Kenneth B.
author list: Agent
  family name: Ding
  given name: Li
doi: 10.7717/peerj.6538
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-03-21
copyright: ©2019 Hong et al.
attribution name: Hong et al.

Association between herd management practices and antimicrobial resistance in Salmonella spp. from cull dairy cattle in Central California
type: item
type: AcademicArticle
description: Background In this study cull dairy cows from six California dairy herds were sampled seasonally over the course of a year. The objectives were to determine the prevalence of antimicrobial resistant (AMR) Salmonella spp. shed in cull cow feces, and the factors associated with fecal shedding of AMR and multidrug resistant (MDR) Salmonella. Methods Six dairy farms located in the San Joaquin Valley of California were identified and enrolled as a convenience sample. On each dairy, and once during each of the four seasons, 10 cull cows were randomly selected for fecal sampling on the day of their removal from the herd. In addition, study personnel completed a survey based on responses of the herd manager to questions related to the previous 4 month’s herd management and the specific cattle sampled. Fecal samples were submitted to the California Animal Health and Food Safety laboratory for Salmonella isolation. Antimicrobial resistance was evaluated using broth microdilution method and a gram-negative assay plate following Clinical Laboratory Standards Institute (CLSI) guidelines and breakpoint references. All statistical models were survey adjusted for number of animals on sampling day. Results A total of 62 Salmonella were isolated from 60 of the 239 fecal samples collected. For 12% (95% confidence interval (CI) [3–20]) of fecal samples a multidrug resistant Salmonella was isolated. The survey-weighted results for the two most common drug classes for which isolates were resistant were tetracycline (39%; 95% CI [27–51]) and ampicillin (18%; 95% CI [9–27]). An important finding was the identification of cephalosporin as the third most common drug class for which isolates were resistant, with ceftriaxone (10%; 95% CI [2–17]) being the most common drug associated with resistance in that class. At the cow-level, reason for culling, prior treatment with antimicrobial drugs as the reason for culling was associated with higher odds of isolating an AMR Salmonella isolate. At the…
format: application/pdf
format: text/html
creator: Richard Pereira
creator: Deniece R. Williams
creator: Paul Rossitto
creator: John Adaska
creator: Emmanuel Okello
creator: John Champagne
creator: Terry W. Lehenbauer
creator: Xunde Li
creator: Jennifer Chase
creator: Tran Nguyen
creator: Alda F. A. Pires
creator: Edward R. Atwill
creator: Sharif S. Aly
subject: Microbiology
subject: Veterinary Medicine
subject: Epidemiology
description: doi:10.7717/peerj.6546
publisher: PeerJ Inc.
rights: © 2019 Pereira et al.
abstract: Background In this study cull dairy cows from six California dairy herds were sampled seasonally over the course of a year. The objectives were to determine the prevalence of antimicrobial resistant (AMR) Salmonella spp. shed in cull cow feces, and the factors associated with fecal shedding of AMR and multidrug resistant (MDR) Salmonella. Methods Six dairy farms located in the San Joaquin Valley of California were identified and enrolled as a convenience sample. On each dairy, and once during each of the four seasons, 10 cull cows were randomly selected for fecal sampling on the day of their removal from the herd. In addition, study personnel completed a survey based on responses of the herd manager to questions related to the previous 4 month’s herd management and the specific cattle sampled. Fecal samples were submitted to the California Animal Health and Food Safety laboratory for Salmonella isolation. Antimicrobial resistance was evaluated using broth microdilution method and a gram-negative assay plate following Clinical Laboratory Standards Institute (CLSI) guidelines and breakpoint references. All statistical models were survey adjusted for number of animals on sampling day. Results A total of 62 Salmonella were isolated from 60 of the 239 fecal samples collected. For 12% (95% confidence interval (CI) [3–20]) of fecal samples a multidrug resistant Salmonella was isolated. The survey-weighted results for the two most common drug classes for which isolates were resistant were tetracycline (39%; 95% CI [27–51]) and ampicillin (18%; 95% CI [9–27]). An important finding was the identification of cephalosporin as the third most common drug class for which isolates were resistant, with ceftriaxone (10%; 95% CI [2–17]) being the most common drug associated with resistance in that class. At the cow-level, reason for culling, prior treatment with antimicrobial drugs as the reason for culling was associated with higher odds of isolating an AMR Salmonella isolate. At the…
bibliographic citation: Pereira et al. (2019) Association between herd management practices and antimicrobial resistance in Salmonella spp. from cull dairy cattle in Central California. PeerJ 7:e6546 https://doi.org/10.7717/peerj.6546
date submitted: 2018-06-19
date accepted: 2019-01-30
issued: 2019-03-21
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Pereira
  given name: Richard
author list: Agent
  family name: Williams
  given name: Deniece R.
author list: Agent
  family name: Rossitto
  given name: Paul
author list: Agent
  family name: Adaska
  given name: John
author list: Agent
  family name: Okello
  given name: Emmanuel
author list: Agent
  family name: Champagne
  given name: John
author list: Agent
  family name: Lehenbauer
  given name: Terry W.
author list: Agent
  family name: Li
  given name: Xunde
author list: Agent
  family name: Chase
  given name: Jennifer
author list: Agent
  family name: Nguyen
  given name: Tran
author list: Agent
  family name: Pires
  given name: Alda F. A.
author list: Agent
  family name: Atwill
  given name: Edward R.
author list: Agent
  family name: Aly
  given name: Sharif S.
doi: 10.7717/peerj.6546
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-03-21
copyright: © 2019 Pereira et al.
attribution name: Pereira et al.

Sea stars of the genus Henricia Gray, 1840 (Echinodermata, Asteroidea) from Vostok Bay, Sea of Japan
type: item
type: AcademicArticle
description: We report seven species of the genus Henricia Gray, 1840 that were found in Vostok Bay, and two species from adjacent area, known from museum collection or seen in underwater footage. while existing literature reported no confirmed species from this area. Most of these species: H. djakonovi, H. alexeyi, H. densispina, H. hayashii, H. granulifera, H. pacifica, H. asiatica, and H. oculata robusta were reported from the Sea of Japan previously. H. nipponica, known from Japan, is reported from Russian seas for the first time. All studied taxa are re-described here using a range of morphological characters and partial 16S rRNA nucleotide sequences, life colorations of several species are reported for the first time, and an identification key is provided. Lectotype designations are fixed for studied series of species described by AM Djakonov.
format: application/pdf
format: text/html
creator: Anton Chichvarkhin
creator: Olga Chichvarkhina
creator: Daiki Wakita
subject: Biodiversity
subject: Marine Biology
subject: Zoology
description: doi:10.7717/peerj.6585
publisher: PeerJ Inc.
rights: © 2019 Chichvarkhin et al.
abstract: We report seven species of the genus Henricia Gray, 1840 that were found in Vostok Bay, and two species from adjacent area, known from museum collection or seen in underwater footage. while existing literature reported no confirmed species from this area. Most of these species: H. djakonovi, H. alexeyi, H. densispina, H. hayashii, H. granulifera, H. pacifica, H. asiatica, and H. oculata robusta were reported from the Sea of Japan previously. H. nipponica, known from Japan, is reported from Russian seas for the first time. All studied taxa are re-described here using a range of morphological characters and partial 16S rRNA nucleotide sequences, life colorations of several species are reported for the first time, and an identification key is provided. Lectotype designations are fixed for studied series of species described by AM Djakonov.
bibliographic citation: Chichvarkhin et al. (2019) Sea stars of the genus Henricia Gray, 1840 (Echinodermata, Asteroidea) from Vostok Bay, Sea of Japan. PeerJ 7:e6585 https://doi.org/10.7717/peerj.6585
date submitted: 2018-03-06
date accepted: 2019-02-08
issued: 2019-03-21
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Chichvarkhin
  given name: Anton
author list: Agent
  family name: Chichvarkhina
  given name: Olga
author list: Agent
  family name: Wakita
  given name: Daiki
doi: 10.7717/peerj.6585
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-03-21
copyright: ©2019 Chichvarkhin et al.
attribution name: Chichvarkhin et al.

Spatial near future modeling of land use and land cover changes in the temperate forests of Mexico
type: item
type: AcademicArticle
description: The loss of temperate forests of Mexico has continued in recent decades despite wide recognition of their importance to maintaining biodiversity. This study analyzes land use/land cover change scenarios, using satellite images from the Landsat sensor. Images corresponded to the years 1990, 2005 and 2017. The scenarios were applied for the temperate forests with the aim of getting a better understanding of the patterns in land use/land cover changes. The Support Vector Machine (SVM) multispectral classification technique served to determine the land use/land cover types, which were validated through the Kappa Index. For the simulation of land use/land cover dynamics, a model developed in Dinamica-EGO was used, which uses stochastic models of Markov Chains, Cellular Automata and Weight of Evidences. For the study, a stationary, an optimistic and a pessimistic scenario were proposed. The projections based on the three scenarios were simulated for the year 2050. Five types of land use/land cover were identified and evaluated. They were primary forest, secondary forest, human settlements, areas without vegetation and water bodies. Results from the land use/land cover change analysis show a substantial gain for the secondary forest. The surface area of the primary forest was reduced from 55.8% in 1990 to 37.7% in 2017. Moreover, the three projected scenarios estimate further losses of the surface are for the primary forest, especially under the stationary and pessimistic scenarios. This highlights the importance and probably urgent implementation of conservation and protection measures to preserve these ecosystems and their services. Based on the accuracy obtained and on the models generated, results from these methodologies can serve as a decision tool to contribute to the sustainable management of the natural resources of a region.
format: application/pdf
format: text/html
creator: Jesús A. Prieto-Amparán
creator: Federico Villarreal-Guerrero
creator: Martin Martínez-Salvador
creator: Carlos Manjarrez-Domínguez
creator: Griselda Vázquez-Quintero
creator: Alfredo Pinedo-Alvarez
subject: Ecology
subject: Natural Resource Management
subject: Forestry
subject: Spatial and Geographic Information Science
description: doi:10.7717/peerj.6617
publisher: PeerJ Inc.
rights: © 2019 Prieto-Amparán et al.
abstract: The loss of temperate forests of Mexico has continued in recent decades despite wide recognition of their importance to maintaining biodiversity. This study analyzes land use/land cover change scenarios, using satellite images from the Landsat sensor. Images corresponded to the years 1990, 2005 and 2017. The scenarios were applied for the temperate forests with the aim of getting a better understanding of the patterns in land use/land cover changes. The Support Vector Machine (SVM) multispectral classification technique served to determine the land use/land cover types, which were validated through the Kappa Index. For the simulation of land use/land cover dynamics, a model developed in Dinamica-EGO was used, which uses stochastic models of Markov Chains, Cellular Automata and Weight of Evidences. For the study, a stationary, an optimistic and a pessimistic scenario were proposed. The projections based on the three scenarios were simulated for the year 2050. Five types of land use/land cover were identified and evaluated. They were primary forest, secondary forest, human settlements, areas without vegetation and water bodies. Results from the land use/land cover change analysis show a substantial gain for the secondary forest. The surface area of the primary forest was reduced from 55.8% in 1990 to 37.7% in 2017. Moreover, the three projected scenarios estimate further losses of the surface are for the primary forest, especially under the stationary and pessimistic scenarios. This highlights the importance and probably urgent implementation of conservation and protection measures to preserve these ecosystems and their services. Based on the accuracy obtained and on the models generated, results from these methodologies can serve as a decision tool to contribute to the sustainable management of the natural resources of a region.
bibliographic citation: Prieto-Amparán et al. (2019) Spatial near future modeling of land use and land cover changes in the temperate forests of Mexico. PeerJ 7:e6617 https://doi.org/10.7717/peerj.6617
date submitted: 2018-09-28
date accepted: 2019-02-11
issued: 2019-03-21
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Prieto-Amparán
  given name: Jesús A.
author list: Agent
  family name: Villarreal-Guerrero
  given name: Federico
author list: Agent
  family name: Martínez-Salvador
  given name: Martin
author list: Agent
  family name: Manjarrez-Domínguez
  given name: Carlos
author list: Agent
  family name: Vázquez-Quintero
  given name: Griselda
author list: Agent
  family name: Pinedo-Alvarez
  given name: Alfredo
doi: 10.7717/peerj.6617
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-03-21
copyright: ©2019 Prieto-Amparán et al.
attribution name: Prieto-Amparán et al.

Improvement of hydrogen production from Chlorella sp. biomass by acid-thermal pretreatment
type: item
type: AcademicArticle
description: Background Owing to the high growth rate, high protein and carbohydrate contents, and an ability to grow autotrophically, microalgal biomass is regarded as a promising feedstock for fermentative hydrogen production. However, the rigid cell wall of microalgae impedes efficient hydrolysis of the biomass, resulting in low availability of assimilable nutrients and, consequently, low hydrogen production. Therefore, pretreatment of the biomass is necessary in order to achieve higher hydrogen yield (HY). In the present study, acid-thermal pretreatment of Chlorella sp. biomass was investigated. Conditions for the pretreatment, as well as those for hydrogen production from the pretreated biomass, were optimized. Acid pretreatment was also conducted for comparison. Results Under optimum conditions (0.75% (v/v) H2SO4, 160 °C, 30 min, and 40 g-biomass/L), acid-thermal pretreatment yielded 151.8 mg-reducing-sugar/g-biomass. This was around 15 times that obtained from the acid pretreatment under optimum conditions (4% (v/v) H2SO4, 150 min, and 40 g-biomass/L). Fermentation of the acid-thermal pretreated biomass gave 1,079 mL-H2/L, with a HY of 54.0 mL-H2/g-volatile-solids (VS), while only 394 mL/L and 26.3 mL-H2/g-VS were obtained from the acid-pretreated biomass. Conclusions Acid-thermal pretreatment was effective in solubilizing the biomass of Chlorella sp. Heat exerted synergistic effect with acid to release nutrients from the biomass. Satisfactory HY obtained with the acid-thermal pretreated biomass demonstrates that this pretreatment method was effective, and that it should be implemented to achieve high HY.
format: application/pdf
format: text/html
creator: Tran T. Giang
creator: Siriporn Lunprom
creator: Qiang Liao
creator: Alissara Reungsang
creator: Apilak Salakkam
subject: Biotechnology
subject: Natural Resource Management
description: doi:10.7717/peerj.6637
publisher: PeerJ Inc.
rights: © 2019 Giang et al.
abstract: Background Owing to the high growth rate, high protein and carbohydrate contents, and an ability to grow autotrophically, microalgal biomass is regarded as a promising feedstock for fermentative hydrogen production. However, the rigid cell wall of microalgae impedes efficient hydrolysis of the biomass, resulting in low availability of assimilable nutrients and, consequently, low hydrogen production. Therefore, pretreatment of the biomass is necessary in order to achieve higher hydrogen yield (HY). In the present study, acid-thermal pretreatment of Chlorella sp. biomass was investigated. Conditions for the pretreatment, as well as those for hydrogen production from the pretreated biomass, were optimized. Acid pretreatment was also conducted for comparison. Results Under optimum conditions (0.75% (v/v) H2SO4, 160 °C, 30 min, and 40 g-biomass/L), acid-thermal pretreatment yielded 151.8 mg-reducing-sugar/g-biomass. This was around 15 times that obtained from the acid pretreatment under optimum conditions (4% (v/v) H2SO4, 150 min, and 40 g-biomass/L). Fermentation of the acid-thermal pretreated biomass gave 1,079 mL-H2/L, with a HY of 54.0 mL-H2/g-volatile-solids (VS), while only 394 mL/L and 26.3 mL-H2/g-VS were obtained from the acid-pretreated biomass. Conclusions Acid-thermal pretreatment was effective in solubilizing the biomass of Chlorella sp. Heat exerted synergistic effect with acid to release nutrients from the biomass. Satisfactory HY obtained with the acid-thermal pretreated biomass demonstrates that this pretreatment method was effective, and that it should be implemented to achieve high HY.
bibliographic citation: Giang et al. (2019) Improvement of hydrogen production from Chlorella sp. biomass by acid-thermal pretreatment. PeerJ 7:e6637 https://doi.org/10.7717/peerj.6637
date submitted: 2018-10-24
date accepted: 2019-02-18
issued: 2019-03-21
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Giang
  given name: Tran T.
author list: Agent
  family name: Lunprom
  given name: Siriporn
author list: Agent
  family name: Liao
  given name: Qiang
author list: Agent
  family name: Reungsang
  given name: Alissara
author list: Agent
  family name: Salakkam
  given name: Apilak
doi: 10.7717/peerj.6637
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-03-21
copyright: ©2019 Giang et al.
attribution name: Giang et al.

The chemical composition of a new “mica sandwich” foraminiferal species from the East Coast of Korea: Capsammina crassa sp. nov.
type: item
type: AcademicArticle
description: We describe a new agglutinated monothalamous foraminiferal species, Capsammina crassa sp. nov., based on integrated observations of the test morphology and the chemical characteristics of materials composing the test. The new species was found at a depth of <60 m on the East coast of Korea. The test morphology is typical of the genus Capsammina, comprising two or more mica plates with a ring of finely agglutinated mineral grains sandwiched between them and surrounding the cell body. There is no distinct test aperture. Elemental analyses of the agglutinated grains revealed 15 different types of mineral grains of which quartz is the most abundant. The surface areas of grains exposed on fractured surfaces ranged from 1.6 to 7,700 μm2 and the large plate-like grains forming the upper and lower surfaces measured about 420–2,350 μm in maximum width. The new species is morphologically similar to C. patelliformis, however, the differences in size, distribution area and depth support that these two species are distinct. This discovery is the first record of the genus Capsammina from the North Pacific. Therefore, it extends the biodiversity and geographical distribution of the genus Capsammina, which has been reported only from the bathyal NE Atlantic. Our finding also suggests the possibility of additional discovery of monothalamous foraminifera from around Korea.
format: application/pdf
format: text/html
creator: Somin Lee
creator: Eric Armynot du Châtelet
creator: Andrew J. Gooday
creator: François Guillot
creator: Philippe Recourt
creator: Fabrizio Frontalini
creator: Wonchoel Lee
subject: Conservation Biology
subject: Taxonomy
description: doi:10.7717/peerj.6642
publisher: PeerJ Inc.
rights: © 2019 Lee et al.
abstract: We describe a new agglutinated monothalamous foraminiferal species, Capsammina crassa sp. nov., based on integrated observations of the test morphology and the chemical characteristics of materials composing the test. The new species was found at a depth of <60 m on the East coast of Korea. The test morphology is typical of the genus Capsammina, comprising two or more mica plates with a ring of finely agglutinated mineral grains sandwiched between them and surrounding the cell body. There is no distinct test aperture. Elemental analyses of the agglutinated grains revealed 15 different types of mineral grains of which quartz is the most abundant. The surface areas of grains exposed on fractured surfaces ranged from 1.6 to 7,700 μm2 and the large plate-like grains forming the upper and lower surfaces measured about 420–2,350 μm in maximum width. The new species is morphologically similar to C. patelliformis, however, the differences in size, distribution area and depth support that these two species are distinct. This discovery is the first record of the genus Capsammina from the North Pacific. Therefore, it extends the biodiversity and geographical distribution of the genus Capsammina, which has been reported only from the bathyal NE Atlantic. Our finding also suggests the possibility of additional discovery of monothalamous foraminifera from around Korea.
bibliographic citation: Lee et al. (2019) The chemical composition of a new “mica sandwich” foraminiferal species from the East Coast of Korea: Capsammina crassa sp. nov.. PeerJ 7:e6642 https://doi.org/10.7717/peerj.6642
date submitted: 2019-01-14
date accepted: 2019-02-19
issued: 2019-03-21
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Lee
  given name: Somin
author list: Agent
  family name: Armynot du Châtelet
  given name: Eric
author list: Agent
  family name: Gooday
  given name: Andrew J.
author list: Agent
  family name: Guillot
  given name: François
author list: Agent
  family name: Recourt
  given name: Philippe
author list: Agent
  family name: Frontalini
  given name: Fabrizio
author list: Agent
  family name: Lee
  given name: Wonchoel
doi: 10.7717/peerj.6642
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-03-21
copyright: © 2019 Lee et al.
attribution name: Lee et al.

Dose-dependent and strain-dependent anti-obesity effects of Lactobacillus sakei in a diet induced obese murine model
type: item
type: AcademicArticle
description: Background Overweight and abdominal obesity, in addition to medical conditions such as high blood pressure, high blood sugar and triglyceride levels, are typical risk factors associated with metabolic syndrome. Yet, considering the complexity of factors and underlying mechanisms leading to these inflammatory conditions, a deeper understanding of this area is still lacking. Some probiotics have a reputation of a relatively-long history of safe use, and an increasing number of studies are confirming benefits including anti-obesity effects when administered in adequate amounts. Recent reports demonstrate that probiotic functions may widely differ with reference to either intra-species or inter-species related data. Such differences do not necessarily reflect or explain strain-specific functions of a probiotic, and thus require further assessment at the intra-species level. Various anti-obesity clinical trials with probiotics have shown discrepant results and require additional consolidated studies in order to clarify the correct dose of application for reliable and constant efficacy over a long period. Methods Three different strains of Lactobacillus sakei were administered in a high-fat diet induced obese murine model using three different doses, 1 × 1010, 1 × 109 and 1 × 108 CFUs, respectively, per day. Changes in body and organ weight were monitored, and serum chemistry analysis was performed for monitoring obesity associated biomarkers. Results Only one strain of L. sakei (CJLS03) induced a dose-dependent anti-obesity effect, while no correlation with either dose or body or adipose tissue weight loss could be detected for the other two L. sakei strains (L338 and L446). The body weight reduction primarily correlated with adipose tissue and obesity-associated serum biomarkers such as triglycerides and aspartate transaminase. Discussion This study shows intraspecies diversity of L. sakei and suggests that anti-obesity effects of probiotics may vary in a strain- and do…
format: application/pdf
format: text/html
creator: Yosep Ji
creator: Young Mee Chung
creator: Soyoung Park
creator: Dahye Jeong
creator: Bongjoon Kim
creator: Wilhelm Heinrich Holzapfel
subject: Biotechnology
subject: Microbiology
description: doi:10.7717/peerj.6651
publisher: PeerJ Inc.
rights: © 2019 Ji et al.
abstract: Background Overweight and abdominal obesity, in addition to medical conditions such as high blood pressure, high blood sugar and triglyceride levels, are typical risk factors associated with metabolic syndrome. Yet, considering the complexity of factors and underlying mechanisms leading to these inflammatory conditions, a deeper understanding of this area is still lacking. Some probiotics have a reputation of a relatively-long history of safe use, and an increasing number of studies are confirming benefits including anti-obesity effects when administered in adequate amounts. Recent reports demonstrate that probiotic functions may widely differ with reference to either intra-species or inter-species related data. Such differences do not necessarily reflect or explain strain-specific functions of a probiotic, and thus require further assessment at the intra-species level. Various anti-obesity clinical trials with probiotics have shown discrepant results and require additional consolidated studies in order to clarify the correct dose of application for reliable and constant efficacy over a long period. Methods Three different strains of Lactobacillus sakei were administered in a high-fat diet induced obese murine model using three different doses, 1 × 1010, 1 × 109 and 1 × 108 CFUs, respectively, per day. Changes in body and organ weight were monitored, and serum chemistry analysis was performed for monitoring obesity associated biomarkers. Results Only one strain of L. sakei (CJLS03) induced a dose-dependent anti-obesity effect, while no correlation with either dose or body or adipose tissue weight loss could be detected for the other two L. sakei strains (L338 and L446). The body weight reduction primarily correlated with adipose tissue and obesity-associated serum biomarkers such as triglycerides and aspartate transaminase. Discussion This study shows intraspecies diversity of L. sakei and suggests that anti-obesity effects of probiotics may vary in a strain- and do…
bibliographic citation: Ji et al. (2019) Dose-dependent and strain-dependent anti-obesity effects of Lactobacillus sakei in a diet induced obese murine model. PeerJ 7:e6651 https://doi.org/10.7717/peerj.6651
date submitted: 2018-09-26
date accepted: 2019-02-20
issued: 2019-03-21
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Ji
  given name: Yosep
author list: Agent
  family name: Chung
  given name: Young Mee
author list: Agent
  family name: Park
  given name: Soyoung
author list: Agent
  family name: Jeong
  given name: Dahye
author list: Agent
  family name: Kim
  given name: Bongjoon
author list: Agent
  family name: Holzapfel
  given name: Wilhelm Heinrich
doi: 10.7717/peerj.6651
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-03-21
copyright: © 2019 Ji et al.
attribution name: Ji et al.

Maintenance of dominant populations in heavily grazed grassland: Inference from a Stipa breviflora seed germination experiment
type: item
type: AcademicArticle
description: An understanding of population adaptation and maintenance mechanisms under interference from large herbivores is lacking and is a major focus of ecological research. In the Eurasian steppe, which has been subjected to continuous interference from domesticated ungulates throughout history and shows increased grazing, it is particularly urgent to analyze the ecological adaptation strategies of widely distributed Stipa plants. In this study, Stipa breviflora in a group of desert steppes in the Mongolian Plateau was selected to study the potential mechanism underlying the maintenance of dominant populations under the continuous interference of heavy grazing from the new perspective of seed germination rate. Laboratory experimental results showed that the values of the phenotypic traits of S. breviflora seeds were lower under a heavy grazing treatment than under a non-grazing treatment, but the seed germination rate did not decrease. The awns of non-grazed seeds significantly affected the seed germination rate, while those of heavily grazed seeds did not. Field observations showed that grazing does not significantly affect the population density of S. breviflora at different growth stages except in extremely wet and dry years. Our study suggests that under heavy grazing, S. breviflora uses an “opportunistic” ecological strategy to ensure population maintenance by increasing the seed germination rate and reducing dispersal via changes in associated seed phenotypic traits.
format: application/pdf
format: text/html
creator: Wenting Liu
creator: Zhijun Wei
creator: Xiaoxia Yang
subject: Biodiversity
subject: Biogeography
subject: Ecology
description: doi:10.7717/peerj.6654
publisher: PeerJ Inc.
rights: © 2019 Liu et al.
abstract: An understanding of population adaptation and maintenance mechanisms under interference from large herbivores is lacking and is a major focus of ecological research. In the Eurasian steppe, which has been subjected to continuous interference from domesticated ungulates throughout history and shows increased grazing, it is particularly urgent to analyze the ecological adaptation strategies of widely distributed Stipa plants. In this study, Stipa breviflora in a group of desert steppes in the Mongolian Plateau was selected to study the potential mechanism underlying the maintenance of dominant populations under the continuous interference of heavy grazing from the new perspective of seed germination rate. Laboratory experimental results showed that the values of the phenotypic traits of S. breviflora seeds were lower under a heavy grazing treatment than under a non-grazing treatment, but the seed germination rate did not decrease. The awns of non-grazed seeds significantly affected the seed germination rate, while those of heavily grazed seeds did not. Field observations showed that grazing does not significantly affect the population density of S. breviflora at different growth stages except in extremely wet and dry years. Our study suggests that under heavy grazing, S. breviflora uses an “opportunistic” ecological strategy to ensure population maintenance by increasing the seed germination rate and reducing dispersal via changes in associated seed phenotypic traits.
bibliographic citation: Liu et al. (2019) Maintenance of dominant populations in heavily grazed grassland: Inference from a Stipa breviflora seed germination experiment. PeerJ 7:e6654 https://doi.org/10.7717/peerj.6654
date submitted: 2018-10-23
date accepted: 2019-02-21
issued: 2019-03-21
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Liu
  given name: Wenting
author list: Agent
  family name: Wei
  given name: Zhijun
author list: Agent
  family name: Yang
  given name: Xiaoxia
doi: 10.7717/peerj.6654
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-03-21
copyright: © 2019 Liu et al.
attribution name: Liu et al.

Minimum inhibitory concentration of nano-silver bactericides for beneficial microbes and its effect on Ralstonia solanacearum and seed germination of Japanese Cucumber (Cucumis sativus)
type: item
type: AcademicArticle
description: Background Plant growth-promoting rhizobacteria (PGPR) are highly promising biofertilizers that contribute to eco-friendly sustainable agriculture. There have been many reports on the anti-microbial properties of nanoparticles (NPs). Toxic effects of NPs under laboratory conditions have also reported; however, there is a lack of information about their uptake and mobility in organisms under environmental conditions. There is an urgent need to determine the highest concentration of NPs which is not detrimental for growth and proliferation of PGPR. Methods Transmission electron microscopy (TEM) and scanning electron microscopy (SEM) were used to measure the size and shape of NPs. Minimum inhibitory concentrations (MIC) of nano-silver on selected beneficial microbes and Ralstonia solanacearum were measured using the microdilution broth method. The percentage of seed germination was measured under in vitro conditions. Results NPs were spherical with a size of 16 ± 6 nm. Nano-silver at 12–40 mg l−1 inhibited the growth of bacteria. Seed application at 40 mg l−1 protected seeds from R. solanacearum and improved the rate of seed germination.
format: application/pdf
format: text/html
creator: Poopak Sotoodehnia
creator: Norida Mazlan
creator: Halimi Mohd Saud
creator: Wahid A. Samsuri
creator: Sheikh Hasna Habib
creator: Amin Soltangheisi
subject: Agricultural Science
subject: Biotechnology
subject: Microbiology
subject: Toxicology
subject: Ecotoxicology
description: doi:10.7717/peerj.6418
publisher: PeerJ Inc.
rights: © 2019 Sotoodehnia et al.
abstract: Background Plant growth-promoting rhizobacteria (PGPR) are highly promising biofertilizers that contribute to eco-friendly sustainable agriculture. There have been many reports on the anti-microbial properties of nanoparticles (NPs). Toxic effects of NPs under laboratory conditions have also reported; however, there is a lack of information about their uptake and mobility in organisms under environmental conditions. There is an urgent need to determine the highest concentration of NPs which is not detrimental for growth and proliferation of PGPR. Methods Transmission electron microscopy (TEM) and scanning electron microscopy (SEM) were used to measure the size and shape of NPs. Minimum inhibitory concentrations (MIC) of nano-silver on selected beneficial microbes and Ralstonia solanacearum were measured using the microdilution broth method. The percentage of seed germination was measured under in vitro conditions. Results NPs were spherical with a size of 16 ± 6 nm. Nano-silver at 12–40 mg l−1 inhibited the growth of bacteria. Seed application at 40 mg l−1 protected seeds from R. solanacearum and improved the rate of seed germination.
bibliographic citation: Sotoodehnia et al. (2019) Minimum inhibitory concentration of nano-silver bactericides for beneficial microbes and its effect on Ralstonia solanacearum and seed germination of Japanese Cucumber (Cucumis sativus). PeerJ 7:e6418 https://doi.org/10.7717/peerj.6418
date submitted: 2018-10-02
date accepted: 2019-01-01
issued: 2019-03-20
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Sotoodehnia
  given name: Poopak
author list: Agent
  family name: Mazlan
  given name: Norida
author list: Agent
  family name: Mohd Saud
  given name: Halimi
author list: Agent
  family name: Samsuri
  given name: Wahid A.
author list: Agent
  family name: Habib
  given name: Sheikh Hasna
author list: Agent
  family name: Soltangheisi
  given name: Amin
doi: 10.7717/peerj.6418
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-03-20
copyright: ©2019 Sotoodehnia et al.
attribution name: Sotoodehnia et al.

Identification of an eight-gene signature for survival prediction for patients with hepatocellular carcinoma based on integrated bioinformatics analysis
type: item
type: AcademicArticle
description: Background Hepatocellular carcinoma (HCC) remains one of the leading causes of cancer-related death worldwide. Despite recent advances in imaging techniques and therapeutic intervention for HCC, the low overall 5-year survival rate of HCC patients remains unsatisfactory. This study aims to find a gene signature to predict clinical outcomes in HCC. Methods Bioinformatics analysis including Cox’s regression analysis, Kaplan-Meier (KM) and receiver operating characteristic curve (ROC) analysis and the random survival forest algorithm were performed to mine the expression profiles of 553 hepatocellular carcinoma (HCC) patients from The Cancer Genome Atlas (TCGA) and Gene Expression Omnibus (GEO) public database. Results We selected a signature comprising eight protein-coding genes (DCAF13, FAM163A, GPR18, LRP10, PVRIG, S100A9, SGCB, and TNNI3K) in the training dataset (AUC = 0.77 at five years, n = 332). The signature stratified patients into high- and low-risk groups with significantly different survival in the training dataset (median 2.20 vs. 8.93 years, log-rank test P < 0.001) and in the test dataset (median 2.68 vs. 4.24 years, log-rank test P = 0.004, n = 221, GSE14520). Further multivariate Cox regression analysis showed that the signature was an independent prognostic factor for patients with HCC. Compared with TNM stage and another reported three-gene model, the signature displayed improved survival prediction power in entire dataset (AUC signature = 0.66 vs. AUC TNM = 0.64 vs. AUC gene model = 0.60, n = 553). Stratification analysis shows that it can be used as an auxiliary marker for many traditional staging models. Conclusions We constructed an eight-gene signature that can be a novel prognostic marker to predict the survival of HCC patients.
format: application/pdf
format: text/html
creator: Guo-jie Qiao
creator: Liang Chen
creator: Jin-cai Wu
creator: Zhou-ri Li
subject: Gastroenterology and Hepatology
subject: Oncology
subject: Data Mining and Machine Learning
description: doi:10.7717/peerj.6548
publisher: PeerJ Inc.
rights: © 2019 Qiao et al.
abstract: Background Hepatocellular carcinoma (HCC) remains one of the leading causes of cancer-related death worldwide. Despite recent advances in imaging techniques and therapeutic intervention for HCC, the low overall 5-year survival rate of HCC patients remains unsatisfactory. This study aims to find a gene signature to predict clinical outcomes in HCC. Methods Bioinformatics analysis including Cox’s regression analysis, Kaplan-Meier (KM) and receiver operating characteristic curve (ROC) analysis and the random survival forest algorithm were performed to mine the expression profiles of 553 hepatocellular carcinoma (HCC) patients from The Cancer Genome Atlas (TCGA) and Gene Expression Omnibus (GEO) public database. Results We selected a signature comprising eight protein-coding genes (DCAF13, FAM163A, GPR18, LRP10, PVRIG, S100A9, SGCB, and TNNI3K) in the training dataset (AUC = 0.77 at five years, n = 332). The signature stratified patients into high- and low-risk groups with significantly different survival in the training dataset (median 2.20 vs. 8.93 years, log-rank test P < 0.001) and in the test dataset (median 2.68 vs. 4.24 years, log-rank test P = 0.004, n = 221, GSE14520). Further multivariate Cox regression analysis showed that the signature was an independent prognostic factor for patients with HCC. Compared with TNM stage and another reported three-gene model, the signature displayed improved survival prediction power in entire dataset (AUC signature = 0.66 vs. AUC TNM = 0.64 vs. AUC gene model = 0.60, n = 553). Stratification analysis shows that it can be used as an auxiliary marker for many traditional staging models. Conclusions We constructed an eight-gene signature that can be a novel prognostic marker to predict the survival of HCC patients.
bibliographic citation: Qiao et al. (2019) Identification of an eight-gene signature for survival prediction for patients with hepatocellular carcinoma based on integrated bioinformatics analysis. PeerJ 7:e6548 https://doi.org/10.7717/peerj.6548
date submitted: 2018-11-09
date accepted: 2019-01-25
issued: 2019-03-20
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Qiao
  given name: Guo-jie
author list: Agent
  family name: Chen
  given name: Liang
author list: Agent
  family name: Wu
  given name: Jin-cai
author list: Agent
  family name: Li
  given name: Zhou-ri
doi: 10.7717/peerj.6548
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-03-20
copyright: ©2019 Qiao et al.
attribution name: Qiao et al.

Effects of handling and short-term captivity: a multi-behaviour approach using red sea urchins, Mesocentrotus franciscanus
type: item
type: AcademicArticle
description: Understanding the effects of captivity-induced stress on wild-caught animals after their release back into the wild is critical for the long-term success of relocation and reintroduction programs. To date, most of the research on captivity stress has focused on vertebrates, with far less attention paid to invertebrates. Here, we examine the effect of short-term captivity (i.e., up to four days) on self-righting, aggregation, and predator-escape behaviours in wild-caught red sea urchins, Mesocentrotus franciscanus, after their release back into the wild. Aggregation behaviour, which has been linked to feeding in sea urchins, was not affected by handling or captivity. In contrast, the sea urchins that had been handled and released immediately, as well as those that were handled and held captive, took longer to right themselves and were poorer at fleeing from predators than wild, unhandled sea urchins. These results indicate that handling rather than captivity impaired these behaviours in the short term. The duration of captivity did not influence the sea urchin behaviours examined. Longer-term monitoring is needed to establish what the fitness consequences of these short-term behavioural changes might be. Our study nevertheless highlights the importance of considering a suite of responses when examining the effects of capture and captivity. Our findings, which are based on a locally abundant species, can inform translocation efforts aimed at bolstering populations of ecologically similar but depleted invertebrate species to retain or restore important ecosystem functions.
format: application/pdf
format: text/html
creator: Aneesh P.H. Bose
creator: Daniel Zayonc
creator: Nikolaos Avrantinis
creator: Natasha Ficzycz
creator: Jonathan Fischer-Rush
creator: Fiona T. Francis
creator: Siobhan Gray
creator: Faye Manning
creator: Haley Robb
creator: Coralee Schmidt
creator: Christine Spice
creator: Aari Umedaly
creator: Jeff Warden
creator: Isabelle M. Côté
subject: Animal Behavior
subject: Marine Biology
description: doi:10.7717/peerj.6556
publisher: PeerJ Inc.
rights: © 2019 Bose et al.
abstract: Understanding the effects of captivity-induced stress on wild-caught animals after their release back into the wild is critical for the long-term success of relocation and reintroduction programs. To date, most of the research on captivity stress has focused on vertebrates, with far less attention paid to invertebrates. Here, we examine the effect of short-term captivity (i.e., up to four days) on self-righting, aggregation, and predator-escape behaviours in wild-caught red sea urchins, Mesocentrotus franciscanus, after their release back into the wild. Aggregation behaviour, which has been linked to feeding in sea urchins, was not affected by handling or captivity. In contrast, the sea urchins that had been handled and released immediately, as well as those that were handled and held captive, took longer to right themselves and were poorer at fleeing from predators than wild, unhandled sea urchins. These results indicate that handling rather than captivity impaired these behaviours in the short term. The duration of captivity did not influence the sea urchin behaviours examined. Longer-term monitoring is needed to establish what the fitness consequences of these short-term behavioural changes might be. Our study nevertheless highlights the importance of considering a suite of responses when examining the effects of capture and captivity. Our findings, which are based on a locally abundant species, can inform translocation efforts aimed at bolstering populations of ecologically similar but depleted invertebrate species to retain or restore important ecosystem functions.
bibliographic citation: Bose et al. (2019) Effects of handling and short-term captivity: a multi-behaviour approach using red sea urchins, Mesocentrotus franciscanus. PeerJ 7:e6556 https://doi.org/10.7717/peerj.6556
date submitted: 2018-11-09
date accepted: 2019-02-02
issued: 2019-03-20
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Bose
  given name: Aneesh P.H.
author list: Agent
  family name: Zayonc
  given name: Daniel
author list: Agent
  family name: Avrantinis
  given name: Nikolaos
author list: Agent
  family name: Ficzycz
  given name: Natasha
author list: Agent
  family name: Fischer-Rush
  given name: Jonathan
author list: Agent
  family name: Francis
  given name: Fiona T.
author list: Agent
  family name: Gray
  given name: Siobhan
author list: Agent
  family name: Manning
  given name: Faye
author list: Agent
  family name: Robb
  given name: Haley
author list: Agent
  family name: Schmidt
  given name: Coralee
author list: Agent
  family name: Spice
  given name: Christine
author list: Agent
  family name: Umedaly
  given name: Aari
author list: Agent
  family name: Warden
  given name: Jeff
author list: Agent
  family name: Côté
  given name: Isabelle M.
doi: 10.7717/peerj.6556
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-03-20
copyright: ©2019 Bose et al.
attribution name: Bose et al.

High virulence gene diversity in Streptococcus pyogenes isolated in Central Italy
type: item
type: AcademicArticle
description: Globally, Streptococcus pyogenes poses a continuous burden on human health, causing both self-limiting and life-threatening diseases. Therefore, studying the profile of virulence genes and their combinations is essential to monitor the epidemiology and pathogenic potential of this important species. Thus, the aim of this study was to analyze related genetic features of clinical strains collected in Italy in 2012 in order to obtain a valid picture of their virulence profile that could be compared to similar studies made in other countries approximately in the same period. We conducted emm typing and fibronectin-collagen-T antigen (FCT) region typing in 122 Streptococcus pyogenes strains. Furthermore, several additional virulence genes were screened by polymerase chain reaction. We found correlations between emm types and FCT region profiles. emm1 strains were mainly associated with FCT2 and FCT6, while emm89 and emm12 strains were associated with FCT4. FCT5 was mainly represented in emm4, emm6, and emm75 strains. Significantly, we defined subtypes for each FCT type based on the differences in single and double loci compared to the reference scheme used for the classification of the FCT region. In addition, new FCT-region variants with differences in multiple loci were also recorded. Cluster analysis based on virulence gene profiling showed a non-random distribution within each emm type. This study added new data to existing studies conducted worldwide and revealed new variability scores in circulating Streptococcus pyogenes strains and new assortments in well-established virulence gene signatures.
format: application/pdf
format: text/html
creator: Daniela Bencardino
creator: Maria Chiara Di Luca
creator: Dezemona Petrelli
creator: Manuela Prenna
creator: Luca Agostino Vitali
subject: Microbiology
subject: Infectious Diseases
description: doi:10.7717/peerj.6613
publisher: PeerJ Inc.
rights: © 2019 Bencardino et al.
abstract: Globally, Streptococcus pyogenes poses a continuous burden on human health, causing both self-limiting and life-threatening diseases. Therefore, studying the profile of virulence genes and their combinations is essential to monitor the epidemiology and pathogenic potential of this important species. Thus, the aim of this study was to analyze related genetic features of clinical strains collected in Italy in 2012 in order to obtain a valid picture of their virulence profile that could be compared to similar studies made in other countries approximately in the same period. We conducted emm typing and fibronectin-collagen-T antigen (FCT) region typing in 122 Streptococcus pyogenes strains. Furthermore, several additional virulence genes were screened by polymerase chain reaction. We found correlations between emm types and FCT region profiles. emm1 strains were mainly associated with FCT2 and FCT6, while emm89 and emm12 strains were associated with FCT4. FCT5 was mainly represented in emm4, emm6, and emm75 strains. Significantly, we defined subtypes for each FCT type based on the differences in single and double loci compared to the reference scheme used for the classification of the FCT region. In addition, new FCT-region variants with differences in multiple loci were also recorded. Cluster analysis based on virulence gene profiling showed a non-random distribution within each emm type. This study added new data to existing studies conducted worldwide and revealed new variability scores in circulating Streptococcus pyogenes strains and new assortments in well-established virulence gene signatures.
bibliographic citation: Bencardino et al. (2019) High virulence gene diversity in Streptococcus pyogenes isolated in Central Italy. PeerJ 7:e6613 https://doi.org/10.7717/peerj.6613
date submitted: 2018-07-19
date accepted: 2019-02-13
issued: 2019-03-20
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Bencardino
  given name: Daniela
author list: Agent
  family name: Di Luca
  given name: Maria Chiara
author list: Agent
  family name: Petrelli
  given name: Dezemona
author list: Agent
  family name: Prenna
  given name: Manuela
author list: Agent
  family name: Vitali
  given name: Luca Agostino
doi: 10.7717/peerj.6613
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-03-20
copyright: © 2019 Bencardino et al.
attribution name: Bencardino et al.

Evolution of host plant use and diversification in a species complex of parasitic weevils (Coleoptera: Curculionidae)
type: item
type: AcademicArticle
description: Weevils (Coleoptera: Curculionoidea) represent one of the most diverse groups of organisms on Earth; interactions with their host plants have been recognized to play a central role in their remarkable diversity, yet the exact mechanisms and factors still remain poorly understood. Using phylogenetic comparative analyses, here we investigate the evolution of host use and its possible role in diversification processes of Rhinusa and Gymnetron, two closely related groups of weevils that feed and develop inside plant tissues of hosts within the families Scrophulariaceae and Plantaginaceae. We found strong evidence for phylogenetic conservatism of host use at the plant family level, most likely due to substantial differences in the chemical composition of hosts, reducing the probability of shifts between host families. In contrast, the use of different plant organs represents a more labile ecological trait and ecological niche expansion that allows a finer partitioning of resources. Rhinusa and Gymnetron weevils initially specialized on plants within Scrophulariaceae and then shifted to the closely related Plantaginaceae; likewise, a gall inducing behavior evolved from non-galler weevils, possibly in response to resource competition, as galls facilitate larval development by providing enhanced nutrition and a favorable microhabitat. Results from trait-dependent diversification analyses suggest that both use of hosts within Plantaginaceae and parasitism on fruits and seed capsules are associated with enhanced diversification of Rhinusa and Gymnetron via low extinction rates. Our study provides quantitative evidence and insights on the ecological factors that can promote diversification in phytophagous insects that feed and develop inside plant tissues.
format: application/pdf
format: text/html
creator: Gerardo Hernández-Vera
creator: Ivo Toševski
creator: Roberto Caldara
creator: Brent C. Emerson
subject: Biodiversity
subject: Ecology
subject: Entomology
subject: Evolutionary Studies
description: doi:10.7717/peerj.6625
publisher: PeerJ Inc.
rights: © 2019 Hernández-Vera et al.
abstract: Weevils (Coleoptera: Curculionoidea) represent one of the most diverse groups of organisms on Earth; interactions with their host plants have been recognized to play a central role in their remarkable diversity, yet the exact mechanisms and factors still remain poorly understood. Using phylogenetic comparative analyses, here we investigate the evolution of host use and its possible role in diversification processes of Rhinusa and Gymnetron, two closely related groups of weevils that feed and develop inside plant tissues of hosts within the families Scrophulariaceae and Plantaginaceae. We found strong evidence for phylogenetic conservatism of host use at the plant family level, most likely due to substantial differences in the chemical composition of hosts, reducing the probability of shifts between host families. In contrast, the use of different plant organs represents a more labile ecological trait and ecological niche expansion that allows a finer partitioning of resources. Rhinusa and Gymnetron weevils initially specialized on plants within Scrophulariaceae and then shifted to the closely related Plantaginaceae; likewise, a gall inducing behavior evolved from non-galler weevils, possibly in response to resource competition, as galls facilitate larval development by providing enhanced nutrition and a favorable microhabitat. Results from trait-dependent diversification analyses suggest that both use of hosts within Plantaginaceae and parasitism on fruits and seed capsules are associated with enhanced diversification of Rhinusa and Gymnetron via low extinction rates. Our study provides quantitative evidence and insights on the ecological factors that can promote diversification in phytophagous insects that feed and develop inside plant tissues.
bibliographic citation: Hernández-Vera et al. (2019) Evolution of host plant use and diversification in a species complex of parasitic weevils (Coleoptera: Curculionidae). PeerJ 7:e6625 https://doi.org/10.7717/peerj.6625
date submitted: 2018-09-25
date accepted: 2019-02-14
issued: 2019-03-20
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Hernández-Vera
  given name: Gerardo
author list: Agent
  family name: Toševski
  given name: Ivo
author list: Agent
  family name: Caldara
  given name: Roberto
author list: Agent
  family name: Emerson
  given name: Brent C.
doi: 10.7717/peerj.6625
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-03-20
copyright: © 2019 Hernández-Vera et al.
attribution name: Hernández-Vera et al.

Transcriptome sequencing of olfactory-related genes in olfactory transduction of large yellow croaker (Larimichthy crocea) in response to bile salts
type: item
type: AcademicArticle
description: Fish produce and release bile salts as chemical signalling substances that act as sensitive olfactory stimuli. To investigate how bile salts affect olfactory signal transduction in large yellow croaker (Larimichthy crocea), deep sequencing of olfactory epithelium was conducted to analyse olfactory-related genes in olfactory transduction. Sodium cholates (SAS) have typical bile salt chemical structures, hence we used four different concentrations of SAS to stimulate L. crocea, and the fish displayed a significant behavioural preference for 0.30% SAS. We then sequenced olfactory epithelium tissues, and identified 9938 unigenes that were significantly differentially expressed between SAS-stimulated and control groups, including 9055 up-regulated and 883 down-regulated unigenes. Subsequent Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses found eight categories linked to the olfactory transduction pathway that was highly enriched with some differentially expressed genes (DEGs), including the olfactory receptor (OR), Adenylate cyclase type 3 (ADCY3) and Calmodulin (CALM). Genes in these categories were analysed by RT-qPCR, which revealed aspects of the pathway transformation between odor detection, and recovery and adaptation. The results provide new insight into the effects of bile salt stimulation in olfactory molecular mechanisms in fishes, and expands our knowledge of olfactory transduction, and signal generation and decline.
format: application/pdf
format: text/html
creator: Jiabao Hu
creator: Yajun Wang
creator: Qijun Le
creator: Na Yu
creator: Xiaohuan Cao
creator: Siwen Kuang
creator: Man Zhang
creator: Weiwei Gu
creator: Yibo Sun
creator: Yang Yang
creator: Xiaojun Yan
subject: Animal Behavior
subject: Aquaculture, Fisheries and Fish Science
subject: Bioinformatics
subject: Marine Biology
description: doi:10.7717/peerj.6627
publisher: PeerJ Inc.
rights: © 2019 Hu et al.
abstract: Fish produce and release bile salts as chemical signalling substances that act as sensitive olfactory stimuli. To investigate how bile salts affect olfactory signal transduction in large yellow croaker (Larimichthy crocea), deep sequencing of olfactory epithelium was conducted to analyse olfactory-related genes in olfactory transduction. Sodium cholates (SAS) have typical bile salt chemical structures, hence we used four different concentrations of SAS to stimulate L. crocea, and the fish displayed a significant behavioural preference for 0.30% SAS. We then sequenced olfactory epithelium tissues, and identified 9938 unigenes that were significantly differentially expressed between SAS-stimulated and control groups, including 9055 up-regulated and 883 down-regulated unigenes. Subsequent Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses found eight categories linked to the olfactory transduction pathway that was highly enriched with some differentially expressed genes (DEGs), including the olfactory receptor (OR), Adenylate cyclase type 3 (ADCY3) and Calmodulin (CALM). Genes in these categories were analysed by RT-qPCR, which revealed aspects of the pathway transformation between odor detection, and recovery and adaptation. The results provide new insight into the effects of bile salt stimulation in olfactory molecular mechanisms in fishes, and expands our knowledge of olfactory transduction, and signal generation and decline.
bibliographic citation: Hu et al. (2019) Transcriptome sequencing of olfactory-related genes in olfactory transduction of large yellow croaker (Larimichthy crocea) in response to bile salts. PeerJ 7:e6627 https://doi.org/10.7717/peerj.6627
date submitted: 2018-11-02
date accepted: 2019-02-15
issued: 2019-03-20
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Hu
  given name: Jiabao
author list: Agent
  family name: Wang
  given name: Yajun
author list: Agent
  family name: Le
  given name: Qijun
author list: Agent
  family name: Yu
  given name: Na
author list: Agent
  family name: Cao
  given name: Xiaohuan
author list: Agent
  family name: Kuang
  given name: Siwen
author list: Agent
  family name: Zhang
  given name: Man
author list: Agent
  family name: Gu
  given name: Weiwei
author list: Agent
  family name: Sun
  given name: Yibo
author list: Agent
  family name: Yang
  given name: Yang
author list: Agent
  family name: Yan
  given name: Xiaojun
doi: 10.7717/peerj.6627
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-03-20
copyright: ©2019 Hu et al.
attribution name: Hu et al.

Low genetic diversity in captive populations of the critically endangered Blue-crowned Laughingthrush (Garrulax courtoisi) revealed by a panel of novel microsatellites
type: item
type: AcademicArticle
description: Background Captive populations permit research and conservation of endangered species in which these efforts are hardly implemented in wild populations. Thus, analysing genetic diversity and structure of captive populations offers unique opportunities. One example is the critically endangered Blue-crowned Laughingthrush, Garrulax courtoisi, which has only two known wild populations in Wuyuan, Jiangxi and Simao, Yunnan, China. We carried out the first conservation genetic study, in order to provide useful implications that allow for successful ex situ conservation and management of the Blue-crowned Laughingthrush. Methods Using the novel microsatellite markers developed by whole-genome sequencing, we genotyped two captive populations, from the Ocean Park Hong Kong, which are of unknown origin, and the Nanchang Zoo, which were introduced from the Wuyuan wild population since the year 2010–2011, respectively. The genetic diversity of captive Blue-crowned Laughingthrush populations was estimated based on genetic polymorphisms revealed by a new microsatellite data set and mitochondrial sequences. Then, we characterised the population structure using STRUCTURE, principal coordinates analysis, population assignment test using the microsatellite data, and haplotype analysis of mitochondrial data. Additionally, we quantified genetic relatedness based on the microsatellite data with ML-Relate. Results Our results showed equally low levels of genetic diversity of the two captive Blue-crowned Laughingthrush populations. The population structure analysis, population assignment test using the microsatellite data, and haplotype analysis of the mitochondrial data showed weak population structuring between these two populations. The average pairwise relatedness coefficient was not significant, and their genetic relatedness was quantified. Discussion This study offers a genetic tool and consequently reveals a low level of genetic diversity within populations of a critically endangere…
format: application/pdf
format: text/html
creator: Guoling Chen
creator: Chenqing Zheng
creator: Nelson Wan
creator: Daoqiang Liu
creator: Vivian Wing Kan Fu
creator: Xu Yang
creator: Yat-tung Yu
creator: Yang Liu
subject: Conservation Biology
subject: Evolutionary Studies
subject: Genetics
subject: Zoology
description: doi:10.7717/peerj.6643
publisher: PeerJ Inc.
rights: © 2019 Chen et al.
abstract: Background Captive populations permit research and conservation of endangered species in which these efforts are hardly implemented in wild populations. Thus, analysing genetic diversity and structure of captive populations offers unique opportunities. One example is the critically endangered Blue-crowned Laughingthrush, Garrulax courtoisi, which has only two known wild populations in Wuyuan, Jiangxi and Simao, Yunnan, China. We carried out the first conservation genetic study, in order to provide useful implications that allow for successful ex situ conservation and management of the Blue-crowned Laughingthrush. Methods Using the novel microsatellite markers developed by whole-genome sequencing, we genotyped two captive populations, from the Ocean Park Hong Kong, which are of unknown origin, and the Nanchang Zoo, which were introduced from the Wuyuan wild population since the year 2010–2011, respectively. The genetic diversity of captive Blue-crowned Laughingthrush populations was estimated based on genetic polymorphisms revealed by a new microsatellite data set and mitochondrial sequences. Then, we characterised the population structure using STRUCTURE, principal coordinates analysis, population assignment test using the microsatellite data, and haplotype analysis of mitochondrial data. Additionally, we quantified genetic relatedness based on the microsatellite data with ML-Relate. Results Our results showed equally low levels of genetic diversity of the two captive Blue-crowned Laughingthrush populations. The population structure analysis, population assignment test using the microsatellite data, and haplotype analysis of the mitochondrial data showed weak population structuring between these two populations. The average pairwise relatedness coefficient was not significant, and their genetic relatedness was quantified. Discussion This study offers a genetic tool and consequently reveals a low level of genetic diversity within populations of a critically endangere…
bibliographic citation: Chen et al. (2019) Low genetic diversity in captive populations of the critically endangered Blue-crowned Laughingthrush (Garrulax courtoisi) revealed by a panel of novel microsatellites. PeerJ 7:e6643 https://doi.org/10.7717/peerj.6643
date submitted: 2018-07-16
date accepted: 2019-02-19
issued: 2019-03-20
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Chen
  given name: Guoling
author list: Agent
  family name: Zheng
  given name: Chenqing
author list: Agent
  family name: Wan
  given name: Nelson
author list: Agent
  family name: Liu
  given name: Daoqiang
author list: Agent
  family name: Fu
  given name: Vivian Wing Kan
author list: Agent
  family name: Yang
  given name: Xu
author list: Agent
  family name: Yu
  given name: Yat-tung
author list: Agent
  family name: Liu
  given name: Yang
doi: 10.7717/peerj.6643
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-03-20
copyright: © 2019 Chen et al.
attribution name: Chen et al.

Fine-scale substrate heterogeneity does not affect arthropod communities on green roofs
type: item
type: AcademicArticle
description: Green roofs, which are roofs with growing substrate and vegetation, can provide habitat for arthropods in cities. Maintaining a diversity of arthropods in an urban environment can enhance the functions they fill, such as pest control and soil development. Theory suggests that the creation of a heterogeneous environment on green roofs would enhance arthropod diversity. Several studies have examined how arthropod diversity can be enhanced on green roofs, and particularly whether substrate properties affect the arthropod community, but a gap remains in identifying the effect of substrate heterogeneity within a green roof on the arthropod community. In this paper, it is hypothesized that creating heterogeneity in the substrate would directly affect the diversity and abundance of some arthropod taxa, and indirectly increase arthropod diversity through increased plant diversity. These hypotheses were tested using green roof plots in four treatments of substrate heterogeneity: (1) homogeneous dispersion; (2) mineral heterogeneity—with increased tuff concentration in subplots; (3) organic heterogeneity—with decreased compost concentrations in subplots; (4) both mineral and organic heterogeneity. Each of the four treatments was replicated twice on each of three roofs (six replicates per treatment) in a Mediterranean region. There was no effect of substrate heterogeneity on arthropod diversity, abundance, or community composition, but there were differences in arthropod communities among roofs. This suggests that the location of a green roof, which can differ in local climatic conditions, can have a strong effect on the composition of the arthropod community. Thus, arthropod diversity may be promoted by building green roofs in a variety of locations throughout a city, even if the roof construction is similar on all roofs.
format: application/pdf
format: text/html
creator: Bracha Y. Schindler
creator: Amiel Vasl
creator: Leon Blaustein
creator: David Gurevich
creator: Gyongyver J. Kadas
creator: Merav Seifan
subject: Conservation Biology
subject: Ecology
subject: Entomology
subject: Coupled Natural and Human Systems
description: doi:10.7717/peerj.6445
publisher: PeerJ Inc.
rights: © 2019 Schindler et al.
abstract: Green roofs, which are roofs with growing substrate and vegetation, can provide habitat for arthropods in cities. Maintaining a diversity of arthropods in an urban environment can enhance the functions they fill, such as pest control and soil development. Theory suggests that the creation of a heterogeneous environment on green roofs would enhance arthropod diversity. Several studies have examined how arthropod diversity can be enhanced on green roofs, and particularly whether substrate properties affect the arthropod community, but a gap remains in identifying the effect of substrate heterogeneity within a green roof on the arthropod community. In this paper, it is hypothesized that creating heterogeneity in the substrate would directly affect the diversity and abundance of some arthropod taxa, and indirectly increase arthropod diversity through increased plant diversity. These hypotheses were tested using green roof plots in four treatments of substrate heterogeneity: (1) homogeneous dispersion; (2) mineral heterogeneity—with increased tuff concentration in subplots; (3) organic heterogeneity—with decreased compost concentrations in subplots; (4) both mineral and organic heterogeneity. Each of the four treatments was replicated twice on each of three roofs (six replicates per treatment) in a Mediterranean region. There was no effect of substrate heterogeneity on arthropod diversity, abundance, or community composition, but there were differences in arthropod communities among roofs. This suggests that the location of a green roof, which can differ in local climatic conditions, can have a strong effect on the composition of the arthropod community. Thus, arthropod diversity may be promoted by building green roofs in a variety of locations throughout a city, even if the roof construction is similar on all roofs.
bibliographic citation: Schindler et al. (2019) Fine-scale substrate heterogeneity does not affect arthropod communities on green roofs. PeerJ 7:e6445 https://doi.org/10.7717/peerj.6445
date submitted: 2018-08-17
date accepted: 2019-01-13
issued: 2019-03-19
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Schindler
  given name: Bracha Y.
author list: Agent
  family name: Vasl
  given name: Amiel
author list: Agent
  family name: Blaustein
  given name: Leon
author list: Agent
  family name: Gurevich
  given name: David
author list: Agent
  family name: Kadas
  given name: Gyongyver J.
author list: Agent
  family name: Seifan
  given name: Merav
doi: 10.7717/peerj.6445
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-03-19
copyright: ©2019 Schindler et al.
attribution name: Schindler et al.

Large carnivore habitat suitability modelling for Romania and associated predictions for protected areas
type: item
type: AcademicArticle
description: Habitat characteristics associated with species occurrences represent important baseline information for wildlife management and conservation, but have rarely been assessed for countries recently joining the EU. We used footprint tracking data and landscape characteristics in Romania to investigate the occurrence of brown bear (Ursus arctos), gray wolf (Canis lupus) and Eurasian lynx (Lynx lynx) and to compare model predictions between Natura 2000 and national-level protected areas (gap analysis). Wolves were more likely to occur where rugged terrain was present. Increasing proportion of forest was positively associated with occurrence of all large carnivores, but forest type (broadleaf, mixed, or conifer) generally varied with carnivore species. Areas where cultivated lands were extensive had little suitable habitat for lynx, whereas bear occurrence probability decreased with increasing proportion of built areas. Pastures were positively associated with wolf and lynx occurrence. Brown bears occurred primarily where national roads with high traffic volumes were at low density, while bears and lynx occurred at medium-high densities of communal roads that had lower traffic volumes. Based on predictions of carnivore distributions, natural areas protected in national parks were most suitable for carnivores, nature parks were less suitable, whereas EU-legislated Natura 2000 sites had the lowest probability of carnivore presence. Our spatially explicit carnivore habitat suitability predictions can be used by managers to amend borders of existing sites, delineate new protected areas, and establish corridors for ecological connectivity. To assist recovery and recolonization, management could also focus on habitat predicted to be suitable but where carnivores were not tracked.
format: application/pdf
format: text/html
creator: Bogdan Cristescu
creator: Csaba Domokos
creator: Kristine J. Teichman
creator: Scott E. Nielsen
subject: Conservation Biology
subject: Ecology
subject: Zoology
subject: Coupled Natural and Human Systems
subject: Natural Resource Management
description: doi:10.7717/peerj.6549
publisher: PeerJ Inc.
rights: © 2019 Cristescu et al.
abstract: Habitat characteristics associated with species occurrences represent important baseline information for wildlife management and conservation, but have rarely been assessed for countries recently joining the EU. We used footprint tracking data and landscape characteristics in Romania to investigate the occurrence of brown bear (Ursus arctos), gray wolf (Canis lupus) and Eurasian lynx (Lynx lynx) and to compare model predictions between Natura 2000 and national-level protected areas (gap analysis). Wolves were more likely to occur where rugged terrain was present. Increasing proportion of forest was positively associated with occurrence of all large carnivores, but forest type (broadleaf, mixed, or conifer) generally varied with carnivore species. Areas where cultivated lands were extensive had little suitable habitat for lynx, whereas bear occurrence probability decreased with increasing proportion of built areas. Pastures were positively associated with wolf and lynx occurrence. Brown bears occurred primarily where national roads with high traffic volumes were at low density, while bears and lynx occurred at medium-high densities of communal roads that had lower traffic volumes. Based on predictions of carnivore distributions, natural areas protected in national parks were most suitable for carnivores, nature parks were less suitable, whereas EU-legislated Natura 2000 sites had the lowest probability of carnivore presence. Our spatially explicit carnivore habitat suitability predictions can be used by managers to amend borders of existing sites, delineate new protected areas, and establish corridors for ecological connectivity. To assist recovery and recolonization, management could also focus on habitat predicted to be suitable but where carnivores were not tracked.
bibliographic citation: Cristescu et al. (2019) Large carnivore habitat suitability modelling for Romania and associated predictions for protected areas. PeerJ 7:e6549 https://doi.org/10.7717/peerj.6549
date submitted: 2017-11-01
date accepted: 2019-01-31
issued: 2019-03-19
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Cristescu
  given name: Bogdan
author list: Agent
  family name: Domokos
  given name: Csaba
author list: Agent
  family name: Teichman
  given name: Kristine J.
author list: Agent
  family name: Nielsen
  given name: Scott E.
doi: 10.7717/peerj.6549
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-03-19
copyright: ©2019 Cristescu et al.
attribution name: Cristescu et al.

Identification of gene-phenotype connectivity associated with flavanone naringenin by functional network analysis
type: item
type: AcademicArticle
description: Naringenin, extracted from grapefruits and citrus fruits, is a bioactive flavonoid with antioxidative, anti-inflammatory, antifibrogenic, and anticancer properties. In the past two decades, the growth of publications of naringenin in PubMed suggests that naringenin is quickly gaining interest. However, systematically regarding its biological functions connected to its direct and indirect target proteins remains difficult but necessary. Herein, we employed a set of bioinformatic platforms to integrate and dissect available published data of naringenin. Analysis based on DrugBank and the Search Tool for the Retrieval of Interacting Genes/Proteins revealed seven direct protein targets and 102 indirect protein targets. The protein–protein interaction (PPI) network of total 109 naringenin-mediated proteins was next visualized using Cytoscape. What’s more, all naringenin-mediated proteins were subject to Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis by the Database for Annotation, Visualization and Integrated Discovery, which resulted in three ESR1-related signaling pathways and prostate cancer pathway. Refined analysis of PPI network and KEGG pathway identified four genes (ESR1, PIK3CA, AKT1, and MAPK1). Further genomic analysis of four genes using cBioPortal indicated that naringenin might exert biological effects via ESR1 signaling axis. In general, this work scrutinized naringenin-relevant knowledge and provided an insight into the regulation and mediation of naringenin on prostate cancer.
format: application/pdf
format: text/html
creator: Suhong Fu
creator: Yongqun Zhang
creator: Jing Shi
creator: Doudou Hao
creator: Pengfei Zhang
subject: Bioinformatics
subject: Genomics
subject: Drugs and Devices
subject: Data Mining and Machine Learning
description: doi:10.7717/peerj.6611
publisher: PeerJ Inc.
rights: © 2019 Fu et al.
abstract: Naringenin, extracted from grapefruits and citrus fruits, is a bioactive flavonoid with antioxidative, anti-inflammatory, antifibrogenic, and anticancer properties. In the past two decades, the growth of publications of naringenin in PubMed suggests that naringenin is quickly gaining interest. However, systematically regarding its biological functions connected to its direct and indirect target proteins remains difficult but necessary. Herein, we employed a set of bioinformatic platforms to integrate and dissect available published data of naringenin. Analysis based on DrugBank and the Search Tool for the Retrieval of Interacting Genes/Proteins revealed seven direct protein targets and 102 indirect protein targets. The protein–protein interaction (PPI) network of total 109 naringenin-mediated proteins was next visualized using Cytoscape. What’s more, all naringenin-mediated proteins were subject to Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis by the Database for Annotation, Visualization and Integrated Discovery, which resulted in three ESR1-related signaling pathways and prostate cancer pathway. Refined analysis of PPI network and KEGG pathway identified four genes (ESR1, PIK3CA, AKT1, and MAPK1). Further genomic analysis of four genes using cBioPortal indicated that naringenin might exert biological effects via ESR1 signaling axis. In general, this work scrutinized naringenin-relevant knowledge and provided an insight into the regulation and mediation of naringenin on prostate cancer.
bibliographic citation: Fu et al. (2019) Identification of gene-phenotype connectivity associated with flavanone naringenin by functional network analysis. PeerJ 7:e6611 https://doi.org/10.7717/peerj.6611
date submitted: 2018-11-02
date accepted: 2019-02-12
issued: 2019-03-19
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Fu
  given name: Suhong
author list: Agent
  family name: Zhang
  given name: Yongqun
author list: Agent
  family name: Shi
  given name: Jing
author list: Agent
  family name: Hao
  given name: Doudou
author list: Agent
  family name: Zhang
  given name: Pengfei
doi: 10.7717/peerj.6611
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-03-19
copyright: © 2019 Fu et al.
attribution name: Fu et al.

Increased risk of thyroid disease in patients with Sjogren's syndrome: a systematic review and meta-analysis
type: item
type: AcademicArticle
description: Background Sjogren’s syndrome (SS) is a chronic autoimmune epithelitis characterized by disruption of epithelial cells, ensuing lymphoplasmocytic infiltration of exocrine glands, and subsequent dryness of the mouth and eyes. Individuals with SS are more likely to have the thyroid disease. However, this association remains controversial. This meta-analysis aimed to evaluate the risk of thyroid disease in patients with SS. Methods We performed this systematic review by searching both English and Chinese literature databases. Random- or fixed-effects models were used to summarize the association between thyroid disease and SS. The results were subjected to meta-analysis with odds ratios (ORs) and corresponding 95% confidence intervals (CIs). Results The eight articles in this meta-analysis included 988 SS cases and 2,884 controls. Overall, the risk of thyroid disease in patients with SS was significantly increased compared with controls (OR, 3.29; 95% CI [2.08–5.21]). The risk of autoimmune thyroid disease (AITD) and non-AITD were also higher in patients with SS than in controls (OR, 3.48; 95% CI [1.59–7.63]; and OR, 2.90; 95% CI [1.51–5.57], respectively). Conclusions To the best of our knowledge, this systematic review is the first to demonstrate that the risk of thyroid disease was increased in SS compared to controls, suggesting that SS patients should be screened for thyroid disease.
format: application/pdf
format: text/html
creator: Xin Sun
creator: Li Lu
creator: Yanbin Li
creator: Rong Yang
creator: Ling Shan
creator: Yang Wang
subject: Diabetes and Endocrinology
subject: Epidemiology
subject: Rheumatology
description: doi:10.7717/peerj.6737
publisher: PeerJ Inc.
rights: © 2019 Sun et al.
abstract: Background Sjogren’s syndrome (SS) is a chronic autoimmune epithelitis characterized by disruption of epithelial cells, ensuing lymphoplasmocytic infiltration of exocrine glands, and subsequent dryness of the mouth and eyes. Individuals with SS are more likely to have the thyroid disease. However, this association remains controversial. This meta-analysis aimed to evaluate the risk of thyroid disease in patients with SS. Methods We performed this systematic review by searching both English and Chinese literature databases. Random- or fixed-effects models were used to summarize the association between thyroid disease and SS. The results were subjected to meta-analysis with odds ratios (ORs) and corresponding 95% confidence intervals (CIs). Results The eight articles in this meta-analysis included 988 SS cases and 2,884 controls. Overall, the risk of thyroid disease in patients with SS was significantly increased compared with controls (OR, 3.29; 95% CI [2.08–5.21]). The risk of autoimmune thyroid disease (AITD) and non-AITD were also higher in patients with SS than in controls (OR, 3.48; 95% CI [1.59–7.63]; and OR, 2.90; 95% CI [1.51–5.57], respectively). Conclusions To the best of our knowledge, this systematic review is the first to demonstrate that the risk of thyroid disease was increased in SS compared to controls, suggesting that SS patients should be screened for thyroid disease.
bibliographic citation: Sun et al. (2019) Increased risk of thyroid disease in patients with Sjogren's syndrome: a systematic review and meta-analysis. PeerJ 7:e6737 https://doi.org/10.7717/peerj.6737
date submitted: 2018-10-22
date accepted: 2019-03-07
issued: 2019-03-19
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Sun
  given name: Xin
author list: Agent
  family name: Lu
  given name: Li
author list: Agent
  family name: Li
  given name: Yanbin
author list: Agent
  family name: Yang
  given name: Rong
author list: Agent
  family name: Shan
  given name: Ling
author list: Agent
  family name: Wang
  given name: Yang
doi: 10.7717/peerj.6737
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-03-19
copyright: © 2019 Sun et al.
attribution name: Sun et al.

Integrated bioinformatics analysis of As, Au, Cd, Pb and Cu heavy metal responsive marker genes through Arabidopsis thaliana GEO datasets
type: item
type: AcademicArticle
description: Background Current environmental pollution factors, particularly the distribution and diffusion of heavy metals in soil and water, are a high risk to local environments and humans. Despite striking advances in methods to detect contaminants by a variety of chemical and physical solutions, these methods have inherent limitations such as small dimensions and very low coverage. Therefore, identifying novel contaminant biomarkers are urgently needed. Methods To better track heavy metal contaminations in soil and water, integrated bioinformatics analysis to identify biomarkers of relevant heavy metal, such as As, Cd, Pb and Cu, is a suitable method for long-term and large-scale surveys of such heavy metal pollutants. Subsequently, the accuracy and stability of the results screened were experimentally validated by quantitative PCR experiment. Results We obtained 168 differentially expressed genes (DEGs) which contained 59 up-regulated genes and 109 down-regulated genes through comparative bioinformatics analyses. Subsequently, the gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichments of these DEGs were performed, respectively. GO analyses found that these DEGs were mainly related to responses to chemicals, responses to stimulus, responses to stress, responses to abiotic stimulus, and so on. KEGG pathway analyses of DEGs were mainly involved in the protein degradation process and other biologic process, such as the phenylpropanoid biosynthesis pathways and nitrogen metabolism. Moreover, we also speculated that nine candidate core biomarker genes (namely, NILR1, PGPS1, WRKY33, BCS1, AR781, CYP81D8, NR1, EAP1 and MYB15) might be tightly correlated with the response or transport of heavy metals. Finally, experimental results displayed that these genes had the same expression trend response to different stresses as mentioned above (Cd, Pb and Cu) and no mentioned above (Zn and Cr). Conclusion In general, the identified biomarker genes could …
format: application/pdf
format: text/html
creator: Chao Niu
creator: Min Jiang
creator: Na Li
creator: Jianguo Cao
creator: Meifang Hou
creator: Di-an Ni
creator: Zhaoqing Chu
subject: Molecular Biology
subject: Plant Science
subject: Data Mining and Machine Learning
subject: Environmental Contamination and Remediation
description: doi:10.7717/peerj.6495
publisher: PeerJ Inc.
rights: © 2019 Niu et al.
abstract: Background Current environmental pollution factors, particularly the distribution and diffusion of heavy metals in soil and water, are a high risk to local environments and humans. Despite striking advances in methods to detect contaminants by a variety of chemical and physical solutions, these methods have inherent limitations such as small dimensions and very low coverage. Therefore, identifying novel contaminant biomarkers are urgently needed. Methods To better track heavy metal contaminations in soil and water, integrated bioinformatics analysis to identify biomarkers of relevant heavy metal, such as As, Cd, Pb and Cu, is a suitable method for long-term and large-scale surveys of such heavy metal pollutants. Subsequently, the accuracy and stability of the results screened were experimentally validated by quantitative PCR experiment. Results We obtained 168 differentially expressed genes (DEGs) which contained 59 up-regulated genes and 109 down-regulated genes through comparative bioinformatics analyses. Subsequently, the gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichments of these DEGs were performed, respectively. GO analyses found that these DEGs were mainly related to responses to chemicals, responses to stimulus, responses to stress, responses to abiotic stimulus, and so on. KEGG pathway analyses of DEGs were mainly involved in the protein degradation process and other biologic process, such as the phenylpropanoid biosynthesis pathways and nitrogen metabolism. Moreover, we also speculated that nine candidate core biomarker genes (namely, NILR1, PGPS1, WRKY33, BCS1, AR781, CYP81D8, NR1, EAP1 and MYB15) might be tightly correlated with the response or transport of heavy metals. Finally, experimental results displayed that these genes had the same expression trend response to different stresses as mentioned above (Cd, Pb and Cu) and no mentioned above (Zn and Cr). Conclusion In general, the identified biomarker genes could …
bibliographic citation: Niu et al. (2019) Integrated bioinformatics analysis of As, Au, Cd, Pb and Cu heavy metal responsive marker genes through Arabidopsis thaliana GEO datasets. PeerJ 7:e6495 https://doi.org/10.7717/peerj.6495
date submitted: 2018-10-26
date accepted: 2019-01-19
issued: 2019-03-18
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Niu
  given name: Chao
author list: Agent
  family name: Jiang
  given name: Min
author list: Agent
  family name: Li
  given name: Na
author list: Agent
  family name: Cao
  given name: Jianguo
author list: Agent
  family name: Hou
  given name: Meifang
author list: Agent
  family name: Ni
  given name: Di-an
author list: Agent
  family name: Chu
  given name: Zhaoqing
doi: 10.7717/peerj.6495
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-03-18
copyright: ©2019 Niu et al.
attribution name: Niu et al.

Long-term high physical activity modulates event-related potential indices of inhibitory control in postmenopausal women
type: item
type: AcademicArticle
description: Background Inhibition processing is sensitive to aging, and an age-related decline in inhibition processing has been associated with an accelerated rate of progression to Alzheimer disease. Elderly women are two to three times more likely than age-matched men to have Alzheimer disease. Therefore, this study examined whether long-term high physical activity affects inhibitory processing, specifically among postmenopausal women. Methods In total, 251 candidates were screened using the Montreal Cognitive Assessment and the Raven’s Standard Progressive Matrices to assess their cognitive abilities and the International Physical Activity Questionnaire (Chinese version) to assess their physical activity levels. The participants were then grouped into either a long-term high physical activity group (defined as more than 3 days of high intensity activity per week and gross metabolic equivalent minutes (MET-minutes) higher than 1,500 MET-minutes/week or a gross MET higher than 3,000 MET-minutes/week obtained through walking or other moderate or high intensity activity) or a control group and matched for demographic and health characteristics as well as cognitive scores. Event-related potentials (ERPs) were recorded as participants performed a Go/No-go task to assess inhibition processing. Results The long-term high physical activity group (n = 30) had faster Go reaction times than the control group (n = 30), whereas no significant difference between the two groups was found in their performance accuracy on the No-go task. For the ERP results, the latency of N2 component was significantly shorter in the long-term high physical activity group than that in the control group. Discussion The results of this study suggested that long-term high physical activity may increase the efficiency of the inhibitory control system by increasing the activity of response monitoring processes.
format: application/pdf
format: text/html
creator: Chang Xu
creator: Yingzhi Lu
creator: Biye Wang
creator: Chenglin Zhou
subject: Neuroscience
subject: Kinesiology
subject: Psychiatry and Psychology
subject: Public Health
subject: Women's Health
description: doi:10.7717/peerj.6523
publisher: PeerJ Inc.
rights: © 2019 Xu et al.
abstract: Background Inhibition processing is sensitive to aging, and an age-related decline in inhibition processing has been associated with an accelerated rate of progression to Alzheimer disease. Elderly women are two to three times more likely than age-matched men to have Alzheimer disease. Therefore, this study examined whether long-term high physical activity affects inhibitory processing, specifically among postmenopausal women. Methods In total, 251 candidates were screened using the Montreal Cognitive Assessment and the Raven’s Standard Progressive Matrices to assess their cognitive abilities and the International Physical Activity Questionnaire (Chinese version) to assess their physical activity levels. The participants were then grouped into either a long-term high physical activity group (defined as more than 3 days of high intensity activity per week and gross metabolic equivalent minutes (MET-minutes) higher than 1,500 MET-minutes/week or a gross MET higher than 3,000 MET-minutes/week obtained through walking or other moderate or high intensity activity) or a control group and matched for demographic and health characteristics as well as cognitive scores. Event-related potentials (ERPs) were recorded as participants performed a Go/No-go task to assess inhibition processing. Results The long-term high physical activity group (n = 30) had faster Go reaction times than the control group (n = 30), whereas no significant difference between the two groups was found in their performance accuracy on the No-go task. For the ERP results, the latency of N2 component was significantly shorter in the long-term high physical activity group than that in the control group. Discussion The results of this study suggested that long-term high physical activity may increase the efficiency of the inhibitory control system by increasing the activity of response monitoring processes.
bibliographic citation: Xu et al. (2019) Long-term high physical activity modulates event-related potential indices of inhibitory control in postmenopausal women. PeerJ 7:e6523 https://doi.org/10.7717/peerj.6523
date submitted: 2017-12-26
date accepted: 2019-01-27
issued: 2019-03-18
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Xu
  given name: Chang
author list: Agent
  family name: Lu
  given name: Yingzhi
author list: Agent
  family name: Wang
  given name: Biye
author list: Agent
  family name: Zhou
  given name: Chenglin
doi: 10.7717/peerj.6523
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-03-18
copyright: © 2019 Xu et al.
attribution name: Xu et al.

Estimating probabilistic context-free grammars for proteins using contact map constraints
type: item
type: AcademicArticle
description: Interactions between amino acids that are close in the spatial structure, but not necessarily in the sequence, play important structural and functional roles in proteins. These non-local interactions ought to be taken into account when modeling collections of proteins. Yet the most popular representations of sets of related protein sequences remain the profile Hidden Markov Models. By modeling independently the distributions of the conserved columns from an underlying multiple sequence alignment of the proteins, these models are unable to capture dependencies between the protein residues. Non-local interactions can be represented by using more expressive grammatical models. However, learning such grammars is difficult. In this work, we propose to use information on protein contacts to facilitate the training of probabilistic context-free grammars representing families of protein sequences. We develop the theory behind the introduction of contact constraints in maximum-likelihood and contrastive estimation schemes and implement it in a machine learning framework for protein grammars. The proposed framework is tested on samples of protein motifs in comparison with learning without contact constraints. The evaluation shows high fidelity of grammatical descriptors to protein structures and improved precision in recognizing sequences. Finally, we present an example of using our method in a practical setting and demonstrate its potential beyond the current state of the art by creating a grammatical model of a meta-family of protein motifs. We conclude that the current piece of research is a significant step towards more flexible and accurate modeling of collections of protein sequences. The software package is made available to the community.
format: application/pdf
format: text/html
creator: Witold Dyrka
creator: Mateusz Pyzik
creator: François Coste
creator: Hugo Talibart
subject: Bioinformatics
subject: Mathematical Biology
subject: Computational Science
subject: Data Mining and Machine Learning
description: doi:10.7717/peerj.6559
publisher: PeerJ Inc.
rights: © 2019 Dyrka et al.
abstract: Interactions between amino acids that are close in the spatial structure, but not necessarily in the sequence, play important structural and functional roles in proteins. These non-local interactions ought to be taken into account when modeling collections of proteins. Yet the most popular representations of sets of related protein sequences remain the profile Hidden Markov Models. By modeling independently the distributions of the conserved columns from an underlying multiple sequence alignment of the proteins, these models are unable to capture dependencies between the protein residues. Non-local interactions can be represented by using more expressive grammatical models. However, learning such grammars is difficult. In this work, we propose to use information on protein contacts to facilitate the training of probabilistic context-free grammars representing families of protein sequences. We develop the theory behind the introduction of contact constraints in maximum-likelihood and contrastive estimation schemes and implement it in a machine learning framework for protein grammars. The proposed framework is tested on samples of protein motifs in comparison with learning without contact constraints. The evaluation shows high fidelity of grammatical descriptors to protein structures and improved precision in recognizing sequences. Finally, we present an example of using our method in a practical setting and demonstrate its potential beyond the current state of the art by creating a grammatical model of a meta-family of protein motifs. We conclude that the current piece of research is a significant step towards more flexible and accurate modeling of collections of protein sequences. The software package is made available to the community.
bibliographic citation: Dyrka et al. (2019) Estimating probabilistic context-free grammars for proteins using contact map constraints. PeerJ 7:e6559 https://doi.org/10.7717/peerj.6559
date submitted: 2018-07-26
date accepted: 2019-02-03
issued: 2019-03-18
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Dyrka
  given name: Witold
author list: Agent
  family name: Pyzik
  given name: Mateusz
author list: Agent
  family name: Coste
  given name: François
author list: Agent
  family name: Talibart
  given name: Hugo
doi: 10.7717/peerj.6559
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-03-18
copyright: ©2019 Dyrka et al.
attribution name: Dyrka et al.

Impact of El Niño-Southern Oscillation 2015-2016 on the soluble proteomic profile and cytolytic activity of Millepora alcicornis (“fire coral”) from the Mexican Caribbean
type: item
type: AcademicArticle
description: Reef-forming cnidarians are extremely susceptible to the “bleaching” phenomenon caused by global warming. The effect of elevated seawater temperature has been extensively studied on Anthozoans; however, to date the impact of thermal stress on the expression of genes and proteins in Hydrozoan species has not been investigated. The present study aimed to determine the differential proteomic profile of Millepora alcicornis, which inhabits the Mexican Caribbean, in response to the El Niño-Southern Oscillation 2015–2016. Additionally, the cytolytic activity of the soluble proteomes obtained from normal and bleached M. alcicornis was assessed. Bleached specimens showed decreased symbiont’s density and chlorophyll a and c2 levels. After bleaching, we observed a differential expression of 17 key proteins, tentatively identified as related to exocytosis, calcium homeostasis, cytoskeletal organization, and potential toxins, including a metalloprotease, a phospholipase A2 (PLA2), and an actitoxin. Although, some of the differentially expressed proteins included potential toxins, the hemolytic, PLA2, and proteolytic activities elicited by the soluble proteomes from bleached and normal specimens were not significantly different. The present study provides heretofore-unknown evidence that thermal stress produces a differential expression of proteins involved in essential cellular processes of Hydrozoan species. Even though our results showed an over-expression of some potential toxin-related proteins, the cytolytic effect (as assessed by hemolytic, PLA2, and caseinolytic activities) was not increased in bleached M. alcicornis, which suggests that the cytolysis is mainly produced by toxins whose expression was not affected by temperature stress. These findings allow hypothesizing that this hydrocoral is able to prey heterotrophically when suffering from moderate bleaching, giving it a better chance to withstand the effects of high temperature.
format: application/pdf
format: text/html
creator: Norma Olguín-López
creator: Víctor Hugo Hérnandez-Elizárraga
creator: Rosalina Hernández-Matehuala
creator: Andrés Cruz-Hernández
creator: Ramón Guevara-González
creator: Juan Caballero-Pérez
creator: César Ibarra-Alvarado
creator: Alejandra Rojas-Molina
subject: Ecology
subject: Climate Change Biology
description: doi:10.7717/peerj.6593
publisher: PeerJ Inc.
rights: © 2019 Olguín-López et al.
abstract: Reef-forming cnidarians are extremely susceptible to the “bleaching” phenomenon caused by global warming. The effect of elevated seawater temperature has been extensively studied on Anthozoans; however, to date the impact of thermal stress on the expression of genes and proteins in Hydrozoan species has not been investigated. The present study aimed to determine the differential proteomic profile of Millepora alcicornis, which inhabits the Mexican Caribbean, in response to the El Niño-Southern Oscillation 2015–2016. Additionally, the cytolytic activity of the soluble proteomes obtained from normal and bleached M. alcicornis was assessed. Bleached specimens showed decreased symbiont’s density and chlorophyll a and c2 levels. After bleaching, we observed a differential expression of 17 key proteins, tentatively identified as related to exocytosis, calcium homeostasis, cytoskeletal organization, and potential toxins, including a metalloprotease, a phospholipase A2 (PLA2), and an actitoxin. Although, some of the differentially expressed proteins included potential toxins, the hemolytic, PLA2, and proteolytic activities elicited by the soluble proteomes from bleached and normal specimens were not significantly different. The present study provides heretofore-unknown evidence that thermal stress produces a differential expression of proteins involved in essential cellular processes of Hydrozoan species. Even though our results showed an over-expression of some potential toxin-related proteins, the cytolytic effect (as assessed by hemolytic, PLA2, and caseinolytic activities) was not increased in bleached M. alcicornis, which suggests that the cytolysis is mainly produced by toxins whose expression was not affected by temperature stress. These findings allow hypothesizing that this hydrocoral is able to prey heterotrophically when suffering from moderate bleaching, giving it a better chance to withstand the effects of high temperature.
bibliographic citation: Olguín-López et al. (2019) Impact of El Niño-Southern Oscillation 2015-2016 on the soluble proteomic profile and cytolytic activity of Millepora alcicornis (“fire coral”) from the Mexican Caribbean. PeerJ 7:e6593 https://doi.org/10.7717/peerj.6593
date submitted: 2018-11-15
date accepted: 2019-02-09
issued: 2019-03-18
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Olguín-López
  given name: Norma
author list: Agent
  family name: Hérnandez-Elizárraga
  given name: Víctor Hugo
author list: Agent
  family name: Hernández-Matehuala
  given name: Rosalina
author list: Agent
  family name: Cruz-Hernández
  given name: Andrés
author list: Agent
  family name: Guevara-González
  given name: Ramón
author list: Agent
  family name: Caballero-Pérez
  given name: Juan
author list: Agent
  family name: Ibarra-Alvarado
  given name: César
author list: Agent
  family name: Rojas-Molina
  given name: Alejandra
doi: 10.7717/peerj.6593
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-03-18
copyright: © 2019 Olguín-López et al.
attribution name: Olguín-López et al.

Genome-wide characterization of endogenous retroviruses in snub-nosed monkeys
type: item
type: AcademicArticle
description: Background Endogenous retroviruses (ERV) are remnants of former exogenous retroviruses that had previously invaded the germ line of the host that can be vertically transmitted across generations. While the majority of ERVs lack infectious capacity due to the accumulation of deleterious mutations, some ERVs remain active and produce potentially infectious viral particles. ERV sequences have been reported in all mammals; however, the distribution and diversity of ERVs in several primate taxa remains unclear. The aim of this study was to identify and classify the ERV sequences in the genomes of the golden snub-nosed monkey (Rhinopithecus roxellana) and the black and white snub-nosed monkey (Rhinopithecus bieti), two endangered primate species that exploit high altitude (2,500–4,500 m) temperate forests in southern and central China. Methods We used a TBLASTN program to search the ERV sequences of golden snub-nosed monkey genome and the black and white snub-nosed monkey genome. We retrieved all complete accession sequences from the homology search and then used the program, RetroTector, to check and identify the ERV sequences. Results We identified 284 and 263 endogenous retrovirus sequences in R. roxellana and R. bieti respectively. The proportion of full-length sequences of all ERV was 30% in R. roxellana and 21% in R. bieti and they were described as class I and class II or gamma-retrovirus and beta-retrovirus genera. The truncation pattern distribution in the two species was virtually identical. By analyzing and comparing ERV orthologues among 6 primate species, we identified the co-evolution of ERVs with their host. We also examined ERV-like sequences and found 48 such genes in R. roxellana and 63 in R. bieti. Some of those genes are associated with diseases, suggesting that ERVs might have involved the abnormal expression of certain genes that have contributed to deleterious consequences for the host. Conclusions Our results indicate that ERV sequences are widely …
format: application/pdf
format: text/html
creator: Xiao Wang
creator: Boshi Wang
creator: Zhijin Liu
creator: Paul A. Garber
creator: Huijuan Pan
subject: Evolutionary Studies
subject: Genetics
subject: Genomics
subject: Molecular Biology
subject: Virology
description: doi:10.7717/peerj.6602
publisher: PeerJ Inc.
rights: © 2019 Wang et al.
abstract: Background Endogenous retroviruses (ERV) are remnants of former exogenous retroviruses that had previously invaded the germ line of the host that can be vertically transmitted across generations. While the majority of ERVs lack infectious capacity due to the accumulation of deleterious mutations, some ERVs remain active and produce potentially infectious viral particles. ERV sequences have been reported in all mammals; however, the distribution and diversity of ERVs in several primate taxa remains unclear. The aim of this study was to identify and classify the ERV sequences in the genomes of the golden snub-nosed monkey (Rhinopithecus roxellana) and the black and white snub-nosed monkey (Rhinopithecus bieti), two endangered primate species that exploit high altitude (2,500–4,500 m) temperate forests in southern and central China. Methods We used a TBLASTN program to search the ERV sequences of golden snub-nosed monkey genome and the black and white snub-nosed monkey genome. We retrieved all complete accession sequences from the homology search and then used the program, RetroTector, to check and identify the ERV sequences. Results We identified 284 and 263 endogenous retrovirus sequences in R. roxellana and R. bieti respectively. The proportion of full-length sequences of all ERV was 30% in R. roxellana and 21% in R. bieti and they were described as class I and class II or gamma-retrovirus and beta-retrovirus genera. The truncation pattern distribution in the two species was virtually identical. By analyzing and comparing ERV orthologues among 6 primate species, we identified the co-evolution of ERVs with their host. We also examined ERV-like sequences and found 48 such genes in R. roxellana and 63 in R. bieti. Some of those genes are associated with diseases, suggesting that ERVs might have involved the abnormal expression of certain genes that have contributed to deleterious consequences for the host. Conclusions Our results indicate that ERV sequences are widely …
bibliographic citation: Wang et al. (2019) Genome-wide characterization of endogenous retroviruses in snub-nosed monkeys. PeerJ 7:e6602 https://doi.org/10.7717/peerj.6602
date submitted: 2018-10-25
date accepted: 2019-02-11
issued: 2019-03-18
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Wang
  given name: Xiao
author list: Agent
  family name: Wang
  given name: Boshi
author list: Agent
  family name: Liu
  given name: Zhijin
author list: Agent
  family name: Garber
  given name: Paul A.
author list: Agent
  family name: Pan
  given name: Huijuan
doi: 10.7717/peerj.6602
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-03-18
copyright: ©2019 Wang et al.
attribution name: Wang et al.

Phytobiomes are compositionally nested from the ground up
type: item
type: AcademicArticle
description: Plant-associated microbes are critical players in host health, fitness and productivity. Despite microbes’ importance in plants, seeds are mostly sterile, and most plant microbes are recruited from an environmental pool. Surprisingly little is known about the processes that govern how environmental microbes assemble on plants in nature. In this study we examine how bacteria are distributed across plant parts, and how these distributions interact with spatial gradients. We sequenced amplicons of bacteria from the surfaces of six plant parts and adjacent soil of Scaevola taccada, a common beach shrub, along a 60 km transect spanning O’ahu island’s windward coast, as well as within a single intensively-sampled site. Bacteria are more strongly partitioned by plant part as compared with location. Within S. taccada plants, microbial communities are highly nested: soil and rhizosphere communities contain much of the diversity found elsewhere, whereas reproductive parts fall at the bottom of the nestedness hierarchy. Nestedness patterns suggest either that microbes follow a source/sink gradient from the ground up, or else that assembly processes correlate with other traits, such as tissue persistence, that are vertically stratified. Our work shines light on the origins and determinants of plant-associated microbes across plant and landscape scales.
format: application/pdf
format: text/html
creator: Anthony S. Amend
creator: Gerald M. Cobian
creator: Aki J. Laruson
creator: Kristina Remple
creator: Sarah J. Tucker
creator: Kirsten E. Poff
creator: Carmen Antaky
creator: Andre Boraks
creator: Casey A. Jones
creator: Donna Kuehu
creator: Becca R. Lensing
creator: Mersedeh Pejhanmehr
creator: Daniel T. Richardson
creator: Paul P. Riley
subject: Ecology
subject: Microbiology
subject: Plant Science
description: doi:10.7717/peerj.6609
publisher: PeerJ Inc.
rights: © 2019 Amend et al.
abstract: Plant-associated microbes are critical players in host health, fitness and productivity. Despite microbes’ importance in plants, seeds are mostly sterile, and most plant microbes are recruited from an environmental pool. Surprisingly little is known about the processes that govern how environmental microbes assemble on plants in nature. In this study we examine how bacteria are distributed across plant parts, and how these distributions interact with spatial gradients. We sequenced amplicons of bacteria from the surfaces of six plant parts and adjacent soil of Scaevola taccada, a common beach shrub, along a 60 km transect spanning O’ahu island’s windward coast, as well as within a single intensively-sampled site. Bacteria are more strongly partitioned by plant part as compared with location. Within S. taccada plants, microbial communities are highly nested: soil and rhizosphere communities contain much of the diversity found elsewhere, whereas reproductive parts fall at the bottom of the nestedness hierarchy. Nestedness patterns suggest either that microbes follow a source/sink gradient from the ground up, or else that assembly processes correlate with other traits, such as tissue persistence, that are vertically stratified. Our work shines light on the origins and determinants of plant-associated microbes across plant and landscape scales.
bibliographic citation: Amend et al. (2019) Phytobiomes are compositionally nested from the ground up. PeerJ 7:e6609 https://doi.org/10.7717/peerj.6609
date submitted: 2018-11-26
date accepted: 2019-02-04
issued: 2019-03-18
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Amend
  given name: Anthony S.
author list: Agent
  family name: Cobian
  given name: Gerald M.
author list: Agent
  family name: Laruson
  given name: Aki J.
author list: Agent
  family name: Remple
  given name: Kristina
author list: Agent
  family name: Tucker
  given name: Sarah J.
author list: Agent
  family name: Poff
  given name: Kirsten E.
author list: Agent
  family name: Antaky
  given name: Carmen
author list: Agent
  family name: Boraks
  given name: Andre
author list: Agent
  family name: Jones
  given name: Casey A.
author list: Agent
  family name: Kuehu
  given name: Donna
author list: Agent
  family name: Lensing
  given name: Becca R.
author list: Agent
  family name: Pejhanmehr
  given name: Mersedeh
author list: Agent
  family name: Richardson
  given name: Daniel T.
author list: Agent
  family name: Riley
  given name: Paul P.
doi: 10.7717/peerj.6609
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-03-18
copyright: ©2019 Amend et al.
attribution name: Amend et al.

A metagenomic study of DNA viruses from samples of local varieties of common bean in Kenya
type: item
type: AcademicArticle
description: Common bean (Phaseolus vulgaris L.) is the primary source of protein and nutrients in the majority of households in sub-Saharan Africa. However, pests and viral diseases are key drivers in the reduction of bean production. To date, the majority of viruses reported in beans have been RNA viruses. In this study, we carried out a viral metagenomic analysis on virus symptomatic bean plants. Our virus detection pipeline identified three viral fragments of the double-stranded DNA virus Pelargonium vein banding virus (PVBV) (family, Caulimoviridae, genus Badnavirus). This is the first report of the dsDNA virus and specifically PVBV in legumes to our knowledge. In addition two previously reported +ssRNA viruses the bean common mosaic necrosis virus (BCMNVA) (Potyviridae) and aphid lethal paralysis virus (ALPV) (Dicistroviridae) were identified. Bayesian phylogenetic analysis of the Badnavirus (PVBV) using amino acid sequences of the RT/RNA-dependent DNA polymerase region showed the Kenyan sequence (SRF019_MK014483) was closely matched with two Badnavirus viruses: Dracaena mottle virus (DrMV) (YP_610965) and Lucky bamboo bacilliform virus (ABR01170). Phylogenetic analysis of BCMNVA was based on amino acid sequences of the Nib region. The BCMNVA phylogenetic tree resolved two clades identified as clade (I and II). Sequence from this study SRF35_MK014482, clustered within clade I with other Kenyan sequences. Conversely, Bayesian phylogenetic analysis of ALPV was based on nucleotide sequences of the hypothetical protein gene 1 and 2. Three main clades were resolved and identified as clades I–III. The Kenyan sequence from this study (SRF35_MK014481) clustered within clade II, and nested within a sub-clade; comprising of sequences from China and an earlier ALPV sequences from Kenya isolated from maize (MF458892). Our findings support the use of viral metagenomics to reveal the nascent viruses, their viral diversity and evolutionary history of these viruses. The detection of ALPV …
format: application/pdf
format: text/html
creator: James M. Wainaina
creator: Elijah Ateka
creator: Timothy Makori
creator: Monica A. Kehoe
creator: Laura M. Boykin
subject: Agricultural Science
subject: Virology
description: doi:10.7717/peerj.6465
publisher: PeerJ Inc.
rights: © 2019 Wainana et al.
abstract: Common bean (Phaseolus vulgaris L.) is the primary source of protein and nutrients in the majority of households in sub-Saharan Africa. However, pests and viral diseases are key drivers in the reduction of bean production. To date, the majority of viruses reported in beans have been RNA viruses. In this study, we carried out a viral metagenomic analysis on virus symptomatic bean plants. Our virus detection pipeline identified three viral fragments of the double-stranded DNA virus Pelargonium vein banding virus (PVBV) (family, Caulimoviridae, genus Badnavirus). This is the first report of the dsDNA virus and specifically PVBV in legumes to our knowledge. In addition two previously reported +ssRNA viruses the bean common mosaic necrosis virus (BCMNVA) (Potyviridae) and aphid lethal paralysis virus (ALPV) (Dicistroviridae) were identified. Bayesian phylogenetic analysis of the Badnavirus (PVBV) using amino acid sequences of the RT/RNA-dependent DNA polymerase region showed the Kenyan sequence (SRF019_MK014483) was closely matched with two Badnavirus viruses: Dracaena mottle virus (DrMV) (YP_610965) and Lucky bamboo bacilliform virus (ABR01170). Phylogenetic analysis of BCMNVA was based on amino acid sequences of the Nib region. The BCMNVA phylogenetic tree resolved two clades identified as clade (I and II). Sequence from this study SRF35_MK014482, clustered within clade I with other Kenyan sequences. Conversely, Bayesian phylogenetic analysis of ALPV was based on nucleotide sequences of the hypothetical protein gene 1 and 2. Three main clades were resolved and identified as clades I–III. The Kenyan sequence from this study (SRF35_MK014481) clustered within clade II, and nested within a sub-clade; comprising of sequences from China and an earlier ALPV sequences from Kenya isolated from maize (MF458892). Our findings support the use of viral metagenomics to reveal the nascent viruses, their viral diversity and evolutionary history of these viruses. The detection of ALPV …
bibliographic citation: Wainaina et al. (2019) A metagenomic study of DNA viruses from samples of local varieties of common bean in Kenya. PeerJ 7:e6465 https://doi.org/10.7717/peerj.6465
date submitted: 2018-07-17
date accepted: 2019-01-16
issued: 2019-03-15
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Wainaina
  given name: James M.
author list: Agent
  family name: Ateka
  given name: Elijah
author list: Agent
  family name: Makori
  given name: Timothy
author list: Agent
  family name: Kehoe
  given name: Monica A.
author list: Agent
  family name: Boykin
  given name: Laura M.
doi: 10.7717/peerj.6465
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-03-15
copyright: © 2019 Wainana et al.
attribution name: Wainana et al.

Vocal recognition of a nest-predator in black grouse
type: item
type: AcademicArticle
description: Corvids count among the important predators of bird nests. They are vocal animals and one can expect that birds threatened by their predation, such as black grouse, are sensitive to and recognize their calls. Within the framework of field studies, we noticed that adult black grouse were alerted by raven calls during periods outside the breeding season. Since black grouse are large, extremely precocial birds, this reaction can hardly be explained by sensitization specifically to the threat of nest predation by ravens. This surprising observation prompted us to study the phenomenon more systematically. According to our knowledge, the response of birds to corvid vocalization has been studied in altricial birds only. We tested whether the black grouse distinguishes and responds specifically to playback calls of the common raven. Black grouse recognized raven calls and were alerted, displaying typical neck stretching, followed by head scanning, and eventual escape. Surprisingly, males tended to react faster and exhibited a longer duration of vigilance behavior compared to females. Although raven calls are recognized by adult black grouse out of the nesting period, they are not directly endangered by the raven. We speculate that the responsiveness of adult grouse to raven calls might be explained as a learned response in juveniles from nesting hens that is then preserved in adults, or by a known association between the raven and the red fox. In that case, calls of the raven would be rather interpreted as a warning signal of probable proximity of the red fox.
format: application/pdf
format: text/html
creator: Richard Policht
creator: Vlastimil Hart
creator: Denis Goncharov
creator: Peter Surový
creator: Vladimír Hanzal
creator: Jaroslav Červený
creator: Hynek Burda
subject: Animal Behavior
subject: Conservation Biology
subject: Zoology
description: doi:10.7717/peerj.6533
publisher: PeerJ Inc.
rights: © 2019 Policht et al.
abstract: Corvids count among the important predators of bird nests. They are vocal animals and one can expect that birds threatened by their predation, such as black grouse, are sensitive to and recognize their calls. Within the framework of field studies, we noticed that adult black grouse were alerted by raven calls during periods outside the breeding season. Since black grouse are large, extremely precocial birds, this reaction can hardly be explained by sensitization specifically to the threat of nest predation by ravens. This surprising observation prompted us to study the phenomenon more systematically. According to our knowledge, the response of birds to corvid vocalization has been studied in altricial birds only. We tested whether the black grouse distinguishes and responds specifically to playback calls of the common raven. Black grouse recognized raven calls and were alerted, displaying typical neck stretching, followed by head scanning, and eventual escape. Surprisingly, males tended to react faster and exhibited a longer duration of vigilance behavior compared to females. Although raven calls are recognized by adult black grouse out of the nesting period, they are not directly endangered by the raven. We speculate that the responsiveness of adult grouse to raven calls might be explained as a learned response in juveniles from nesting hens that is then preserved in adults, or by a known association between the raven and the red fox. In that case, calls of the raven would be rather interpreted as a warning signal of probable proximity of the red fox.
bibliographic citation: Policht et al. (2019) Vocal recognition of a nest-predator in black grouse. PeerJ 7:e6533 https://doi.org/10.7717/peerj.6533
date submitted: 2018-12-12
date accepted: 2019-01-26
issued: 2019-03-15
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Policht
  given name: Richard
author list: Agent
  family name: Hart
  given name: Vlastimil
author list: Agent
  family name: Goncharov
  given name: Denis
author list: Agent
  family name: Surový
  given name: Peter
author list: Agent
  family name: Hanzal
  given name: Vladimír
author list: Agent
  family name: Červený
  given name: Jaroslav
author list: Agent
  family name: Burda
  given name: Hynek
doi: 10.7717/peerj.6533
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-03-15
copyright: ©2019 Policht et al.
attribution name: Policht et al.

Phylogenetic signal analysis in the basicranium of Ursidae (Carnivora, Mammalia)
type: item
type: AcademicArticle
description: Ursidae is a monophyletic group comprised of three subfamilies: Tremarctinae, Ursinae and Ailuropodinae, all of which have a rich geographical distribution. The phylogenetic relationships within the Ursidae group have been underexamined, especially regarding morphological traits such as the basicranium. Importantly, the basicranium is a highly complex region that covers a small portion of the skull, combining both structural and functional aspects that determine its morphology. Phylogenetic hypotheses of the Ursidae (including Tremarctinae) have been made based on morphological characters that considers skull, mandible and teeth features, while specific characters of the auditory region and basicranium have not been taken into account. To do this, we analyse the shape and size macroevolution of the basicranium of Ursidae, testing its morphological disparity in a phylogenetic context, which is quantified by means of the phylogenetic signal. We investigated phylogenetical autocorrelation by shape (depicted by Principal Components Analysis scores from previous published analyses) and basicranium size (depicted by centroid size, CS) using an orthonormal decomposition analysis and Abouheif C mean. The main advantages of these methods are that they rely exclusively on cladogram topology and do not require branch-length estimates. Also, an optimisation of the ancestral nodes was performed using TNT 1.5 software. In relation to the phylogenetic signal, both methods showed similar results: the presence of autocorrelation was detected in PC1 and PC2, while in PC3, PC4 and PC5 and in the size of the basicranium (CS), the absence of autocorrelation occurred. The most significant nodes (where there is autocorrelation) are the basal nodes ‘Ursidae’ and ‘Ursinae-Tremarctinae’. Within this last group, distinctive basicranium morphology is observed, being more conservative in Tremarctinae than in Ursinae. The differences between these subfamilies could be related to historical event…
format: application/pdf
format: text/html
creator: María Eugenia Arnaudo
creator: Néstor Toledo
creator: Leopoldo Soibelzon
creator: Paula Bona
subject: Evolutionary Studies
subject: Paleontology
description: doi:10.7717/peerj.6597
publisher: PeerJ Inc.
rights: © 2019 Arnaudo et al.
abstract: Ursidae is a monophyletic group comprised of three subfamilies: Tremarctinae, Ursinae and Ailuropodinae, all of which have a rich geographical distribution. The phylogenetic relationships within the Ursidae group have been underexamined, especially regarding morphological traits such as the basicranium. Importantly, the basicranium is a highly complex region that covers a small portion of the skull, combining both structural and functional aspects that determine its morphology. Phylogenetic hypotheses of the Ursidae (including Tremarctinae) have been made based on morphological characters that considers skull, mandible and teeth features, while specific characters of the auditory region and basicranium have not been taken into account. To do this, we analyse the shape and size macroevolution of the basicranium of Ursidae, testing its morphological disparity in a phylogenetic context, which is quantified by means of the phylogenetic signal. We investigated phylogenetical autocorrelation by shape (depicted by Principal Components Analysis scores from previous published analyses) and basicranium size (depicted by centroid size, CS) using an orthonormal decomposition analysis and Abouheif C mean. The main advantages of these methods are that they rely exclusively on cladogram topology and do not require branch-length estimates. Also, an optimisation of the ancestral nodes was performed using TNT 1.5 software. In relation to the phylogenetic signal, both methods showed similar results: the presence of autocorrelation was detected in PC1 and PC2, while in PC3, PC4 and PC5 and in the size of the basicranium (CS), the absence of autocorrelation occurred. The most significant nodes (where there is autocorrelation) are the basal nodes ‘Ursidae’ and ‘Ursinae-Tremarctinae’. Within this last group, distinctive basicranium morphology is observed, being more conservative in Tremarctinae than in Ursinae. The differences between these subfamilies could be related to historical event…
bibliographic citation: Arnaudo et al. (2019) Phylogenetic signal analysis in the basicranium of Ursidae (Carnivora, Mammalia). PeerJ 7:e6597 https://doi.org/10.7717/peerj.6597
date submitted: 2018-03-08
date accepted: 2019-02-09
issued: 2019-03-15
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Arnaudo
  given name: María Eugenia
author list: Agent
  family name: Toledo
  given name: Néstor
author list: Agent
  family name: Soibelzon
  given name: Leopoldo
author list: Agent
  family name: Bona
  given name: Paula
doi: 10.7717/peerj.6597
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-03-15
copyright: ©2019 Arnaudo et al.
attribution name: Arnaudo et al.

Predicting electrocardiogram interpretation performance in Advanced Cardiovascular Life Support simulation: comparing knowledge tests and simulation performance among Mexican medical students
type: item
type: AcademicArticle
description: Background Simulation plays a key role in assessing performance in Advanced Cardiovascular Life Support (ACLS). Traditional knowledge tests are also important for assessing the cognitive elements of ACLS performance. However, the association between the two has not been established. In this study, we focus on one important element in ACLS—interpretation of electrocardiograms (ECG)—and the potential of knowledge tests to serve as predictors of improvement in ACLS performance. Methods We looked at the correlation between Mexican medical students’ improvement in ECG interpretation performance in ACLS megacode simulations (from the start of the semester to the end of the semester), and their scores on ECG interpretation knowledge tests. Results We found significant improvement in ECG interpretation in ACLS megacode simulation (from pre-semester to post-semester), but this was not predicted by the ECG interpretation knowledge test scores. The correlation was .079 (p = 0.66). Conclusions These results suggest that even cognitive tasks such as ECG interpretation can be expressed and assessed differently in simulation versus traditional knowledge testing.
format: application/pdf
format: text/html
creator: Michael William Smith
creator: David Abarca Rondero
subject: Cardiology
subject: Emergency and Critical Care
subject: Science and Medical Education
description: doi:10.7717/peerj.6632
publisher: PeerJ Inc.
rights: © 2019 Smith and Abarca Rondero
abstract: Background Simulation plays a key role in assessing performance in Advanced Cardiovascular Life Support (ACLS). Traditional knowledge tests are also important for assessing the cognitive elements of ACLS performance. However, the association between the two has not been established. In this study, we focus on one important element in ACLS—interpretation of electrocardiograms (ECG)—and the potential of knowledge tests to serve as predictors of improvement in ACLS performance. Methods We looked at the correlation between Mexican medical students’ improvement in ECG interpretation performance in ACLS megacode simulations (from the start of the semester to the end of the semester), and their scores on ECG interpretation knowledge tests. Results We found significant improvement in ECG interpretation in ACLS megacode simulation (from pre-semester to post-semester), but this was not predicted by the ECG interpretation knowledge test scores. The correlation was .079 (p = 0.66). Conclusions These results suggest that even cognitive tasks such as ECG interpretation can be expressed and assessed differently in simulation versus traditional knowledge testing.
bibliographic citation: Smith et al. (2019) Predicting electrocardiogram interpretation performance in Advanced Cardiovascular Life Support simulation: comparing knowledge tests and simulation performance among Mexican medical students. PeerJ 7:e6632 https://doi.org/10.7717/peerj.6632
date submitted: 2018-10-16
date accepted: 2019-02-16
issued: 2019-03-15
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Smith
  given name: Michael William
author list: Agent
  family name: Abarca Rondero
  given name: David
doi: 10.7717/peerj.6632
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-03-15
copyright: © 2019 Smith and Abarca Rondero
attribution name: Smith and Abarca Rondero

Genome-wide analysis of the Catalpa bungei caffeic acid O-methyltransferase (COMT) gene family: identification and expression profiles in normal, tension, and opposite wood
type: item
type: AcademicArticle
description: Caffeic acid O-methyltransferase (COMT) is an important protein that participates in lignin synthesis and is associated with the ratio of G-/S-type lignin in plants. COMTs are associated with the wood properties of forest trees; however, little known about the COMT family in Catalpa bungei, a valuable timber tree species in China . We performed a comprehensive analysis of COMT genes in the C. bungei genome by describing the gene structure and phylogenetic relationships of each family member using bioinformatics-based methods. A total of 23 putative COMT genes were identified using the conserved domain sequences and amino acid sequences of COMTs from Arabidopsis thaliana and Populus trichocarpa as probes. Phylogenetic analysis showed that 23 CbuCOMTs can be divided into three groups based on their structural characteristics; five conserved domains were found in the COMT family. Promoter analysis indicated that the CbuCOMT promoters included various cis-acting elements related to growth and development. Real-time quantitative polymerase chain reaction (PCR) analysis showed differential expression among CbuCOMTs. CbuCOMT2, 7, 8, 9, 10, 12, 13, 14, 21, and 23 were mainly expressed in xylem. Only CbuCOMT23 was significantly downregulated in tension wood and upregulated in opposite wood compared to normal wood. Our study provides new information about the CbuCOMT gene family and will facilitate functional characterisation in further research.
format: application/pdf
format: text/html
creator: Nan Lu
creator: Wenjun Ma
creator: Donghua Han
creator: Ying Liu
creator: Zhi Wang
creator: Nan Wang
creator: Guijuan Yang
creator: Guanzheng Qu
creator: Qiuxia Wang
creator: Kun Zhao
creator: Junhui Wang
subject: Agricultural Science
subject: Forestry
description: doi:10.7717/peerj.6520
publisher: PeerJ Inc.
rights: © 2019 Lu et al.
abstract: Caffeic acid O-methyltransferase (COMT) is an important protein that participates in lignin synthesis and is associated with the ratio of G-/S-type lignin in plants. COMTs are associated with the wood properties of forest trees; however, little known about the COMT family in Catalpa bungei, a valuable timber tree species in China . We performed a comprehensive analysis of COMT genes in the C. bungei genome by describing the gene structure and phylogenetic relationships of each family member using bioinformatics-based methods. A total of 23 putative COMT genes were identified using the conserved domain sequences and amino acid sequences of COMTs from Arabidopsis thaliana and Populus trichocarpa as probes. Phylogenetic analysis showed that 23 CbuCOMTs can be divided into three groups based on their structural characteristics; five conserved domains were found in the COMT family. Promoter analysis indicated that the CbuCOMT promoters included various cis-acting elements related to growth and development. Real-time quantitative polymerase chain reaction (PCR) analysis showed differential expression among CbuCOMTs. CbuCOMT2, 7, 8, 9, 10, 12, 13, 14, 21, and 23 were mainly expressed in xylem. Only CbuCOMT23 was significantly downregulated in tension wood and upregulated in opposite wood compared to normal wood. Our study provides new information about the CbuCOMT gene family and will facilitate functional characterisation in further research.
bibliographic citation: Lu et al. (2019) Genome-wide analysis of the Catalpa bungei caffeic acid O-methyltransferase (COMT) gene family: identification and expression profiles in normal, tension, and opposite wood. PeerJ 7:e6520 https://doi.org/10.7717/peerj.6520
date submitted: 2018-11-20
date accepted: 2019-01-22
issued: 2019-03-14
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Lu
  given name: Nan
author list: Agent
  family name: Ma
  given name: Wenjun
author list: Agent
  family name: Han
  given name: Donghua
author list: Agent
  family name: Liu
  given name: Ying
author list: Agent
  family name: Wang
  given name: Zhi
author list: Agent
  family name: Wang
  given name: Nan
author list: Agent
  family name: Yang
  given name: Guijuan
author list: Agent
  family name: Qu
  given name: Guanzheng
author list: Agent
  family name: Wang
  given name: Qiuxia
author list: Agent
  family name: Zhao
  given name: Kun
author list: Agent
  family name: Wang
  given name: Junhui
doi: 10.7717/peerj.6520
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-03-14
copyright: ©2019 Lu et al.
attribution name: Lu et al.

Identification of four hub genes associated with adrenocortical carcinoma progression by WGCNA
type: item
type: AcademicArticle
description: Background Adrenocortical carcinoma (ACC) is a rare and aggressive malignant cancer in the adrenal cortex with poor prognosis. Though previous research has attempted to elucidate the progression of ACC, its molecular mechanism remains poorly understood. Methods Gene transcripts per million (TPM) data were downloaded from the UCSC Xena database, which included ACC (The Cancer Genome Atlas, n = 77) and normal samples (Genotype Tissue Expression, n = 128). We used weighted gene co-expression network analysis to identify gene connections. Overall survival (OS) was determined using the univariate Cox model. A protein–protein interaction (PPI) network was constructed by the search tool for the retrieval of interacting genes. Results To determine the critical genes involved in ACC progression, we obtained 2,953 significantly differentially expressed genes and nine modules. Among them, the blue module demonstrated significant correlation with the “Stage” of ACC. Enrichment analysis revealed that genes in the blue module were mainly enriched in cell division, cell cycle, and DNA replication. Combined with the PPI and co-expression networks, we identified four hub genes (i.e., TOP2A, TTK, CHEK1, and CENPA) that were highly expressed in ACC and negatively correlated with OS. Thus, these identified genes may play important roles in the progression of ACC and serve as potential biomarkers for future diagnosis.
format: application/pdf
format: text/html
creator: Wang-Xiao Xia
creator: Qin Yu
creator: Gong-Hua Li
creator: Yao-Wen Liu
creator: Fu-Hui Xiao
creator: Li-Qin Yang
creator: Zia Ur Rahman
creator: Hao-Tian Wang
creator: Qing-Peng Kong
subject: Bioinformatics
subject: Genetics
subject: Oncology
description: doi:10.7717/peerj.6555
publisher: PeerJ Inc.
rights: © 2019 Xia et al.
abstract: Background Adrenocortical carcinoma (ACC) is a rare and aggressive malignant cancer in the adrenal cortex with poor prognosis. Though previous research has attempted to elucidate the progression of ACC, its molecular mechanism remains poorly understood. Methods Gene transcripts per million (TPM) data were downloaded from the UCSC Xena database, which included ACC (The Cancer Genome Atlas, n = 77) and normal samples (Genotype Tissue Expression, n = 128). We used weighted gene co-expression network analysis to identify gene connections. Overall survival (OS) was determined using the univariate Cox model. A protein–protein interaction (PPI) network was constructed by the search tool for the retrieval of interacting genes. Results To determine the critical genes involved in ACC progression, we obtained 2,953 significantly differentially expressed genes and nine modules. Among them, the blue module demonstrated significant correlation with the “Stage” of ACC. Enrichment analysis revealed that genes in the blue module were mainly enriched in cell division, cell cycle, and DNA replication. Combined with the PPI and co-expression networks, we identified four hub genes (i.e., TOP2A, TTK, CHEK1, and CENPA) that were highly expressed in ACC and negatively correlated with OS. Thus, these identified genes may play important roles in the progression of ACC and serve as potential biomarkers for future diagnosis.
bibliographic citation: Xia et al. (2019) Identification of four hub genes associated with adrenocortical carcinoma progression by WGCNA. PeerJ 7:e6555 https://doi.org/10.7717/peerj.6555
date submitted: 2018-10-25
date accepted: 2019-02-02
issued: 2019-03-14
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Xia
  given name: Wang-Xiao
author list: Agent
  family name: Yu
  given name: Qin
author list: Agent
  family name: Li
  given name: Gong-Hua
author list: Agent
  family name: Liu
  given name: Yao-Wen
author list: Agent
  family name: Xiao
  given name: Fu-Hui
author list: Agent
  family name: Yang
  given name: Li-Qin
author list: Agent
  family name: Rahman
  given name: Zia Ur
author list: Agent
  family name: Wang
  given name: Hao-Tian
author list: Agent
  family name: Kong
  given name: Qing-Peng
doi: 10.7717/peerj.6555
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-03-14
copyright: © 2019 Xia et al.
attribution name: Xia et al.

Acute toxicity and responses of antioxidant systems to dibutyl phthalate in neonate and adult Daphnia magna
type: item
type: AcademicArticle
description: Dibutyl phthalate (DBP) poses a severe threat to aquatic ecosystems, introducing hazards to both aquatic species and human health. The ecotoxic effects of DBP on aquatic organisms have not been fully investigated. This study investigates acute toxicity, oxidative damage, and antioxidant enzyme parameters in neonate and adult Daphnia magna exposed to DBP. The obtained results show comparable DBP toxic responses in neonates and adults. The median lethal concentrations (LC50) of DBP in neonates exposed for 24 and 48 h were 3.48 and 2.83 mg/L, respectively. The LC50 of adults for the same DBP exposure durations were 4.92 and 4.31 mg/L, respectively. Increased hydrogen peroxide and malondialdehyde were found in neonates and adults at both 24 and 48 h, while the total antioxidant capacity decreased. Superoxide dismutase activity increased significantly in neonates and adults exposed to 0.5 mg/L DBP, and subsequently diminished at higher DBP concentrations and prolonged exposure. Catalase and glutathione S-transferases activities both decreased markedly in neonates and adults. The changes observed were found to be time and concentration dependent. Overall, these data indicated that the acute toxic effects of DBP exposure on neonates were more pronounced than in adults, and oxidative injury may be the main mechanism of DBP toxicity. These results provide a functional link for lipid peroxidation, antioxidant capacity, and antioxidant enzyme levels in the Daphnia magna response to DBP exposure.
format: application/pdf
format: text/html
creator: Chenchen Shen
creator: Jie Wei
creator: Tianyi Wang
creator: Yuan Wang
subject: Ecotoxicology
subject: Freshwater Biology
description: doi:10.7717/peerj.6584
publisher: PeerJ Inc.
rights: © 2019 Shen et al.
abstract: Dibutyl phthalate (DBP) poses a severe threat to aquatic ecosystems, introducing hazards to both aquatic species and human health. The ecotoxic effects of DBP on aquatic organisms have not been fully investigated. This study investigates acute toxicity, oxidative damage, and antioxidant enzyme parameters in neonate and adult Daphnia magna exposed to DBP. The obtained results show comparable DBP toxic responses in neonates and adults. The median lethal concentrations (LC50) of DBP in neonates exposed for 24 and 48 h were 3.48 and 2.83 mg/L, respectively. The LC50 of adults for the same DBP exposure durations were 4.92 and 4.31 mg/L, respectively. Increased hydrogen peroxide and malondialdehyde were found in neonates and adults at both 24 and 48 h, while the total antioxidant capacity decreased. Superoxide dismutase activity increased significantly in neonates and adults exposed to 0.5 mg/L DBP, and subsequently diminished at higher DBP concentrations and prolonged exposure. Catalase and glutathione S-transferases activities both decreased markedly in neonates and adults. The changes observed were found to be time and concentration dependent. Overall, these data indicated that the acute toxic effects of DBP exposure on neonates were more pronounced than in adults, and oxidative injury may be the main mechanism of DBP toxicity. These results provide a functional link for lipid peroxidation, antioxidant capacity, and antioxidant enzyme levels in the Daphnia magna response to DBP exposure.
bibliographic citation: Shen et al. (2019) Acute toxicity and responses of antioxidant systems to dibutyl phthalate in neonate and adult Daphnia magna. PeerJ 7:e6584 https://doi.org/10.7717/peerj.6584
date submitted: 2018-11-25
date accepted: 2019-02-06
issued: 2019-03-14
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Shen
  given name: Chenchen
author list: Agent
  family name: Wei
  given name: Jie
author list: Agent
  family name: Wang
  given name: Tianyi
author list: Agent
  family name: Wang
  given name: Yuan
doi: 10.7717/peerj.6584
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-03-14
copyright: © 2019 Shen et al.
attribution name: Shen et al.

Staphylococcus spp. associated with subclinical bovine mastitis in central and northeast provinces of Thailand
type: item
type: AcademicArticle
description: Background Staphylococcus spp. are major cause of bovine mastitis (BM) worldwide leading to economic damage to dairy farms and public health threat. Recently, a newly emerged Staphylococcus argenteus has been found as a human and animal pathogen. Molecular characteristics, virulence and antibiotic resistant phenotypes of bacteria causing BM in Thailand are rare. This study aimed to investigated Staphylococcus spp. associated with subclinical bovine mastitis (SCM) in Thailand. Methods Milk samples were collected from 224 cows of 52 dairy herds in four central and northeast provinces. Total somatic cell counts (SCC) and California mastitis test (CMT) were used to identify SCM cows. Milk samples were cultured for Staphylococcus spp. Coagulase-positive isolates were subjected to pulsed-field gel electrophoresis (PFGE) and multilocus sequence typing (MLST). Organisms suspected as S. argenteus were verified by detecting nonribosomal peptide synthetase gene. All isolates were checked for antibiograms and the presence of various virulence genes. Results From the 224 milk samples of 224 cows, 132 (59%) were positive for SCM by SCC and CMT and 229 staphylococcal isolates were recovered. They were 32 coagulase-positive (24 S. aureus and eight S. argenteus) and 197 coagulase-negative. PFGE of the S. aureus and S. argenteus revealed 11 clusters and a non-typeable pattern. MLST of representatives of the 11 PFGE clusters, three PFGE non-typeable S. aureus isolates from different locations and S. argenteus showed 12 sequence types. The eight S. argenteus isolates belonged to ST1223 (three isolates), ST2250 (two isolates), and ST2793 (two isolates). The antimicrobial tests identified 11 (46%) methicillin-resistant S. aureus and 25 (13%) methicillin-resistant coagulase-negative isolates, while seven S. argenteus were methicillin-susceptible and one isolate was methicillin-resistant. All of the 229 isolates were multiply resistant to other antibiotics. The most prevalent virulence gen…
format: application/pdf
format: text/html
creator: Natapol Pumipuntu
creator: Witawat Tunyong
creator: Narisara Chantratita
creator: Pornphan Diraphat
creator: Pornpan Pumirat
creator: Nitat Sookrung
creator: Wanpen Chaicumpa
creator: Nitaya Indrawattana
subject: Agricultural Science
subject: Microbiology
description: doi:10.7717/peerj.6587
publisher: PeerJ Inc.
rights: © 2019 Pumipuntu et al.
abstract: Background Staphylococcus spp. are major cause of bovine mastitis (BM) worldwide leading to economic damage to dairy farms and public health threat. Recently, a newly emerged Staphylococcus argenteus has been found as a human and animal pathogen. Molecular characteristics, virulence and antibiotic resistant phenotypes of bacteria causing BM in Thailand are rare. This study aimed to investigated Staphylococcus spp. associated with subclinical bovine mastitis (SCM) in Thailand. Methods Milk samples were collected from 224 cows of 52 dairy herds in four central and northeast provinces. Total somatic cell counts (SCC) and California mastitis test (CMT) were used to identify SCM cows. Milk samples were cultured for Staphylococcus spp. Coagulase-positive isolates were subjected to pulsed-field gel electrophoresis (PFGE) and multilocus sequence typing (MLST). Organisms suspected as S. argenteus were verified by detecting nonribosomal peptide synthetase gene. All isolates were checked for antibiograms and the presence of various virulence genes. Results From the 224 milk samples of 224 cows, 132 (59%) were positive for SCM by SCC and CMT and 229 staphylococcal isolates were recovered. They were 32 coagulase-positive (24 S. aureus and eight S. argenteus) and 197 coagulase-negative. PFGE of the S. aureus and S. argenteus revealed 11 clusters and a non-typeable pattern. MLST of representatives of the 11 PFGE clusters, three PFGE non-typeable S. aureus isolates from different locations and S. argenteus showed 12 sequence types. The eight S. argenteus isolates belonged to ST1223 (three isolates), ST2250 (two isolates), and ST2793 (two isolates). The antimicrobial tests identified 11 (46%) methicillin-resistant S. aureus and 25 (13%) methicillin-resistant coagulase-negative isolates, while seven S. argenteus were methicillin-susceptible and one isolate was methicillin-resistant. All of the 229 isolates were multiply resistant to other antibiotics. The most prevalent virulence gen…
bibliographic citation: Pumipuntu et al. (2019) Staphylococcus spp. associated with subclinical bovine mastitis in central and northeast provinces of Thailand. PeerJ 7:e6587 https://doi.org/10.7717/peerj.6587
date submitted: 2018-11-12
date accepted: 2019-02-10
issued: 2019-03-14
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Pumipuntu
  given name: Natapol
author list: Agent
  family name: Tunyong
  given name: Witawat
author list: Agent
  family name: Chantratita
  given name: Narisara
author list: Agent
  family name: Diraphat
  given name: Pornphan
author list: Agent
  family name: Pumirat
  given name: Pornpan
author list: Agent
  family name: Sookrung
  given name: Nitat
author list: Agent
  family name: Chaicumpa
  given name: Wanpen
author list: Agent
  family name: Indrawattana
  given name: Nitaya
doi: 10.7717/peerj.6587
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-03-14
copyright: © 2019 Pumipuntu et al.
attribution name: Pumipuntu et al.

Circadian disruption and divergent microbiota acquisition under extended photoperiod regimens in chicken
type: item
type: AcademicArticle
description: The gut microbiota is crucial for metabolic homeostasis, immunity, growth and overall health, and it is recognized that early-life microbiota acquisition is a pivotal event for later-life health. Recent studies show that gut microbiota diversity and functional activity are synchronized with the host circadian rhythms in healthy individuals, and circadian disruption elicits dysbiosis in mammalian models. However, no studies have determined the associations between circadian disruption in early life, microbiota colonization, and the consequences for microbiota structure in birds. Chickens, as a major source of protein around the world, are one of the most important agricultural species, and their gut and metabolic health are significant concerns. The poultry industry routinely employs extended photoperiods (>18 h light) as a management tool, and their impacts on the chicken circadian, its role in gut microbiota acquisition in early life (first 3 weeks of life), and consequences for later life microbiota structure remain unknown. In this study, the objectives were to (a) characterize circadian activity under two different light regimes in layer chicken (12/12 h′ Light/Dark (LD) and 23/1 h LD), (b) characterize gut microbiota acquisition and composition in the first 4 weeks of life, (c) determine if gut microbiota oscillate in synchrony with the host circadian rhythm, and (d) to determine if fecal microbiota is representative of cecal microbiota in early life. Expression of clock genes (clock, bmal1, and per2) was assayed, and fecal and cecal microbiotas were characterized using 16S rRNA gene amplicon analyses from birds raised under two photoperiod treatments. Chickens raised under 12/12 LD photoperiods exhibited rhythmic clock gene activity, which was absent in birds raised under the extended (23/1 LD) photoperiod. There was differential microbiota acquisition under different photoperiod regimes in newly hatched chicks. Gut microbiota members showed a similar oscillat…
format: application/pdf
format: text/html
creator: Anne-Sophie Charlotte Hieke
creator: Shawna Marie Hubert
creator: Giridhar Athrey
subject: Agricultural Science
subject: Genomics
subject: Microbiology
description: doi:10.7717/peerj.6592
publisher: PeerJ Inc.
rights: © 2019 Hieke et al.
abstract: The gut microbiota is crucial for metabolic homeostasis, immunity, growth and overall health, and it is recognized that early-life microbiota acquisition is a pivotal event for later-life health. Recent studies show that gut microbiota diversity and functional activity are synchronized with the host circadian rhythms in healthy individuals, and circadian disruption elicits dysbiosis in mammalian models. However, no studies have determined the associations between circadian disruption in early life, microbiota colonization, and the consequences for microbiota structure in birds. Chickens, as a major source of protein around the world, are one of the most important agricultural species, and their gut and metabolic health are significant concerns. The poultry industry routinely employs extended photoperiods (>18 h light) as a management tool, and their impacts on the chicken circadian, its role in gut microbiota acquisition in early life (first 3 weeks of life), and consequences for later life microbiota structure remain unknown. In this study, the objectives were to (a) characterize circadian activity under two different light regimes in layer chicken (12/12 h′ Light/Dark (LD) and 23/1 h LD), (b) characterize gut microbiota acquisition and composition in the first 4 weeks of life, (c) determine if gut microbiota oscillate in synchrony with the host circadian rhythm, and (d) to determine if fecal microbiota is representative of cecal microbiota in early life. Expression of clock genes (clock, bmal1, and per2) was assayed, and fecal and cecal microbiotas were characterized using 16S rRNA gene amplicon analyses from birds raised under two photoperiod treatments. Chickens raised under 12/12 LD photoperiods exhibited rhythmic clock gene activity, which was absent in birds raised under the extended (23/1 LD) photoperiod. There was differential microbiota acquisition under different photoperiod regimes in newly hatched chicks. Gut microbiota members showed a similar oscillat…
bibliographic citation: Hieke et al. (2019) Circadian disruption and divergent microbiota acquisition under extended photoperiod regimens in chicken. PeerJ 7:e6592 https://doi.org/10.7717/peerj.6592
date submitted: 2018-08-09
date accepted: 2019-02-09
issued: 2019-03-14
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Hieke
  given name: Anne-Sophie Charlotte
author list: Agent
  family name: Hubert
  given name: Shawna Marie
author list: Agent
  family name: Athrey
  given name: Giridhar
doi: 10.7717/peerj.6592
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-03-14
copyright: © 2019 Hieke et al.
attribution name: Hieke et al.

Recognizing two new Hippolyte species (Decapoda, Caridea, Hippolytidae) from the South China Sea based on integrative taxonomy
type: item
type: AcademicArticle
description: Hippolyte shrimps exhibit abundant biological diversity and display great ecological significance in seaweed bed ecosystems. Dozens of Hippolyte specimens were collected from Hainan Island and the Xisha Islands in the South China Sea. Detailed examination indicates that some of these specimens represent new Hippolyte species. Based on morphological, genetic, and ecological data, Hippolyte chacei sp. nov. and H. nanhaiensis sp. nov. are described. H. chacei sp. nov. was collected from the Sargassum sp. biotope in Hainan Island and is distinguished from congeners by its unique mandible and the dactylus of the third to fifth pereiopods; this species has a basal position in the Indo-West Pacific species clade in the phylogenetic tree which is reconstructed based on 16S rRNA gene. H. nanhaiensis sp. nov. was collected from the biotopes of Galaxaura sp. or Halimeda sp. in the Xisha Islands, and it differs from congeners in a series of characters associated with rostrum, scaphocerite, antennular peduncle, and spines on the dactylus of the third to fifth pereiopods. Additionally, it is sister to H. australiensis in the phylogenetic tree. A key to identifying mature female Hippolyte species of the Indo-West Pacific and neighboring seas is provided.
format: application/pdf
format: text/html
creator: Zhi-Bin Gan
creator: Xin-Zheng Li
subject: Biodiversity
subject: Genetics
subject: Marine Biology
subject: Taxonomy
description: doi:10.7717/peerj.6605
publisher: PeerJ Inc.
rights: © 2019 Gan and Li
abstract: Hippolyte shrimps exhibit abundant biological diversity and display great ecological significance in seaweed bed ecosystems. Dozens of Hippolyte specimens were collected from Hainan Island and the Xisha Islands in the South China Sea. Detailed examination indicates that some of these specimens represent new Hippolyte species. Based on morphological, genetic, and ecological data, Hippolyte chacei sp. nov. and H. nanhaiensis sp. nov. are described. H. chacei sp. nov. was collected from the Sargassum sp. biotope in Hainan Island and is distinguished from congeners by its unique mandible and the dactylus of the third to fifth pereiopods; this species has a basal position in the Indo-West Pacific species clade in the phylogenetic tree which is reconstructed based on 16S rRNA gene. H. nanhaiensis sp. nov. was collected from the biotopes of Galaxaura sp. or Halimeda sp. in the Xisha Islands, and it differs from congeners in a series of characters associated with rostrum, scaphocerite, antennular peduncle, and spines on the dactylus of the third to fifth pereiopods. Additionally, it is sister to H. australiensis in the phylogenetic tree. A key to identifying mature female Hippolyte species of the Indo-West Pacific and neighboring seas is provided.
bibliographic citation: Gan et al. (2019) Recognizing two new Hippolyte species (Decapoda, Caridea, Hippolytidae) from the South China Sea based on integrative taxonomy. PeerJ 7:e6605 https://doi.org/10.7717/peerj.6605
date submitted: 2018-12-04
date accepted: 2019-02-11
issued: 2019-03-14
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Gan
  given name: Zhi-Bin
author list: Agent
  family name: Li
  given name: Xin-Zheng
doi: 10.7717/peerj.6605
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-03-14
copyright: © 2019 Gan and Li
attribution name: Gan and Li

HOXC6 promotes migration, invasion and proliferation of esophageal squamous cell carcinoma cells via modulating expression of genes involved in malignant phenotypes
type: item
type: AcademicArticle
description: Background HOXC6 is a member of the HOX gene family. The elevated expression of this gene occurs in prostate and breast cancers. However, the role of HOXC6 in esophageal squamous cell carcinoma (ESCC) remains largely uninvestigated. Methods The expression of HOXC6 was examined by immunohistochemistry, quantitative real-time PCR and immunoblotting assays. The lentivirus-mediated expression of HOXC6 was verified at mRNA and protein levels. Wound healing and Matrigel assays were performed to assess the effect of HOXC6 on the migration and invasion of cancer cells. The growth curving, CCK8, and colony formation assays were utilized to access the proliferation capacities. RNA-seq was performed to evaluate the downstream targets of HOXC6. Bioinformatic tool was used to analyze the gene expression. Results HOXC6 was highly expressed in ESCC tissues. HOXC6 overexpression promoted the migration, invasion, and proliferation of both Eca109 and TE10 cells. There were 2,155 up-regulated and 759 down-regulated genes in Eca109-HOXC6 cells and 95 up-regulated and 47 down-regulated genes in TE10-HOXC6 cells compared with the results of control. Interestingly, there were only 20 common genes, including 17 up-regulated and three down-regulated genes with similar changes upon HOXC6 transfection in both cell lines. HOXC6 activated several crucial genes implicated in the malignant phenotype of cancer cells. Discussion HOXC6 is highly expressed in ESCC and promotes malignant phenotype of ESCC cells. HOXC6 can be used as a new therapeutic target of ESCC.
format: application/pdf
format: text/html
creator: Li Tang
creator: Yong Cao
creator: Xueqin Song
creator: Xiaoyan Wang
creator: Yan Li
creator: Minglan Yu
creator: Mingying Li
creator: Xu Liu
creator: Fang Huang
creator: Feng Chen
creator: Haisu Wan
subject: Cell Biology
subject: Molecular Biology
subject: Oncology
description: doi:10.7717/peerj.6607
publisher: PeerJ Inc.
rights: © 2019 Tang et al.
abstract: Background HOXC6 is a member of the HOX gene family. The elevated expression of this gene occurs in prostate and breast cancers. However, the role of HOXC6 in esophageal squamous cell carcinoma (ESCC) remains largely uninvestigated. Methods The expression of HOXC6 was examined by immunohistochemistry, quantitative real-time PCR and immunoblotting assays. The lentivirus-mediated expression of HOXC6 was verified at mRNA and protein levels. Wound healing and Matrigel assays were performed to assess the effect of HOXC6 on the migration and invasion of cancer cells. The growth curving, CCK8, and colony formation assays were utilized to access the proliferation capacities. RNA-seq was performed to evaluate the downstream targets of HOXC6. Bioinformatic tool was used to analyze the gene expression. Results HOXC6 was highly expressed in ESCC tissues. HOXC6 overexpression promoted the migration, invasion, and proliferation of both Eca109 and TE10 cells. There were 2,155 up-regulated and 759 down-regulated genes in Eca109-HOXC6 cells and 95 up-regulated and 47 down-regulated genes in TE10-HOXC6 cells compared with the results of control. Interestingly, there were only 20 common genes, including 17 up-regulated and three down-regulated genes with similar changes upon HOXC6 transfection in both cell lines. HOXC6 activated several crucial genes implicated in the malignant phenotype of cancer cells. Discussion HOXC6 is highly expressed in ESCC and promotes malignant phenotype of ESCC cells. HOXC6 can be used as a new therapeutic target of ESCC.
bibliographic citation: Tang et al. (2019) HOXC6 promotes migration, invasion and proliferation of esophageal squamous cell carcinoma cells via modulating expression of genes involved in malignant phenotypes. PeerJ 7:e6607 https://doi.org/10.7717/peerj.6607
date submitted: 2018-11-02
date accepted: 2019-02-10
issued: 2019-03-14
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Tang
  given name: Li
author list: Agent
  family name: Cao
  given name: Yong
author list: Agent
  family name: Song
  given name: Xueqin
author list: Agent
  family name: Wang
  given name: Xiaoyan
author list: Agent
  family name: Li
  given name: Yan
author list: Agent
  family name: Yu
  given name: Minglan
author list: Agent
  family name: Li
  given name: Mingying
author list: Agent
  family name: Liu
  given name: Xu
author list: Agent
  family name: Huang
  given name: Fang
author list: Agent
  family name: Chen
  given name: Feng
author list: Agent
  family name: Wan
  given name: Haisu
doi: 10.7717/peerj.6607
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-03-14
copyright: © 2019 Tang et al.
attribution name: Tang et al.

Fatty liver is a risk factor for liver metastasis in Chinese patients with non-small cell lung cancer
type: item
type: AcademicArticle
description: Background The hepatic microenvironment, which may include chronic inflammation and fibrosis, is considered to contribute to the development of liver metastases. Hepatic steatosis (HS) might cause liver inflammation and fibrosis. However, to date, no studies have investigated the impact of HS on liver metastasis in patients with non-small cell lung cancer (NSCLC). Methods A retrospective cohort study was performed on patients who received NSCLC treatment at two hospitals affiliated with the Southern Medical University from January 2005 to December 2015. The patients were grouped according to the presence of HS. The clinicopathological features of patients between the two groups were compared. The effect of HS on liver metastasis and overall metastasis was evaluated, adjusting for other confounders using Cox regression analyses. Results In total, 1,873 patients with NSCLC with no distant metastases were included in this study, and 408 (21.8%) patients were diagnosed with HS (at the time of diagnosis or before diagnosis). Liver metastases occurred in 166 (8.9%) patients. Liver metastasis-free survival was significantly worse in the study (HS) group (hazard ratio (HR) 1.42; (95% CI [1.03–1.96]); P = 0.031). Multivariate regression analysis demonstrated that HS was an independent risk factor for liver metastasis (HR 1.43; 95% CI [1.02–2.01]; P = 0.039). However, HS was not associated with overall metastasis of NSCLC (HR 0.99; 95% CI [0.84–1.17]; P = 0.895). Conclusion Hepatic steatosis was an independent predictor of liver metastasis from in patients with NSCLC.
format: application/pdf
format: text/html
creator: Wenyu Wu
creator: Haiyan Liao
creator: Weilin Ye
creator: Xi Li
creator: Jian Zhang
creator: Junguo Bu
subject: Epidemiology
subject: Evidence Based Medicine
subject: Oncology
description: doi:10.7717/peerj.6612
publisher: PeerJ Inc.
rights: © 2019 Wu et al.
abstract: Background The hepatic microenvironment, which may include chronic inflammation and fibrosis, is considered to contribute to the development of liver metastases. Hepatic steatosis (HS) might cause liver inflammation and fibrosis. However, to date, no studies have investigated the impact of HS on liver metastasis in patients with non-small cell lung cancer (NSCLC). Methods A retrospective cohort study was performed on patients who received NSCLC treatment at two hospitals affiliated with the Southern Medical University from January 2005 to December 2015. The patients were grouped according to the presence of HS. The clinicopathological features of patients between the two groups were compared. The effect of HS on liver metastasis and overall metastasis was evaluated, adjusting for other confounders using Cox regression analyses. Results In total, 1,873 patients with NSCLC with no distant metastases were included in this study, and 408 (21.8%) patients were diagnosed with HS (at the time of diagnosis or before diagnosis). Liver metastases occurred in 166 (8.9%) patients. Liver metastasis-free survival was significantly worse in the study (HS) group (hazard ratio (HR) 1.42; (95% CI [1.03–1.96]); P = 0.031). Multivariate regression analysis demonstrated that HS was an independent risk factor for liver metastasis (HR 1.43; 95% CI [1.02–2.01]; P = 0.039). However, HS was not associated with overall metastasis of NSCLC (HR 0.99; 95% CI [0.84–1.17]; P = 0.895). Conclusion Hepatic steatosis was an independent predictor of liver metastasis from in patients with NSCLC.
bibliographic citation: Wu et al. (2019) Fatty liver is a risk factor for liver metastasis in Chinese patients with non-small cell lung cancer. PeerJ 7:e6612 https://doi.org/10.7717/peerj.6612
date submitted: 2018-12-14
date accepted: 2019-02-13
issued: 2019-03-14
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Wu
  given name: Wenyu
author list: Agent
  family name: Liao
  given name: Haiyan
author list: Agent
  family name: Ye
  given name: Weilin
author list: Agent
  family name: Li
  given name: Xi
author list: Agent
  family name: Zhang
  given name: Jian
author list: Agent
  family name: Bu
  given name: Junguo
doi: 10.7717/peerj.6612
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-03-14
copyright: © 2019 Wu et al.
attribution name: Wu et al.

Effects of habitat fragmentation and human disturbance on the population dynamics of the Yunnan snub-nosed monkey from 1994 to 2016
type: item
type: AcademicArticle
description: In this study, we integrate data from field investigations, spatial analysis, genetic analysis, and Generalized Linear Models (GLMs) to evaluate the effects of habitat fragmentation on the population dynamics, genetic diversity, and range shifts in the endangered Yunnan snub-nosed monkey (Rhinopithecus bieti). The results indicate that from 1994 to 2016, R. bieti population size increased from less than 2,000 to approximately 3,000 individuals. A primary factor promoting population recovery was the establishment of protected nature reserves. We also found that subpopulation growth rates were uneven, with the groups in some areas, and the formation of new groups. Both the fragmentation index, defined as the ratio of the number of forest patches to the total area of forest patches (e.g., increased fragmentation), and increasing human population size had a negative effect on population growth in R. bieti. We recommend that government conservation plans prioritize the protection of particular R. bieti populations, such as the Baimei and Jisichang populations, which have uncommon haplotypes. In addition, effective conservation strategies need to include an expansion of migration corridors to enable individuals from larger populations such as Guyoulong (Guilong) to serve as a source population to increase the genetic diversity of smaller R. bieti subpopulations. We argue that policies designed to protect endangered primates should not focus solely on total population size but also need to determine the amount of genetic diversity present across different subpopulations and use this information as a measure of the effectiveness of current conservation policies and the basis for new conservation policies.
format: application/pdf
format: text/html
creator: Xumao Zhao
creator: Baoping Ren
creator: Dayong Li
creator: Zuofu Xiang
creator: Paul A. Garber
creator: Ming Li
subject: Conservation Biology
subject: Ecology
subject: Zoology
description: doi:10.7717/peerj.6633
publisher: PeerJ Inc.
rights: © 2019 Zhao et al.
abstract: In this study, we integrate data from field investigations, spatial analysis, genetic analysis, and Generalized Linear Models (GLMs) to evaluate the effects of habitat fragmentation on the population dynamics, genetic diversity, and range shifts in the endangered Yunnan snub-nosed monkey (Rhinopithecus bieti). The results indicate that from 1994 to 2016, R. bieti population size increased from less than 2,000 to approximately 3,000 individuals. A primary factor promoting population recovery was the establishment of protected nature reserves. We also found that subpopulation growth rates were uneven, with the groups in some areas, and the formation of new groups. Both the fragmentation index, defined as the ratio of the number of forest patches to the total area of forest patches (e.g., increased fragmentation), and increasing human population size had a negative effect on population growth in R. bieti. We recommend that government conservation plans prioritize the protection of particular R. bieti populations, such as the Baimei and Jisichang populations, which have uncommon haplotypes. In addition, effective conservation strategies need to include an expansion of migration corridors to enable individuals from larger populations such as Guyoulong (Guilong) to serve as a source population to increase the genetic diversity of smaller R. bieti subpopulations. We argue that policies designed to protect endangered primates should not focus solely on total population size but also need to determine the amount of genetic diversity present across different subpopulations and use this information as a measure of the effectiveness of current conservation policies and the basis for new conservation policies.
bibliographic citation: Zhao et al. (2019) Effects of habitat fragmentation and human disturbance on the population dynamics of the Yunnan snub-nosed monkey from 1994 to 2016. PeerJ 7:e6633 https://doi.org/10.7717/peerj.6633
date submitted: 2018-10-30
date accepted: 2019-02-18
issued: 2019-03-14
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Zhao
  given name: Xumao
author list: Agent
  family name: Ren
  given name: Baoping
author list: Agent
  family name: Li
  given name: Dayong
author list: Agent
  family name: Xiang
  given name: Zuofu
author list: Agent
  family name: Garber
  given name: Paul A.
author list: Agent
  family name: Li
  given name: Ming
doi: 10.7717/peerj.6633
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-03-14
copyright: © 2019 Zhao et al.
attribution name: Zhao et al.

The choice of tree prior and molecular clock does not substantially affect phylogenetic inferences of diversification rates
type: item
type: AcademicArticle
description: Comparative methods allow researchers to make inferences about evolutionary processes and patterns from phylogenetic trees. In Bayesian phylogenetics, estimating a phylogeny requires specifying priors on parameters characterizing the branching process and rates of substitution among lineages, in addition to others. Accordingly, characterizing the effect of prior selection on phylogenies is an active area of research. The choice of priors may systematically bias phylogenetic reconstruction and, subsequently, affect conclusions drawn from the resulting phylogeny. Here, we focus on the impact of priors in Bayesian phylogenetic inference and evaluate how they affect the estimation of parameters in macroevolutionary models of lineage diversification. Specifically, we simulate trees under combinations of tree priors and molecular clocks, simulate sequence data, estimate trees, and estimate diversification parameters (e.g., speciation and extinction rates) from these trees. When substitution rate heterogeneity is large, diversification rate estimates deviate substantially from those estimated under the simulation conditions when not captured by an appropriate choice of relaxed molecular clock. However, in general, we find that the choice of tree prior and molecular clock has relatively little impact on the estimation of diversification rates insofar as the sequence data are sufficiently informative and substitution rate heterogeneity among lineages is low-to-moderate.
format: application/pdf
format: text/html
creator: Brice A.J. Sarver
creator: Matthew W. Pennell
creator: Joseph W. Brown
creator: Sara Keeble
creator: Kayla M. Hardwick
creator: Jack Sullivan
creator: Luke J. Harmon
subject: Computational Biology
subject: Evolutionary Studies
description: doi:10.7717/peerj.6334
publisher: PeerJ Inc.
rights: © 2019 Sarver et al.
abstract: Comparative methods allow researchers to make inferences about evolutionary processes and patterns from phylogenetic trees. In Bayesian phylogenetics, estimating a phylogeny requires specifying priors on parameters characterizing the branching process and rates of substitution among lineages, in addition to others. Accordingly, characterizing the effect of prior selection on phylogenies is an active area of research. The choice of priors may systematically bias phylogenetic reconstruction and, subsequently, affect conclusions drawn from the resulting phylogeny. Here, we focus on the impact of priors in Bayesian phylogenetic inference and evaluate how they affect the estimation of parameters in macroevolutionary models of lineage diversification. Specifically, we simulate trees under combinations of tree priors and molecular clocks, simulate sequence data, estimate trees, and estimate diversification parameters (e.g., speciation and extinction rates) from these trees. When substitution rate heterogeneity is large, diversification rate estimates deviate substantially from those estimated under the simulation conditions when not captured by an appropriate choice of relaxed molecular clock. However, in general, we find that the choice of tree prior and molecular clock has relatively little impact on the estimation of diversification rates insofar as the sequence data are sufficiently informative and substitution rate heterogeneity among lineages is low-to-moderate.
bibliographic citation: Sarver et al. (2019) The choice of tree prior and molecular clock does not substantially affect phylogenetic inferences of diversification rates. PeerJ 7:e6334 https://doi.org/10.7717/peerj.6334
date submitted: 2018-08-30
date accepted: 2018-12-23
issued: 2019-03-13
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Sarver
  given name: Brice A.J.
author list: Agent
  family name: Pennell
  given name: Matthew W.
author list: Agent
  family name: Brown
  given name: Joseph W.
author list: Agent
  family name: Keeble
  given name: Sara
author list: Agent
  family name: Hardwick
  given name: Kayla M.
author list: Agent
  family name: Sullivan
  given name: Jack
author list: Agent
  family name: Harmon
  given name: Luke J.
doi: 10.7717/peerj.6334
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-03-13
copyright: © 2019 Sarver et al.
attribution name: Sarver et al.

Adaptation of metal and antibiotic resistant traits in novel β-Proteobacterium Achromobacter xylosoxidans BHW-15
type: item
type: AcademicArticle
description: Chromosomal co-existence of metal and antibiotic resistance genes in bacteria offers a new perspective to the bacterial resistance proliferation in contaminated environment. In this study, an arsenotrophic bacterium Achromobacter xylosoxidans BHW-15, isolated from Arsenic (As) contaminated tubewell water in the Bogra district of Bangladesh, was analyzed using high throughput Ion Torrent Personal Genome Machine (PGM) complete genome sequencing scheme to reveal its adaptive potentiality. The assembled draft genome of A. xylosoxidans BHW-15 was 6.3 Mbp containing 5,782 functional genes, 1,845 pseudo genes, and three incomplete phage signature regions. Comparative genome study suggested the bacterium to be a novel strain of A. xylosoxidans showing significant dissimilarity with other relevant strains in metal resistance gene islands. A total of 35 metal resistance genes along with arsenite-oxidizing aioSXBA, arsenate reducing arsRCDAB, and mercury resistance merRTPADE operonic gene cluster and 20 broad range antibiotic resistance genes including β-lactams, aminoglycosides, and multiple multidrug resistance (MDR) efflux gene complex with a tripartite system OM-IM-MFP were found co-existed within the genome. Genomic synteny analysis with reported arsenotrophic bacteria revealed the characteristic genetic organization of ars and mer operonic genes, rarely described in β-Proteobacteria. A transposon Tn21 and mobile element protein genes were also detected to the end of mer (mercury) operonic genes, possibly a carrier for the gene transposition. In vitro antibiotic susceptibility assay showed a broad range of resistance against antibiotics belonging to β-lactams, aminoglycosides, cephalosporins (1st, 2nd, and 3rd generations), monobactams and even macrolides, some of the resistome determinants were predicted during in silico analysis. KEGG functional orthology analysis revealed the potential of the bacterium to utilize multiple carbon sources including one carbon pool by fol…
format: application/pdf
format: text/html
creator: Arif Istiaq
creator: Md. Sadikur Rahman Shuvo
creator: Khondaker Md. Jaminur Rahman
creator: Mohammad Anwar Siddique
creator: M. Anwar Hossain
creator: Munawar Sultana
subject: Bioinformatics
subject: Ecology
subject: Microbiology
subject: Freshwater Biology
subject: Environmental Impacts
description: doi:10.7717/peerj.6537
publisher: PeerJ Inc.
rights: © 2019 Istiaq et al.
abstract: Chromosomal co-existence of metal and antibiotic resistance genes in bacteria offers a new perspective to the bacterial resistance proliferation in contaminated environment. In this study, an arsenotrophic bacterium Achromobacter xylosoxidans BHW-15, isolated from Arsenic (As) contaminated tubewell water in the Bogra district of Bangladesh, was analyzed using high throughput Ion Torrent Personal Genome Machine (PGM) complete genome sequencing scheme to reveal its adaptive potentiality. The assembled draft genome of A. xylosoxidans BHW-15 was 6.3 Mbp containing 5,782 functional genes, 1,845 pseudo genes, and three incomplete phage signature regions. Comparative genome study suggested the bacterium to be a novel strain of A. xylosoxidans showing significant dissimilarity with other relevant strains in metal resistance gene islands. A total of 35 metal resistance genes along with arsenite-oxidizing aioSXBA, arsenate reducing arsRCDAB, and mercury resistance merRTPADE operonic gene cluster and 20 broad range antibiotic resistance genes including β-lactams, aminoglycosides, and multiple multidrug resistance (MDR) efflux gene complex with a tripartite system OM-IM-MFP were found co-existed within the genome. Genomic synteny analysis with reported arsenotrophic bacteria revealed the characteristic genetic organization of ars and mer operonic genes, rarely described in β-Proteobacteria. A transposon Tn21 and mobile element protein genes were also detected to the end of mer (mercury) operonic genes, possibly a carrier for the gene transposition. In vitro antibiotic susceptibility assay showed a broad range of resistance against antibiotics belonging to β-lactams, aminoglycosides, cephalosporins (1st, 2nd, and 3rd generations), monobactams and even macrolides, some of the resistome determinants were predicted during in silico analysis. KEGG functional orthology analysis revealed the potential of the bacterium to utilize multiple carbon sources including one carbon pool by fol…
bibliographic citation: Istiaq et al. (2019) Adaptation of metal and antibiotic resistant traits in novel β-Proteobacterium Achromobacter xylosoxidans BHW-15. PeerJ 7:e6537 https://doi.org/10.7717/peerj.6537
date submitted: 2018-10-15
date accepted: 2019-01-29
issued: 2019-03-13
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Istiaq
  given name: Arif
author list: Agent
  family name: Shuvo
  given name: Md. Sadikur Rahman
author list: Agent
  family name: Rahman
  given name: Khondaker Md. Jaminur
author list: Agent
  family name: Siddique
  given name: Mohammad Anwar
author list: Agent
  family name: Hossain
  given name: M. Anwar
author list: Agent
  family name: Sultana
  given name: Munawar
doi: 10.7717/peerj.6537
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-03-13
copyright: © 2019 Istiaq et al.
attribution name: Istiaq et al.

Identification of Austwickia chelonae as cause of cutaneous granuloma in endangered crocodile lizards using metataxonomics
type: item
type: AcademicArticle
description: The crocodile lizard (Shinisaurus crocodilurus Ahl, 1930) is an endangered reptile species, and in recent years many have died from diseases, especially the rescued and breeding individuals. However, pathogens underlying these diseases are unclear. In this study, we report our effort in rapidly identifying and isolating the pathogen that causes high mortality in crocodile lizards from Guangdong Luokeng Shinisaurus crocodilurus National Nature Reserve. The typical symptom is cutaneous granuloma in the infected crocodile lizards. Metagenomic next-generation sequencing (mNGS) is a comprehensive approach for sequence-based identification of pathogenic microbes. In this study, 16S rDNA based mNGS was used for rapid identification of pathogens, and microscopy and microbe isolation were used to confirm the results. Austwickia chelonae was identified to be the dominant pathogen in the granuloma using 16S rDNA based mNGS. Chinese skinks were used as an animal model to verify the pathogenicity of A. chelonae to fulfill Koch’s postulates. As expected, subcutaneous inoculation of A. chelonae induced granulomas in the healthy Chinese skinks and the A. chelonae was re-isolated from the induced granulomas. Therefore, A. chelonae was the primary pathogen that caused this high mortality disease, cutaneous granuloma, in crocodile lizards from Guangdong Luokeng Shinisaurus crocodilurus National Nature Reserve. Antibiotics analysis demonstrated that A. chelonae was sensitive to cephalothin, minocycline and ampicillin, but not to kanamycin, gentamicin, streptomycin and clarithromycin, suggesting a possible treatment for the infected crocodile lizards. However, surgical resection of the nodules as early as possible was recommended. This study is the first report of pathogenic analysis in crocodile lizards and provides a reference for disease control and conservations of the endangered crocodile lizards and other reptiles. In addition, this study indicated that mNGS of lesions could be us…
format: application/pdf
format: text/html
creator: Haiying Jiang
creator: Xiujuan Zhang
creator: Linmiao Li
creator: Jinge Ma
creator: Nan He
creator: Haiyang Liu
creator: Richou Han
creator: Huiming Li
creator: Zhengjun Wu
creator: Jinping Chen
subject: Conservation Biology
subject: Microbiology
subject: Veterinary Medicine
description: doi:10.7717/peerj.6574
publisher: PeerJ Inc.
rights: © 2019 Jiang et al.
abstract: The crocodile lizard (Shinisaurus crocodilurus Ahl, 1930) is an endangered reptile species, and in recent years many have died from diseases, especially the rescued and breeding individuals. However, pathogens underlying these diseases are unclear. In this study, we report our effort in rapidly identifying and isolating the pathogen that causes high mortality in crocodile lizards from Guangdong Luokeng Shinisaurus crocodilurus National Nature Reserve. The typical symptom is cutaneous granuloma in the infected crocodile lizards. Metagenomic next-generation sequencing (mNGS) is a comprehensive approach for sequence-based identification of pathogenic microbes. In this study, 16S rDNA based mNGS was used for rapid identification of pathogens, and microscopy and microbe isolation were used to confirm the results. Austwickia chelonae was identified to be the dominant pathogen in the granuloma using 16S rDNA based mNGS. Chinese skinks were used as an animal model to verify the pathogenicity of A. chelonae to fulfill Koch’s postulates. As expected, subcutaneous inoculation of A. chelonae induced granulomas in the healthy Chinese skinks and the A. chelonae was re-isolated from the induced granulomas. Therefore, A. chelonae was the primary pathogen that caused this high mortality disease, cutaneous granuloma, in crocodile lizards from Guangdong Luokeng Shinisaurus crocodilurus National Nature Reserve. Antibiotics analysis demonstrated that A. chelonae was sensitive to cephalothin, minocycline and ampicillin, but not to kanamycin, gentamicin, streptomycin and clarithromycin, suggesting a possible treatment for the infected crocodile lizards. However, surgical resection of the nodules as early as possible was recommended. This study is the first report of pathogenic analysis in crocodile lizards and provides a reference for disease control and conservations of the endangered crocodile lizards and other reptiles. In addition, this study indicated that mNGS of lesions could be us…
bibliographic citation: Jiang et al. (2019) Identification of Austwickia chelonae as cause of cutaneous granuloma in endangered crocodile lizards using metataxonomics. PeerJ 7:e6574 https://doi.org/10.7717/peerj.6574
date submitted: 2018-10-02
date accepted: 2019-02-05
issued: 2019-03-13
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Jiang
  given name: Haiying
author list: Agent
  family name: Zhang
  given name: Xiujuan
author list: Agent
  family name: Li
  given name: Linmiao
author list: Agent
  family name: Ma
  given name: Jinge
author list: Agent
  family name: He
  given name: Nan
author list: Agent
  family name: Liu
  given name: Haiyang
author list: Agent
  family name: Han
  given name: Richou
author list: Agent
  family name: Li
  given name: Huiming
author list: Agent
  family name: Wu
  given name: Zhengjun
author list: Agent
  family name: Chen
  given name: Jinping
doi: 10.7717/peerj.6574
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-03-13
copyright: ©2019 Jiang et al.
attribution name: Jiang et al.

Geochemical characteristics of dissolved heavy metals in Zhujiang River, Southwest China: spatial-temporal distribution, source, export flux estimation, and a water quality assessment
type: item
type: AcademicArticle
description: To investigate the sources and spatial-temporal distribution of dissolved heavy metals in river water, and to evaluate the water quality, a total of 162 water samples were collected from 81 key sampling points in high and low flow seasons separately in the Zhujiang River, Southwest China. Ten dissolved heavy metals (V, Cr, Mn, Co, Ni, Cu, Mo, Cd, Ba, and Pb) in the Zhujiang River water exhibit little variation at temporal scale, but vary with a significant spatial heterogeneity. Furthermore, different metals present different variation trends along the main channel of the Zhujiang River. Our results suggest that Ba (14.72 μg L−1 in low flow season and 12.50 μg L−1 in high flow season) and Cr (6.85 μg L−1 in low flow season and 7.52 μg L−1 in high flow season) are consistently the most abundant metals in the two sampling periods. According to the water quality index (WQI values ranged from 1.3 to 43.9) and health risk assessment, metals investigated in Zhujiang River are below the hazard level (all hazard index (HI) < 1). Application of statistical approaches, including correlation matrix and principal component analysis (PCA), identify three principal components that account for 61.74% of the total variance, the results conclude that the anthropogenic heavy metals (V, Cr, Ni, and Cu) are greatly impacted by the dilution effect, and the heavy metals in Zhujiang River are mainly presented a natural sources signature from the perspective of entire basin. Moreover, our results reveal that the estimated export budget of several heavy metals including V (735.6 t year−1), Cr (1,561.1 t year−1), Ni (498.2 t year−1), and Mo (118.9 t year−1) to the ocean are higher than the world average.
format: application/pdf
format: text/html
creator: Jie Zeng
creator: Guilin Han
creator: Qixin Wu
creator: Yang Tang
subject: Aquatic and Marine Chemistry
subject: Biogeochemistry
subject: Environmental Contamination and Remediation
subject: Environmental Impacts
description: doi:10.7717/peerj.6578
publisher: PeerJ Inc.
rights: © 2019 Zeng et al.
abstract: To investigate the sources and spatial-temporal distribution of dissolved heavy metals in river water, and to evaluate the water quality, a total of 162 water samples were collected from 81 key sampling points in high and low flow seasons separately in the Zhujiang River, Southwest China. Ten dissolved heavy metals (V, Cr, Mn, Co, Ni, Cu, Mo, Cd, Ba, and Pb) in the Zhujiang River water exhibit little variation at temporal scale, but vary with a significant spatial heterogeneity. Furthermore, different metals present different variation trends along the main channel of the Zhujiang River. Our results suggest that Ba (14.72 μg L−1 in low flow season and 12.50 μg L−1 in high flow season) and Cr (6.85 μg L−1 in low flow season and 7.52 μg L−1 in high flow season) are consistently the most abundant metals in the two sampling periods. According to the water quality index (WQI values ranged from 1.3 to 43.9) and health risk assessment, metals investigated in Zhujiang River are below the hazard level (all hazard index (HI) < 1). Application of statistical approaches, including correlation matrix and principal component analysis (PCA), identify three principal components that account for 61.74% of the total variance, the results conclude that the anthropogenic heavy metals (V, Cr, Ni, and Cu) are greatly impacted by the dilution effect, and the heavy metals in Zhujiang River are mainly presented a natural sources signature from the perspective of entire basin. Moreover, our results reveal that the estimated export budget of several heavy metals including V (735.6 t year−1), Cr (1,561.1 t year−1), Ni (498.2 t year−1), and Mo (118.9 t year−1) to the ocean are higher than the world average.
bibliographic citation: Zeng et al. (2019) Geochemical characteristics of dissolved heavy metals in Zhujiang River, Southwest China: spatial-temporal distribution, source, export flux estimation, and a water quality assessment. PeerJ 7:e6578 https://doi.org/10.7717/peerj.6578
date submitted: 2018-12-06
date accepted: 2019-02-06
issued: 2019-03-13
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Zeng
  given name: Jie
author list: Agent
  family name: Han
  given name: Guilin
author list: Agent
  family name: Wu
  given name: Qixin
author list: Agent
  family name: Tang
  given name: Yang
doi: 10.7717/peerj.6578
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-03-13
copyright: © 2019 Zeng et al.
attribution name: Zeng et al.

Just a small bunch of flowers: the botanical knowledge of students and the positive effects of courses in plant identification at German universities
type: item
type: AcademicArticle
description: Background In the light of the ongoing loss of species the knowledge about and the ability to identify species becomes increasingly important for effective monitoring and conservation measures. Learning about identifying biodiversity is a central task for future biologists and biology teachers and universities play an important role in educating future experts and multipliers. It builds one basis for conservation literacy. Methods We analyzed undergraduate students’ prior knowledge on plant species, identification and their knowledge gain from introductory plant identification courses at eight German universities. Using the Visual Classification Method—a combination of a presentation and standardized questionnaires—we evaluated the learning success of more than 500 students regarding (a) ‘declarative species knowledge’ of plant species names and (b) ‘taxonomic concept knowledge’, which is seen as knowledge on a higher level of complexity. From comparison of paired pre- and post-tests we calculated the individual knowledge gain. Using Linear Mixed Effects Models (LMMs) we analyzed effects of knowledge levels, learner-specific resources and learning environment on the knowledge gain. Results We found that university course instructors have to start teaching at an almost zero level with respect to undergraduates’ prior knowledge: on average 2.6 of 32 common plant species were known. Overall, the introductory courses resulted in a significant but weak knowledge gain. We detected a higher knowledge gain in ‘taxonomic concept knowledge’ than in ‘declarative species knowledge’. We showed that the learning success was influenced by learner-specific resources, such as prior knowledge or aspects of motivation towards the subject matter, and by learning environment such as teaching methodology. Discussion We discuss didactical demands and aspects of teaching methodologies that could facilitate learning the complex task of plant identification in university courses. Plant ident…
format: application/pdf
format: text/html
creator: Thorsten Buck
creator: Ines Bruchmann
creator: Pascale Zumstein
creator: Claudia Drees
subject: Biodiversity
subject: Conservation Biology
subject: Ecology
subject: Plant Science
subject: Science and Medical Education
description: doi:10.7717/peerj.6581
publisher: PeerJ Inc.
rights: © 2019 Buck et al.
abstract: Background In the light of the ongoing loss of species the knowledge about and the ability to identify species becomes increasingly important for effective monitoring and conservation measures. Learning about identifying biodiversity is a central task for future biologists and biology teachers and universities play an important role in educating future experts and multipliers. It builds one basis for conservation literacy. Methods We analyzed undergraduate students’ prior knowledge on plant species, identification and their knowledge gain from introductory plant identification courses at eight German universities. Using the Visual Classification Method—a combination of a presentation and standardized questionnaires—we evaluated the learning success of more than 500 students regarding (a) ‘declarative species knowledge’ of plant species names and (b) ‘taxonomic concept knowledge’, which is seen as knowledge on a higher level of complexity. From comparison of paired pre- and post-tests we calculated the individual knowledge gain. Using Linear Mixed Effects Models (LMMs) we analyzed effects of knowledge levels, learner-specific resources and learning environment on the knowledge gain. Results We found that university course instructors have to start teaching at an almost zero level with respect to undergraduates’ prior knowledge: on average 2.6 of 32 common plant species were known. Overall, the introductory courses resulted in a significant but weak knowledge gain. We detected a higher knowledge gain in ‘taxonomic concept knowledge’ than in ‘declarative species knowledge’. We showed that the learning success was influenced by learner-specific resources, such as prior knowledge or aspects of motivation towards the subject matter, and by learning environment such as teaching methodology. Discussion We discuss didactical demands and aspects of teaching methodologies that could facilitate learning the complex task of plant identification in university courses. Plant ident…
bibliographic citation: Buck et al. (2019) Just a small bunch of flowers: the botanical knowledge of students and the positive effects of courses in plant identification at German universities. PeerJ 7:e6581 https://doi.org/10.7717/peerj.6581
date submitted: 2018-07-18
date accepted: 2019-02-07
issued: 2019-03-13
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Buck
  given name: Thorsten
author list: Agent
  family name: Bruchmann
  given name: Ines
author list: Agent
  family name: Zumstein
  given name: Pascale
author list: Agent
  family name: Drees
  given name: Claudia
doi: 10.7717/peerj.6581
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-03-13
copyright: ©2019 Buck et al.
attribution name: Buck et al.

Coral-algal interactions at Weizhou Island in the northern South China Sea: variations by taxa and the exacerbating impact of sediments trapped in turf algae
type: item
type: AcademicArticle
description: Competitive interactions between corals and benthic algae are increasingly frequent on degrading coral reefs, but the processes and mechanisms surrounding the interactions, as well as the exacerbating effects of sediments trapped in turf algae, are poorly described. We surveyed the frequency, proportion, and outcomes of interactions between benthic algae (turf algae and macroalgae) and 631 corals (genera: Porites, Favites, Favia, Platygyra, and Pavona) on a degenerating reef in the northern South China Sea, with a specific focus on the negative effects of algal contact on corals. Our data indicated that turf algae were the main algal competitors for each surveyed coral genus and the proportion of algal contact along the coral edges varied significantly among the coral genera and the algal types. The proportions of algal wins between corals and turf algae or macroalgae differed significantly among coral genera. Compared to macroalgae, turf algae consistently yielded more algal wins and fewer coral wins on all coral genera. Amongst the coral genera, Porites was the most easily damaged by algal competition. The proportions of turf algal wins on the coral genera increased 1.1–1.9 times in the presence of sediments. Furthermore, the proportions of algal wins on massive and encrusting corals significantly increased with the combination of sediments and turf algae as the algal type. However, the variation in proportions of algal wins between massive and encrusting corals disappeared as sediments became trapped in turf algae. Sediments bound within turf algae further induced damage to corals and reduced the competitive advantage of the different coral growth forms in their competitive interactions with adjacent turf algae.
format: application/pdf
format: text/html
creator: Zhiheng Liao
creator: Kefu Yu
creator: Yinghui Wang
creator: Xueyong Huang
creator: Lijia Xu
subject: Biodiversity
subject: Ecology
subject: Marine Biology
description: doi:10.7717/peerj.6590
publisher: PeerJ Inc.
rights: © 2019 Liao et al.
abstract: Competitive interactions between corals and benthic algae are increasingly frequent on degrading coral reefs, but the processes and mechanisms surrounding the interactions, as well as the exacerbating effects of sediments trapped in turf algae, are poorly described. We surveyed the frequency, proportion, and outcomes of interactions between benthic algae (turf algae and macroalgae) and 631 corals (genera: Porites, Favites, Favia, Platygyra, and Pavona) on a degenerating reef in the northern South China Sea, with a specific focus on the negative effects of algal contact on corals. Our data indicated that turf algae were the main algal competitors for each surveyed coral genus and the proportion of algal contact along the coral edges varied significantly among the coral genera and the algal types. The proportions of algal wins between corals and turf algae or macroalgae differed significantly among coral genera. Compared to macroalgae, turf algae consistently yielded more algal wins and fewer coral wins on all coral genera. Amongst the coral genera, Porites was the most easily damaged by algal competition. The proportions of turf algal wins on the coral genera increased 1.1–1.9 times in the presence of sediments. Furthermore, the proportions of algal wins on massive and encrusting corals significantly increased with the combination of sediments and turf algae as the algal type. However, the variation in proportions of algal wins between massive and encrusting corals disappeared as sediments became trapped in turf algae. Sediments bound within turf algae further induced damage to corals and reduced the competitive advantage of the different coral growth forms in their competitive interactions with adjacent turf algae.
bibliographic citation: Liao et al. (2019) Coral-algal interactions at Weizhou Island in the northern South China Sea: variations by taxa and the exacerbating impact of sediments trapped in turf algae. PeerJ 7:e6590 https://doi.org/10.7717/peerj.6590
date submitted: 2018-03-12
date accepted: 2019-02-10
issued: 2019-03-13
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Liao
  given name: Zhiheng
author list: Agent
  family name: Yu
  given name: Kefu
author list: Agent
  family name: Wang
  given name: Yinghui
author list: Agent
  family name: Huang
  given name: Xueyong
author list: Agent
  family name: Xu
  given name: Lijia
doi: 10.7717/peerj.6590
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-03-13
copyright: © 2019 Liao et al.
attribution name: Liao et al.

Assessing alignment-based taxonomic classification of ancient microbial DNA
type: item
type: AcademicArticle
description: The field of palaeomicrobiology—the study of ancient microorganisms—is rapidly growing due to recent methodological and technological advancements. It is now possible to obtain vast quantities of DNA data from ancient specimens in a high-throughput manner and use this information to investigate the dynamics and evolution of past microbial communities. However, we still know very little about how the characteristics of ancient DNA influence our ability to accurately assign microbial taxonomies (i.e. identify species) within ancient metagenomic samples. Here, we use both simulated and published metagenomic data sets to investigate how ancient DNA characteristics affect alignment-based taxonomic classification. We find that nucleotide-to-nucleotide, rather than nucleotide-to-protein, alignments are preferable when assigning taxonomies to short DNA fragment lengths routinely identified within ancient specimens (<60 bp). We determine that deamination (a form of ancient DNA damage) and random sequence substitutions corresponding to ∼100,000 years of genomic divergence minimally impact alignment-based classification. We also test four different reference databases and find that database choice can significantly bias the results of alignment-based taxonomic classification in ancient metagenomic studies. Finally, we perform a reanalysis of previously published ancient dental calculus data, increasing the number of microbial DNA sequences assigned taxonomically by an average of 64.2-fold and identifying microbial species previously unidentified in the original study. Overall, this study enhances our understanding of how ancient DNA characteristics influence alignment-based taxonomic classification of ancient microorganisms and provides recommendations for future palaeomicrobiological studies.
format: application/pdf
format: text/html
creator: Raphael Eisenhofer
creator: Laura Susan Weyrich
subject: Bioinformatics
subject: Evolutionary Studies
subject: Microbiology
description: doi:10.7717/peerj.6594
publisher: PeerJ Inc.
rights: © 2019 Eisenhofer and Weyrich
abstract: The field of palaeomicrobiology—the study of ancient microorganisms—is rapidly growing due to recent methodological and technological advancements. It is now possible to obtain vast quantities of DNA data from ancient specimens in a high-throughput manner and use this information to investigate the dynamics and evolution of past microbial communities. However, we still know very little about how the characteristics of ancient DNA influence our ability to accurately assign microbial taxonomies (i.e. identify species) within ancient metagenomic samples. Here, we use both simulated and published metagenomic data sets to investigate how ancient DNA characteristics affect alignment-based taxonomic classification. We find that nucleotide-to-nucleotide, rather than nucleotide-to-protein, alignments are preferable when assigning taxonomies to short DNA fragment lengths routinely identified within ancient specimens (<60 bp). We determine that deamination (a form of ancient DNA damage) and random sequence substitutions corresponding to ∼100,000 years of genomic divergence minimally impact alignment-based classification. We also test four different reference databases and find that database choice can significantly bias the results of alignment-based taxonomic classification in ancient metagenomic studies. Finally, we perform a reanalysis of previously published ancient dental calculus data, increasing the number of microbial DNA sequences assigned taxonomically by an average of 64.2-fold and identifying microbial species previously unidentified in the original study. Overall, this study enhances our understanding of how ancient DNA characteristics influence alignment-based taxonomic classification of ancient microorganisms and provides recommendations for future palaeomicrobiological studies.
bibliographic citation: Eisenhofer et al. (2019) Assessing alignment-based taxonomic classification of ancient microbial DNA. PeerJ 7:e6594 https://doi.org/10.7717/peerj.6594
date submitted: 2018-08-30
date accepted: 2019-02-09
issued: 2019-03-13
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Eisenhofer
  given name: Raphael
author list: Agent
  family name: Weyrich
  given name: Laura Susan
doi: 10.7717/peerj.6594
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-03-13
copyright: © 2019 Eisenhofer and Weyrich
attribution name: Eisenhofer and Weyrich

Microgeographic variation in body condition of three Mexican garter snakes in central Mexico
type: item
type: AcademicArticle
description: Background Geographic variation in body size and condition can reveal differential local adaptation to resource availability or climatic factors. Body size and condition are related to fitness in garter snakes (Thamnophis), thus good body condition may increase survival, fecundity in females, and mating success in males. Phylogenetically related species in sympatry are predicted to exhibit similar body condition when they experience similar environmental conditions. We focused on interspecific and geographical variation in body size and condition in three sympatric Mexican garter snakes from the highlands of Central Mexico. Methods We assessed SVL, mass, and body condition (obtained from Major axis linear regression of ln-transformed body mass on ln-transformed SVL) in adults and juveniles of both sexes of Thamnophis eques, T. melanogaster, and T. scalaris sampled at different locations and ranges from 3–11 years over a 20-year period. Results We provide a heterogeneous pattern of sexual and ontogenic reproductive status variations of body size and condition among local populations. Each garter snake species shows locations with good and poor body condition; juvenile snakes show similar body condition between populations, adults show varying body condition between populations, and adults also show sex differences in body condition. We discuss variations in body condition as possibly related to the snakes’ life cycle differences.
format: application/pdf
format: text/html
creator: Erika Valencia-Flores
creator: Crystian S. Venegas-Barrera
creator: Victor Fajardo
creator: Javier Manjarrez
subject: Ecology
subject: Zoology
description: doi:10.7717/peerj.6601
publisher: PeerJ Inc.
rights: © 2019 Valencia-Flores et al.
abstract: Background Geographic variation in body size and condition can reveal differential local adaptation to resource availability or climatic factors. Body size and condition are related to fitness in garter snakes (Thamnophis), thus good body condition may increase survival, fecundity in females, and mating success in males. Phylogenetically related species in sympatry are predicted to exhibit similar body condition when they experience similar environmental conditions. We focused on interspecific and geographical variation in body size and condition in three sympatric Mexican garter snakes from the highlands of Central Mexico. Methods We assessed SVL, mass, and body condition (obtained from Major axis linear regression of ln-transformed body mass on ln-transformed SVL) in adults and juveniles of both sexes of Thamnophis eques, T. melanogaster, and T. scalaris sampled at different locations and ranges from 3–11 years over a 20-year period. Results We provide a heterogeneous pattern of sexual and ontogenic reproductive status variations of body size and condition among local populations. Each garter snake species shows locations with good and poor body condition; juvenile snakes show similar body condition between populations, adults show varying body condition between populations, and adults also show sex differences in body condition. We discuss variations in body condition as possibly related to the snakes’ life cycle differences.
bibliographic citation: Valencia-Flores et al. (2019) Microgeographic variation in body condition of three Mexican garter snakes in central Mexico. PeerJ 7:e6601 https://doi.org/10.7717/peerj.6601
date submitted: 2018-09-13
date accepted: 2019-02-07
issued: 2019-03-13
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Valencia-Flores
  given name: Erika
author list: Agent
  family name: Venegas-Barrera
  given name: Crystian S.
author list: Agent
  family name: Fajardo
  given name: Victor
author list: Agent
  family name: Manjarrez
  given name: Javier
doi: 10.7717/peerj.6601
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-03-13
copyright: ©2019 Valencia-Flores et al.
attribution name: Valencia-Flores et al.

Seroprevalence and risk factors of Toxoplasma gondii infection in children with leukemia in Shandong Province, Eastern China: a case—control prospective study
type: item
type: AcademicArticle
description: Limited information is available concerning the epidemiology of Toxoplasma gondii infection in children with leukemia in Eastern China. Therefore, a case-control study was conducted to estimate the seroprevalence of toxoplasmosis in this patient group and to identify risk factors and possible routes of infection. Serum samples were collected from 339 children with leukemia and 339 age matched health control subjects in Qingdao from September 2014 to March 2018. Enzyme linked immunoassays were used to screen anti- T. gondii IgG and anti- T. gondii IgM antibodies. Forty-eight (14.2%) children with leukemia and 31 (9.1%) control subjects were positive for anti-T. gondii IgG antibodies (P < 0.05), while 13 (3.8%) patients and 14 (4.1%) controls were positive for anti-T. gondii IgM antibodies (P = 0.84). Multivariate analysis showed exposure to soil and a history of blood transfusion were risk factors for T. gondii infection. Compared with IgG, patients with a history of blood transfusion were more likely to present anti- T. gondii IgM (P = 0.003). Moreover, patients with chronic lymphocytic leukemia and acute lymphocytic leukemia had higher T. gondii seroprevalence in comparison to control subjects (P = 0.002 and P = 0.016, respectively). The results indicated that the seroprevalence of T. gondii infection in children with leukemia is higher than that of healthy children in Eastern China. This information may be used to guide future research and clinical management, and further studies are necessary to elucidate the role of T. gondii in children with leukemia.
format: application/pdf
format: text/html
creator: Na Zhou
creator: Haiyang Fu
creator: Zhongjun Wang
creator: Hailei Shi
creator: Yang Yu
creator: Tingting Qu
creator: Longlong Wang
creator: Xiangyan Zhang
creator: Lin Wang
subject: Hematology
subject: Infectious Diseases
subject: Pediatrics
description: doi:10.7717/peerj.6604
publisher: PeerJ Inc.
rights: © 2019 Zhou et al.
abstract: Limited information is available concerning the epidemiology of Toxoplasma gondii infection in children with leukemia in Eastern China. Therefore, a case-control study was conducted to estimate the seroprevalence of toxoplasmosis in this patient group and to identify risk factors and possible routes of infection. Serum samples were collected from 339 children with leukemia and 339 age matched health control subjects in Qingdao from September 2014 to March 2018. Enzyme linked immunoassays were used to screen anti- T. gondii IgG and anti- T. gondii IgM antibodies. Forty-eight (14.2%) children with leukemia and 31 (9.1%) control subjects were positive for anti-T. gondii IgG antibodies (P < 0.05), while 13 (3.8%) patients and 14 (4.1%) controls were positive for anti-T. gondii IgM antibodies (P = 0.84). Multivariate analysis showed exposure to soil and a history of blood transfusion were risk factors for T. gondii infection. Compared with IgG, patients with a history of blood transfusion were more likely to present anti- T. gondii IgM (P = 0.003). Moreover, patients with chronic lymphocytic leukemia and acute lymphocytic leukemia had higher T. gondii seroprevalence in comparison to control subjects (P = 0.002 and P = 0.016, respectively). The results indicated that the seroprevalence of T. gondii infection in children with leukemia is higher than that of healthy children in Eastern China. This information may be used to guide future research and clinical management, and further studies are necessary to elucidate the role of T. gondii in children with leukemia.
bibliographic citation: Zhou et al. (2019) Seroprevalence and risk factors of Toxoplasma gondii infection in children with leukemia in Shandong Province, Eastern China: a case—control prospective study. PeerJ 7:e6604 https://doi.org/10.7717/peerj.6604
date submitted: 2018-11-16
date accepted: 2019-02-12
issued: 2019-03-13
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Zhou
  given name: Na
author list: Agent
  family name: Fu
  given name: Haiyang
author list: Agent
  family name: Wang
  given name: Zhongjun
author list: Agent
  family name: Shi
  given name: Hailei
author list: Agent
  family name: Yu
  given name: Yang
author list: Agent
  family name: Qu
  given name: Tingting
author list: Agent
  family name: Wang
  given name: Longlong
author list: Agent
  family name: Zhang
  given name: Xiangyan
author list: Agent
  family name: Wang
  given name: Lin
doi: 10.7717/peerj.6604
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-03-13
copyright: ©2019 Zhou et al.
attribution name: Zhou et al.

A new ancient lineage of frog (Anura: Nyctibatrachidae: Astrobatrachinae subfam. nov.) endemic to the Western Ghats of Peninsular India
type: item
type: AcademicArticle
description: The Western Ghats (WG) is an escarpment on the west coast of Peninsular India, housing one of the richest assemblages of frogs in the world, with three endemic families. Here, we report the discovery of a new ancient lineage from a high-elevation massif in the Wayanad Plateau of the southern WG. Phylogenetic analysis reveals that the lineage belongs to Natatanura and clusters with Nyctibatrachidae, a family endemic to the WG/Sri Lanka biodiversity hotspot. Based on geographic distribution, unique morphological traits, deep genetic divergence, and phylogenetic position that distinguishes the lineage from the two nyctibatrachid subfamilies Nyctibatrachinae Blommers-Schlösser, 1993 and Lankanectinae Dubois & Ohler, 2001, we erect a new subfamily Astrobatrachinae subfam. nov. (endemic to the WG, Peninsular India), and describe a new genus Astrobatrachus gen. nov. and species, Astrobatrachus kurichiyana sp. nov. The discovery of this species adds to the list of deeply divergent and monotypic or depauperate lineages with narrow geographic ranges in the southern massifs of the WG. The southern regions of the WG have long been considered geographic and climatic refugia, and this new relict lineage underscores their evolutionary significance. The small range of this species exclusively outside protected areas highlights the significance of reserve forest tracts in the WG in housing evolutionary novelty. This reinforces the need for intensive sampling to uncover new lineages and advance our understanding of the historical biogeography of this ancient landmass.
format: application/pdf
format: text/html
creator: Seenapuram Palaniswamy Vijayakumar
creator: Robert Alexander Pyron
creator: K. P. Dinesh
creator: Varun R. Torsekar
creator: Achyuthan N. Srikanthan
creator: Priyanka Swamy
creator: Edward L. Stanley
creator: David C. Blackburn
creator: Kartik Shanker
subject: Evolutionary Studies
subject: Taxonomy
description: doi:10.7717/peerj.6457
publisher: PeerJ Inc.
rights: © 2019 Vijayakumar et al.
abstract: The Western Ghats (WG) is an escarpment on the west coast of Peninsular India, housing one of the richest assemblages of frogs in the world, with three endemic families. Here, we report the discovery of a new ancient lineage from a high-elevation massif in the Wayanad Plateau of the southern WG. Phylogenetic analysis reveals that the lineage belongs to Natatanura and clusters with Nyctibatrachidae, a family endemic to the WG/Sri Lanka biodiversity hotspot. Based on geographic distribution, unique morphological traits, deep genetic divergence, and phylogenetic position that distinguishes the lineage from the two nyctibatrachid subfamilies Nyctibatrachinae Blommers-Schlösser, 1993 and Lankanectinae Dubois & Ohler, 2001, we erect a new subfamily Astrobatrachinae subfam. nov. (endemic to the WG, Peninsular India), and describe a new genus Astrobatrachus gen. nov. and species, Astrobatrachus kurichiyana sp. nov. The discovery of this species adds to the list of deeply divergent and monotypic or depauperate lineages with narrow geographic ranges in the southern massifs of the WG. The southern regions of the WG have long been considered geographic and climatic refugia, and this new relict lineage underscores their evolutionary significance. The small range of this species exclusively outside protected areas highlights the significance of reserve forest tracts in the WG in housing evolutionary novelty. This reinforces the need for intensive sampling to uncover new lineages and advance our understanding of the historical biogeography of this ancient landmass.
bibliographic citation: Vijayakumar et al. (2019) A new ancient lineage of frog (Anura: Nyctibatrachidae: Astrobatrachinae subfam. nov.) endemic to the Western Ghats of Peninsular India. PeerJ 7:e6457 https://doi.org/10.7717/peerj.6457
date submitted: 2018-12-02
date accepted: 2019-01-16
issued: 2019-03-12
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Vijayakumar
  given name: Seenapuram Palaniswamy
author list: Agent
  family name: Pyron
  given name: Robert Alexander
author list: Agent
  family name: Dinesh
  given name: K. P.
author list: Agent
  family name: Torsekar
  given name: Varun R.
author list: Agent
  family name: Srikanthan
  given name: Achyuthan N.
author list: Agent
  family name: Swamy
  given name: Priyanka
author list: Agent
  family name: Stanley
  given name: Edward L.
author list: Agent
  family name: Blackburn
  given name: David C.
author list: Agent
  family name: Shanker
  given name: Kartik
doi: 10.7717/peerj.6457
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-03-12
copyright: © 2019 Vijayakumar et al.
attribution name: Vijayakumar et al.

Habitat differentiation and conservation gap of Magnolia biondii, M. denudata, and M. sprengeri in China
type: item
type: AcademicArticle
description: The flower buds of Magnolia biondii, M. denudata, and M. sprengeri are the materials of Xinyi, a traditional Chinese medicine. The harvest of flower buds and habitat fragmentation caused by human disturbance heavily threatens the natural regeneration and survival of these three Magnolia species. With the aim to support the conservation and improve the effectiveness of conservation, we performed an assessment on habitat suitability, influences of environmental variables on habitat suitability, and the conservation gap of these three Magnolia species, based on the Maxent modeling method. The results indicated that: (1) altitude, annual mean temperature, extreme temperature, temperature fluctuation, annual precipitation, and extreme precipitation are the most influential environmental variables for the distribution of M. sprengeri, M. biondii, and M. denudata; (2) obvious habitat differentiations were observed among M. biondii, M. denudata, and M. sprengeri. M. sprengeri tends to be located in further northern areas with higher altitudes, lower temperatures, and lower precipitation compared to M. biondii and M. denudata; and (3) a large proportion of suitable habitats have been left without protection. Woodland and forest shared the largest area out of the suitable habitats. However, grassland, agricultural land, residential land, and mining and industry areas also occupied large areas of suitable habitats.
format: application/pdf
format: text/html
creator: Chuangye Song
creator: Huiming Liu
subject: Biogeography
subject: Conservation Biology
subject: Ecology
subject: Forestry
description: doi:10.7717/peerj.6126
publisher: PeerJ Inc.
rights: © 2019 Song and Liu
abstract: The flower buds of Magnolia biondii, M. denudata, and M. sprengeri are the materials of Xinyi, a traditional Chinese medicine. The harvest of flower buds and habitat fragmentation caused by human disturbance heavily threatens the natural regeneration and survival of these three Magnolia species. With the aim to support the conservation and improve the effectiveness of conservation, we performed an assessment on habitat suitability, influences of environmental variables on habitat suitability, and the conservation gap of these three Magnolia species, based on the Maxent modeling method. The results indicated that: (1) altitude, annual mean temperature, extreme temperature, temperature fluctuation, annual precipitation, and extreme precipitation are the most influential environmental variables for the distribution of M. sprengeri, M. biondii, and M. denudata; (2) obvious habitat differentiations were observed among M. biondii, M. denudata, and M. sprengeri. M. sprengeri tends to be located in further northern areas with higher altitudes, lower temperatures, and lower precipitation compared to M. biondii and M. denudata; and (3) a large proportion of suitable habitats have been left without protection. Woodland and forest shared the largest area out of the suitable habitats. However, grassland, agricultural land, residential land, and mining and industry areas also occupied large areas of suitable habitats.
bibliographic citation: Song et al. (2019) Habitat differentiation and conservation gap of Magnolia biondii, M. denudata, and M. sprengeri in China. PeerJ 6:e6126 https://doi.org/10.7717/peerj.6126
date submitted: 2018-07-31
date accepted: 2018-11-17
issued: 2019-03-12
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Song
  given name: Chuangye
author list: Agent
  family name: Liu
  given name: Huiming
doi: 10.7717/peerj.6126
volume: 6
issn: 2167-8359
publication name: PeerJ
publication date: 2019-03-12
copyright: © 2019 Song and Liu
attribution name: Song and Liu

Determination of two fluoroquinolones and their combinations with hyaluronan effect in in vitro canine cartilage explants
type: item
type: AcademicArticle
description: Background Previous studies reported the effect of enrofloxacin (Enro) and marbofloxacin (Mar) on cell death and alteration of the key genes involved in catabolic and anabolic processes and demonstrated the beneficial effects of hyaluronan (HA) combined with fluoroquinolones (FQs) on primary canine chondrocytes. This study further determines the effects of these treatments on canine cartilage explants in both normal and interleukin-1 beta (IL-1β)-stimulated conditions. Methods We examined sulfate glycosaminoglycan (s-GAG) release, uronic acid (UA) content, and safranin-O staining, as well as the expression patterns of inflammatory, extracellular matrix (ECM) component and enzymes. Results Enro treatment alone effectively stimulated proteoglycan anabolism by increasing UA content and glycosaminoglycans (GAGs) in normal and pre-IL-1β-stimulated explant, whereas Mar showed opposite results. The combination of HA and FQs increased s-GAG release and UA content in normal explants in addition to effective down-regulated expression of MMP3. HA reduced the adverse effects of Mar by enhancing UA and GAG contents in both normal and pre-IL-1β-explants. Moreover, HA effectively induced HAS1and ACANup-regulation and reduced MMP9, TNF, PTGS2,and NFKB1 expression for a long term. Discussion Our results suggest the direct effects of Enro and Mar may selectively stimulate the conditioned explants to express MMP-codinggenes and promote gene expression involved in matrix production, pro-inflammatory cytokines, and cell degradation in different directions. HA successfully reduced the adverse effects of FQs by enhancing s-GAG and UA contents and down-regulated expression of MMPs.
format: application/pdf
format: text/html
creator: Puntita Siengdee
creator: Waranee Pradit
creator: Siriwadee Chomdej
creator: Korakot Nganvongpanit
subject: Veterinary Medicine
subject: Pharmacology
subject: Rheumatology
description: doi:10.7717/peerj.6553
publisher: PeerJ Inc.
rights: © 2019 Siengdee et al.
abstract: Background Previous studies reported the effect of enrofloxacin (Enro) and marbofloxacin (Mar) on cell death and alteration of the key genes involved in catabolic and anabolic processes and demonstrated the beneficial effects of hyaluronan (HA) combined with fluoroquinolones (FQs) on primary canine chondrocytes. This study further determines the effects of these treatments on canine cartilage explants in both normal and interleukin-1 beta (IL-1β)-stimulated conditions. Methods We examined sulfate glycosaminoglycan (s-GAG) release, uronic acid (UA) content, and safranin-O staining, as well as the expression patterns of inflammatory, extracellular matrix (ECM) component and enzymes. Results Enro treatment alone effectively stimulated proteoglycan anabolism by increasing UA content and glycosaminoglycans (GAGs) in normal and pre-IL-1β-stimulated explant, whereas Mar showed opposite results. The combination of HA and FQs increased s-GAG release and UA content in normal explants in addition to effective down-regulated expression of MMP3. HA reduced the adverse effects of Mar by enhancing UA and GAG contents in both normal and pre-IL-1β-explants. Moreover, HA effectively induced HAS1and ACANup-regulation and reduced MMP9, TNF, PTGS2,and NFKB1 expression for a long term. Discussion Our results suggest the direct effects of Enro and Mar may selectively stimulate the conditioned explants to express MMP-codinggenes and promote gene expression involved in matrix production, pro-inflammatory cytokines, and cell degradation in different directions. HA successfully reduced the adverse effects of FQs by enhancing s-GAG and UA contents and down-regulated expression of MMPs.
bibliographic citation: Siengdee et al. (2019) Determination of two fluoroquinolones and their combinations with hyaluronan effect in in vitro canine cartilage explants. PeerJ 7:e6553 https://doi.org/10.7717/peerj.6553
date submitted: 2018-10-17
date accepted: 2019-02-02
issued: 2019-03-12
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Siengdee
  given name: Puntita
author list: Agent
  family name: Pradit
  given name: Waranee
author list: Agent
  family name: Chomdej
  given name: Siriwadee
author list: Agent
  family name: Nganvongpanit
  given name: Korakot
doi: 10.7717/peerj.6553
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-03-12
copyright: ©2019 Siengdee et al.
attribution name: Siengdee et al.

The effects of Solidago canadensis water extracts on maize seedling growth in association with the biomass allocation pattern
type: item
type: AcademicArticle
description: Background Solidago canadensis L. is an aggressive exotic plant species in China that has potential allelopathic effects on competing plant species. Effects of hormesis are frequently observed in studies of allelopathy; however, the mechanisms of such effects need to be elucidated. Allelopathic compounds may affect the growth of recipient plants via alteration of biomass allocation patterns or photosynthetic capacity. The aim of this study was to determine how water extracts from S. canadensis affected the shoot and root growth of recipient plants and whether the underlying mechanism was related to the biomass allocation pattern or photosynthetic gas exchange capacity. Methods The water extracts from S. canadensis shoots at 12 different concentrations in the range of 0–0.25 g/ml were applied thrice in 9 days to maize seedlings cultivated in silica sand. The growth (shoot height, leaf length and area and root length) and biomass accumulation and allocation (specific leaf area (SLA), leaf area ratio (LAR) and leaf mass ratio (LMR)) were compared among maize seedlings exposed to different treatment concentrations. Gas exchange (photosynthetic light response curve) was measured and compared among maize seedlings exposed to three concentrations of water extract (0, 0.0125 and 0.2 g/ml) before and after the first application, and seedling growth was measured after the third and final application. Results The growth of seedlings (shoot height, leaf length and area and root length) was promoted at concentrations below 0.125 g/ml and inhibited at concentrations above this level (P < 0.05). The pattern of change in biomass accumulation and allocation was similar to that of shoot growth, but biomass accumulation and allocation was not significantly affected by the water extract treatments (P > 0.05). The water extract treatments did not significantly affect the photosynthetic capacity (P > 0.05), but the dark respiration rate was higher in the low-dose treatment than that in t…
format: application/pdf
format: text/html
creator: Xiao qi Ye
creator: Jin liu Meng
creator: Ming Wu
subject: Agricultural Science
subject: Biodiversity
subject: Ecology
subject: Plant Science
description: doi:10.7717/peerj.6564
publisher: PeerJ Inc.
rights: © 2019 Ye et al.
abstract: Background Solidago canadensis L. is an aggressive exotic plant species in China that has potential allelopathic effects on competing plant species. Effects of hormesis are frequently observed in studies of allelopathy; however, the mechanisms of such effects need to be elucidated. Allelopathic compounds may affect the growth of recipient plants via alteration of biomass allocation patterns or photosynthetic capacity. The aim of this study was to determine how water extracts from S. canadensis affected the shoot and root growth of recipient plants and whether the underlying mechanism was related to the biomass allocation pattern or photosynthetic gas exchange capacity. Methods The water extracts from S. canadensis shoots at 12 different concentrations in the range of 0–0.25 g/ml were applied thrice in 9 days to maize seedlings cultivated in silica sand. The growth (shoot height, leaf length and area and root length) and biomass accumulation and allocation (specific leaf area (SLA), leaf area ratio (LAR) and leaf mass ratio (LMR)) were compared among maize seedlings exposed to different treatment concentrations. Gas exchange (photosynthetic light response curve) was measured and compared among maize seedlings exposed to three concentrations of water extract (0, 0.0125 and 0.2 g/ml) before and after the first application, and seedling growth was measured after the third and final application. Results The growth of seedlings (shoot height, leaf length and area and root length) was promoted at concentrations below 0.125 g/ml and inhibited at concentrations above this level (P < 0.05). The pattern of change in biomass accumulation and allocation was similar to that of shoot growth, but biomass accumulation and allocation was not significantly affected by the water extract treatments (P > 0.05). The water extract treatments did not significantly affect the photosynthetic capacity (P > 0.05), but the dark respiration rate was higher in the low-dose treatment than that in t…
bibliographic citation: Ye et al. (2019) The effects of Solidago canadensis water extracts on maize seedling growth in association with the biomass allocation pattern. PeerJ 7:e6564 https://doi.org/10.7717/peerj.6564
date submitted: 2018-07-03
date accepted: 2019-02-02
issued: 2019-03-12
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Ye
  given name: Xiao qi
author list: Agent
  family name: Meng
  given name: Jin liu
author list: Agent
  family name: Wu
  given name: Ming
doi: 10.7717/peerj.6564
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-03-12
copyright: © 2019 Ye et al.
attribution name: Ye et al.

Anywhere but here: local conditions motivate dispersal in Daphnia
type: item
type: AcademicArticle
description: Dispersal is fundamental to population dynamics. However, it is increasingly apparent that, despite most models treating dispersal as a constant, many organisms make dispersal decisions based upon information gathered from the environment. Ideally, organisms would make fully informed decisions, with knowledge of both intra-patch conditions (conditions in their current location) and extra-patch conditions (conditions in alternative locations). Acquiring information is energetically costly, however, and extra-patch information will typically be costlier to obtain than intra-patch information. As a consequence, theory suggests that organisms will often make partially informed dispersal decisions, utilising intra-patch information only. We test this proposition in an experimental two-patch system using populations of the aquatic crustacean, Daphnia carinata. We manipulated conditions (food availability) in the population’s home patch, and in its alternative patch. We found that D. carinata made use of intra-patch information (resource availability in the home patch induced a 10-fold increase in dispersal probability) but either ignored or were incapable of using of extra-patch information (resource availability in the alternative patch did not affect dispersal probability). We also observed a small apparent increase in dispersal in replicates with higher population densities, but this effect was smaller than the effect of resource constraint, and not found to be significant. Our work highlights the considerable influence that information can have on dispersal probability, but also that dispersal decisions will often be made in only a partially informed manner. The magnitude of the response we observed also adds to the growing chorus that condition-dependence may be a significant driver of variation in dispersal.
format: application/pdf
format: text/html
creator: Philip Erm
creator: Matthew D. Hall
creator: Ben L. Phillips
subject: Animal Behavior
subject: Ecology
subject: Zoology
subject: Freshwater Biology
description: doi:10.7717/peerj.6599
publisher: PeerJ Inc.
rights: © 2019 Erm et al.
abstract: Dispersal is fundamental to population dynamics. However, it is increasingly apparent that, despite most models treating dispersal as a constant, many organisms make dispersal decisions based upon information gathered from the environment. Ideally, organisms would make fully informed decisions, with knowledge of both intra-patch conditions (conditions in their current location) and extra-patch conditions (conditions in alternative locations). Acquiring information is energetically costly, however, and extra-patch information will typically be costlier to obtain than intra-patch information. As a consequence, theory suggests that organisms will often make partially informed dispersal decisions, utilising intra-patch information only. We test this proposition in an experimental two-patch system using populations of the aquatic crustacean, Daphnia carinata. We manipulated conditions (food availability) in the population’s home patch, and in its alternative patch. We found that D. carinata made use of intra-patch information (resource availability in the home patch induced a 10-fold increase in dispersal probability) but either ignored or were incapable of using of extra-patch information (resource availability in the alternative patch did not affect dispersal probability). We also observed a small apparent increase in dispersal in replicates with higher population densities, but this effect was smaller than the effect of resource constraint, and not found to be significant. Our work highlights the considerable influence that information can have on dispersal probability, but also that dispersal decisions will often be made in only a partially informed manner. The magnitude of the response we observed also adds to the growing chorus that condition-dependence may be a significant driver of variation in dispersal.
bibliographic citation: Erm et al. (2019) Anywhere but here: local conditions motivate dispersal in Daphnia. PeerJ 7:e6599 https://doi.org/10.7717/peerj.6599
date submitted: 2018-11-15
date accepted: 2019-02-11
issued: 2019-03-12
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Erm
  given name: Philip
author list: Agent
  family name: Hall
  given name: Matthew D.
author list: Agent
  family name: Phillips
  given name: Ben L.
doi: 10.7717/peerj.6599
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-03-12
copyright: © 2019 Erm et al.
attribution name: Erm et al.

Quality-of-life among Syrian refugees residing outside camps in Jordan relative to Jordanians and other countries
type: item
type: AcademicArticle
description: Background Since the beginning of the Syrian humanitarian crisis, Syrians sought refuge in many safer countries. Many aspects of Syrian refugees’ lives have been affected, hence affecting the overall quality of their lives. However, only one study has investigated their quality of life (QOL). The aim of this study was to assess the QOL of Syrian refugees residing outside camps in Jordan and compare it to the QOL of Jordanians and to other refugees and populations around the globe. Methods Data were obtained from Syrian refugees residing outside camps in Jordan, and from two Jordanian groups; low socioeconomic status (LSES) Jordanians and average socioeconomic status (ASES) Jordanians in 2017. A total of 661 Syrians, 208 LSES Jordanians and 714 ASES Jordanians, aged between 18 and 75 years were included. The World Health Organization Quality of Life instrument (WHOQOL-BREF) questionnaire was used as the QOL assessment tool. Analysis of Variance “ANOVA” and post hoc Tukey-Honest tests were used to find the differences between the means of QOL questions in the three groups (Syrians, ASES, and LSES). Stepwise multivariate linear regression was performed for each domain to determine the most associated risk factors. Results No significant difference was found between Syrian refugees and LSES Jordanians in the physical health domain. Syrian refugees scored significantly lower than LSES Jordanians in the psychological health and social relationship domain. Syrian refugees scored significantly higher than LSES Jordanians in the environmental domain. ASES Jordanians scored significantly higher than the other two groups in all domains, with all its scores above the average. Discussion Despite the support Jordan provides to the Syrian refugees, they still seem to suffer from poor psychological health, social relationships and environmental domains, with scores below 50 on (0–100) scale. Nonetheless, no significant difference was found between Syrian refugees and LSES Jordanian…
format: application/pdf
format: text/html
creator: Nour Abdo
creator: Faten Sweidan
creator: Anwar Batieha
subject: Epidemiology
subject: Global Health
subject: Public Health
subject: Ethical Issues
subject: Coupled Natural and Human Systems
description: doi:10.7717/peerj.6454
publisher: PeerJ Inc.
rights: © 2019 Abdo et al.
abstract: Background Since the beginning of the Syrian humanitarian crisis, Syrians sought refuge in many safer countries. Many aspects of Syrian refugees’ lives have been affected, hence affecting the overall quality of their lives. However, only one study has investigated their quality of life (QOL). The aim of this study was to assess the QOL of Syrian refugees residing outside camps in Jordan and compare it to the QOL of Jordanians and to other refugees and populations around the globe. Methods Data were obtained from Syrian refugees residing outside camps in Jordan, and from two Jordanian groups; low socioeconomic status (LSES) Jordanians and average socioeconomic status (ASES) Jordanians in 2017. A total of 661 Syrians, 208 LSES Jordanians and 714 ASES Jordanians, aged between 18 and 75 years were included. The World Health Organization Quality of Life instrument (WHOQOL-BREF) questionnaire was used as the QOL assessment tool. Analysis of Variance “ANOVA” and post hoc Tukey-Honest tests were used to find the differences between the means of QOL questions in the three groups (Syrians, ASES, and LSES). Stepwise multivariate linear regression was performed for each domain to determine the most associated risk factors. Results No significant difference was found between Syrian refugees and LSES Jordanians in the physical health domain. Syrian refugees scored significantly lower than LSES Jordanians in the psychological health and social relationship domain. Syrian refugees scored significantly higher than LSES Jordanians in the environmental domain. ASES Jordanians scored significantly higher than the other two groups in all domains, with all its scores above the average. Discussion Despite the support Jordan provides to the Syrian refugees, they still seem to suffer from poor psychological health, social relationships and environmental domains, with scores below 50 on (0–100) scale. Nonetheless, no significant difference was found between Syrian refugees and LSES Jordanian…
bibliographic citation: Abdo et al. (2019) Quality-of-life among Syrian refugees residing outside camps in Jordan relative to Jordanians and other countries. PeerJ 7:e6454 https://doi.org/10.7717/peerj.6454
date submitted: 2018-10-02
date accepted: 2019-01-15
issued: 2019-03-11
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Abdo
  given name: Nour
author list: Agent
  family name: Sweidan
  given name: Faten
author list: Agent
  family name: Batieha
  given name: Anwar
doi: 10.7717/peerj.6454
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-03-11
copyright: © 2019 Abdo et al.
attribution name: Abdo et al.

The effect of sewage sludge and BAF inoculant on plant condition and yield as well as biochemical and microbial activity of soil in willow (Salix viminalis L.) culture as an energy crop
type: item
type: AcademicArticle
description: Excessive amounts of sewage sludge produced in sewage treatment plants along with the ban on its storage and dumping require rapid solutions to the problem of sewage sludge management. An example of a rational and environmentally viable method may be provided by its application in agriculture and environmental management. The optimal solution is to use sludge as a fertiliser for industrial plants, including energy crops, that is, those not used in food production. For environmental reasons it is essential to control soil quality and condition following sludge application. Analyses of the residual effect of sewage sludge and bacteria, actinobacteria, fungi microbial inoculant (BAF) on selected physiological parameters of plants and microbial activity of soil were conducted in the years 2013–2015 on experimental fields of the Poznan University of Life Sciences. The results indicate that the application of sewage sludge increased yields and improved selected photosynthesis activity and biometric traits of willow. Among the tested combinations the best results were obtained following the application of sewage sludge combined with the BAF medium microbial inoculant. Similar dependencies were observed when evaluating soil microbial activity.
format: application/pdf
format: text/html
creator: Katarzyna Panasiewicz
creator: Alicja Niewiadomska
creator: Hanna Sulewska
creator: Agnieszka Wolna-Maruwka
creator: Klaudia Borowiak
creator: Anna Budka
creator: Karolina Ratajczak
subject: Agricultural Science
subject: Microbiology
subject: Plant Science
description: doi:10.7717/peerj.6434
publisher: PeerJ Inc.
rights: © 2019 Panasiewicz et al.
abstract: Excessive amounts of sewage sludge produced in sewage treatment plants along with the ban on its storage and dumping require rapid solutions to the problem of sewage sludge management. An example of a rational and environmentally viable method may be provided by its application in agriculture and environmental management. The optimal solution is to use sludge as a fertiliser for industrial plants, including energy crops, that is, those not used in food production. For environmental reasons it is essential to control soil quality and condition following sludge application. Analyses of the residual effect of sewage sludge and bacteria, actinobacteria, fungi microbial inoculant (BAF) on selected physiological parameters of plants and microbial activity of soil were conducted in the years 2013–2015 on experimental fields of the Poznan University of Life Sciences. The results indicate that the application of sewage sludge increased yields and improved selected photosynthesis activity and biometric traits of willow. Among the tested combinations the best results were obtained following the application of sewage sludge combined with the BAF medium microbial inoculant. Similar dependencies were observed when evaluating soil microbial activity.
bibliographic citation: Panasiewicz et al. (2019) The effect of sewage sludge and BAF inoculant on plant condition and yield as well as biochemical and microbial activity of soil in willow (Salix viminalis L.) culture as an energy crop. PeerJ 7:e6434 https://doi.org/10.7717/peerj.6434
date submitted: 2018-10-04
date accepted: 2019-01-11
issued: 2019-03-11
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Panasiewicz
  given name: Katarzyna
author list: Agent
  family name: Niewiadomska
  given name: Alicja
author list: Agent
  family name: Sulewska
  given name: Hanna
author list: Agent
  family name: Wolna-Maruwka
  given name: Agnieszka
author list: Agent
  family name: Borowiak
  given name: Klaudia
author list: Agent
  family name: Budka
  given name: Anna
author list: Agent
  family name: Ratajczak
  given name: Karolina
doi: 10.7717/peerj.6434
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-03-11
copyright: © 2019 Panasiewicz et al.
attribution name: Panasiewicz et al.

Draft Aphaenogaster genomes expand our view of ant genome size variation across climate gradients
type: item
type: AcademicArticle
description: Given the abundance, broad distribution, and diversity of roles that ants play in many ecosystems, they are an ideal group to serve as ecosystem indicators of climatic change. At present, only a few whole-genome sequences of ants are available (19 of >16,000 species), mostly from tropical and sub-tropical species. To address this limited sampling, we sequenced genomes of temperate-latitude species from the genus Aphaenogaster, a genus with important seed dispersers. In total, we sampled seven colonies of six species: Aphaenogaster ashmeadi, Aphaenogaster floridana, Aphaenogaster fulva, Aphaenogaster miamiana, Aphaenogaster picea, and Aphaenogaster rudis. The geographic ranges of these species collectively span eastern North America from southern Florida to southern Canada, which encompasses a latitudinal gradient in which many climatic variables are changing rapidly. For the six genomes, we assembled an average of 271,039 contigs into 47,337 scaffolds. The Aphaenogaster genomes displayed high levels of completeness with 96.1% to 97.6% of Hymenoptera BUSCOs completely represented, relative to currently sequenced ant genomes which ranged from 88.2% to 98.5%. Additionally, the mean genome size was 370.5 Mb, ranging from 310.3 to 429.7, which is comparable to that of other sequenced ant genomes (212.8–396.0 Mb) and flow cytometry estimates (210.7–690.4 Mb). In an analysis of currently sequenced ant genomes and the new Aphaenogaster sequences, we found that after controlling for both spatial autocorrelation and phylogenetics ant genome size was marginally correlated with sample site climate similarity. Of all examined climate variables, minimum temperature, and annual precipitation had the strongest correlations with genome size, with ants from locations with colder minimum temperatures and higher levels of precipitation having larger genomes. These results suggest that climate extremes could be a selective force acting on ant genomes and point to the need for more exten…
format: application/pdf
format: text/html
creator: Matthew K. Lau
creator: Aaron M. Ellison
creator: Andrew Nguyen
creator: Clint Penick
creator: Bernice DeMarco
creator: Nicholas J. Gotelli
creator: Nathan J. Sanders
creator: Robert R. Dunn
creator: Sara Helms Cahan
subject: Ecology
subject: Genomics
description: doi:10.7717/peerj.6447
publisher: PeerJ Inc.
rights: © 2019 Lau et al.
abstract: Given the abundance, broad distribution, and diversity of roles that ants play in many ecosystems, they are an ideal group to serve as ecosystem indicators of climatic change. At present, only a few whole-genome sequences of ants are available (19 of >16,000 species), mostly from tropical and sub-tropical species. To address this limited sampling, we sequenced genomes of temperate-latitude species from the genus Aphaenogaster, a genus with important seed dispersers. In total, we sampled seven colonies of six species: Aphaenogaster ashmeadi, Aphaenogaster floridana, Aphaenogaster fulva, Aphaenogaster miamiana, Aphaenogaster picea, and Aphaenogaster rudis. The geographic ranges of these species collectively span eastern North America from southern Florida to southern Canada, which encompasses a latitudinal gradient in which many climatic variables are changing rapidly. For the six genomes, we assembled an average of 271,039 contigs into 47,337 scaffolds. The Aphaenogaster genomes displayed high levels of completeness with 96.1% to 97.6% of Hymenoptera BUSCOs completely represented, relative to currently sequenced ant genomes which ranged from 88.2% to 98.5%. Additionally, the mean genome size was 370.5 Mb, ranging from 310.3 to 429.7, which is comparable to that of other sequenced ant genomes (212.8–396.0 Mb) and flow cytometry estimates (210.7–690.4 Mb). In an analysis of currently sequenced ant genomes and the new Aphaenogaster sequences, we found that after controlling for both spatial autocorrelation and phylogenetics ant genome size was marginally correlated with sample site climate similarity. Of all examined climate variables, minimum temperature, and annual precipitation had the strongest correlations with genome size, with ants from locations with colder minimum temperatures and higher levels of precipitation having larger genomes. These results suggest that climate extremes could be a selective force acting on ant genomes and point to the need for more exten…
bibliographic citation: Lau et al. (2019) Draft Aphaenogaster genomes expand our view of ant genome size variation across climate gradients. PeerJ 7:e6447 https://doi.org/10.7717/peerj.6447
date submitted: 2018-04-25
date accepted: 2019-01-10
issued: 2019-03-11
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Lau
  given name: Matthew K.
author list: Agent
  family name: Ellison
  given name: Aaron M.
author list: Agent
  family name: Nguyen
  given name: Andrew
author list: Agent
  family name: Penick
  given name: Clint
author list: Agent
  family name: DeMarco
  given name: Bernice
author list: Agent
  family name: Gotelli
  given name: Nicholas J.
author list: Agent
  family name: Sanders
  given name: Nathan J.
author list: Agent
  family name: Dunn
  given name: Robert R.
author list: Agent
  family name: Helms Cahan
  given name: Sara
doi: 10.7717/peerj.6447
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-03-11
copyright: © 2019 Lau et al.
attribution name: Lau et al.

A systematic comparison of eight new plastome sequences from Ipomoea L
type: item
type: AcademicArticle
description: Background Ipomoea is the largest genus in the family Convolvulaceae. The species in this genus have been widely used in many fields, such as agriculture, nutrition, and medicine. With the development of next-generation sequencing, more than 50 chloroplast genomes of Ipomoea species have been sequenced. However, the repeats and divergence regions in Ipomoea have not been well investigated. In the present study, we sequenced and assembled eight chloroplast genomes from sweet potato’s close wild relatives. By combining these with 32 published chloroplast genomes, we conducted a detailed comparative analysis of a broad range of Ipomoea species. Methods Eight chloroplast genomes were assembled using short DNA sequences generated by next-generation sequencing technology. By combining these chloroplast genomes with 32 other published Ipomoea chloroplast genomes downloaded from GenBank and the Oxford Research Archive, we conducted a comparative analysis of the repeat sequences and divergence regions across the Ipomoea genus. In addition, separate analyses of the Batatas group and Quamoclit group were also performed. Results The eight newly sequenced chloroplast genomes ranged from 161,225 to 161,721 bp in length and displayed the typical circular quadripartite structure, consisting of a pair of inverted repeat (IR) regions (30,798–30,910 bp each) separated by a large single copy (LSC) region (87,575–88,004 bp) and a small single copy (SSC) region (12,018–12,051 bp). The average guanine-cytosine (GC) content was approximately 40.5% in the IR region, 36.1% in the LSC region, 32.2% in the SSC regions, and 37.5% in complete sequence for all the generated plastomes. The eight chloroplast genome sequences from this study included 80 protein-coding genes, four rRNAs (rrn23, rrn16, rrn5, and rrn4.5), and 37 tRNAs. The boundaries of single copy regions and IR regions were highly conserved in the eight chloroplast genomes. In Ipomoea, 57–89 pairs of repetitive sequences and 39–64 si…
format: application/pdf
format: text/html
creator: Jianying Sun
creator: Xiaofeng Dong
creator: Qinghe Cao
creator: Tao Xu
creator: Mingku Zhu
creator: Jian Sun
creator: Tingting Dong
creator: Daifu Ma
creator: Yonghua Han
creator: Zongyun Li
subject: Bioinformatics
subject: Genetics
subject: Genomics
subject: Plant Science
description: doi:10.7717/peerj.6563
publisher: PeerJ Inc.
rights: © 2019 Sun et al.
abstract: Background Ipomoea is the largest genus in the family Convolvulaceae. The species in this genus have been widely used in many fields, such as agriculture, nutrition, and medicine. With the development of next-generation sequencing, more than 50 chloroplast genomes of Ipomoea species have been sequenced. However, the repeats and divergence regions in Ipomoea have not been well investigated. In the present study, we sequenced and assembled eight chloroplast genomes from sweet potato’s close wild relatives. By combining these with 32 published chloroplast genomes, we conducted a detailed comparative analysis of a broad range of Ipomoea species. Methods Eight chloroplast genomes were assembled using short DNA sequences generated by next-generation sequencing technology. By combining these chloroplast genomes with 32 other published Ipomoea chloroplast genomes downloaded from GenBank and the Oxford Research Archive, we conducted a comparative analysis of the repeat sequences and divergence regions across the Ipomoea genus. In addition, separate analyses of the Batatas group and Quamoclit group were also performed. Results The eight newly sequenced chloroplast genomes ranged from 161,225 to 161,721 bp in length and displayed the typical circular quadripartite structure, consisting of a pair of inverted repeat (IR) regions (30,798–30,910 bp each) separated by a large single copy (LSC) region (87,575–88,004 bp) and a small single copy (SSC) region (12,018–12,051 bp). The average guanine-cytosine (GC) content was approximately 40.5% in the IR region, 36.1% in the LSC region, 32.2% in the SSC regions, and 37.5% in complete sequence for all the generated plastomes. The eight chloroplast genome sequences from this study included 80 protein-coding genes, four rRNAs (rrn23, rrn16, rrn5, and rrn4.5), and 37 tRNAs. The boundaries of single copy regions and IR regions were highly conserved in the eight chloroplast genomes. In Ipomoea, 57–89 pairs of repetitive sequences and 39–64 si…
bibliographic citation: Sun et al. (2019) A systematic comparison of eight new plastome sequences from Ipomoea L. PeerJ 7:e6563 https://doi.org/10.7717/peerj.6563
date submitted: 2018-08-28
date accepted: 2019-02-04
issued: 2019-03-11
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Sun
  given name: Jianying
author list: Agent
  family name: Dong
  given name: Xiaofeng
author list: Agent
  family name: Cao
  given name: Qinghe
author list: Agent
  family name: Xu
  given name: Tao
author list: Agent
  family name: Zhu
  given name: Mingku
author list: Agent
  family name: Sun
  given name: Jian
author list: Agent
  family name: Dong
  given name: Tingting
author list: Agent
  family name: Ma
  given name: Daifu
author list: Agent
  family name: Han
  given name: Yonghua
author list: Agent
  family name: Li
  given name: Zongyun
doi: 10.7717/peerj.6563
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-03-11
copyright: © 2019 Sun et al.
attribution name: Sun et al.

The distributive and structural characteristics of bronchus-associated lymphoid tissue (BALT) in Bactrian camels (Camelus bactrianus)
type: item
type: AcademicArticle
description: Background Bronchus-associated lymphoid tissue (BALT), distributed in the bronchial mucosa, plays a critical role in maintaining the mucosal immune homeostasis of the lower respiratory tract. The bronchial tree is a functional structure for gas exchange with the outside environment and maintains basic lung morphology. Methods To explore the structural and distributive characteristics of BALT in Bactrian camels, twelve healthy adult Bactrian camels were divided into two groups (six in each group). The lungs, bronchial tree and BALT were observed and analysed systematically through anatomical and histological methods. Results The results showed that Bactrian camel lungs were constituted by the left cranial lobe, left caudal lobe, right cranial lobe, right caudal lobe and accessory lobe, but lacked the middle lobe. The cranial lobe was narrow and small, the caudal lobe was extremely developed (almost four times the cranial lobe in size), and the accessory lobe was smaller than the cranial lobe; the bronchial tree, an unequal dichotomy with a tracheobronchial branch, was composed of dorsal, ventral, lateral and medial bronchiole systems. Isolated lymphoid follicles (the chief type) and aggregates of lymphoid follicles revealed two types of BALT, and germinal centres, follicle-associated epithelium and high endothelial venules could be observed in some well-developed BALT. Additionally, BALT was scattered along the bronchial tree in the entire lung, and the density increased from the trachea to the lower graded branches (densest in the bronchioles) and then decreased, with the occasional location around respiratory bronchioles or among the pulmonary mesenchyme. In the conducting portion, BALT was primarily located in the mucosa lamina propria but was also found in the submucosa, under the muscular layer, and around the submucosal glands and cartilage. Conclusion The results demonstrated that the lung morphology of Bactrian camels was similar to that of horses, but the br…
format: application/pdf
format: text/html
creator: Wanhong He
creator: Wangdong Zhang
creator: Cuicui Cheng
creator: Jianfei Li
creator: Xiuping Wu
creator: Min Li
creator: Zhihua Chen
creator: Wenhui Wang
subject: Agricultural Science
subject: Veterinary Medicine
subject: Zoology
subject: Respiratory Medicine
subject: Histology
description: doi:10.7717/peerj.6571
publisher: PeerJ Inc.
rights: © 2019 He et al.
abstract: Background Bronchus-associated lymphoid tissue (BALT), distributed in the bronchial mucosa, plays a critical role in maintaining the mucosal immune homeostasis of the lower respiratory tract. The bronchial tree is a functional structure for gas exchange with the outside environment and maintains basic lung morphology. Methods To explore the structural and distributive characteristics of BALT in Bactrian camels, twelve healthy adult Bactrian camels were divided into two groups (six in each group). The lungs, bronchial tree and BALT were observed and analysed systematically through anatomical and histological methods. Results The results showed that Bactrian camel lungs were constituted by the left cranial lobe, left caudal lobe, right cranial lobe, right caudal lobe and accessory lobe, but lacked the middle lobe. The cranial lobe was narrow and small, the caudal lobe was extremely developed (almost four times the cranial lobe in size), and the accessory lobe was smaller than the cranial lobe; the bronchial tree, an unequal dichotomy with a tracheobronchial branch, was composed of dorsal, ventral, lateral and medial bronchiole systems. Isolated lymphoid follicles (the chief type) and aggregates of lymphoid follicles revealed two types of BALT, and germinal centres, follicle-associated epithelium and high endothelial venules could be observed in some well-developed BALT. Additionally, BALT was scattered along the bronchial tree in the entire lung, and the density increased from the trachea to the lower graded branches (densest in the bronchioles) and then decreased, with the occasional location around respiratory bronchioles or among the pulmonary mesenchyme. In the conducting portion, BALT was primarily located in the mucosa lamina propria but was also found in the submucosa, under the muscular layer, and around the submucosal glands and cartilage. Conclusion The results demonstrated that the lung morphology of Bactrian camels was similar to that of horses, but the br…
bibliographic citation: He et al. (2019) The distributive and structural characteristics of bronchus-associated lymphoid tissue (BALT) in Bactrian camels (Camelus bactrianus). PeerJ 7:e6571 https://doi.org/10.7717/peerj.6571
date submitted: 2018-10-23
date accepted: 2019-02-04
issued: 2019-03-11
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: He
  given name: Wanhong
author list: Agent
  family name: Zhang
  given name: Wangdong
author list: Agent
  family name: Cheng
  given name: Cuicui
author list: Agent
  family name: Li
  given name: Jianfei
author list: Agent
  family name: Wu
  given name: Xiuping
author list: Agent
  family name: Li
  given name: Min
author list: Agent
  family name: Chen
  given name: Zhihua
author list: Agent
  family name: Wang
  given name: Wenhui
doi: 10.7717/peerj.6571
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-03-11
copyright: ©2019 He et al.
attribution name: He et al.

Anatomical location of AICA loop in CPA as a prognostic factor for ISSNHL
type: item
type: AcademicArticle
description: The cerebellopontine angle (CPA) is a triangular-shaped space that lies at the junction of the pons and cerebellum. It contains cranial nerves and the anterior inferior cerebellar artery (AICA). The anatomical shape and location of the AICA is variable within the CPA and internal auditory canal (IAC). A possible etiology of idiopathic sudden sensorineural hearing loss (ISSNHL) is ischemia of the labyrinthine artery, which is a branch of the AICA. As such, the position of the AICA within the CPA and IAC may be related to the clinical development of ISSNHL. We adopted two methods to classify the anatomic position of the AICA, then analyzed whether these classifications affected the clinical features and prognosis of ISSNHL. We retrospectively reviewed patient data from January 2015 to March 2018. Two established classification methods designed by Cahvada and Gorrie et al. were used. Pure tone threshold at four different frequencies (0.5, 1, 4, and 8 kHz), at two different time points (at initial presentation and three months after treatment), were analyzed. We compared the affected and unaffected ears, and investigated whether there were any differences in hearing recovery and symptoms between the two classification types. There was no difference in AICA types between ears with and without ISSNHL. Patients who had combined symptoms such as tinnitus and vertigo did not show a different AICA distribution compared with patients who did not. There were differences in quantitative hearing improvement between AICA types, although without statistic significance (p = 0.09–0.13). At two frequencies, 1 and 4 kHz, there were differences in Chavda types between hearing improvement and no improvement (p < 0.05). Anatomical variances of the AICA loop position did not affect the incidence of ISSNHL or co-morbid symptoms including tinnitus and vertigo. In contrast, comparisons of hearing improvement based on Chavda type classification showed a statistical difference, with a higher pr…
format: application/pdf
format: text/html
creator: Sang Hyub Kim
creator: Yeo Rim Ju
creator: Ji Eun Choi
creator: Jae Yun Jung
creator: Sang Yoon Kim
creator: Min Young Lee
subject: Anatomy and Physiology
subject: Neurology
subject: Otorhinolaryngology
subject: Radiology and Medical Imaging
description: doi:10.7717/peerj.6582
publisher: PeerJ Inc.
rights: © 2019 Kim et al.
abstract: The cerebellopontine angle (CPA) is a triangular-shaped space that lies at the junction of the pons and cerebellum. It contains cranial nerves and the anterior inferior cerebellar artery (AICA). The anatomical shape and location of the AICA is variable within the CPA and internal auditory canal (IAC). A possible etiology of idiopathic sudden sensorineural hearing loss (ISSNHL) is ischemia of the labyrinthine artery, which is a branch of the AICA. As such, the position of the AICA within the CPA and IAC may be related to the clinical development of ISSNHL. We adopted two methods to classify the anatomic position of the AICA, then analyzed whether these classifications affected the clinical features and prognosis of ISSNHL. We retrospectively reviewed patient data from January 2015 to March 2018. Two established classification methods designed by Cahvada and Gorrie et al. were used. Pure tone threshold at four different frequencies (0.5, 1, 4, and 8 kHz), at two different time points (at initial presentation and three months after treatment), were analyzed. We compared the affected and unaffected ears, and investigated whether there were any differences in hearing recovery and symptoms between the two classification types. There was no difference in AICA types between ears with and without ISSNHL. Patients who had combined symptoms such as tinnitus and vertigo did not show a different AICA distribution compared with patients who did not. There were differences in quantitative hearing improvement between AICA types, although without statistic significance (p = 0.09–0.13). At two frequencies, 1 and 4 kHz, there were differences in Chavda types between hearing improvement and no improvement (p < 0.05). Anatomical variances of the AICA loop position did not affect the incidence of ISSNHL or co-morbid symptoms including tinnitus and vertigo. In contrast, comparisons of hearing improvement based on Chavda type classification showed a statistical difference, with a higher pr…
bibliographic citation: Kim et al. (2019) Anatomical location of AICA loop in CPA as a prognostic factor for ISSNHL. PeerJ 7:e6582 https://doi.org/10.7717/peerj.6582
date submitted: 2018-10-05
date accepted: 2019-02-05
issued: 2019-03-11
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Kim
  given name: Sang Hyub
author list: Agent
  family name: Ju
  given name: Yeo Rim
author list: Agent
  family name: Choi
  given name: Ji Eun
author list: Agent
  family name: Jung
  given name: Jae Yun
author list: Agent
  family name: Kim
  given name: Sang Yoon
author list: Agent
  family name: Lee
  given name: Min Young
doi: 10.7717/peerj.6582
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-03-11
copyright: ©2019 Kim et al.
attribution name: Kim et al.

Numerical ability and improvement through interindividual cooperation varied between two cyprinid fish species, qingbo and crucian carp
type: item
type: AcademicArticle
description: We used qingbo (Spinibarbus sinensis) and Chinese crucian carp (Carassius auratus) to test whether numerical discrimination could be improved by the coexistence and possible cooperation of conspecies or heterospecies. We conducted a spontaneous shoal choice test of singletons, conspecific dyads and heterospecific dyads under different numerical comparisons (8 vs. 12, 9 vs. 12 and 10 vs. 12). Singletons of qingbo could discriminate only 8 vs. 12, whereas the dyads of qingbo showed better numerical acuity, as they could discriminate 10 vs. 12. Crucian carp may have poor numerical ability, as both singleton and dyads showed no significant preference for larger stimulus shoals, even at the ‘easier’ numerical discrimination, that is, 8 vs. 12. Furthermore, heterospecific dyads of crucian carp and qingbo did not show significant preference for larger shoals at any numerical comparison in the present study. It is suggested that both the numerical ability and the possibility for improvement by interindividual interaction and hence cooperation might vary among fish species, and the interaction between heterospecies in the present study showed negative effect on numerical ability possibly due to the different behavioural and cognitive traits which make the information transfer and consensus difficult to reach.
format: application/pdf
format: text/html
creator: Wei Xiong
creator: Lian-Chun Yi
creator: Zhong-Hua Tang
creator: Shi-Jian Fu
subject: Animal Behavior
subject: Freshwater Biology
description: doi:10.7717/peerj.6619
publisher: PeerJ Inc.
rights: © 2019 Xiong et al.
abstract: We used qingbo (Spinibarbus sinensis) and Chinese crucian carp (Carassius auratus) to test whether numerical discrimination could be improved by the coexistence and possible cooperation of conspecies or heterospecies. We conducted a spontaneous shoal choice test of singletons, conspecific dyads and heterospecific dyads under different numerical comparisons (8 vs. 12, 9 vs. 12 and 10 vs. 12). Singletons of qingbo could discriminate only 8 vs. 12, whereas the dyads of qingbo showed better numerical acuity, as they could discriminate 10 vs. 12. Crucian carp may have poor numerical ability, as both singleton and dyads showed no significant preference for larger stimulus shoals, even at the ‘easier’ numerical discrimination, that is, 8 vs. 12. Furthermore, heterospecific dyads of crucian carp and qingbo did not show significant preference for larger shoals at any numerical comparison in the present study. It is suggested that both the numerical ability and the possibility for improvement by interindividual interaction and hence cooperation might vary among fish species, and the interaction between heterospecies in the present study showed negative effect on numerical ability possibly due to the different behavioural and cognitive traits which make the information transfer and consensus difficult to reach.
bibliographic citation: Xiong et al. (2019) Numerical ability and improvement through interindividual cooperation varied between two cyprinid fish species, qingbo and crucian carp. PeerJ 7:e6619 https://doi.org/10.7717/peerj.6619
date submitted: 2019-01-02
date accepted: 2019-02-14
issued: 2019-03-11
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Xiong
  given name: Wei
author list: Agent
  family name: Yi
  given name: Lian-Chun
author list: Agent
  family name: Tang
  given name: Zhong-Hua
author list: Agent
  family name: Fu
  given name: Shi-Jian
doi: 10.7717/peerj.6619
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-03-11
copyright: © 2019 Xiong et al.
attribution name: Xiong et al.

Chronic fluoxetine treatment of juvenile zebrafish (Danio rerio) does not elicit changes in basal cortisol levels and anxiety-like behavior in adulthood
type: item
type: AcademicArticle
description: Exposure to selective serotonin reuptake inhibitors (SSRIs) during development may elicit long-term neuroadaptive changes that could alter the basal regulation of stress-associated physiological and behavioral processes later in life. Currently, the effects of juvenile fluoxetine exposure in rodent models appear to be dependent on the developmental window targeted as well as the duration of drug exposure. The zebrafish (Danio rerio) model is rapidly becoming a useful tool in pharmacological research and can be used to help elucidate some of the long-term effects of fluoxetine exposure prior to sexual maturation on neuroendocrine and behavioral stress markers. In the current study, juvenile zebrafish were chronically exposed to fluoxetine hydrochloride (0 or 100 μg/L) for 14 days (31–44 days post-fertilization (dpf)), then were left untreated until young adulthood. Starting at 90 dpf, basal neuroendocrine stress and behavioral responses of zebrafish were assessed. Cortisol was extracted from the young adult zebrafish body (trunk) and quantified via enzyme-linked immunosorbent assay (ELISA). Anxiety-like behaviors were assessed in response to introduction to the novel tank test. It was expected that juvenile exposure to fluoxetine would (1) reduce basal cortisol levels and (2) elicit anxiolytic effects in the novel tank test in adulthood. However, fluoxetine exposure during the juvenile period was not associated with alterations in basal levels of cortisol nor were there any significant changes in anxiety-like behavior in the young adult zebrafish. Thus, in zebrafish, it does not appear that SSRI exposure during the juvenile period has a long-term adverse or maladaptive impact on the basal expression of cortisol and anxiety-like behavior in adulthood. Further studies are needed to determine if SSRI exposure during this developmental window influences neuroendocrine and behavioral responses to acute stress.
format: application/pdf
format: text/html
creator: Maureen L. Petrunich-Rutherford
subject: Animal Behavior
subject: Developmental Biology
subject: Neuroscience
subject: Pharmacology
description: doi:10.7717/peerj.6407
publisher: PeerJ Inc.
rights: © 2019 Petrunich-Rutherford
abstract: Exposure to selective serotonin reuptake inhibitors (SSRIs) during development may elicit long-term neuroadaptive changes that could alter the basal regulation of stress-associated physiological and behavioral processes later in life. Currently, the effects of juvenile fluoxetine exposure in rodent models appear to be dependent on the developmental window targeted as well as the duration of drug exposure. The zebrafish (Danio rerio) model is rapidly becoming a useful tool in pharmacological research and can be used to help elucidate some of the long-term effects of fluoxetine exposure prior to sexual maturation on neuroendocrine and behavioral stress markers. In the current study, juvenile zebrafish were chronically exposed to fluoxetine hydrochloride (0 or 100 μg/L) for 14 days (31–44 days post-fertilization (dpf)), then were left untreated until young adulthood. Starting at 90 dpf, basal neuroendocrine stress and behavioral responses of zebrafish were assessed. Cortisol was extracted from the young adult zebrafish body (trunk) and quantified via enzyme-linked immunosorbent assay (ELISA). Anxiety-like behaviors were assessed in response to introduction to the novel tank test. It was expected that juvenile exposure to fluoxetine would (1) reduce basal cortisol levels and (2) elicit anxiolytic effects in the novel tank test in adulthood. However, fluoxetine exposure during the juvenile period was not associated with alterations in basal levels of cortisol nor were there any significant changes in anxiety-like behavior in the young adult zebrafish. Thus, in zebrafish, it does not appear that SSRI exposure during the juvenile period has a long-term adverse or maladaptive impact on the basal expression of cortisol and anxiety-like behavior in adulthood. Further studies are needed to determine if SSRI exposure during this developmental window influences neuroendocrine and behavioral responses to acute stress.
bibliographic citation: Petrunich-Rutherford (2019) Chronic fluoxetine treatment of juvenile zebrafish (Danio rerio) does not elicit changes in basal cortisol levels and anxiety-like behavior in adulthood. PeerJ 7:e6407 https://doi.org/10.7717/peerj.6407
date submitted: 2018-08-22
date accepted: 2019-01-08
issued: 2019-03-08
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Petrunich-Rutherford
  given name: Maureen L.
doi: 10.7717/peerj.6407
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-03-08
copyright: © 2019 Petrunich-Rutherford
attribution name: Petrunich-Rutherford

In vitro observation: the GFP-E. coli adhering to porcine erythrocytes can be removed by porcine alveolar macrophages
type: item
type: AcademicArticle
description: Although the activation of pathogen phagocytosis via complement system has been studied, erythrocyte-phagocyte interactions in pigs are not clearly understood. Therefore, we sought to investigate the ability of porcine erythrocytes to clear immune complexes (ICs) by using laser confocal microscopy and flow cytometry to observe the immune adhesion of porcine erythrocytes to fluorescent bacilli and the immune presentation process of transferring fluorescent bacilli to macrophages. Isolated porcine alveolar macrophages (PAMs) had uniform morphology and size, and a survival rate of 97.2%. The phagocytosis rate was 98.8%. After WT E. coli was labeled with Fluorescein Isothiocyanate (FITC), the bacteria showed a bright green fluorescence, and the labeling rate was 92.3%. When laser confocal microscopy was utilized to observe the co-incubation system of porcine erythrocytes, PAM, and fluorescent E. coli, the fluorescence intensity of bacilli decreased with increasing observation time and even disappeared. Flow Cytometry examination showed that the average fluorescence intensity of PAMs co-incubated with porcine erythrocytes adhered to WT-E. coli-FITC, was significantly higher than that of normal PAMs. Furthermore, when porcine erythrocytes adhered to WT E. coli were incubated with PAMs, the surface mean fluorescence intensity of porcine erythrocytes was significantly higher than that of the blank control group. This shows that PAMs can competitively bind to the oposinized E. coli adhered to the surface of porcine erythrocytes, and these oposinized pathogens can enter macrophages by the process of phagocytosis, which promoting the internalization of ICs or pathogens. During this process, the physical morphology of porcine erythrocytes was not damaged, but the levels of its main functional protein CR1-like were reduced.
format: application/pdf
format: text/html
creator: Wei Yin
creator: Chun Wang
creator: Kuohai Fan
creator: Na Sun
creator: Yaogui Sun
creator: Hongquan Li
subject: Immunology
description: doi:10.7717/peerj.6439
publisher: PeerJ Inc.
rights: © 2019 Yin et al.
abstract: Although the activation of pathogen phagocytosis via complement system has been studied, erythrocyte-phagocyte interactions in pigs are not clearly understood. Therefore, we sought to investigate the ability of porcine erythrocytes to clear immune complexes (ICs) by using laser confocal microscopy and flow cytometry to observe the immune adhesion of porcine erythrocytes to fluorescent bacilli and the immune presentation process of transferring fluorescent bacilli to macrophages. Isolated porcine alveolar macrophages (PAMs) had uniform morphology and size, and a survival rate of 97.2%. The phagocytosis rate was 98.8%. After WT E. coli was labeled with Fluorescein Isothiocyanate (FITC), the bacteria showed a bright green fluorescence, and the labeling rate was 92.3%. When laser confocal microscopy was utilized to observe the co-incubation system of porcine erythrocytes, PAM, and fluorescent E. coli, the fluorescence intensity of bacilli decreased with increasing observation time and even disappeared. Flow Cytometry examination showed that the average fluorescence intensity of PAMs co-incubated with porcine erythrocytes adhered to WT-E. coli-FITC, was significantly higher than that of normal PAMs. Furthermore, when porcine erythrocytes adhered to WT E. coli were incubated with PAMs, the surface mean fluorescence intensity of porcine erythrocytes was significantly higher than that of the blank control group. This shows that PAMs can competitively bind to the oposinized E. coli adhered to the surface of porcine erythrocytes, and these oposinized pathogens can enter macrophages by the process of phagocytosis, which promoting the internalization of ICs or pathogens. During this process, the physical morphology of porcine erythrocytes was not damaged, but the levels of its main functional protein CR1-like were reduced.
bibliographic citation: Yin et al. (2019) In vitro observation: the GFP-E. coli adhering to porcine erythrocytes can be removed by porcine alveolar macrophages. PeerJ 7:e6439 https://doi.org/10.7717/peerj.6439
date submitted: 2018-04-19
date accepted: 2019-01-11
issued: 2019-03-08
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Yin
  given name: Wei
author list: Agent
  family name: Wang
  given name: Chun
author list: Agent
  family name: Fan
  given name: Kuohai
author list: Agent
  family name: Sun
  given name: Na
author list: Agent
  family name: Sun
  given name: Yaogui
author list: Agent
  family name: Li
  given name: Hongquan
doi: 10.7717/peerj.6439
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-03-08
copyright: © 2019 Yin et al.
attribution name: Yin et al.

A multi-year experiment shows that lower precipitation predictability encourages plants’ early life stages and enhances population viability
type: item
type: AcademicArticle
description: Climate change is a key factor that may cause the extinction of species. The associated reduced weather predictability may alter the survival of plants, especially during their early life stages, when individuals are most fragile. While it is expected that extreme weather events will be highly detrimental for species, the effects of more subtle environmental changes have been little considered. In a four-year experiment on two herbaceous plants, Papaver rhoeas and Onobrychis viciifolia, we manipulated the predictability of precipitation by changing the temporal correlation of precipitation events while maintaining average precipitation constant, leading to more and less predictable treatments. We assessed the effect of predictability on plant viability in terms of seedling emergence, survival, seed production, and population growth rate. We found greater seedling emergence, survival, and population growth for plants experiencing lower intra-seasonal predictability, but more so during early compared to late life stages. Since predictability levels were maintained across four generations, we have also tested whether descendants exhibited transgenerational responses to previous predictability conditions. In P. rhoeas, descendants had increased the seedling emergence compared to ancestors under both treatments, but more so under lower precipitation predictability. However, higher predictability in the late treatment induced higher survival in descendants, showing that these conditions may benefit long-term survival. This experiment highlights the ability of some plants to rapidly exploit environmental resources and increase their survival under less predictable conditions, especially during early life stages. Therefore, this study provides relevant evidence of the survival capacity of some species under current and future short-term environmental alterations.
format: application/pdf
format: text/html
creator: Martí March-Salas
creator: Patrick S. Fitze
subject: Ecology
subject: Evolutionary Studies
subject: Plant Science
subject: Climate Change Biology
description: doi:10.7717/peerj.6443
publisher: PeerJ Inc.
rights: © 2019 March-Salas and Fitze
abstract: Climate change is a key factor that may cause the extinction of species. The associated reduced weather predictability may alter the survival of plants, especially during their early life stages, when individuals are most fragile. While it is expected that extreme weather events will be highly detrimental for species, the effects of more subtle environmental changes have been little considered. In a four-year experiment on two herbaceous plants, Papaver rhoeas and Onobrychis viciifolia, we manipulated the predictability of precipitation by changing the temporal correlation of precipitation events while maintaining average precipitation constant, leading to more and less predictable treatments. We assessed the effect of predictability on plant viability in terms of seedling emergence, survival, seed production, and population growth rate. We found greater seedling emergence, survival, and population growth for plants experiencing lower intra-seasonal predictability, but more so during early compared to late life stages. Since predictability levels were maintained across four generations, we have also tested whether descendants exhibited transgenerational responses to previous predictability conditions. In P. rhoeas, descendants had increased the seedling emergence compared to ancestors under both treatments, but more so under lower precipitation predictability. However, higher predictability in the late treatment induced higher survival in descendants, showing that these conditions may benefit long-term survival. This experiment highlights the ability of some plants to rapidly exploit environmental resources and increase their survival under less predictable conditions, especially during early life stages. Therefore, this study provides relevant evidence of the survival capacity of some species under current and future short-term environmental alterations.
bibliographic citation: March-Salas et al. (2019) A multi-year experiment shows that lower precipitation predictability encourages plants’ early life stages and enhances population viability. PeerJ 7:e6443 https://doi.org/10.7717/peerj.6443
date submitted: 2018-11-22
date accepted: 2019-01-14
issued: 2019-03-08
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: March-Salas
  given name: Martí
author list: Agent
  family name: Fitze
  given name: Patrick S.
doi: 10.7717/peerj.6443
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-03-08
copyright: © 2019 March-Salas and Fitze
attribution name: March-Salas and Fitze

Modulating pain thresholds through classical conditioning
type: item
type: AcademicArticle
description: Background Classical conditioning has frequently been shown to be capable of evoking fear of pain and avoidance behavior in the context of chronic pain. However, whether pain itself can be conditioned has rarely been investigated and remains a matter of debate. Therefore, the present study investigated whether pain threshold ratings can be modified by the presence of conditioned non-nociceptive sensory stimuli in healthy participant. Methods In 51 healthy volunteers, pain threshold to electrocutaneous stimuli was determined prior to participation in a simultaneous conditioning paradigm. Participants underwent an acquisition phase in which one non-painful vibrotactile stimulus (CS+) was repeatedly paired with a painful electrocutaneous stimulus, whereas a second vibrotactile stimulus of the same quality and intensity (CS−) was paired with a non-painful electrocutaneous stimulus. Stimulation was provided on the lower back with close proximity between the conditioned stimulus and the unconditioned stimulus. In the test phase, electrocutaneous stimuli at the individually-set threshold intensity were simultaneously delivered together with either a CS+ or CS−. Pain intensity ratings were obtained after each trial; expectancy ratings were obtained after each block. The primary outcome was the percentage of test stimuli that were rated as painful. Results Test stimuli were more likely to be rated as painful when they were paired with the CS+ than when they were paired with the CS−. This effect was not influenced by contingency awareness, nor by expectancies or mood states. Discussion The findings support the notion that the judgement of an event being painful or non-painful can be influenced by classical conditioning and corroborate the possible role of associative learning in the development and maintenance of chronic pain.
format: application/pdf
format: text/html
creator: Juliane Traxler
creator: Victoria J. Madden
creator: G. Lorimer Moseley
creator: Johan W.S. Vlaeyen
subject: Anesthesiology and Pain Management
subject: Psychiatry and Psychology
description: doi:10.7717/peerj.6486
publisher: PeerJ Inc.
rights: © 2019 Traxler et al.
abstract: Background Classical conditioning has frequently been shown to be capable of evoking fear of pain and avoidance behavior in the context of chronic pain. However, whether pain itself can be conditioned has rarely been investigated and remains a matter of debate. Therefore, the present study investigated whether pain threshold ratings can be modified by the presence of conditioned non-nociceptive sensory stimuli in healthy participant. Methods In 51 healthy volunteers, pain threshold to electrocutaneous stimuli was determined prior to participation in a simultaneous conditioning paradigm. Participants underwent an acquisition phase in which one non-painful vibrotactile stimulus (CS+) was repeatedly paired with a painful electrocutaneous stimulus, whereas a second vibrotactile stimulus of the same quality and intensity (CS−) was paired with a non-painful electrocutaneous stimulus. Stimulation was provided on the lower back with close proximity between the conditioned stimulus and the unconditioned stimulus. In the test phase, electrocutaneous stimuli at the individually-set threshold intensity were simultaneously delivered together with either a CS+ or CS−. Pain intensity ratings were obtained after each trial; expectancy ratings were obtained after each block. The primary outcome was the percentage of test stimuli that were rated as painful. Results Test stimuli were more likely to be rated as painful when they were paired with the CS+ than when they were paired with the CS−. This effect was not influenced by contingency awareness, nor by expectancies or mood states. Discussion The findings support the notion that the judgement of an event being painful or non-painful can be influenced by classical conditioning and corroborate the possible role of associative learning in the development and maintenance of chronic pain.
bibliographic citation: Traxler et al. (2019) Modulating pain thresholds through classical conditioning. PeerJ 7:e6486 https://doi.org/10.7717/peerj.6486
date submitted: 2018-08-28
date accepted: 2019-01-17
issued: 2019-03-08
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Traxler
  given name: Juliane
author list: Agent
  family name: Madden
  given name: Victoria J.
author list: Agent
  family name: Moseley
  given name: G. Lorimer
author list: Agent
  family name: Vlaeyen
  given name: Johan W.S.
doi: 10.7717/peerj.6486
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-03-08
copyright: © 2019 Traxler et al.
attribution name: Traxler et al.

Aboveground carbon of community-managed Chirpine (Pinus roxburghii Sarg.) forests of Nepal based on stand types and geographic aspects
type: item
type: AcademicArticle
description: On a global scale, about 15.5% of forests are administered through community-based forestry programs that offer the opportunity for enhanced carbon sequestration while maintaining the supply of more traditional goods and services such as cooking fuels, animal fodder and bedding. A challenge in community forest (CF) management is to realize their carbon value without compromising their role in the provision of these traditional goods and services. In this study of CF dominated by Pinus roxburghii in the Phalebas region of Nepal, the impacts of stand composition and geographic aspect on aboveground forest carbon is investigated as a means to optimize CF management for both traditional values and for emerging carbon market values. The aboveground carbon of mixed and monospecific stands of Pinus roxburghii was estimated using a combination of destructive sampling and species-specific allometric equations. On average, monospecific stands contained 106.2 Mg C ha−1 in aboveground tree biomass, significantly more than mixed stands at 73.1 Mg C ha−1 (p = 0.022). Similarly, stands growing on northern aspects (northeast 124.8 Mg C ha−1, northwest 100.9 Mg C ha−1) stored significantly more carbon (p = 0.002) than southern aspects (southeast 75.3 Mg C ha−1, southwest 57.6 Mg C ha−1), reflecting the more favorable growing conditions of northern aspects. These results suggest monospecific stands planted on northern aspects may be best suited for management to achieve carbon benefits, whilst mixed-species stands on southern aspects may be better suited for biodiversity conservation and supporting livelihoods. To maintain and increase carbon value, community forestry may need to implement nutrient return practices to limit the impact of sustained nutrient removals on stand productivity.
format: application/pdf
format: text/html
creator: Shiva Pariyar
creator: Liubov Volkova
creator: Ram P. Sharma
creator: Ramesh Sunam
creator: Christopher J. Weston
subject: Climate Change Biology
subject: Natural Resource Management
subject: Forestry
description: doi:10.7717/peerj.6494
publisher: PeerJ Inc.
rights: © 2019 Pariyar et al.
abstract: On a global scale, about 15.5% of forests are administered through community-based forestry programs that offer the opportunity for enhanced carbon sequestration while maintaining the supply of more traditional goods and services such as cooking fuels, animal fodder and bedding. A challenge in community forest (CF) management is to realize their carbon value without compromising their role in the provision of these traditional goods and services. In this study of CF dominated by Pinus roxburghii in the Phalebas region of Nepal, the impacts of stand composition and geographic aspect on aboveground forest carbon is investigated as a means to optimize CF management for both traditional values and for emerging carbon market values. The aboveground carbon of mixed and monospecific stands of Pinus roxburghii was estimated using a combination of destructive sampling and species-specific allometric equations. On average, monospecific stands contained 106.2 Mg C ha−1 in aboveground tree biomass, significantly more than mixed stands at 73.1 Mg C ha−1 (p = 0.022). Similarly, stands growing on northern aspects (northeast 124.8 Mg C ha−1, northwest 100.9 Mg C ha−1) stored significantly more carbon (p = 0.002) than southern aspects (southeast 75.3 Mg C ha−1, southwest 57.6 Mg C ha−1), reflecting the more favorable growing conditions of northern aspects. These results suggest monospecific stands planted on northern aspects may be best suited for management to achieve carbon benefits, whilst mixed-species stands on southern aspects may be better suited for biodiversity conservation and supporting livelihoods. To maintain and increase carbon value, community forestry may need to implement nutrient return practices to limit the impact of sustained nutrient removals on stand productivity.
bibliographic citation: Pariyar et al. (2019) Aboveground carbon of community-managed Chirpine (Pinus roxburghii Sarg.) forests of Nepal based on stand types and geographic aspects. PeerJ 7:e6494 https://doi.org/10.7717/peerj.6494
date submitted: 2018-07-31
date accepted: 2019-01-20
issued: 2019-03-08
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Pariyar
  given name: Shiva
author list: Agent
  family name: Volkova
  given name: Liubov
author list: Agent
  family name: Sharma
  given name: Ram P.
author list: Agent
  family name: Sunam
  given name: Ramesh
author list: Agent
  family name: Weston
  given name: Christopher J.
doi: 10.7717/peerj.6494
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-03-08
copyright: © 2019 Pariyar et al.
attribution name: Pariyar et al.

cRegulome: an R package for accessing microRNA and transcription factor-gene expression correlations in cancer
type: item
type: AcademicArticle
description: Background Transcription factors and microRNAs play a critical role in regulating the gene expression in normal physiology and pathological conditions. Many bioinformatics tools were built to predict and identify transcription factor and microRNA targets and their role in the development of diseases including cancers. The availability of public access high-throughput data allows researchers to make data-driven predictions. Implementation Here, we developed an R package called cRegulome to access, manage and visualize data from open source databases. The package provides a programmatic access to the regulome (transcription factor and microRNA) expression correlations with target genes of different cancer types. It obtains a local instance of Cistrome Cancer and miRCancerdb databases and provides classes and methods to query, interact with and visualize the correlation data. Availability cRegulome is available on the comprehensive R archive network (CRAN) and the source code is hosted on GitHub as part of the ROpenSci on-boarding collection, https://github.com/ropensci/cRegulome.
format: application/pdf
format: text/html
creator: Mahmoud Ahmed
creator: Deok Ryong Kim
subject: Cell Biology
subject: Computational Biology
subject: Molecular Biology
description: doi:10.7717/peerj.6509
publisher: PeerJ Inc.
rights: © 2019 Ahmed et al.
abstract: Background Transcription factors and microRNAs play a critical role in regulating the gene expression in normal physiology and pathological conditions. Many bioinformatics tools were built to predict and identify transcription factor and microRNA targets and their role in the development of diseases including cancers. The availability of public access high-throughput data allows researchers to make data-driven predictions. Implementation Here, we developed an R package called cRegulome to access, manage and visualize data from open source databases. The package provides a programmatic access to the regulome (transcription factor and microRNA) expression correlations with target genes of different cancer types. It obtains a local instance of Cistrome Cancer and miRCancerdb databases and provides classes and methods to query, interact with and visualize the correlation data. Availability cRegulome is available on the comprehensive R archive network (CRAN) and the source code is hosted on GitHub as part of the ROpenSci on-boarding collection, https://github.com/ropensci/cRegulome.
bibliographic citation: Ahmed et al. (2019) cRegulome: an R package for accessing microRNA and transcription factor-gene expression correlations in cancer. PeerJ 7:e6509 https://doi.org/10.7717/peerj.6509
date submitted: 2018-10-29
date accepted: 2019-01-24
issued: 2019-03-08
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Ahmed
  given name: Mahmoud
author list: Agent
  family name: Kim
  given name: Deok Ryong
doi: 10.7717/peerj.6509
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-03-08
copyright: ©2019 Ahmed et al.
attribution name: Ahmed et al.

Comparison of laboratory indices of non-alcoholic fatty liver disease for the detection of incipient kidney dysfunction
type: item
type: AcademicArticle
description: Non-alcoholic fatty liver disease (NAFLD) is closely linked to insulin resistance and related adverse health outcomes. We investigated the non-invasive index of NAFLD that has the best performance in estimating the renal manifestations of metabolic disturbances. This nation-wide, cross-sectional study included 11,836 subjects, using various non-invasive assessments comprising routinely measured clinical and laboratory variables. The subjects were native Koreans aged 20 years or older and had no diabetes, history of liver or kidney disease. All participants were divided into quintiles according to their fibrosis-4 (FIB-4) results. Participants in the highest quintile were more hypertensive and obese with greater glycemic exposure, poor lipid profiles, and impaired kidney function, than those in the other quintiles. Multiple logistic regression, adjusted for age, sex, smoking, systolic blood pressure, white blood cell, platelet, fasting plasma glucose, and triglyceride, demonstrated that FIB-4, the hepatic steatosis index, the aspartate aminotransferase/alanine aminotransferase (AST/ALT) ratio, Gholam’s model for non-alcoholic steatohepatitis, and the BARD score were independently associated with kidney dysfunction. ROC curve analysis revealed that FIB-4 (AUC = 0.6227, 95% CI [0.5929–0.6526], p = 0.0258) was the most precise in predicting kidney dysfunction. Our findings suggest that FIB-4 may be a favorable screening tool for the renal manifestation of hepatic metabolic disturbances.
format: application/pdf
format: text/html
creator: Jong Wook Choi
creator: Chang Hwa Lee
creator: Joon-Sung Park
subject: Gastroenterology and Hepatology
subject: Nephrology
description: doi:10.7717/peerj.6524
publisher: PeerJ Inc.
rights: © 2019 Choi et al.
abstract: Non-alcoholic fatty liver disease (NAFLD) is closely linked to insulin resistance and related adverse health outcomes. We investigated the non-invasive index of NAFLD that has the best performance in estimating the renal manifestations of metabolic disturbances. This nation-wide, cross-sectional study included 11,836 subjects, using various non-invasive assessments comprising routinely measured clinical and laboratory variables. The subjects were native Koreans aged 20 years or older and had no diabetes, history of liver or kidney disease. All participants were divided into quintiles according to their fibrosis-4 (FIB-4) results. Participants in the highest quintile were more hypertensive and obese with greater glycemic exposure, poor lipid profiles, and impaired kidney function, than those in the other quintiles. Multiple logistic regression, adjusted for age, sex, smoking, systolic blood pressure, white blood cell, platelet, fasting plasma glucose, and triglyceride, demonstrated that FIB-4, the hepatic steatosis index, the aspartate aminotransferase/alanine aminotransferase (AST/ALT) ratio, Gholam’s model for non-alcoholic steatohepatitis, and the BARD score were independently associated with kidney dysfunction. ROC curve analysis revealed that FIB-4 (AUC = 0.6227, 95% CI [0.5929–0.6526], p = 0.0258) was the most precise in predicting kidney dysfunction. Our findings suggest that FIB-4 may be a favorable screening tool for the renal manifestation of hepatic metabolic disturbances.
bibliographic citation: Choi et al. (2019) Comparison of laboratory indices of non-alcoholic fatty liver disease for the detection of incipient kidney dysfunction. PeerJ 7:e6524 https://doi.org/10.7717/peerj.6524
date submitted: 2018-10-24
date accepted: 2019-01-26
issued: 2019-03-08
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Choi
  given name: Jong Wook
author list: Agent
  family name: Lee
  given name: Chang Hwa
author list: Agent
  family name: Park
  given name: Joon-Sung
doi: 10.7717/peerj.6524
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-03-08
copyright: ©2019 Choi et al.
attribution name: Choi et al.

Transcriptome sequencing and comparative analysis of adult ovary and testis identify potential gonadal maintenance-related genes in Mauremys reevesii with temperature-dependent sex determination
type: item
type: AcademicArticle
description: Mauremys reevesii is a classical organism with temperature-dependent sex determination (TSD). Gonad development in early life has recently received considerable attention but gonadal maintenance after sex differentiation in turtles with TSD remains a mystery. In this study, we sequenced the transcriptomes for the adult testis and ovary using RNA-seq, and 36,221 transcripts were identified. In total, 1,594 differentially expressed genes (DEGs) were identified where 756 DEGs were upregulated in the testis and 838 DEGs were upregulated in the ovary. Gene Ontology and Kyoto Encyclopedia of Genes and Genomes pathway analysis suggested that the TGF-beta signaling pathway and Hedgehog signaling pathway have important roles in testis maintenance and spermatogenesis, whereas the Hippo signaling pathway and Wnt signaling pathway are likely to participate in ovary maintenance. We determined the existence of antagonistic networks containing significant specific-expressed genes and pathways related to gonadal maintenance and gametogenesis in the adult gonads of M. reevesii. The candidate gene Fibronectin type 3 and ankyrin repeat domains 1 (FANK1) might be involved with the regulation of testis spermatogenesis.
format: application/pdf
format: text/html
creator: Lei Xiong
creator: Jinxiu Dong
creator: Hui Jiang
creator: Jiawei Zan
creator: Jiucui Tong
creator: Jianjun Liu
creator: Meng Wang
creator: Liuwang Nie
subject: Bioinformatics
subject: Genomics
subject: Zoology
description: doi:10.7717/peerj.6557
publisher: PeerJ Inc.
rights: © 2019 Xiong et al.
abstract: Mauremys reevesii is a classical organism with temperature-dependent sex determination (TSD). Gonad development in early life has recently received considerable attention but gonadal maintenance after sex differentiation in turtles with TSD remains a mystery. In this study, we sequenced the transcriptomes for the adult testis and ovary using RNA-seq, and 36,221 transcripts were identified. In total, 1,594 differentially expressed genes (DEGs) were identified where 756 DEGs were upregulated in the testis and 838 DEGs were upregulated in the ovary. Gene Ontology and Kyoto Encyclopedia of Genes and Genomes pathway analysis suggested that the TGF-beta signaling pathway and Hedgehog signaling pathway have important roles in testis maintenance and spermatogenesis, whereas the Hippo signaling pathway and Wnt signaling pathway are likely to participate in ovary maintenance. We determined the existence of antagonistic networks containing significant specific-expressed genes and pathways related to gonadal maintenance and gametogenesis in the adult gonads of M. reevesii. The candidate gene Fibronectin type 3 and ankyrin repeat domains 1 (FANK1) might be involved with the regulation of testis spermatogenesis.
bibliographic citation: Xiong et al. (2019) Transcriptome sequencing and comparative analysis of adult ovary and testis identify potential gonadal maintenance-related genes in Mauremys reevesii with temperature-dependent sex determination. PeerJ 7:e6557 https://doi.org/10.7717/peerj.6557
date submitted: 2018-10-23
date accepted: 2019-02-03
issued: 2019-03-08
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Xiong
  given name: Lei
author list: Agent
  family name: Dong
  given name: Jinxiu
author list: Agent
  family name: Jiang
  given name: Hui
author list: Agent
  family name: Zan
  given name: Jiawei
author list: Agent
  family name: Tong
  given name: Jiucui
author list: Agent
  family name: Liu
  given name: Jianjun
author list: Agent
  family name: Wang
  given name: Meng
author list: Agent
  family name: Nie
  given name: Liuwang
doi: 10.7717/peerj.6557
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-03-08
copyright: © 2019 Xiong et al.
attribution name: Xiong et al.

Patterns of hepatitis B virus S gene escape mutants and reverse transcriptase mutations among genotype D isolates in Jordan
type: item
type: AcademicArticle
description: Background Hepatitis B virus (HBV) is an important infectious cause of morbidity and mortality in Jordan. HBV genotype D is the most prevalent in the country. Virus escape mutants in the HBV S region is an important public health problem halting preventive efforts. The aim of the current study was to investigate patterns of HBV escape and resistance mutations and to assess domestic transmission of the virus. Methods Patients infected with HBV were recruited at Jordan University Hospital (n = 56) and were diagnosed during (1984–2012). A total of 37 partial HBV S sequences were generated using Sanger’s method. Mutation analysis was done using the HIV grade HBV drug resistance interpretation online tool and Geno2pheno (HBV) online tools. Domestic transmission of HBV was assessed using maximum likelihood phylogenetic inference with similar GenBank sequences. Results Genotyping revealed an exclusive presence of sub-genotype D1. Typical HBV escape mutants were identified in seven patients. These mutations included: L109R, Q129R, M133L, S143L and D144E with overall prevalence of 18.9% (95% CI [9.5–34.2]). Reverse transcriptase (RT) sequence analysis showed mutations in three patients with overall prevalence of 8.1% (95% CI [2.8–21.3]). RT mutations included: V173L, S202I, L180M, M204V and T184A. Transmission cluster analysis revealed a relatively high proportion of infections taking place as a result of domestic spread (29.7%). Conclusions Based on our findings, RT mutation analysis appears to be of high value before the initiation of therapy in patients with chronic HBV infection in Jordan. Phylogenetic analyses revealed a considerable proportion of local spread in the country which should be considered in the preventive infection control efforts.
format: application/pdf
format: text/html
creator: Nidaa A. Ababneh
creator: Malik Sallam
creator: Doaa Kaddomi
creator: Abdelrahman M. Attili
creator: Isam Bsisu
creator: Nadia Khamees
creator: Amer Khatib
creator: Azmi Mahafzah
subject: Virology
subject: Epidemiology
subject: Gastroenterology and Hepatology
subject: Infectious Diseases
description: doi:10.7717/peerj.6583
publisher: PeerJ Inc.
rights: © 2019 Ababneh et al.
abstract: Background Hepatitis B virus (HBV) is an important infectious cause of morbidity and mortality in Jordan. HBV genotype D is the most prevalent in the country. Virus escape mutants in the HBV S region is an important public health problem halting preventive efforts. The aim of the current study was to investigate patterns of HBV escape and resistance mutations and to assess domestic transmission of the virus. Methods Patients infected with HBV were recruited at Jordan University Hospital (n = 56) and were diagnosed during (1984–2012). A total of 37 partial HBV S sequences were generated using Sanger’s method. Mutation analysis was done using the HIV grade HBV drug resistance interpretation online tool and Geno2pheno (HBV) online tools. Domestic transmission of HBV was assessed using maximum likelihood phylogenetic inference with similar GenBank sequences. Results Genotyping revealed an exclusive presence of sub-genotype D1. Typical HBV escape mutants were identified in seven patients. These mutations included: L109R, Q129R, M133L, S143L and D144E with overall prevalence of 18.9% (95% CI [9.5–34.2]). Reverse transcriptase (RT) sequence analysis showed mutations in three patients with overall prevalence of 8.1% (95% CI [2.8–21.3]). RT mutations included: V173L, S202I, L180M, M204V and T184A. Transmission cluster analysis revealed a relatively high proportion of infections taking place as a result of domestic spread (29.7%). Conclusions Based on our findings, RT mutation analysis appears to be of high value before the initiation of therapy in patients with chronic HBV infection in Jordan. Phylogenetic analyses revealed a considerable proportion of local spread in the country which should be considered in the preventive infection control efforts.
bibliographic citation: Ababneh et al. (2019) Patterns of hepatitis B virus S gene escape mutants and reverse transcriptase mutations among genotype D isolates in Jordan. PeerJ 7:e6583 https://doi.org/10.7717/peerj.6583
date submitted: 2018-10-10
date accepted: 2019-02-08
issued: 2019-03-08
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Ababneh
  given name: Nidaa A.
author list: Agent
  family name: Sallam
  given name: Malik
author list: Agent
  family name: Kaddomi
  given name: Doaa
author list: Agent
  family name: Attili
  given name: Abdelrahman M.
author list: Agent
  family name: Bsisu
  given name: Isam
author list: Agent
  family name: Khamees
  given name: Nadia
author list: Agent
  family name: Khatib
  given name: Amer
author list: Agent
  family name: Mahafzah
  given name: Azmi
doi: 10.7717/peerj.6583
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-03-08
copyright: © 2019 Ababneh et al.
attribution name: Ababneh et al.

Osteogenic capacity and cytotherapeutic potential of periodontal ligament cells for periodontal regeneration in vitro and in vivo
type: item
type: AcademicArticle
description: Background The periodontal ligament cells (PDLCs) contain heterogeneous cell populations and possess stem-cell-like properties. PDLCs have attracted considerable attention as an option for periodontal regeneration. However, the osteogenic differentiation of PDLCs remains obscure owing to variable osteo-inductive methods and whether PDLCs could be directly used for periodontal regeneration without stem cell enrichment is uncertain. The aim of the present study was to clarify the osteogenic differentiation capacity of PDLCs and test PDLCs as an alternative to stem cells for periodontal regeneration. Methods We tested the performance of human PDLCs in osteo-inductive culture and transplantation in vivo while taking human bone marrow derived mesenchymal stem cells (hMSCs) as positive control. Proliferation of PDLCs and hMSCs in osteo-inductive condition were examined by MTT assay and colony formation assay. The osteogenic differentiations of PDLCs and hMSCs were assessed by Alkaline phosphatase (ALP) activity measurement, von Kossa staining, Alizarin red S staining and quantitative RT-PCR of osteogenic marker gene including RUNX2, ALP, OCN, Col I, BSP, OPN. We transplanted osteo-inductive PDLCs and hMSCs with hydroxyapatite/tricalcium phosphate (HA/TCP) scaffolds to immunodeficient mice to explore their biological behaviors in vivo by histological staining and immunohistochemical evaluation. Results After 14 days of osteo-induction, PDLCs exhibited significantly higher proliferation rate but lower colony-forming ability comparing with hMSCs. PDLCs demonstrated lower ALP activity and generated fewer mineralized nodules than hMSCs. PDLCs showed overall up-regulated expression of RUNX2, ALP, OCN, Col I, BSP, OPN after osteo-induction. Col I level of PDLCs in osteo-inductive group was significantly higher while RUNX2, ALP, OCN were lower than that of hMSCs. Massive fiber bundles were produced linking or circling the scaffold while the bone-like structures were limited in th…
format: application/pdf
format: text/html
creator: Jinghui Li
creator: Fangming Zhang
creator: Ning Zhang
creator: Xuefei Geng
creator: Cen Meng
creator: Xiaoying Wang
creator: Ying Yang
subject: Cell Biology
subject: Dentistry
subject: Translational Medicine
description: doi:10.7717/peerj.6589
publisher: PeerJ Inc.
rights: © 2019 Li et al.
abstract: Background The periodontal ligament cells (PDLCs) contain heterogeneous cell populations and possess stem-cell-like properties. PDLCs have attracted considerable attention as an option for periodontal regeneration. However, the osteogenic differentiation of PDLCs remains obscure owing to variable osteo-inductive methods and whether PDLCs could be directly used for periodontal regeneration without stem cell enrichment is uncertain. The aim of the present study was to clarify the osteogenic differentiation capacity of PDLCs and test PDLCs as an alternative to stem cells for periodontal regeneration. Methods We tested the performance of human PDLCs in osteo-inductive culture and transplantation in vivo while taking human bone marrow derived mesenchymal stem cells (hMSCs) as positive control. Proliferation of PDLCs and hMSCs in osteo-inductive condition were examined by MTT assay and colony formation assay. The osteogenic differentiations of PDLCs and hMSCs were assessed by Alkaline phosphatase (ALP) activity measurement, von Kossa staining, Alizarin red S staining and quantitative RT-PCR of osteogenic marker gene including RUNX2, ALP, OCN, Col I, BSP, OPN. We transplanted osteo-inductive PDLCs and hMSCs with hydroxyapatite/tricalcium phosphate (HA/TCP) scaffolds to immunodeficient mice to explore their biological behaviors in vivo by histological staining and immunohistochemical evaluation. Results After 14 days of osteo-induction, PDLCs exhibited significantly higher proliferation rate but lower colony-forming ability comparing with hMSCs. PDLCs demonstrated lower ALP activity and generated fewer mineralized nodules than hMSCs. PDLCs showed overall up-regulated expression of RUNX2, ALP, OCN, Col I, BSP, OPN after osteo-induction. Col I level of PDLCs in osteo-inductive group was significantly higher while RUNX2, ALP, OCN were lower than that of hMSCs. Massive fiber bundles were produced linking or circling the scaffold while the bone-like structures were limited in th…
bibliographic citation: Li et al. (2019) Osteogenic capacity and cytotherapeutic potential of periodontal ligament cells for periodontal regeneration in vitro and in vivo. PeerJ 7:e6589 https://doi.org/10.7717/peerj.6589
date submitted: 2018-10-23
date accepted: 2019-02-10
issued: 2019-03-08
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Li
  given name: Jinghui
author list: Agent
  family name: Zhang
  given name: Fangming
author list: Agent
  family name: Zhang
  given name: Ning
author list: Agent
  family name: Geng
  given name: Xuefei
author list: Agent
  family name: Meng
  given name: Cen
author list: Agent
  family name: Wang
  given name: Xiaoying
author list: Agent
  family name: Yang
  given name: Ying
doi: 10.7717/peerj.6589
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-03-08
copyright: © 2019 Li et al.
attribution name: Li et al.

Environmental inactivation and irrigation-mediated regrowth of Escherichia coli O157:H7 on romaine lettuce when inoculated in a fecal slurry matrix
type: item
type: AcademicArticle
description: Field trials were conducted in July–August and October 2012 to quantify the inactivation rate of Escherichia coli O157:H7 when mixed with fecal slurry and applied to romaine lettuce leaves. Lettuce was grown under commercial conditions in Salinas Valley, California. One-half milliliter of rabbit, chicken, or pig fecal slurry, containing an average of 4.05 × 107 CFU E. coli O157:H7 (C0), was inoculated onto the upper (adaxial) surface of a lower leaf on 288 heads of lettuce per trial immediately following a 2.5 h irrigation event. To estimate the bacterial inactivation rate as a function of time, fecal matrix, irrigation and seasonal climate effects, sets of lettuce heads (n = 28) were sampled each day over 10 days and the concentration of E. coli O157:H7 (Ct) determined. E. coli O157:H7 was detected on 100% of heads during the 10-day duration, with concentrations ranging from ≤340 MPN/head (∼5-log reduction) to >3.45 × 1012 MPN/head (∼5-log growth). Relative to C0, on day 10 (Ct = 12) we observed an overall 2.6-log and 3.2-log mean reduction of E. coli O157:H7 in July and October, respectively. However, we observed relative maximum concentrations due to bacterial growth on day 6 (maximum Ct = 8) apparently stimulated by foliar irrigation on day 5. From this maximum there was a mean 5.3-log and 5.1-log reduction by day 10 (Ct = 12) for the July and October trials, respectively. This study provides insight into the inactivation and growth kinetics of E. coli O157:H7 on romaine lettuce leaves under natural field conditions. This study provides evidence that harvesting within 24 h post irrigation has the potential to increase the concentration of E. coli O157:H7 contamination, if present on heads of romaine lettuce; foliar irrigation can temporarily stimulate substantial regrowth of E. coli O157:H7.
format: application/pdf
format: text/html
creator: Jennifer A. Chase
creator: Melissa L. Partyka
creator: Ronald F. Bond
creator: Edward R. Atwill
subject: Agricultural Science
subject: Microbiology
subject: Epidemiology
subject: Infectious Diseases
subject: Public Health
description: doi:10.7717/peerj.6591
publisher: PeerJ Inc.
rights: © 2019 Chase et al.
abstract: Field trials were conducted in July–August and October 2012 to quantify the inactivation rate of Escherichia coli O157:H7 when mixed with fecal slurry and applied to romaine lettuce leaves. Lettuce was grown under commercial conditions in Salinas Valley, California. One-half milliliter of rabbit, chicken, or pig fecal slurry, containing an average of 4.05 × 107 CFU E. coli O157:H7 (C0), was inoculated onto the upper (adaxial) surface of a lower leaf on 288 heads of lettuce per trial immediately following a 2.5 h irrigation event. To estimate the bacterial inactivation rate as a function of time, fecal matrix, irrigation and seasonal climate effects, sets of lettuce heads (n = 28) were sampled each day over 10 days and the concentration of E. coli O157:H7 (Ct) determined. E. coli O157:H7 was detected on 100% of heads during the 10-day duration, with concentrations ranging from ≤340 MPN/head (∼5-log reduction) to >3.45 × 1012 MPN/head (∼5-log growth). Relative to C0, on day 10 (Ct = 12) we observed an overall 2.6-log and 3.2-log mean reduction of E. coli O157:H7 in July and October, respectively. However, we observed relative maximum concentrations due to bacterial growth on day 6 (maximum Ct = 8) apparently stimulated by foliar irrigation on day 5. From this maximum there was a mean 5.3-log and 5.1-log reduction by day 10 (Ct = 12) for the July and October trials, respectively. This study provides insight into the inactivation and growth kinetics of E. coli O157:H7 on romaine lettuce leaves under natural field conditions. This study provides evidence that harvesting within 24 h post irrigation has the potential to increase the concentration of E. coli O157:H7 contamination, if present on heads of romaine lettuce; foliar irrigation can temporarily stimulate substantial regrowth of E. coli O157:H7.
bibliographic citation: Chase et al. (2019) Environmental inactivation and irrigation-mediated regrowth of Escherichia coli O157:H7 on romaine lettuce when inoculated in a fecal slurry matrix. PeerJ 7:e6591 https://doi.org/10.7717/peerj.6591
date submitted: 2018-11-29
date accepted: 2019-02-09
issued: 2019-03-08
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Chase
  given name: Jennifer A.
author list: Agent
  family name: Partyka
  given name: Melissa L.
author list: Agent
  family name: Bond
  given name: Ronald F.
author list: Agent
  family name: Atwill
  given name: Edward R.
doi: 10.7717/peerj.6591
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-03-08
copyright: © 2019 Chase et al.
attribution name: Chase et al.

Exotic urban trees conserve similar natural enemy communities to native congeners but have fewer pests
type: item
type: AcademicArticle
description: Urban trees serve a critical conservation function by supporting arthropod and vertebrate communities but are often subject to arthropod pest infestations. Native trees are thought to support richer arthropod communities than exotic trees but may also be more susceptible to herbivorous pests. Exotic trees may be less susceptible to herbivores but provide less conservation value as a consequence. We tested the hypotheses that native species in Acer and Quercus would have more herbivorous pests than exotic congeners and different communities of arthropod natural enemies. The density of scale insects, common urban tree pests, was greatest on a native Acer and a native Quercus than exotic congeners in both years of our research (2012 and 2016) and sometimes reached damaging levels. However, differences in predator and parasitoid abundance, diversity, and communities were not consistent between native and exotic species in either genus and were generally similar. For example, in 2012 neither predator nor parasitoid abundance differed among native and exotic Acer congeners but in 2016 a native species, A. saccharum, had the least of both groups. A native, Q. phellos, had significantly more predators and parasitoids in 2012 than its native and exotic congeners but no differences in 2016. Parasitoid communities were significantly different among Acer species and Quercus species due in each case to greater abundance of a single family on one native tree species. These native and exotic tree species could help conserve arthropod natural enemies and achieve pest management goals.
format: application/pdf
format: text/html
creator: Steven D. Frank
creator: Kristi M. Backe
creator: Casey McDaniel
creator: Matthew Green
creator: Sarah Widney
creator: Robert R. Dunn
subject: Conservation Biology
subject: Ecology
subject: Entomology
description: doi:10.7717/peerj.6531
publisher: PeerJ Inc.
rights: © 2019 Frank et al.
abstract: Urban trees serve a critical conservation function by supporting arthropod and vertebrate communities but are often subject to arthropod pest infestations. Native trees are thought to support richer arthropod communities than exotic trees but may also be more susceptible to herbivorous pests. Exotic trees may be less susceptible to herbivores but provide less conservation value as a consequence. We tested the hypotheses that native species in Acer and Quercus would have more herbivorous pests than exotic congeners and different communities of arthropod natural enemies. The density of scale insects, common urban tree pests, was greatest on a native Acer and a native Quercus than exotic congeners in both years of our research (2012 and 2016) and sometimes reached damaging levels. However, differences in predator and parasitoid abundance, diversity, and communities were not consistent between native and exotic species in either genus and were generally similar. For example, in 2012 neither predator nor parasitoid abundance differed among native and exotic Acer congeners but in 2016 a native species, A. saccharum, had the least of both groups. A native, Q. phellos, had significantly more predators and parasitoids in 2012 than its native and exotic congeners but no differences in 2016. Parasitoid communities were significantly different among Acer species and Quercus species due in each case to greater abundance of a single family on one native tree species. These native and exotic tree species could help conserve arthropod natural enemies and achieve pest management goals.
bibliographic citation: Frank et al. (2019) Exotic urban trees conserve similar natural enemy communities to native congeners but have fewer pests. PeerJ 7:e6531 https://doi.org/10.7717/peerj.6531
date submitted: 2018-10-26
date accepted: 2019-01-28
issued: 2019-03-07
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Frank
  given name: Steven D.
author list: Agent
  family name: Backe
  given name: Kristi M.
author list: Agent
  family name: McDaniel
  given name: Casey
author list: Agent
  family name: Green
  given name: Matthew
author list: Agent
  family name: Widney
  given name: Sarah
author list: Agent
  family name: Dunn
  given name: Robert R.
doi: 10.7717/peerj.6531
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-03-07
copyright: © 2019 Frank et al.
attribution name: Frank et al.

Experimental mechanical strain measurement of tissues
type: item
type: AcademicArticle
description: Strain, an important biomechanical factor, occurs at different scales from molecules and cells to tissues and organs in physiological conditions. Under mechanical strain, the strength of tissues and their micro- and nanocomponents, the structure, proliferation, differentiation and apoptosis of cells and even the cytokines expressed by cells probably shift. Thus, the measurement of mechanical strain (i.e., relative displacement or deformation) is critical to understand functional changes in tissues, and to elucidate basic relationships between mechanical loading and tissue response. In the last decades, a great number of methods have been developed and applied to measure the deformations and mechanical strains in tissues comprising bone, tendon, ligament, muscle and brain as well as blood vessels. In this article, we have reviewed the mechanical strain measurement from six aspects: electro-based, light-based, ultrasound-based, magnetic resonance-based and computed tomography-based techniques, and the texture correlation-based image processing method. The review may help solving the problems of experimental and mechanical strain measurement of tissues under different measurement environments.
format: application/pdf
format: text/html
creator: Lingwei Huang
creator: Rami K. Korhonen
creator: Mikael J. Turunen
creator: Mikko A.J. Finnilä
subject: Bioengineering
subject: Biophysics
subject: Cell Biology
subject: Orthopedics
description: doi:10.7717/peerj.6545
publisher: PeerJ Inc.
rights: © 2019 Huang et al.
abstract: Strain, an important biomechanical factor, occurs at different scales from molecules and cells to tissues and organs in physiological conditions. Under mechanical strain, the strength of tissues and their micro- and nanocomponents, the structure, proliferation, differentiation and apoptosis of cells and even the cytokines expressed by cells probably shift. Thus, the measurement of mechanical strain (i.e., relative displacement or deformation) is critical to understand functional changes in tissues, and to elucidate basic relationships between mechanical loading and tissue response. In the last decades, a great number of methods have been developed and applied to measure the deformations and mechanical strains in tissues comprising bone, tendon, ligament, muscle and brain as well as blood vessels. In this article, we have reviewed the mechanical strain measurement from six aspects: electro-based, light-based, ultrasound-based, magnetic resonance-based and computed tomography-based techniques, and the texture correlation-based image processing method. The review may help solving the problems of experimental and mechanical strain measurement of tissues under different measurement environments.
bibliographic citation: Huang et al. (2019) Experimental mechanical strain measurement of tissues. PeerJ 7:e6545 https://doi.org/10.7717/peerj.6545
date submitted: 2018-05-24
date accepted: 2019-01-31
issued: 2019-03-07
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Huang
  given name: Lingwei
author list: Agent
  family name: Korhonen
  given name: Rami K.
author list: Agent
  family name: Turunen
  given name: Mikael J.
author list: Agent
  family name: Finnilä
  given name: Mikko A.J.
doi: 10.7717/peerj.6545
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-03-07
copyright: ©2019 Huang et al.
attribution name: Huang et al.

Identification of differentially expressed key genes between glioblastoma and low-grade glioma by bioinformatics analysis
type: item
type: AcademicArticle
description: Gliomas are a very diverse group of brain tumors that are most commonly primary tumor and difficult to cure in central nervous system. It’s necessary to distinguish low-grade tumors from high-grade tumors by understanding the molecular basis of different grades of glioma, which is an important step in defining new biomarkers and therapeutic strategies. We have chosen the gene expression profile GSE52009 from gene expression omnibus (GEO) database to detect important differential genes. GSE52009 contains 120 samples, including 60 WHO II samples and 24 WHO IV samples that were selected in our analysis. We used the GEO2R tool to pick out differently expressed genes (DEGs) between low-grade glioma and high-grade glioma, and then we used the database for annotation, visualization and integrated discovery to perform gene ontology analysis and Kyoto encyclopedia of gene and genome pathway analysis. Furthermore, we used the Cytoscape search tool for the retrieval of interacting genes with molecular complex detection plug-in applied to achieve the visualization of protein–protein interaction (PPI). We selected 15 hub genes with higher degrees of connectivity, including tissue inhibitors metalloproteinases-1 and serum amyloid A1; additionally, we used GSE53733 containing 70 glioblastoma samples to conduct Gene Set Enrichment Analysis. In conclusion, our bioinformatics analysis showed that DEGs and hub genes may be defined as new biomarkers for diagnosis and for guiding the therapeutic strategies of glioblastoma.
format: application/pdf
format: text/html
creator: Yang Xu
creator: Rongxin Geng
creator: Fan’en Yuan
creator: Qian Sun
creator: Baohui Liu
creator: Qianxue Chen
subject: Bioinformatics
subject: Neurology
subject: Oncology
description: doi:10.7717/peerj.6560
publisher: PeerJ Inc.
rights: © 2019 Xu et al.
abstract: Gliomas are a very diverse group of brain tumors that are most commonly primary tumor and difficult to cure in central nervous system. It’s necessary to distinguish low-grade tumors from high-grade tumors by understanding the molecular basis of different grades of glioma, which is an important step in defining new biomarkers and therapeutic strategies. We have chosen the gene expression profile GSE52009 from gene expression omnibus (GEO) database to detect important differential genes. GSE52009 contains 120 samples, including 60 WHO II samples and 24 WHO IV samples that were selected in our analysis. We used the GEO2R tool to pick out differently expressed genes (DEGs) between low-grade glioma and high-grade glioma, and then we used the database for annotation, visualization and integrated discovery to perform gene ontology analysis and Kyoto encyclopedia of gene and genome pathway analysis. Furthermore, we used the Cytoscape search tool for the retrieval of interacting genes with molecular complex detection plug-in applied to achieve the visualization of protein–protein interaction (PPI). We selected 15 hub genes with higher degrees of connectivity, including tissue inhibitors metalloproteinases-1 and serum amyloid A1; additionally, we used GSE53733 containing 70 glioblastoma samples to conduct Gene Set Enrichment Analysis. In conclusion, our bioinformatics analysis showed that DEGs and hub genes may be defined as new biomarkers for diagnosis and for guiding the therapeutic strategies of glioblastoma.
bibliographic citation: Xu et al. (2019) Identification of differentially expressed key genes between glioblastoma and low-grade glioma by bioinformatics analysis. PeerJ 7:e6560 https://doi.org/10.7717/peerj.6560
date submitted: 2018-10-24
date accepted: 2019-02-04
issued: 2019-03-07
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Xu
  given name: Yang
author list: Agent
  family name: Geng
  given name: Rongxin
author list: Agent
  family name: Yuan
  given name: Fan’en
author list: Agent
  family name: Sun
  given name: Qian
author list: Agent
  family name: Liu
  given name: Baohui
author list: Agent
  family name: Chen
  given name: Qianxue
doi: 10.7717/peerj.6560
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-03-07
copyright: © 2019 Xu et al.
attribution name: Xu et al.

Lightweight data management with dtool
type: item
type: AcademicArticle
description: The explosion in volumes and types of data has led to substantial challenges in data management. These challenges are often faced by front-line researchers who are already dealing with rapidly changing technologies and have limited time to devote to data management. There are good high-level guidelines for managing and processing scientific data. However, there is a lack of simple, practical tools to implement these guidelines. This is particularly problematic in a highly distributed research environment where needs differ substantially from group to group and centralised solutions are difficult to implement and storage technologies change rapidly. To meet these challenges we have developed dtool, a command line tool for managing data. The tool packages data and metadata into a unified whole, which we call a dataset. The dataset provides consistency checking and the ability to access metadata for both the whole dataset and individual files. The tool can store these datasets on several different storage systems, including a traditional file system, object store (S3 and Azure) and iRODS. It includes an application programming interface that can be used to incorporate it into existing pipelines and workflows. The tool has provided substantial process, cost, and peace-of-mind benefits to our data management practices and we want to share these benefits. The tool is open source and available freely online at http://dtool.readthedocs.io.
format: application/pdf
format: text/html
creator: Tjelvar S.G. Olsson
creator: Matthew Hartley
subject: Bioinformatics
subject: Computational Biology
subject: Genomics
description: doi:10.7717/peerj.6562
publisher: PeerJ Inc.
rights: © 2019 Olsson and Hartley
abstract: The explosion in volumes and types of data has led to substantial challenges in data management. These challenges are often faced by front-line researchers who are already dealing with rapidly changing technologies and have limited time to devote to data management. There are good high-level guidelines for managing and processing scientific data. However, there is a lack of simple, practical tools to implement these guidelines. This is particularly problematic in a highly distributed research environment where needs differ substantially from group to group and centralised solutions are difficult to implement and storage technologies change rapidly. To meet these challenges we have developed dtool, a command line tool for managing data. The tool packages data and metadata into a unified whole, which we call a dataset. The dataset provides consistency checking and the ability to access metadata for both the whole dataset and individual files. The tool can store these datasets on several different storage systems, including a traditional file system, object store (S3 and Azure) and iRODS. It includes an application programming interface that can be used to incorporate it into existing pipelines and workflows. The tool has provided substantial process, cost, and peace-of-mind benefits to our data management practices and we want to share these benefits. The tool is open source and available freely online at http://dtool.readthedocs.io.
bibliographic citation: Olsson et al. (2019) Lightweight data management with dtool. PeerJ 7:e6562 https://doi.org/10.7717/peerj.6562
date submitted: 2018-10-04
date accepted: 2019-02-04
issued: 2019-03-07
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Olsson
  given name: Tjelvar S.G.
author list: Agent
  family name: Hartley
  given name: Matthew
doi: 10.7717/peerj.6562
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-03-07
copyright: ©2019 Olsson and Hartley
attribution name: Olsson and Hartley

Climate change and conservation in a warm North American desert: effect in shrubby plants
type: item
type: AcademicArticle
description: Background Deserts are biologically rich habitats with a vast array of animals and plants adapted to xeric conditions, and most deserts are among the planet’s last remaining areas of total wilderness. Among North American deserts, the Chihuahuan Desert has the highest levels of diversity and endemism. To understand the effect of future climate change on plants distributed in this arid land and propose effective conservation planning, we focused on five endemic shrubby species that characterize the Chihuahuan Desert and used an integrative approach. Methods Ecological niche-based modeling, spatial genetics and ecological resistance analyses were carried out to identify the effect of global warming on the studied five shrubby species. Key areas that need to be preserved were identified taking into account the existing protected areas within the Chihuahuan Desert. Results The extent of future distribution will vary among these species, and on average expansion will occur in the western part of the Chihuahuan Desert. For most species low environmental resistance to gene flow was predicted, while higher future resistance was predicted for one species that would lead to increased population isolation. The highest haplotype diversity was identified in three hotspots. Based on future suitability of habitat and in the haplotype diversity we suggest preserving two hotspots of genetic diversity in the Sierra Madre Oriental, located in areas without protection. The third hotspot was detected in the well preserved Tehuacán-Cuicatlán Man and Biosphere Reserve. Conclusion Global climate change will have an effect in arid adapted plants, favoring expansion in the western of the Chihuahuan Desert however negatively affecting others with high ecological resistance disrupting gene flow. Two hotspots of genetic diversity in the Sierra Madre Oriental should be protected.
format: application/pdf
format: text/html
creator: Victoria Sosa
creator: Israel Loera
creator: Diego F. Angulo
creator: Marilyn Vásquez-Cruz
creator: Etelvina Gándara
subject: Biodiversity
subject: Ecology
subject: Evolutionary Studies
subject: Genetics
description: doi:10.7717/peerj.6572
publisher: PeerJ Inc.
rights: © 2019 Sosa et al.
abstract: Background Deserts are biologically rich habitats with a vast array of animals and plants adapted to xeric conditions, and most deserts are among the planet’s last remaining areas of total wilderness. Among North American deserts, the Chihuahuan Desert has the highest levels of diversity and endemism. To understand the effect of future climate change on plants distributed in this arid land and propose effective conservation planning, we focused on five endemic shrubby species that characterize the Chihuahuan Desert and used an integrative approach. Methods Ecological niche-based modeling, spatial genetics and ecological resistance analyses were carried out to identify the effect of global warming on the studied five shrubby species. Key areas that need to be preserved were identified taking into account the existing protected areas within the Chihuahuan Desert. Results The extent of future distribution will vary among these species, and on average expansion will occur in the western part of the Chihuahuan Desert. For most species low environmental resistance to gene flow was predicted, while higher future resistance was predicted for one species that would lead to increased population isolation. The highest haplotype diversity was identified in three hotspots. Based on future suitability of habitat and in the haplotype diversity we suggest preserving two hotspots of genetic diversity in the Sierra Madre Oriental, located in areas without protection. The third hotspot was detected in the well preserved Tehuacán-Cuicatlán Man and Biosphere Reserve. Conclusion Global climate change will have an effect in arid adapted plants, favoring expansion in the western of the Chihuahuan Desert however negatively affecting others with high ecological resistance disrupting gene flow. Two hotspots of genetic diversity in the Sierra Madre Oriental should be protected.
bibliographic citation: Sosa et al. (2019) Climate change and conservation in a warm North American desert: effect in shrubby plants. PeerJ 7:e6572 https://doi.org/10.7717/peerj.6572
date submitted: 2018-07-30
date accepted: 2019-02-05
issued: 2019-03-07
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Sosa
  given name: Victoria
author list: Agent
  family name: Loera
  given name: Israel
author list: Agent
  family name: Angulo
  given name: Diego F.
author list: Agent
  family name: Vásquez-Cruz
  given name: Marilyn
author list: Agent
  family name: Gándara
  given name: Etelvina
doi: 10.7717/peerj.6572
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-03-07
copyright: © 2019 Sosa et al.
attribution name: Sosa et al.

Three odorant-binding proteins are involved in the behavioral response of Sogatella furcifera to rice plant volatiles
type: item
type: AcademicArticle
description: Plant volatiles play an important role in regulating insect behavior. Odorant binding proteins (OBPs) are involved in the first step of the olfactory signal transduction pathway and plant volatiles recognition. Sogatella furcifera is one of the most destructive pests of rice crops. Understanding the functions of S. furcifera OBPs (SfurOBPs) in the host plant location and the behavioral responses of S. furcifera to rice plant volatiles could lead to improved, more environmentally-friendly, methods for controlling this pest. We found that SfurOBP1 displayed only weak binding with all the tested volatiles. SfurOBP2, SfurOBP3 and SfurOBP11 had different binding affinities to β-ionone. SfurOBP2 and SfurOBP11 had strong binding affinities to β-caryophyllene (Ki = 2.23 µM) and plant alcohol (Ki = 2.98 µM), respectively. The results of Y-olfactometer experiments indicate that S. furcifera was significantly repelled by octanal and n-octane but strongly attracted by (+)-limonene, acetophenone, 2-heptanone, n-hendecane, α-farnesene and β-ionone. Furthermore, the dsRNA-mediated gene silencing of SfurOBP2, SfurOBP3 and SfurOBP11 shifted the olfactory behavior of S. furcifera for β-ionone, α-farnesene and plant alcohol, respectively. These results suggest that the SfurOBPs are involved in the recognition of rice plant volatiles, and several potential repellants and lures for controlling this pest.
format: application/pdf
format: text/html
creator: Kui Hu
creator: Sheng Liu
creator: Lin Qiu
creator: Youzhi Li
subject: Agricultural Science
subject: Animal Behavior
subject: Entomology
subject: Molecular Biology
description: doi:10.7717/peerj.6576
publisher: PeerJ Inc.
rights: © 2019 Hu et al.
abstract: Plant volatiles play an important role in regulating insect behavior. Odorant binding proteins (OBPs) are involved in the first step of the olfactory signal transduction pathway and plant volatiles recognition. Sogatella furcifera is one of the most destructive pests of rice crops. Understanding the functions of S. furcifera OBPs (SfurOBPs) in the host plant location and the behavioral responses of S. furcifera to rice plant volatiles could lead to improved, more environmentally-friendly, methods for controlling this pest. We found that SfurOBP1 displayed only weak binding with all the tested volatiles. SfurOBP2, SfurOBP3 and SfurOBP11 had different binding affinities to β-ionone. SfurOBP2 and SfurOBP11 had strong binding affinities to β-caryophyllene (Ki = 2.23 µM) and plant alcohol (Ki = 2.98 µM), respectively. The results of Y-olfactometer experiments indicate that S. furcifera was significantly repelled by octanal and n-octane but strongly attracted by (+)-limonene, acetophenone, 2-heptanone, n-hendecane, α-farnesene and β-ionone. Furthermore, the dsRNA-mediated gene silencing of SfurOBP2, SfurOBP3 and SfurOBP11 shifted the olfactory behavior of S. furcifera for β-ionone, α-farnesene and plant alcohol, respectively. These results suggest that the SfurOBPs are involved in the recognition of rice plant volatiles, and several potential repellants and lures for controlling this pest.
bibliographic citation: Hu et al. (2019) Three odorant-binding proteins are involved in the behavioral response of Sogatella furcifera to rice plant volatiles. PeerJ 7:e6576 https://doi.org/10.7717/peerj.6576
date submitted: 2018-12-26
date accepted: 2019-02-06
issued: 2019-03-07
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Hu
  given name: Kui
author list: Agent
  family name: Liu
  given name: Sheng
author list: Agent
  family name: Qiu
  given name: Lin
author list: Agent
  family name: Li
  given name: Youzhi
doi: 10.7717/peerj.6576
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-03-07
copyright: ©2019 Hu et al.
attribution name: Hu et al.

An assessment for health education and health promotion in chronic disease demonstration districts: a comparative study from Hunan Province, China
type: item
type: AcademicArticle
description: Background Cost-effective strategies of chronic disease control, integrated health education and health promotion play important roles in the programs of chronic disease demonstration districts in China. The performance of these districts can be directly assessed by their health education and promotion work. However, there have been only a few performance assessments done on these programs, most of which made without the inclusion of proper quality indicators. This study was designed to establish a framework of indicators for outcome evaluation of health education and promotion efforts in Chinese districts, and explore the factors involved in promoting these efforts. Methods A modified two-round Delphi survey was first used to construct quality indicators on a nine-point Likert scale. With those indicators, the rank sum ratio (RSR) method was then conducted through rank conversion and parametric statistics, to assess and classify the performance of ten districts or counties randomly chosen both from demonstration and non-demonstration districts in the Hunan province. Results The Delphi process produced seven themes and 25 sub-themes as quality indicators. The seven themes included organizational management, financial support, professional personnel, health education and promotion, residents’ health awareness and behaviors, residents’ satisfaction, and residents’ health literacy. The districts were classified into four levels by RSR as follows: One demonstration district at the first-ranked level, five other demonstration districts at the second-ranked level, all non-demonstration districts at the third-ranked level. None were at the fourth-qualified level. Discussion Chronic disease demonstration districts performed better on the work of health education and health promotion than the non-demonstration districts. The work should be focused on the following measures of chronic diseases: organizational management, financial support, media-related broadcasting, technica…
format: application/pdf
format: text/html
creator: Qiaohua Xu
creator: Biyun Chen
creator: Donghui Jin
creator: Li Yin
creator: Yuelong Huang
subject: Health Policy
subject: Public Health
subject: Science and Medical Education
description: doi:10.7717/peerj.6579
publisher: PeerJ Inc.
rights: © 2019 Xu et al.
abstract: Background Cost-effective strategies of chronic disease control, integrated health education and health promotion play important roles in the programs of chronic disease demonstration districts in China. The performance of these districts can be directly assessed by their health education and promotion work. However, there have been only a few performance assessments done on these programs, most of which made without the inclusion of proper quality indicators. This study was designed to establish a framework of indicators for outcome evaluation of health education and promotion efforts in Chinese districts, and explore the factors involved in promoting these efforts. Methods A modified two-round Delphi survey was first used to construct quality indicators on a nine-point Likert scale. With those indicators, the rank sum ratio (RSR) method was then conducted through rank conversion and parametric statistics, to assess and classify the performance of ten districts or counties randomly chosen both from demonstration and non-demonstration districts in the Hunan province. Results The Delphi process produced seven themes and 25 sub-themes as quality indicators. The seven themes included organizational management, financial support, professional personnel, health education and promotion, residents’ health awareness and behaviors, residents’ satisfaction, and residents’ health literacy. The districts were classified into four levels by RSR as follows: One demonstration district at the first-ranked level, five other demonstration districts at the second-ranked level, all non-demonstration districts at the third-ranked level. None were at the fourth-qualified level. Discussion Chronic disease demonstration districts performed better on the work of health education and health promotion than the non-demonstration districts. The work should be focused on the following measures of chronic diseases: organizational management, financial support, media-related broadcasting, technica…
bibliographic citation: Xu et al. (2019) An assessment for health education and health promotion in chronic disease demonstration districts: a comparative study from Hunan Province, China. PeerJ 7:e6579 https://doi.org/10.7717/peerj.6579
date submitted: 2018-10-11
date accepted: 2019-02-06
issued: 2019-03-07
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Xu
  given name: Qiaohua
author list: Agent
  family name: Chen
  given name: Biyun
author list: Agent
  family name: Jin
  given name: Donghui
author list: Agent
  family name: Yin
  given name: Li
author list: Agent
  family name: Huang
  given name: Yuelong
doi: 10.7717/peerj.6579
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-03-07
copyright: ©2019 Xu et al.
attribution name: Xu et al.

Ultra-performance liquid chromatography-mass spectrometry for precise fatty acid profiling of oilseed crops
type: item
type: AcademicArticle
description: Oilseed crops are one of the most important sources of vegetable oils for food and industry. Nutritional and technical properties of vegetable oil are primarily determined by its fatty acid (FA) composition. The content and composition of FAs in plants are commonly determined using gas chromatography-mass spectrometry (GS-MS) or gas chromatography-flame ionization detection (GC-FID) techniques. In the present work, we applied ultra-performance liquid chromatography-mass spectrometry (UPLC-MS) technique to FA profiling of sunflower and rapeseed seeds and compared this method with the GC-FID technique. GC-FID detected 11 FAs in sunflower and 13 FAs in rapeseed, while UPLC-MS appeared to be more sensitive, detecting about 2.5 times higher numbers of FAs in both plants. In addition to even-chain FAs, UPLC-MS was able to detect odd-chain FAs. The longest FA detected using GC-FID was an FA with 24 carbon atoms, whereas UPLC-MS could reveal the presence of longer FAs with the tails of up to 28 carbon atoms. Based on our results, we may conclude that UPLC-MS has great potential to be used for the assessment of FA profiles of oil crops.
format: application/pdf
format: text/html
creator: Alina Chernova
creator: Pavel Mazin
creator: Svetlana Goryunova
creator: Denis Goryunov
creator: Yakov Demurin
creator: Lyudmila Gorlova
creator: Anna Vanyushkina
creator: Waltraud Mair
creator: Nikolai Anikanov
creator: Ekaterina Yushina
creator: Anna Pavlova
creator: Elena Martynova
creator: Sergei Garkusha
creator: Zhanna Mukhina
creator: Elena Savenko
creator: Philipp Khaitovich
subject: Agricultural Science
subject: Plant Science
description: doi:10.7717/peerj.6547
publisher: PeerJ Inc.
rights: © 2019 Chernova et al.
abstract: Oilseed crops are one of the most important sources of vegetable oils for food and industry. Nutritional and technical properties of vegetable oil are primarily determined by its fatty acid (FA) composition. The content and composition of FAs in plants are commonly determined using gas chromatography-mass spectrometry (GS-MS) or gas chromatography-flame ionization detection (GC-FID) techniques. In the present work, we applied ultra-performance liquid chromatography-mass spectrometry (UPLC-MS) technique to FA profiling of sunflower and rapeseed seeds and compared this method with the GC-FID technique. GC-FID detected 11 FAs in sunflower and 13 FAs in rapeseed, while UPLC-MS appeared to be more sensitive, detecting about 2.5 times higher numbers of FAs in both plants. In addition to even-chain FAs, UPLC-MS was able to detect odd-chain FAs. The longest FA detected using GC-FID was an FA with 24 carbon atoms, whereas UPLC-MS could reveal the presence of longer FAs with the tails of up to 28 carbon atoms. Based on our results, we may conclude that UPLC-MS has great potential to be used for the assessment of FA profiles of oil crops.
bibliographic citation: Chernova et al. (2019) Ultra-performance liquid chromatography-mass spectrometry for precise fatty acid profiling of oilseed crops. PeerJ 7:e6547 https://doi.org/10.7717/peerj.6547
date submitted: 2018-10-30
date accepted: 2019-01-31
issued: 2019-03-06
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Chernova
  given name: Alina
author list: Agent
  family name: Mazin
  given name: Pavel
author list: Agent
  family name: Goryunova
  given name: Svetlana
author list: Agent
  family name: Goryunov
  given name: Denis
author list: Agent
  family name: Demurin
  given name: Yakov
author list: Agent
  family name: Gorlova
  given name: Lyudmila
author list: Agent
  family name: Vanyushkina
  given name: Anna
author list: Agent
  family name: Mair
  given name: Waltraud
author list: Agent
  family name: Anikanov
  given name: Nikolai
author list: Agent
  family name: Yushina
  given name: Ekaterina
author list: Agent
  family name: Pavlova
  given name: Anna
author list: Agent
  family name: Martynova
  given name: Elena
author list: Agent
  family name: Garkusha
  given name: Sergei
author list: Agent
  family name: Mukhina
  given name: Zhanna
author list: Agent
  family name: Savenko
  given name: Elena
author list: Agent
  family name: Khaitovich
  given name: Philipp
doi: 10.7717/peerj.6547
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-03-06
copyright: ©2019 Chernova et al.
attribution name: Chernova et al.

Agrobacterium rhizogenes—mediated transformation of Pisum sativum L. roots as a tool for studying the mycorrhizal and root nodule symbioses
type: item
type: AcademicArticle
description: In this study, we demonstrated the successful transformation of two pea (Pisum sativum L.) cultivars using Agrobacterium rhizogenes, whereby transgenic roots in the resulting composite plants showed expression of the gene encoding the green fluorescent protein. Subsequent to infection with A. rhizogenes, approximately 70%–80% of pea seedlings developed transgenic hairy roots. We found out that the transgenic roots can be efficiently nodulated by Rhizobium leguminosarum bv. viciae and infected by the arbuscular mycorrhizal (AM) fungus Rhizophagus irregularis. The morphology of nodules in the transgenic roots was found to be identical to that of nodules observed in wild-type roots, and we also observed the effective induction of markers typical of the symbiotic association with AM fungi. The convenient protocol for highly efficient A. rhizogenes-mediated transformation developed in this study would be a rapid and effective tool for investigating those genes involved in the development of the two types of symbioses found in pea plants.
format: application/pdf
format: text/html
creator: Irina V. Leppyanen
creator: Anna N. Kirienko
creator: Elena A. Dolgikh
subject: Agricultural Science
subject: Microbiology
subject: Plant Science
description: doi:10.7717/peerj.6552
publisher: PeerJ Inc.
rights: © 2019 Leppyanen et al.
abstract: In this study, we demonstrated the successful transformation of two pea (Pisum sativum L.) cultivars using Agrobacterium rhizogenes, whereby transgenic roots in the resulting composite plants showed expression of the gene encoding the green fluorescent protein. Subsequent to infection with A. rhizogenes, approximately 70%–80% of pea seedlings developed transgenic hairy roots. We found out that the transgenic roots can be efficiently nodulated by Rhizobium leguminosarum bv. viciae and infected by the arbuscular mycorrhizal (AM) fungus Rhizophagus irregularis. The morphology of nodules in the transgenic roots was found to be identical to that of nodules observed in wild-type roots, and we also observed the effective induction of markers typical of the symbiotic association with AM fungi. The convenient protocol for highly efficient A. rhizogenes-mediated transformation developed in this study would be a rapid and effective tool for investigating those genes involved in the development of the two types of symbioses found in pea plants.
bibliographic citation: Leppyanen et al. (2019) Agrobacterium rhizogenes—mediated transformation of Pisum sativum L. roots as a tool for studying the mycorrhizal and root nodule symbioses. PeerJ 7:e6552 https://doi.org/10.7717/peerj.6552
date submitted: 2018-11-22
date accepted: 2019-02-01
issued: 2019-03-06
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Leppyanen
  given name: Irina V.
author list: Agent
  family name: Kirienko
  given name: Anna N.
author list: Agent
  family name: Dolgikh
  given name: Elena A.
doi: 10.7717/peerj.6552
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-03-06
copyright: ©2019 Leppyanen et al.
attribution name: Leppyanen et al.

Association of late-onset postpartum depression of mothers with expressive language development during infancy and early childhood: the HBC study
type: item
type: AcademicArticle
description: Background While it has been implied that an infant’s exposure to maternal postpartum depression (PPD) may be associated with delayed development of expressive language, it remains unclear whether such a delay persists into childhood and whether the onset of PPD onset—early (within 4 weeks after childbirth) vs. late (between 5 and 12 weeks postpartum)—is relevant in this context. Objective To examine whether children of mothers with early- or late-onset PPD have reduced expressive language scores during infancy and early childhood (up to 40 months of age). Methods This longitudinal, observational study was conducted as a part of the Hamamatsu Birth Cohort for Mothers and Children (HBC Study), a population-representative sample in Japan. A total of 969 neonates and their mothers were included in the analysis. Exposures Early- and late-onset PPD was measured using the Edinburgh Postnatal Depression Scale. Main Outcomes and Measures Expressive language development was measured using the Mullen Scales of Early Learning. Six points over time were monitored (10, 14, 18, 24, 32, and 40 months postpartum). The relationship between the exposure variable and any change in expressive language score was evaluated using multiple linear regression analysis and growth curve analysis, both adjusted for covariates. Results Results from the adjusted regression analysis showed that children of mothers with late-onset PPD had significantly lower expressive language scores at 18 months of age and beyond, with a score reduction of approximately 0.6 standard deviations from the reference value at 40 months of age (95% CI [−0.888 to −0.265], p < .001). This association was confirmed on growth curve analysis, which revealed a significant, monotonic decline of expressive language development between 10 and 40 months of age among children of mothers with late-onset PPD, but not among children of mothers with early-onset PPD. Conclusion Exposure to late-onset PPD may lead to a persistent decli…
format: application/pdf
format: text/html
creator: Sona-Sanae Aoyagi
creator: Nori Takei
creator: Tomoko Nishimura
creator: Yoko Nomura
creator: Kenji J. Tsuchiya
subject: Epidemiology
subject: Pediatrics
subject: Psychiatry and Psychology
subject: Public Health
subject: Women’s Health
description: doi:10.7717/peerj.6566
publisher: PeerJ Inc.
rights: © 2019 Aoyagi et al.
abstract: Background While it has been implied that an infant’s exposure to maternal postpartum depression (PPD) may be associated with delayed development of expressive language, it remains unclear whether such a delay persists into childhood and whether the onset of PPD onset—early (within 4 weeks after childbirth) vs. late (between 5 and 12 weeks postpartum)—is relevant in this context. Objective To examine whether children of mothers with early- or late-onset PPD have reduced expressive language scores during infancy and early childhood (up to 40 months of age). Methods This longitudinal, observational study was conducted as a part of the Hamamatsu Birth Cohort for Mothers and Children (HBC Study), a population-representative sample in Japan. A total of 969 neonates and their mothers were included in the analysis. Exposures Early- and late-onset PPD was measured using the Edinburgh Postnatal Depression Scale. Main Outcomes and Measures Expressive language development was measured using the Mullen Scales of Early Learning. Six points over time were monitored (10, 14, 18, 24, 32, and 40 months postpartum). The relationship between the exposure variable and any change in expressive language score was evaluated using multiple linear regression analysis and growth curve analysis, both adjusted for covariates. Results Results from the adjusted regression analysis showed that children of mothers with late-onset PPD had significantly lower expressive language scores at 18 months of age and beyond, with a score reduction of approximately 0.6 standard deviations from the reference value at 40 months of age (95% CI [−0.888 to −0.265], p < .001). This association was confirmed on growth curve analysis, which revealed a significant, monotonic decline of expressive language development between 10 and 40 months of age among children of mothers with late-onset PPD, but not among children of mothers with early-onset PPD. Conclusion Exposure to late-onset PPD may lead to a persistent decli…
bibliographic citation: Aoyagi et al. (2019) Association of late-onset postpartum depression of mothers with expressive language development during infancy and early childhood: the HBC study. PeerJ 7:e6566 https://doi.org/10.7717/peerj.6566
date submitted: 2018-10-31
date accepted: 2019-01-30
issued: 2019-03-06
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Aoyagi
  given name: Sona-Sanae
author list: Agent
  family name: Takei
  given name: Nori
author list: Agent
  family name: Nishimura
  given name: Tomoko
author list: Agent
  family name: Nomura
  given name: Yoko
author list: Agent
  family name: Tsuchiya
  given name: Kenji J.
doi: 10.7717/peerj.6566
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-03-06
copyright: ©2019 Aoyagi et al.
attribution name: Aoyagi et al.

A glucagon-like peptide-1 analog, liraglutide, ameliorates endothelial dysfunction through miRNAs to inhibit apoptosis in rats
type: item
type: AcademicArticle
description: Background and Aims Many studies have revealed that glucagon-like peptide-1 has vasoprotective effects. In this study, we investigated whether liraglutide suppressed endothelial dysfunction and explored the mechanism involved. Methods Experimental diabetes was induced through combined high-fat diet administration and intraperitoneal streptozotocin injections. Rats were randomly divided into the following four groups: control, diabetes, diabetes + a low liraglutide dose (0.2 mg/kg/d), and diabetes + a high liraglutide dose (0.4 mg/kg/d). Endothelial function and metabolic parameters were measured after 8 weeks of treatment. miRNA arrays were analyzed to identify the differentially expressed miRNAs. Results We found that liraglutide significantly improved aortic endothelial function in diabetic rats. Liraglutide inhibited miR-93-5p, miR-181a-5p and miR-34a-5p expression, and activated miR-26a-5p expression. miRNA mimic transfection experiments indicated negative relationships between miR-93-5p, miR-181a-5p, miR-34a-5p, and miR-26a-5p and Sirt1, Creb, Bcl-2, and Pten expression, respectively. Moreover, liraglutide increased Sirt1, Creb, and Bcl-2 expression levels and reduced Pten expression level. Conclusion Our results demonstrate the role of key miRNAs in the liraglutide-mediated regulation of endothelial cell function in diabetic rats.
format: application/pdf
format: text/html
creator: Qian Zhang
creator: Xinhua Xiao
creator: Jia Zheng
creator: Ming Li
subject: Diabetes and Endocrinology
description: doi:10.7717/peerj.6567
publisher: PeerJ Inc.
rights: © 2019 Zhang et al.
abstract: Background and Aims Many studies have revealed that glucagon-like peptide-1 has vasoprotective effects. In this study, we investigated whether liraglutide suppressed endothelial dysfunction and explored the mechanism involved. Methods Experimental diabetes was induced through combined high-fat diet administration and intraperitoneal streptozotocin injections. Rats were randomly divided into the following four groups: control, diabetes, diabetes + a low liraglutide dose (0.2 mg/kg/d), and diabetes + a high liraglutide dose (0.4 mg/kg/d). Endothelial function and metabolic parameters were measured after 8 weeks of treatment. miRNA arrays were analyzed to identify the differentially expressed miRNAs. Results We found that liraglutide significantly improved aortic endothelial function in diabetic rats. Liraglutide inhibited miR-93-5p, miR-181a-5p and miR-34a-5p expression, and activated miR-26a-5p expression. miRNA mimic transfection experiments indicated negative relationships between miR-93-5p, miR-181a-5p, miR-34a-5p, and miR-26a-5p and Sirt1, Creb, Bcl-2, and Pten expression, respectively. Moreover, liraglutide increased Sirt1, Creb, and Bcl-2 expression levels and reduced Pten expression level. Conclusion Our results demonstrate the role of key miRNAs in the liraglutide-mediated regulation of endothelial cell function in diabetic rats.
bibliographic citation: Zhang et al. (2019) A glucagon-like peptide-1 analog, liraglutide, ameliorates endothelial dysfunction through miRNAs to inhibit apoptosis in rats. PeerJ 7:e6567 https://doi.org/10.7717/peerj.6567
date submitted: 2018-12-08
date accepted: 2019-02-05
issued: 2019-03-06
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Zhang
  given name: Qian
author list: Agent
  family name: Xiao
  given name: Xinhua
author list: Agent
  family name: Zheng
  given name: Jia
author list: Agent
  family name: Li
  given name: Ming
doi: 10.7717/peerj.6567
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-03-06
copyright: © 2019 Zhang et al.
attribution name: Zhang et al.

Public perception of the vegetative state/unresponsive wakefulness syndrome: a crowdsourced study
type: item
type: AcademicArticle
description: Background The vegetative state (VS)/unresponsive wakefulness syndrome (UWS) denotes brain-injured, awake patients who are seemingly without awareness. Still, up to 15% of these patients show signs of covert consciousness when examined by functional magnetic resonance imaging (fMRI) or EEG, which is known as cognitive motor dissociation (CMD). Experts often prefer the term unresponsive wakefulness syndrome to avoid the negative connotations associated with vegetative state and to highlight the possibility for CMD. However, the perception of VS/UWS by the public has never been studied systematically. Methods Using an online crowdsourcing platform, we recruited 1,297 lay people from 32 countries. We investigated if vegetative state and unresponsive wakefulness syndrome might have a different influence on attitudes towards VS/UWS and the concept of CMD. Results Participants randomized to be inquired about the vegetative state believed that CMD was less plausible (mean estimated frequency in unresponsive patients 38.07% ± SD 25.15) than participants randomized to unresponsive wakefulness syndrome (42.29% ± SD 26.63; Cohen’s d 0.164; p = 0.016). Attitudes towards treatment withdrawal were similar. Most participants preferred unresponsive wakefulness syndrome (60.05%), although a sizeable minority favored vegetative state (24.21%; difference 35.84%, 95% CI 29.36 to 41.87; p < 0.0001). Searches on PubMed and Google Trends revealed that unresponsive wakefulness syndrome is increasingly used by academics but not lay people. Discussion Simply replacing vegetative state with unresponsive wakefulness syndrome may not be fully appropriate given that one of four prefer the first term. We suggest that physicians take advantage of the controversy around the terminology to explain relatives the concept of CMD and its ethical implications.
format: application/pdf
format: text/html
creator: Daniel Kondziella
creator: Man Cheung Cheung
creator: Anirban Dutta
subject: Cognitive Disorders
subject: Emergency and Critical Care
subject: Neurology
subject: Ethical Issues
subject: Palliative Care
description: doi:10.7717/peerj.6575
publisher: PeerJ Inc.
rights: © 2019 Kondziella et al.
abstract: Background The vegetative state (VS)/unresponsive wakefulness syndrome (UWS) denotes brain-injured, awake patients who are seemingly without awareness. Still, up to 15% of these patients show signs of covert consciousness when examined by functional magnetic resonance imaging (fMRI) or EEG, which is known as cognitive motor dissociation (CMD). Experts often prefer the term unresponsive wakefulness syndrome to avoid the negative connotations associated with vegetative state and to highlight the possibility for CMD. However, the perception of VS/UWS by the public has never been studied systematically. Methods Using an online crowdsourcing platform, we recruited 1,297 lay people from 32 countries. We investigated if vegetative state and unresponsive wakefulness syndrome might have a different influence on attitudes towards VS/UWS and the concept of CMD. Results Participants randomized to be inquired about the vegetative state believed that CMD was less plausible (mean estimated frequency in unresponsive patients 38.07% ± SD 25.15) than participants randomized to unresponsive wakefulness syndrome (42.29% ± SD 26.63; Cohen’s d 0.164; p = 0.016). Attitudes towards treatment withdrawal were similar. Most participants preferred unresponsive wakefulness syndrome (60.05%), although a sizeable minority favored vegetative state (24.21%; difference 35.84%, 95% CI 29.36 to 41.87; p < 0.0001). Searches on PubMed and Google Trends revealed that unresponsive wakefulness syndrome is increasingly used by academics but not lay people. Discussion Simply replacing vegetative state with unresponsive wakefulness syndrome may not be fully appropriate given that one of four prefer the first term. We suggest that physicians take advantage of the controversy around the terminology to explain relatives the concept of CMD and its ethical implications.
bibliographic citation: Kondziella et al. (2019) Public perception of the vegetative state/unresponsive wakefulness syndrome: a crowdsourced study. PeerJ 7:e6575 https://doi.org/10.7717/peerj.6575
date submitted: 2018-12-18
date accepted: 2019-02-05
issued: 2019-03-06
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Kondziella
  given name: Daniel
author list: Agent
  family name: Cheung
  given name: Man Cheung
author list: Agent
  family name: Dutta
  given name: Anirban
doi: 10.7717/peerj.6575
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-03-06
copyright: ©2019 Kondziella et al.
attribution name: Kondziella et al.

Genome-wide analysis of long non-coding RNA expression profile in porcine circovirus 2-infected intestinal porcine epithelial cell line by RNA sequencing
type: item
type: AcademicArticle
description: Porcine circovirus-associated disease (PCVAD), which is induced by porcine circovirus type 2 (PCV2), is responsible for severe economic losses. Recently, the role of noncoding RNAs, and in particular microRNAs, in PCV2 infection has received great attention. However, the role of long noncoding RNA (lncRNA) in PCV2 infection is unclear. Here, for the first time, we describe the expression profiles of lncRNAs in an intestinal porcine epithelial cell line (IPEC-J2) after PCV2 infection, and analyze the features of differently expressed lncRNAs and their potential target genes. After strict filtering of approximately 150 million reads, we identified 13,520 lncRNAs, including 199 lncRNAs that were differentially expressed in non-infected and PCV2-infected cells. Furthermore, trans analysis found lncRNA-regulated target genes enriched for specific Gene Ontology terms (P < 0.05), such as DNA binding, RNA binding, and transcription factor activity, which are closely associated with PCV2 infection. In addition, we analyzed the predicted target genes of differentially expressed lncRNAs, including SOD2, TNFAIP3, and ARG1, all of which are involved in infectious diseases. Our study identifies many candidate lncRNAs involved in PCV2 infection and provides new insight into the mechanisms underlying the pathogenesis of PCVAD.
format: application/pdf
format: text/html
creator: Manxin Fang
creator: Yi Yang
creator: Naidong Wang
creator: Aibing Wang
creator: Yanfeng He
creator: Jiaoshun Wang
creator: You Jiang
creator: Zhibang Deng
subject: Agricultural Science
subject: Bioinformatics
subject: Virology
description: doi:10.7717/peerj.6577
publisher: PeerJ Inc.
rights: © 2019 Fang et al.
abstract: Porcine circovirus-associated disease (PCVAD), which is induced by porcine circovirus type 2 (PCV2), is responsible for severe economic losses. Recently, the role of noncoding RNAs, and in particular microRNAs, in PCV2 infection has received great attention. However, the role of long noncoding RNA (lncRNA) in PCV2 infection is unclear. Here, for the first time, we describe the expression profiles of lncRNAs in an intestinal porcine epithelial cell line (IPEC-J2) after PCV2 infection, and analyze the features of differently expressed lncRNAs and their potential target genes. After strict filtering of approximately 150 million reads, we identified 13,520 lncRNAs, including 199 lncRNAs that were differentially expressed in non-infected and PCV2-infected cells. Furthermore, trans analysis found lncRNA-regulated target genes enriched for specific Gene Ontology terms (P < 0.05), such as DNA binding, RNA binding, and transcription factor activity, which are closely associated with PCV2 infection. In addition, we analyzed the predicted target genes of differentially expressed lncRNAs, including SOD2, TNFAIP3, and ARG1, all of which are involved in infectious diseases. Our study identifies many candidate lncRNAs involved in PCV2 infection and provides new insight into the mechanisms underlying the pathogenesis of PCVAD.
bibliographic citation: Fang et al. (2019) Genome-wide analysis of long non-coding RNA expression profile in porcine circovirus 2-infected intestinal porcine epithelial cell line by RNA sequencing. PeerJ 7:e6577 https://doi.org/10.7717/peerj.6577
date submitted: 2018-10-02
date accepted: 2019-02-05
issued: 2019-03-06
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Fang
  given name: Manxin
author list: Agent
  family name: Yang
  given name: Yi
author list: Agent
  family name: Wang
  given name: Naidong
author list: Agent
  family name: Wang
  given name: Aibing
author list: Agent
  family name: He
  given name: Yanfeng
author list: Agent
  family name: Wang
  given name: Jiaoshun
author list: Agent
  family name: Jiang
  given name: You
author list: Agent
  family name: Deng
  given name: Zhibang
doi: 10.7717/peerj.6577
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-03-06
copyright: © 2019 Fang et al.
attribution name: Fang et al.

Electric resistance tomography and stress wave tomography for decay detection in trees—a comparison study
type: item
type: AcademicArticle
description: Background To ensure the safety of trees, two NDT (nondestructive testing) techniques, electric resistance tomography and stress wave tomography, were employed to quantitatively detect and characterize the internal decay of standing trees. Comparisons between those two techniques were done to make full use of the individual capability for decay detection. Methods Eighty trees (40 Manchurian ash and 40 Populus simonii) were detected, then wood increment cores were obtained from each cross disc trial. The Dt, which was defined as the value determined by the mass loss ratio of each wood core, was regarded as the true severity of decay. Using ordinary least-squares regression to analyze the relationship between Dt and De (De was defined as the severity of decay determined by electric resistance tomography) and between Dt and Ds (Ds was defined as the severity of decay determined by stress wave tomography). Results The results showed that both methods could estimate the severity of decay in trees. In terms of different stages of decay, when Dt < 30%, De had a strong positive correlation with Dt (R2 = 0.677, P < 0.01), while, when Dt ≥ 30%, Ds had a significant positive correlation relationship with Dt (R2 = 0.645, P < 0.01). Conclusion Electric resistance tomography was better than stress wave tomography for testing in the early stages of decay, while stress wave tomography can be used effectively in the late stage of decay. It is suggested that each technique can be used in the practice of internal decay testing of standing trees based on decay stages and operating conditions.
format: application/pdf
format: text/html
creator: Xiaoquan Yue
creator: Lihai Wang
creator: James P. Wacker
creator: Zhiming Zhu
subject: Forestry
description: doi:10.7717/peerj.6444
publisher: PeerJ Inc.
rights: © 2019 Yue et al.
abstract: Background To ensure the safety of trees, two NDT (nondestructive testing) techniques, electric resistance tomography and stress wave tomography, were employed to quantitatively detect and characterize the internal decay of standing trees. Comparisons between those two techniques were done to make full use of the individual capability for decay detection. Methods Eighty trees (40 Manchurian ash and 40 Populus simonii) were detected, then wood increment cores were obtained from each cross disc trial. The Dt, which was defined as the value determined by the mass loss ratio of each wood core, was regarded as the true severity of decay. Using ordinary least-squares regression to analyze the relationship between Dt and De (De was defined as the severity of decay determined by electric resistance tomography) and between Dt and Ds (Ds was defined as the severity of decay determined by stress wave tomography). Results The results showed that both methods could estimate the severity of decay in trees. In terms of different stages of decay, when Dt < 30%, De had a strong positive correlation with Dt (R2 = 0.677, P < 0.01), while, when Dt ≥ 30%, Ds had a significant positive correlation relationship with Dt (R2 = 0.645, P < 0.01). Conclusion Electric resistance tomography was better than stress wave tomography for testing in the early stages of decay, while stress wave tomography can be used effectively in the late stage of decay. It is suggested that each technique can be used in the practice of internal decay testing of standing trees based on decay stages and operating conditions.
bibliographic citation: Yue et al. (2019) Electric resistance tomography and stress wave tomography for decay detection in trees—a comparison study. PeerJ 7:e6444 https://doi.org/10.7717/peerj.6444
date submitted: 2018-10-09
date accepted: 2019-01-14
issued: 2019-03-05
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Yue
  given name: Xiaoquan
author list: Agent
  family name: Wang
  given name: Lihai
author list: Agent
  family name: Wacker
  given name: James P.
author list: Agent
  family name: Zhu
  given name: Zhiming
doi: 10.7717/peerj.6444
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-03-05
copyright: ©2019 Yue et al.
attribution name: Yue et al.

Potential invasive plant expansion in global ecoregions under climate change
type: item
type: AcademicArticle
description: Climate change is increasing the risk of invasive plant expansion worldwide. However, few studies have specified the relationship between invasive plant expansion and ecoregions at the global scale under climate change. To address this gap, we provide risk maps highlighting the response of invasive plant species (IPS), with a focus on terrestrial and freshwater ecoregions to climate change, and further explore the climatic features of ecosystems with a high potential for invasive plant expansion under climate change. We use species distribution modelling to predict the suitable habitats of IPS with records at the global scale. Hotspots with a potential risk of IPS (such as aquatic plants, trees, and herbs) expanding in global ecoregions were distributed in Northern Europe, the UK, South America, North America, southwest China, and New Zealand. Temperature changes were related to the potential of IPS expansion in global ecoregions under climate change. Coastal and high latitude ecoregions, such as temperate forests, alpine vegetation, and coastal rivers, were severely infiltrated by IPS under climate change. Monitoring strategies should be defined for climate change for IPS, particularly for aquatic plants, trees, and herbs in the biomes of regions with coastal or high latitudes. The role of climate change on the potential for IPS expansion should be taken into consideration for biological conservation and risk evaluation of IPS at ecoregional scales.
format: application/pdf
format: text/html
creator: Chun-Jing Wang
creator: Qiang-Feng Li
creator: Ji-Zhong Wan
subject: Biogeography
subject: Ecology
subject: Ecosystem Science
subject: Plant Science
subject: Climate Change Biology
description: doi:10.7717/peerj.6479
publisher: PeerJ Inc.
rights: © 2019 Wang et al.
abstract: Climate change is increasing the risk of invasive plant expansion worldwide. However, few studies have specified the relationship between invasive plant expansion and ecoregions at the global scale under climate change. To address this gap, we provide risk maps highlighting the response of invasive plant species (IPS), with a focus on terrestrial and freshwater ecoregions to climate change, and further explore the climatic features of ecosystems with a high potential for invasive plant expansion under climate change. We use species distribution modelling to predict the suitable habitats of IPS with records at the global scale. Hotspots with a potential risk of IPS (such as aquatic plants, trees, and herbs) expanding in global ecoregions were distributed in Northern Europe, the UK, South America, North America, southwest China, and New Zealand. Temperature changes were related to the potential of IPS expansion in global ecoregions under climate change. Coastal and high latitude ecoregions, such as temperate forests, alpine vegetation, and coastal rivers, were severely infiltrated by IPS under climate change. Monitoring strategies should be defined for climate change for IPS, particularly for aquatic plants, trees, and herbs in the biomes of regions with coastal or high latitudes. The role of climate change on the potential for IPS expansion should be taken into consideration for biological conservation and risk evaluation of IPS at ecoregional scales.
bibliographic citation: Wang et al. (2019) Potential invasive plant expansion in global ecoregions under climate change. PeerJ 7:e6479 https://doi.org/10.7717/peerj.6479
date submitted: 2018-07-24
date accepted: 2019-01-20
issued: 2019-03-05
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Wang
  given name: Chun-Jing
author list: Agent
  family name: Li
  given name: Qiang-Feng
author list: Agent
  family name: Wan
  given name: Ji-Zhong
doi: 10.7717/peerj.6479
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-03-05
copyright: © 2019 Wang et al.
attribution name: Wang et al.

Improved taxonomic assignment of rumen bacterial 16S rRNA sequences using a revised SILVA taxonomic framework
type: item
type: AcademicArticle
description: The taxonomy and associated nomenclature of many taxa of rumen bacteria are poorly defined within databases of 16S rRNA genes. This lack of resolution results in inadequate definition of microbial community structures, with large parts of the community designated as incertae sedis, unclassified, or uncultured within families, orders, or even classes. We have begun resolving these poorly-defined groups of rumen bacteria, based on our desire to name these for use in microbial community profiling. We used the previously-reported global rumen census (GRC) dataset consisting of >4.5 million partial bacterial 16S rRNA gene sequences amplified from 684 rumen samples and representing a wide range of animal hosts and diets. Representative sequences from the 8,985 largest operational units (groups of sequence sharing >97% sequence similarity, and covering 97.8% of all sequences in the GRC dataset) were used to identify 241 pre-defined clusters (mainly at genus or family level) of abundant rumen bacteria in the ARB SILVA 119 framework. A total of 99 of these clusters (containing 63.8% of all GRC sequences) had no unique or had inadequate taxonomic identifiers, and each was given a unique nomenclature. We assessed this improved framework by comparing taxonomic assignments of bacterial 16S rRNA gene sequence data in the GRC dataset with those made using the original SILVA 119 framework, and three other frameworks. The two SILVA frameworks performed best at assigning sequences to genus-level taxa. The SILVA 119 framework allowed 55.4% of the sequence data to be assigned to 751 uniquely identifiable genus-level groups. The improved framework increased this to 87.1% of all sequences being assigned to one of 871 uniquely identifiable genus-level groups. The new designations were included in the SILVA 123 release (https://www.arb-silva.de/documentation/release-123/) and will be perpetuated in future releases.
format: application/pdf
format: text/html
creator: Gemma Henderson
creator: Pelin Yilmaz
creator: Sandeep Kumar
creator: Robert J. Forster
creator: William J. Kelly
creator: Sinead C. Leahy
creator: Le Luo Guan
creator: Peter H. Janssen
subject: Agricultural Science
subject: Microbiology
description: doi:10.7717/peerj.6496
publisher: PeerJ Inc.
rights: © 2019 Henderson et al.
abstract: The taxonomy and associated nomenclature of many taxa of rumen bacteria are poorly defined within databases of 16S rRNA genes. This lack of resolution results in inadequate definition of microbial community structures, with large parts of the community designated as incertae sedis, unclassified, or uncultured within families, orders, or even classes. We have begun resolving these poorly-defined groups of rumen bacteria, based on our desire to name these for use in microbial community profiling. We used the previously-reported global rumen census (GRC) dataset consisting of >4.5 million partial bacterial 16S rRNA gene sequences amplified from 684 rumen samples and representing a wide range of animal hosts and diets. Representative sequences from the 8,985 largest operational units (groups of sequence sharing >97% sequence similarity, and covering 97.8% of all sequences in the GRC dataset) were used to identify 241 pre-defined clusters (mainly at genus or family level) of abundant rumen bacteria in the ARB SILVA 119 framework. A total of 99 of these clusters (containing 63.8% of all GRC sequences) had no unique or had inadequate taxonomic identifiers, and each was given a unique nomenclature. We assessed this improved framework by comparing taxonomic assignments of bacterial 16S rRNA gene sequence data in the GRC dataset with those made using the original SILVA 119 framework, and three other frameworks. The two SILVA frameworks performed best at assigning sequences to genus-level taxa. The SILVA 119 framework allowed 55.4% of the sequence data to be assigned to 751 uniquely identifiable genus-level groups. The improved framework increased this to 87.1% of all sequences being assigned to one of 871 uniquely identifiable genus-level groups. The new designations were included in the SILVA 123 release (https://www.arb-silva.de/documentation/release-123/) and will be perpetuated in future releases.
bibliographic citation: Henderson et al. (2019) Improved taxonomic assignment of rumen bacterial 16S rRNA sequences using a revised SILVA taxonomic framework. PeerJ 7:e6496 https://doi.org/10.7717/peerj.6496
date submitted: 2018-07-30
date accepted: 2019-01-21
issued: 2019-03-05
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Henderson
  given name: Gemma
author list: Agent
  family name: Yilmaz
  given name: Pelin
author list: Agent
  family name: Kumar
  given name: Sandeep
author list: Agent
  family name: Forster
  given name: Robert J.
author list: Agent
  family name: Kelly
  given name: William J.
author list: Agent
  family name: Leahy
  given name: Sinead C.
author list: Agent
  family name: Guan
  given name: Le Luo
author list: Agent
  family name: Janssen
  given name: Peter H.
doi: 10.7717/peerj.6496
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-03-05
copyright: © 2019 Henderson et al.
attribution name: Henderson et al.

The Malacca Strait separates distinct faunas of poorly-flying Cautires net-winged beetles
type: item
type: AcademicArticle
description: We investigated the spatial and temporal patterns of Cautires diversification on the Malay Peninsula and Sumatra to understand if the narrow and frequently dry Malacca Strait separates different faunas. Moreover, we analyzed the origin of Cautires in Malayan and Sumatran mountains. We sampled 18 localities and present the mtDNA-based phylogeny of 76 species represented by 388 individuals. The phylogenetic tree was dated using mtDNA evolution rates and the ancestral ranges were estimated using the maximum likelihood approach. The phylogeny identified multiple lineages on the Malay Peninsula since the Upper Eocene (35 million years ago, mya) and a delayed evolution of diversity in Sumatra since the Upper Oligocene (26 mya). A limited number of colonization events across the Malacca Strait was identified up to the Pliocene and more intensive faunal exchange since the Pleistocene. The early colonization events were commonly followed by in situ diversification. As a result, the Malacca Strait now separates two faunas with a high species-level turnover. The montane fauna diversified in a limited space and seldom took part in colonization events across the Strait. Besides isolation by open sea or a savannah corridor, mimetic patterns could decrease the colonization capacity of Cautires. The Malay fauna is phylogenetically more diverse and has a higher value if conservation priorities should be defined.
format: application/pdf
format: text/html
creator: Alice Jiruskova
creator: Michal Motyka
creator: Matej Bocek
creator: Ladislav Bocak
subject: Entomology
subject: Evolutionary Studies
subject: Molecular Biology
description: doi:10.7717/peerj.6511
publisher: PeerJ Inc.
rights: © 2019 Jiruskova et al.
abstract: We investigated the spatial and temporal patterns of Cautires diversification on the Malay Peninsula and Sumatra to understand if the narrow and frequently dry Malacca Strait separates different faunas. Moreover, we analyzed the origin of Cautires in Malayan and Sumatran mountains. We sampled 18 localities and present the mtDNA-based phylogeny of 76 species represented by 388 individuals. The phylogenetic tree was dated using mtDNA evolution rates and the ancestral ranges were estimated using the maximum likelihood approach. The phylogeny identified multiple lineages on the Malay Peninsula since the Upper Eocene (35 million years ago, mya) and a delayed evolution of diversity in Sumatra since the Upper Oligocene (26 mya). A limited number of colonization events across the Malacca Strait was identified up to the Pliocene and more intensive faunal exchange since the Pleistocene. The early colonization events were commonly followed by in situ diversification. As a result, the Malacca Strait now separates two faunas with a high species-level turnover. The montane fauna diversified in a limited space and seldom took part in colonization events across the Strait. Besides isolation by open sea or a savannah corridor, mimetic patterns could decrease the colonization capacity of Cautires. The Malay fauna is phylogenetically more diverse and has a higher value if conservation priorities should be defined.
bibliographic citation: Jiruskova et al. (2019) The Malacca Strait separates distinct faunas of poorly-flying Cautires net-winged beetles. PeerJ 7:e6511 https://doi.org/10.7717/peerj.6511
date submitted: 2018-03-07
date accepted: 2019-01-22
issued: 2019-03-05
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Jiruskova
  given name: Alice
author list: Agent
  family name: Motyka
  given name: Michal
author list: Agent
  family name: Bocek
  given name: Matej
author list: Agent
  family name: Bocak
  given name: Ladislav
doi: 10.7717/peerj.6511
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-03-05
copyright: © 2019 Jiruskova et al.
attribution name: Jiruskova et al.

Transcriptome analysis of osmotic-responsive genes in ABA-dependent and -independent pathways in wheat (Triticum aestivum L.) roots
type: item
type: AcademicArticle
description: Bread wheat is one of the most important crops in the world. However, osmotic stress significantly inhibits wheat growth and development, and reduces crop yield and quality. Plants respond to osmotic stress mainly through abscisic acid (ABA)-dependent and -independent pathways. In this study, root transcriptome profiles of wheat seedlings exposed to osmotic stress and exogenous ABA were analysed to identify osmotic-responsive genes belonging to the ABA-dependent or -independent pathways. We found that osmotic stress promoted proline biosynthesis in the ABA-dependent pathway, and trehalose biosynthesis is likely promoted among soluble sugars to maintain protein bioactivity under osmotic stress. In wheat roots subjected to osmotic stress, calcium ions, and glutathione exert their functions mainly through calcium-binding protein (CaM/CML) and glutathione-S-transferase, respectively, depending on both pathways. In addition, a complex relationship among phytohormones signal transduction was observed in response to osmotic stress. The findings of this study deepen our understanding of the molecular mechanisms of osmotic-stress resistance, and provide several candidate osmotic-responsive genes for further study.
format: application/pdf
format: text/html
creator: Chunxi Li
creator: Wenli Zhang
creator: Meng Yuan
creator: Lina Jiang
creator: Bo Sun
creator: Daijing Zhang
creator: Yun Shao
creator: Anqi Liu
creator: Xueqing Liu
creator: Jianhui Ma
subject: Bioinformatics
subject: Genomics
subject: Plant Science
description: doi:10.7717/peerj.6519
publisher: PeerJ Inc.
rights: © 2019 Li et al.
abstract: Bread wheat is one of the most important crops in the world. However, osmotic stress significantly inhibits wheat growth and development, and reduces crop yield and quality. Plants respond to osmotic stress mainly through abscisic acid (ABA)-dependent and -independent pathways. In this study, root transcriptome profiles of wheat seedlings exposed to osmotic stress and exogenous ABA were analysed to identify osmotic-responsive genes belonging to the ABA-dependent or -independent pathways. We found that osmotic stress promoted proline biosynthesis in the ABA-dependent pathway, and trehalose biosynthesis is likely promoted among soluble sugars to maintain protein bioactivity under osmotic stress. In wheat roots subjected to osmotic stress, calcium ions, and glutathione exert their functions mainly through calcium-binding protein (CaM/CML) and glutathione-S-transferase, respectively, depending on both pathways. In addition, a complex relationship among phytohormones signal transduction was observed in response to osmotic stress. The findings of this study deepen our understanding of the molecular mechanisms of osmotic-stress resistance, and provide several candidate osmotic-responsive genes for further study.
bibliographic citation: Li et al. (2019) Transcriptome analysis of osmotic-responsive genes in ABA-dependent and -independent pathways in wheat (Triticum aestivum L.) roots. PeerJ 7:e6519 https://doi.org/10.7717/peerj.6519
date submitted: 2018-05-13
date accepted: 2019-01-21
issued: 2019-03-05
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Li
  given name: Chunxi
author list: Agent
  family name: Zhang
  given name: Wenli
author list: Agent
  family name: Yuan
  given name: Meng
author list: Agent
  family name: Jiang
  given name: Lina
author list: Agent
  family name: Sun
  given name: Bo
author list: Agent
  family name: Zhang
  given name: Daijing
author list: Agent
  family name: Shao
  given name: Yun
author list: Agent
  family name: Liu
  given name: Anqi
author list: Agent
  family name: Liu
  given name: Xueqing
author list: Agent
  family name: Ma
  given name: Jianhui
doi: 10.7717/peerj.6519
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-03-05
copyright: © 2019 Li et al.
attribution name: Li et al.

Serial monogamy benefits both sexes in the biparental convict cichlid
type: item
type: AcademicArticle
description: Monogamy can be either long-term or serial, with new pairs formed with each breeding bout. Costs and benefits are associated with each strategy. Because biparental convict cichlids (Amatitlania nigrofasciata) typically switch mates, exhibiting serial monogamy, we tested for the costs associated with forcing individuals to remain with the same mate. Convict cichlids were observed over two successive breeding bouts, either with the same or a new, equally experienced, mate. Parental behavior did not differ between breeding bouts, nor did brood size. Surprisingly, fish that remained with their original partner for a second bout took significantly longer to produce a brood compared to fish that paired with new partners. New partners were also more likely to successfully produce a second brood than re-mated partners. This is in contrast to the majority of bird studies that show many benefits to staying with the same partner for multiple broods. In convict cichlids, there seems to be no benefit associated with remaining with the same partner and switching mates reduces duration between broods for both males and females, potentially increasing overall reproductive success.
format: application/pdf
format: text/html
creator: Jennifer L. Snekser
creator: Murray Itzkowitz
subject: Animal Behavior
subject: Aquaculture, Fisheries and Fish Science
subject: Evolutionary Studies
description: doi:10.7717/peerj.6535
publisher: PeerJ Inc.
rights: © 2019 Snekser and Itzkowitz
abstract: Monogamy can be either long-term or serial, with new pairs formed with each breeding bout. Costs and benefits are associated with each strategy. Because biparental convict cichlids (Amatitlania nigrofasciata) typically switch mates, exhibiting serial monogamy, we tested for the costs associated with forcing individuals to remain with the same mate. Convict cichlids were observed over two successive breeding bouts, either with the same or a new, equally experienced, mate. Parental behavior did not differ between breeding bouts, nor did brood size. Surprisingly, fish that remained with their original partner for a second bout took significantly longer to produce a brood compared to fish that paired with new partners. New partners were also more likely to successfully produce a second brood than re-mated partners. This is in contrast to the majority of bird studies that show many benefits to staying with the same partner for multiple broods. In convict cichlids, there seems to be no benefit associated with remaining with the same partner and switching mates reduces duration between broods for both males and females, potentially increasing overall reproductive success.
bibliographic citation: Snekser et al. (2019) Serial monogamy benefits both sexes in the biparental convict cichlid. PeerJ 7:e6535 https://doi.org/10.7717/peerj.6535
date submitted: 2018-10-16
date accepted: 2019-01-28
issued: 2019-03-05
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Snekser
  given name: Jennifer L.
author list: Agent
  family name: Itzkowitz
  given name: Murray
doi: 10.7717/peerj.6535
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-03-05
copyright: © 2019 Snekser and Itzkowitz
attribution name: Snekser and Itzkowitz

Effect of the flavonoid baicalin on the proliferative capacity of bovine mammary cells and their ability to regulate oxidative stress
type: item
type: AcademicArticle
description: Background High-yielding dairy cows are prone to oxidative stress due to the high metabolic needs of homeostasis and milk production. Oxidative stress and inflammation are tightly linked; therefore, anti-inflammatory and/or natural antioxidant compounds may help improve mammary cell health. Baicalin, one of the major flavonoids in Scutellaria baicalensis, has natural antioxidant and anti-inflammatory properties in various cell types, but its effects on bovine mammary epithelial cells (BMECs) have not been investigated. Methods Explants from bovine mammary glands were collected by biopsy at the peak of lactation (approximately 60 days after the start of lactation) (n = three animals) to isolate BMECs corresponding to mature secretory cells. Cell viability, apoptosis, proliferative capacity and reactive oxygen species (ROS) production by BMECs were measured after increasing doses of baicalin were added to the culture media in the absence or presence of H2O2, which was used as an in vitro model of oxidative stress. Results Low doses of baicalin (1–10 µg/mL) had no or only slightly positive effects on the proliferation and viability of BMECs, whereas higher doses (100 or 200 µg/mL) markedly decreased BMEC proliferation. Baicalin decreased apoptosis rate at low concentrations (10 µg/mL) but increased apoptosis at higher doses. ROS production was decreased in BMECs treated with increasing doses of baicalin compared with untreated cells, and this decreased production was associated with increased intracellular concentrations of catalase and NRF-2. Irrespective of the dose, baicalin pretreatment attenuated H2O2-induced ROS production. Discussion These results indicate that baicalin exerts protective antioxidant effects on bovine mammary cells. This finding suggests that baicalin could be used to prevent oxidative metabolic disorders in dairy cows.
format: application/pdf
format: text/html
creator: Marie-Hélène Perruchot
creator: Florence Gondret
creator: Fabrice Robert
creator: Emilien Dupuis
creator: Hélène Quesnel
creator: Frédéric Dessauge
subject: Agricultural Science
subject: Veterinary Medicine
description: doi:10.7717/peerj.6565
publisher: PeerJ Inc.
rights: © 2019 Perruchot et al.
abstract: Background High-yielding dairy cows are prone to oxidative stress due to the high metabolic needs of homeostasis and milk production. Oxidative stress and inflammation are tightly linked; therefore, anti-inflammatory and/or natural antioxidant compounds may help improve mammary cell health. Baicalin, one of the major flavonoids in Scutellaria baicalensis, has natural antioxidant and anti-inflammatory properties in various cell types, but its effects on bovine mammary epithelial cells (BMECs) have not been investigated. Methods Explants from bovine mammary glands were collected by biopsy at the peak of lactation (approximately 60 days after the start of lactation) (n = three animals) to isolate BMECs corresponding to mature secretory cells. Cell viability, apoptosis, proliferative capacity and reactive oxygen species (ROS) production by BMECs were measured after increasing doses of baicalin were added to the culture media in the absence or presence of H2O2, which was used as an in vitro model of oxidative stress. Results Low doses of baicalin (1–10 µg/mL) had no or only slightly positive effects on the proliferation and viability of BMECs, whereas higher doses (100 or 200 µg/mL) markedly decreased BMEC proliferation. Baicalin decreased apoptosis rate at low concentrations (10 µg/mL) but increased apoptosis at higher doses. ROS production was decreased in BMECs treated with increasing doses of baicalin compared with untreated cells, and this decreased production was associated with increased intracellular concentrations of catalase and NRF-2. Irrespective of the dose, baicalin pretreatment attenuated H2O2-induced ROS production. Discussion These results indicate that baicalin exerts protective antioxidant effects on bovine mammary cells. This finding suggests that baicalin could be used to prevent oxidative metabolic disorders in dairy cows.
bibliographic citation: Perruchot et al. (2019) Effect of the flavonoid baicalin on the proliferative capacity of bovine mammary cells and their ability to regulate oxidative stress. PeerJ 7:e6565 https://doi.org/10.7717/peerj.6565
date submitted: 2018-11-09
date accepted: 2019-02-01
issued: 2019-03-05
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Perruchot
  given name: Marie-Hélène
author list: Agent
  family name: Gondret
  given name: Florence
author list: Agent
  family name: Robert
  given name: Fabrice
author list: Agent
  family name: Dupuis
  given name: Emilien
author list: Agent
  family name: Quesnel
  given name: Hélène
author list: Agent
  family name: Dessauge
  given name: Frédéric
doi: 10.7717/peerj.6565
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-03-05
copyright: © 2019 Perruchot et al.
attribution name: Perruchot et al.

DNA metabarcoding allows non-invasive identification of arthropod prey provisioned to nestling Rufous hummingbirds (Selasphorus rufus)
type: item
type: AcademicArticle
description: Hummingbirds consume sugars from nectar, sap and honeydew, and obtain protein, fat and minerals from arthropods. To date, the identity of arthropod taxa in hummingbird diets has been investigated by observation of foraging or examination of alimentary tract contents. Direct examination of nestling provisioning adds the extra complication of disturbance to the young and mother. Here, we show that arthropod food items provisioned to Rufous hummingbird (Selasphorus rufus) nestlings can be identified by a safe and non-invasive protocol using next-generation sequencing (NGS) of DNA from nestling fecal pellets collected post-fledging. We found that females on southern Vancouver Island (British Columbia, Canada) provisioned nestlings with a wide range of arthropod taxa. The samples examined contained three Classes, eight Orders, 48 Families, and 87 Genera, with from one to 15 Families being identified in a single pellet. Soft-bodied Dipterans were found most frequently and had the highest relative abundance; hard-bodied prey items were absent from almost all samples. Substantial differences in taxa were found within season and between years, indicating the importance of multi-year sampling when defining a prey spectrum.
format: application/pdf
format: text/html
creator: Alison J. Moran
creator: Sean W.J. Prosser
creator: Jonathan A. Moran
subject: Biodiversity
subject: Ecology
subject: Molecular Biology
subject: Zoology
description: doi:10.7717/peerj.6596
publisher: PeerJ Inc.
rights: © 2019 Moran et al.
abstract: Hummingbirds consume sugars from nectar, sap and honeydew, and obtain protein, fat and minerals from arthropods. To date, the identity of arthropod taxa in hummingbird diets has been investigated by observation of foraging or examination of alimentary tract contents. Direct examination of nestling provisioning adds the extra complication of disturbance to the young and mother. Here, we show that arthropod food items provisioned to Rufous hummingbird (Selasphorus rufus) nestlings can be identified by a safe and non-invasive protocol using next-generation sequencing (NGS) of DNA from nestling fecal pellets collected post-fledging. We found that females on southern Vancouver Island (British Columbia, Canada) provisioned nestlings with a wide range of arthropod taxa. The samples examined contained three Classes, eight Orders, 48 Families, and 87 Genera, with from one to 15 Families being identified in a single pellet. Soft-bodied Dipterans were found most frequently and had the highest relative abundance; hard-bodied prey items were absent from almost all samples. Substantial differences in taxa were found within season and between years, indicating the importance of multi-year sampling when defining a prey spectrum.
bibliographic citation: Moran et al. (2019) DNA metabarcoding allows non-invasive identification of arthropod prey provisioned to nestling Rufous hummingbirds (Selasphorus rufus). PeerJ 7:e6596 https://doi.org/10.7717/peerj.6596
date submitted: 2018-12-08
date accepted: 2019-02-08
issued: 2019-03-05
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Moran
  given name: Alison J.
author list: Agent
  family name: Prosser
  given name: Sean W.J.
author list: Agent
  family name: Moran
  given name: Jonathan A.
doi: 10.7717/peerj.6596
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-03-05
copyright: ©2019 Moran et al.
attribution name: Moran et al.

Capturing complexity: field-testing the use of ‘structure from motion’ derived virtual models to replicate standard measures of reef physical structure
type: item
type: AcademicArticle
description: Reef structural complexity provides important refuge habitat for a range of marine organisms, and is a useful indicator of the health and resilience of reefs as a whole. Marine scientists have recently begun to use ‘Structure from Motion’ (SfM) photogrammetry in order to accurately and repeatably capture the 3D structure of physical objects underwater, including reefs. There has however been limited research on the comparability of this new method with existing analogue methods already used widely for measuring and monitoring 3D structure, such as ‘tape and chain rugosity index (RI)’ and graded visual assessments. Our findings show that analogue and SfM RI can be reliably converted over a standard 10-m reef section (SfM RI = 1.348 × chain RI—0.359, r2 = 0.82; and Chain RI = 0.606 × SfM RI + 0.465) for RI values up to 2.0; however, SfM RI values above this number become increasingly divergent from traditional tape and chain measurements. Additionally, we found SfM RI correlates well with visual assessment grades of coral reefs over a 10 × 10 m area (SfM RI = 0.1461 × visual grade + 1.117; r2 = 0.83). The SfM method is shown to be affordable and non-destructive whilst also allowing the data collected to be archival, less biased by the observer, and broader in its scope of applications than standard methods. This work allows researchers to easily transition from analogue to digital structural assessment techniques, facilitating continued long-term monitoring, whilst also improving the quality and additional research value of the data collected.
format: application/pdf
format: text/html
creator: Daniel T.I. Bayley
creator: Andrew O.M. Mogg
creator: Heather Koldewey
creator: Andy Purvis
subject: Conservation Biology
subject: Marine Biology
subject: Computational Science
subject: Climate Change Biology
subject: Spatial and Geographic Information Science
description: doi:10.7717/peerj.6540
publisher: PeerJ Inc.
rights: © 2019 Bayley et al.
abstract: Reef structural complexity provides important refuge habitat for a range of marine organisms, and is a useful indicator of the health and resilience of reefs as a whole. Marine scientists have recently begun to use ‘Structure from Motion’ (SfM) photogrammetry in order to accurately and repeatably capture the 3D structure of physical objects underwater, including reefs. There has however been limited research on the comparability of this new method with existing analogue methods already used widely for measuring and monitoring 3D structure, such as ‘tape and chain rugosity index (RI)’ and graded visual assessments. Our findings show that analogue and SfM RI can be reliably converted over a standard 10-m reef section (SfM RI = 1.348 × chain RI—0.359, r2 = 0.82; and Chain RI = 0.606 × SfM RI + 0.465) for RI values up to 2.0; however, SfM RI values above this number become increasingly divergent from traditional tape and chain measurements. Additionally, we found SfM RI correlates well with visual assessment grades of coral reefs over a 10 × 10 m area (SfM RI = 0.1461 × visual grade + 1.117; r2 = 0.83). The SfM method is shown to be affordable and non-destructive whilst also allowing the data collected to be archival, less biased by the observer, and broader in its scope of applications than standard methods. This work allows researchers to easily transition from analogue to digital structural assessment techniques, facilitating continued long-term monitoring, whilst also improving the quality and additional research value of the data collected.
bibliographic citation: Bayley et al. (2019) Capturing complexity: field-testing the use of ‘structure from motion’ derived virtual models to replicate standard measures of reef physical structure. PeerJ 7:e6540 https://doi.org/10.7717/peerj.6540
date submitted: 2018-10-18
date accepted: 2019-01-30
issued: 2019-03-04
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Bayley
  given name: Daniel T.I.
author list: Agent
  family name: Mogg
  given name: Andrew O.M.
author list: Agent
  family name: Koldewey
  given name: Heather
author list: Agent
  family name: Purvis
  given name: Andy
doi: 10.7717/peerj.6540
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-03-04
copyright: © 2019 Bayley et al.
attribution name: Bayley et al.

A new method of gall mite management: application of artificial defoliation to control Aceria pallida
type: item
type: AcademicArticle
description: Artificial defoliant is widely applied to cotton to facilitate mechanical harvesting and successfully controls leaf diseases by blocking pathogen epidemical cycles; however, this technique is rarely used to control herbivores. Because many eriophyoid mites live and reproduce in galls, the control of these mites by pesticides is usually limited. However, the abscission of galled foliage is lethal to tiny mites with low mobility. Therefore, artificial defoliation should be effective in controlling gall mites. Here, the effects of defoliant on the control of the goji berry Lycium barbarum L. gall mite Aceria pallida Keifer were compared with those of pesticides under field conditions over 3 years. Our results showed that artificial defoliation enabled almost complete defoliation and timely refoliation. A. pallida galls fell off with the defoliation, and then regenerated foliage escaped from mite attack. After defoliant application, the densities of mite galls decreased by 84.1%, 80.3% and 80.3% compared with those found in the pesticide (undefoliated) treatment in 2012, 2013 and 2014, respectively. Artificial defoliation achieved much better control of gall mites than pesticides.
format: application/pdf
format: text/html
creator: Jianling Li
creator: Sai Liu
creator: Kun Guo
creator: Haili Qiao
creator: Rong Xu
creator: Changqing Xu
creator: Jun Chen
subject: Agricultural Science
subject: Entomology
subject: Plant Science
subject: Zoology
subject: Forestry
description: doi:10.7717/peerj.6503
publisher: PeerJ Inc.
rights: © 2019 Li et al.
abstract: Artificial defoliant is widely applied to cotton to facilitate mechanical harvesting and successfully controls leaf diseases by blocking pathogen epidemical cycles; however, this technique is rarely used to control herbivores. Because many eriophyoid mites live and reproduce in galls, the control of these mites by pesticides is usually limited. However, the abscission of galled foliage is lethal to tiny mites with low mobility. Therefore, artificial defoliation should be effective in controlling gall mites. Here, the effects of defoliant on the control of the goji berry Lycium barbarum L. gall mite Aceria pallida Keifer were compared with those of pesticides under field conditions over 3 years. Our results showed that artificial defoliation enabled almost complete defoliation and timely refoliation. A. pallida galls fell off with the defoliation, and then regenerated foliage escaped from mite attack. After defoliant application, the densities of mite galls decreased by 84.1%, 80.3% and 80.3% compared with those found in the pesticide (undefoliated) treatment in 2012, 2013 and 2014, respectively. Artificial defoliation achieved much better control of gall mites than pesticides.
bibliographic citation: Li et al. (2019) A new method of gall mite management: application of artificial defoliation to control Aceria pallida. PeerJ 7:e6503 https://doi.org/10.7717/peerj.6503
date submitted: 2018-08-30
date accepted: 2019-01-22
issued: 2019-03-04
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Li
  given name: Jianling
author list: Agent
  family name: Liu
  given name: Sai
author list: Agent
  family name: Guo
  given name: Kun
author list: Agent
  family name: Qiao
  given name: Haili
author list: Agent
  family name: Xu
  given name: Rong
author list: Agent
  family name: Xu
  given name: Changqing
author list: Agent
  family name: Chen
  given name: Jun
doi: 10.7717/peerj.6503
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-03-04
copyright: ©2019 Li et al.
attribution name: Li et al.

Amorphous silica nanoparticles induce tumorigenesis via regulating ATP5H/SOD1-related oxidative stress, oxidative phosphorylation and EIF4G2/PABPC1-associated translational initiation
type: item
type: AcademicArticle
description: Background Recent studies indicate amorphous silica nanoparticles (SiNPs), one of the widely applied nanomaterials, have potential toxicity in humans and induces cell malignant transformation. However, its carcinogenic mechanisms remain poorly understood. This study’s purpose was to investigate the underlying toxic mechanisms of amorphous SiNPs on human lung epithelial cells model by using microarray data. Methods Microarray dataset GSE82062 was collected from Gene Expression Omnibus database, including three repeats of Beas-2B exposed to amorphous SiNPs for 40 passages and three repeats of passage-matched control Beas-2B cells. Differentially expressed genes (DEGs) were identified using linear models for microarray data method. Protein–protein interaction (PPI) network was constructed using data from the STRING database followed by module analysis. The miRwalk2 database was used to predict the underlying target genes of differentially miRNAs. Function enrichment analysis was performed using the Database for Annotation, Visualization and Integrated Discovery (DAVID) online tool. Results A total of 323 genes were identified as DEGs, including 280 downregulated (containing 12 pre-miRNAs) and 43 upregulated genes (containing 29 pre-miRNAs). Function enrichment indicated these genes were involved in translational initiation (i.e., eukaryotic translation initiation factor 4 gamma 2 (EIF4G2), poly (A) binding protein cytoplasmic 1 (PABPC1)), response to reactive oxygen species (i.e., superoxide dismutase 1 (SOD1)) and oxidative phosphorylation (i.e., ATP5H). PABPC1 (degree = 15), ATP5H (degree = 11) and SOD1 (degree = 8)] were proved to be hub genes after PPI-module analyses. ATP5H/SOD1 and EIF4G2/PABPC1 were overlapped with the target genes of differentially expressed pre-miR-3648/572/661 and pre-miR-4521. Conclusions Amorphous SiNPs may induce tumorigenesis via influencing ATP5H/SOD1-related oxidative stress, oxidative phosphorylation and EIF4G2/PABPC1-associated transl…
format: application/pdf
format: text/html
creator: Dongli Xie
creator: Yang Zhou
creator: Xiaogang Luo
subject: Bioinformatics
subject: Toxicology
subject: Ecotoxicology
subject: Environmental Impacts
description: doi:10.7717/peerj.6455
publisher: PeerJ Inc.
rights: © 2019 Xie et al.
abstract: Background Recent studies indicate amorphous silica nanoparticles (SiNPs), one of the widely applied nanomaterials, have potential toxicity in humans and induces cell malignant transformation. However, its carcinogenic mechanisms remain poorly understood. This study’s purpose was to investigate the underlying toxic mechanisms of amorphous SiNPs on human lung epithelial cells model by using microarray data. Methods Microarray dataset GSE82062 was collected from Gene Expression Omnibus database, including three repeats of Beas-2B exposed to amorphous SiNPs for 40 passages and three repeats of passage-matched control Beas-2B cells. Differentially expressed genes (DEGs) were identified using linear models for microarray data method. Protein–protein interaction (PPI) network was constructed using data from the STRING database followed by module analysis. The miRwalk2 database was used to predict the underlying target genes of differentially miRNAs. Function enrichment analysis was performed using the Database for Annotation, Visualization and Integrated Discovery (DAVID) online tool. Results A total of 323 genes were identified as DEGs, including 280 downregulated (containing 12 pre-miRNAs) and 43 upregulated genes (containing 29 pre-miRNAs). Function enrichment indicated these genes were involved in translational initiation (i.e., eukaryotic translation initiation factor 4 gamma 2 (EIF4G2), poly (A) binding protein cytoplasmic 1 (PABPC1)), response to reactive oxygen species (i.e., superoxide dismutase 1 (SOD1)) and oxidative phosphorylation (i.e., ATP5H). PABPC1 (degree = 15), ATP5H (degree = 11) and SOD1 (degree = 8)] were proved to be hub genes after PPI-module analyses. ATP5H/SOD1 and EIF4G2/PABPC1 were overlapped with the target genes of differentially expressed pre-miR-3648/572/661 and pre-miR-4521. Conclusions Amorphous SiNPs may induce tumorigenesis via influencing ATP5H/SOD1-related oxidative stress, oxidative phosphorylation and EIF4G2/PABPC1-associated transl…
bibliographic citation: Xie et al. (2019) Amorphous silica nanoparticles induce tumorigenesis via regulating ATP5H/SOD1-related oxidative stress, oxidative phosphorylation and EIF4G2/PABPC1-associated translational initiation. PeerJ 7:e6455 https://doi.org/10.7717/peerj.6455
date submitted: 2018-11-19
date accepted: 2019-01-16
issued: 2019-03-04
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Xie
  given name: Dongli
author list: Agent
  family name: Zhou
  given name: Yang
author list: Agent
  family name: Luo
  given name: Xiaogang
doi: 10.7717/peerj.6455
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-03-04
copyright: © 2019 Xie et al.
attribution name: Xie et al.

Employing toxin-antitoxin genome markers for identification of Bifidobacterium and Lactobacillus strains in human metagenomes
type: item
type: AcademicArticle
description: Recent research has indicated that in addition to the unique genotype each individual may also have a unique microbiota composition. Difference in microbiota composition may emerge from both its species and strain constituents. It is important to know the precise composition especially for the gut microbiota (GM), since it can contribute to the health assessment, personalized treatment, and disease prevention for individuals and groups (cohorts). The existing methods for species and strain composition in microbiota are not always precise and usually not so easy to use. Probiotic bacteria of the genus Bifidobacterium and Lactobacillus make an essential component of human GM. Previously we have shown that in certain Bifidobacterium and Lactobacillus species the RelBE and MazEF superfamily of toxin-antitoxin (TA) systems may be used as functional biomarkers to differentiate these groups of bacteria at the species and strain levels. We have composed a database of TA genes of these superfamily specific for all lactobacilli and bifidobacteria species with complete genome sequence and confirmed that in all Lactobacillus and Bifidobacterium species TA gene composition is species and strain specific. To analyze composition of species and strains of two bacteria genera, Bifidobacterium and Lactobacillus, in human GM we developed TAGMA (toxin antitoxin genes for metagenomes analyses) software based on polymorphism in TA genes. TAGMA was tested on gut metagenomic samples. The results of our analysis have shown that TAGMA can be used to characterize species and strains of Lactobacillus and Bifidobacterium in metagenomes.
format: application/pdf
format: text/html
creator: Ksenia M. Klimina
creator: Artem S. Kasianov
creator: Elena U. Poluektova
creator: Kirill V. Emelyanov
creator: Viktoriya N. Voroshilova
creator: Natalia V. Zakharevich
creator: Anna V. Kudryavtseva
creator: Vsevolod J. Makeev
creator: Valery N. Danilenko
subject: Bioinformatics
subject: Computational Biology
subject: Genetics
description: doi:10.7717/peerj.6554
publisher: PeerJ Inc.
rights: © 2019 Klimina et al.
abstract: Recent research has indicated that in addition to the unique genotype each individual may also have a unique microbiota composition. Difference in microbiota composition may emerge from both its species and strain constituents. It is important to know the precise composition especially for the gut microbiota (GM), since it can contribute to the health assessment, personalized treatment, and disease prevention for individuals and groups (cohorts). The existing methods for species and strain composition in microbiota are not always precise and usually not so easy to use. Probiotic bacteria of the genus Bifidobacterium and Lactobacillus make an essential component of human GM. Previously we have shown that in certain Bifidobacterium and Lactobacillus species the RelBE and MazEF superfamily of toxin-antitoxin (TA) systems may be used as functional biomarkers to differentiate these groups of bacteria at the species and strain levels. We have composed a database of TA genes of these superfamily specific for all lactobacilli and bifidobacteria species with complete genome sequence and confirmed that in all Lactobacillus and Bifidobacterium species TA gene composition is species and strain specific. To analyze composition of species and strains of two bacteria genera, Bifidobacterium and Lactobacillus, in human GM we developed TAGMA (toxin antitoxin genes for metagenomes analyses) software based on polymorphism in TA genes. TAGMA was tested on gut metagenomic samples. The results of our analysis have shown that TAGMA can be used to characterize species and strains of Lactobacillus and Bifidobacterium in metagenomes.
bibliographic citation: Klimina et al. (2019) Employing toxin-antitoxin genome markers for identification of Bifidobacterium and Lactobacillus strains in human metagenomes. PeerJ 7:e6554 https://doi.org/10.7717/peerj.6554
date submitted: 2018-09-13
date accepted: 2019-02-02
issued: 2019-03-04
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Klimina
  given name: Ksenia M.
author list: Agent
  family name: Kasianov
  given name: Artem S.
author list: Agent
  family name: Poluektova
  given name: Elena U.
author list: Agent
  family name: Emelyanov
  given name: Kirill V.
author list: Agent
  family name: Voroshilova
  given name: Viktoriya N.
author list: Agent
  family name: Zakharevich
  given name: Natalia V.
author list: Agent
  family name: Kudryavtseva
  given name: Anna V.
author list: Agent
  family name: Makeev
  given name: Vsevolod J.
author list: Agent
  family name: Danilenko
  given name: Valery N.
doi: 10.7717/peerj.6554
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-03-04
copyright: © 2019 Klimina et al.
attribution name: Klimina et al.

PCR effects of melting temperature adjustment of individual primers in degenerate primer pools
type: item
type: AcademicArticle
description: Deep sequencing of small subunit ribosomal RNA (SSU rRNA) gene amplicons continues to be the most common approach for characterization of complex microbial communities. PCR amplifications of conserved regions of SSU rRNA genes often employ degenerate pools of primers to enable targeting of a broad spectrum of organisms. One little noticed feature of such degenerate primer sets is the potential for a wide range of melting temperatures between the primer variants. The melting temperature variation of primers in a degenerate pool could lead to variable amplification efficiencies and PCR bias. Thus, we sought to adjust the melting temperature of each primer variant individually. Individual primer modifications were used to reduce theoretical melting temperature variation between primers, as well as to introduce inter-cluster nucleotide diversity during Illumina sequencing of primer regions. We demonstrate here the suitability of such primers for microbial community analysis. However, no substantial differences in microbial community structure were revealed when using primers with adjusted melting temperatures, though the optimal annealing temperature decreased.
format: application/pdf
format: text/html
creator: Ankur Naqib
creator: Trisha Jeon
creator: Kevin Kunstman
creator: Weihua Wang
creator: Yiding Shen
creator: Dagmar Sweeney
creator: Marieta Hyde
creator: Stefan J. Green
subject: Bioengineering
subject: Bioinformatics
subject: Microbiology
subject: Molecular Biology
description: doi:10.7717/peerj.6570
publisher: PeerJ Inc.
rights: © 2019 Naqib et al.
abstract: Deep sequencing of small subunit ribosomal RNA (SSU rRNA) gene amplicons continues to be the most common approach for characterization of complex microbial communities. PCR amplifications of conserved regions of SSU rRNA genes often employ degenerate pools of primers to enable targeting of a broad spectrum of organisms. One little noticed feature of such degenerate primer sets is the potential for a wide range of melting temperatures between the primer variants. The melting temperature variation of primers in a degenerate pool could lead to variable amplification efficiencies and PCR bias. Thus, we sought to adjust the melting temperature of each primer variant individually. Individual primer modifications were used to reduce theoretical melting temperature variation between primers, as well as to introduce inter-cluster nucleotide diversity during Illumina sequencing of primer regions. We demonstrate here the suitability of such primers for microbial community analysis. However, no substantial differences in microbial community structure were revealed when using primers with adjusted melting temperatures, though the optimal annealing temperature decreased.
bibliographic citation: Naqib et al. (2019) PCR effects of melting temperature adjustment of individual primers in degenerate primer pools. PeerJ 7:e6570 https://doi.org/10.7717/peerj.6570
date submitted: 2018-11-15
date accepted: 2019-02-05
issued: 2019-03-04
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Naqib
  given name: Ankur
author list: Agent
  family name: Jeon
  given name: Trisha
author list: Agent
  family name: Kunstman
  given name: Kevin
author list: Agent
  family name: Wang
  given name: Weihua
author list: Agent
  family name: Shen
  given name: Yiding
author list: Agent
  family name: Sweeney
  given name: Dagmar
author list: Agent
  family name: Hyde
  given name: Marieta
author list: Agent
  family name: Green
  given name: Stefan J.
doi: 10.7717/peerj.6570
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-03-04
copyright: ©2019 Naqib et al.
attribution name: Naqib et al.

Feeding traces attributable to juvenile Tyrannosaurus rex offer insight into ontogenetic dietary trends
type: item
type: AcademicArticle
description: Theropod dinosaur feeding traces and tooth marks yield paleobiological and paleoecological implications for social interactions, feeding behaviors, and direct evidence of cannibalism and attempted predation. However, ascertaining the taxonomic origin of a tooth mark is largely dependent on both the known regional biostratigraphy and the ontogenetic stage of the taxon. Currently, most recorded theropod feeding traces and bite marks are attributed to adult theropods, whereas juvenile and subadult tooth marks have been rarely reported in the literature. Here we describe feeding traces attributable to a late-stage juvenile Tyrannosaurus rex on a caudal vertebra of a hadrosaurid dinosaur. The dimensions and spacing of the traces were compared to the dentition of Tyrannosaurus rex maxillae and dentaries of different ontogenetic stages. These comparisons reveal that the tooth marks present on the vertebra closely match the maxillary teeth of a late-stage juvenile Tyrannosaurus rex specimen histologically determined to be 11–12 years of age. These results demonstrate that late-stage juvenile and subadult tyrannosaurs were already utilizing the same large-bodied food sources as adults despite lacking the bone-crushing abilities of adults. Further identification of tyrannosaur feeding traces coupled with experimental studies of the biomechanics of tyrannosaur bite forces from younger ontogenetic stages may reveal dynamic dietary trends and ecological roles of Tyrannosaurus rex throughout ontogeny.
format: application/pdf
format: text/html
creator: Joseph E. Peterson
creator: Karsen N. Daus
subject: Ecology
subject: Paleontology
description: doi:10.7717/peerj.6573
publisher: PeerJ Inc.
rights: © 2019 Peterson and Daus
abstract: Theropod dinosaur feeding traces and tooth marks yield paleobiological and paleoecological implications for social interactions, feeding behaviors, and direct evidence of cannibalism and attempted predation. However, ascertaining the taxonomic origin of a tooth mark is largely dependent on both the known regional biostratigraphy and the ontogenetic stage of the taxon. Currently, most recorded theropod feeding traces and bite marks are attributed to adult theropods, whereas juvenile and subadult tooth marks have been rarely reported in the literature. Here we describe feeding traces attributable to a late-stage juvenile Tyrannosaurus rex on a caudal vertebra of a hadrosaurid dinosaur. The dimensions and spacing of the traces were compared to the dentition of Tyrannosaurus rex maxillae and dentaries of different ontogenetic stages. These comparisons reveal that the tooth marks present on the vertebra closely match the maxillary teeth of a late-stage juvenile Tyrannosaurus rex specimen histologically determined to be 11–12 years of age. These results demonstrate that late-stage juvenile and subadult tyrannosaurs were already utilizing the same large-bodied food sources as adults despite lacking the bone-crushing abilities of adults. Further identification of tyrannosaur feeding traces coupled with experimental studies of the biomechanics of tyrannosaur bite forces from younger ontogenetic stages may reveal dynamic dietary trends and ecological roles of Tyrannosaurus rex throughout ontogeny.
bibliographic citation: Peterson et al. (2019) Feeding traces attributable to juvenile Tyrannosaurus rex offer insight into ontogenetic dietary trends. PeerJ 7:e6573 https://doi.org/10.7717/peerj.6573
date submitted: 2018-11-29
date accepted: 2019-02-05
issued: 2019-03-04
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Peterson
  given name: Joseph E.
author list: Agent
  family name: Daus
  given name: Karsen N.
doi: 10.7717/peerj.6573
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-03-04
copyright: ©2019 Peterson and Daus
attribution name: Peterson and Daus

Arbuscular mycorrhizal fungi in soil, roots and rhizosphere of Medicago truncatula: diversity and heterogeneity under semi-arid conditions
type: item
type: AcademicArticle
description: Mycorrhizal symbioses are considered indicators of ecosystem biodiversity. However, their diversity and relevance in arid and semi-arid ecosystems are poorly understood. This study addressed this subject, the main objective being to evaluate arbuscular mycorrhizal fungi (AMF) diversity and heterogeneity in a semi-arid region. Samples of bulk and rhizosphere soil and fine roots of Medicago truncatula were collected at four different sites with the same aridity index (6.1), in Bou-Hedma National Park, Tunisia, a semi-arid ecosystem. AMF taxa were assessed by 454- pyrosequencing and identified by BLAST matching of operational taxonomic units (OTUs) against the MaarjAM database, targeting AMF SSU rRNA gene diversity. Roots were the hotspots of AMF diversity (107 OTUs out of a total of 138). Of the 138 OTUs, 113 found correspondence in the MaarjAM database, with 32 AMF virtual taxa (VTX),19 Site-exclusive (SE) and 13 common to at least two sites (Non-site exclusive, NSE); the remaining 25 OTUs grouped in 16 putative new AMF taxa (pNTX), each one consisting of OTUs sharing pairwise distances not higher than 3%. We found a high diversity and heterogeneity of AMF across the four sites, which showed, in a regression analysis, significant relation to six out of the eight environmental parameters evaluated: grazing activity and soil texture, electrical conductivity, organic matter, total phosphorus and total nitrogen. AMF colonization of plants also presented significant differences among the four sites, as well as spore density, microbial biomass and several enzymatic activities (dehydrogenase, β-glucosidase and phosphatase) evaluated in rhizosphere soils. The four sites clustered in two groups in a hierarchical clustering evaluation based on their AMF diversity (total numbers of OTU, VTX and pNTX) and the parameters referred above. The crucial role of abiotic factors, other than aridity index, on AMF community composition, was evidenced by the high heterogeneity found betwee…
format: application/pdf
format: text/html
creator: Neji Mahmoudi
creator: Cristina Cruz
creator: Mosbah Mahdhi
creator: Mohamed Mars
creator: Maria F. Caeiro
subject: Biodiversity
subject: Plant Science
subject: Soil Science
description: doi:10.7717/peerj.6401
publisher: PeerJ Inc.
rights: © 2019 Mahmoudi et al.
abstract: Mycorrhizal symbioses are considered indicators of ecosystem biodiversity. However, their diversity and relevance in arid and semi-arid ecosystems are poorly understood. This study addressed this subject, the main objective being to evaluate arbuscular mycorrhizal fungi (AMF) diversity and heterogeneity in a semi-arid region. Samples of bulk and rhizosphere soil and fine roots of Medicago truncatula were collected at four different sites with the same aridity index (6.1), in Bou-Hedma National Park, Tunisia, a semi-arid ecosystem. AMF taxa were assessed by 454- pyrosequencing and identified by BLAST matching of operational taxonomic units (OTUs) against the MaarjAM database, targeting AMF SSU rRNA gene diversity. Roots were the hotspots of AMF diversity (107 OTUs out of a total of 138). Of the 138 OTUs, 113 found correspondence in the MaarjAM database, with 32 AMF virtual taxa (VTX),19 Site-exclusive (SE) and 13 common to at least two sites (Non-site exclusive, NSE); the remaining 25 OTUs grouped in 16 putative new AMF taxa (pNTX), each one consisting of OTUs sharing pairwise distances not higher than 3%. We found a high diversity and heterogeneity of AMF across the four sites, which showed, in a regression analysis, significant relation to six out of the eight environmental parameters evaluated: grazing activity and soil texture, electrical conductivity, organic matter, total phosphorus and total nitrogen. AMF colonization of plants also presented significant differences among the four sites, as well as spore density, microbial biomass and several enzymatic activities (dehydrogenase, β-glucosidase and phosphatase) evaluated in rhizosphere soils. The four sites clustered in two groups in a hierarchical clustering evaluation based on their AMF diversity (total numbers of OTU, VTX and pNTX) and the parameters referred above. The crucial role of abiotic factors, other than aridity index, on AMF community composition, was evidenced by the high heterogeneity found betwee…
bibliographic citation: Mahmoudi et al. (2019) Arbuscular mycorrhizal fungi in soil, roots and rhizosphere of Medicago truncatula: diversity and heterogeneity under semi-arid conditions. PeerJ 7:e6401 https://doi.org/10.7717/peerj.6401
date submitted: 2018-07-17
date accepted: 2019-01-05
issued: 2019-03-01
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Mahmoudi
  given name: Neji
author list: Agent
  family name: Cruz
  given name: Cristina
author list: Agent
  family name: Mahdhi
  given name: Mosbah
author list: Agent
  family name: Mars
  given name: Mohamed
author list: Agent
  family name: Caeiro
  given name: Maria F.
doi: 10.7717/peerj.6401
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-03-01
copyright: ©2019 Mahmoudi et al.
attribution name: Mahmoudi et al.

https://peerj.com/articles/6464
type: item
type: AcademicArticle
title: Functional genomics screen with pooled shRNA library and gene expression profiling with extracts of Azadirachta indica identify potential pathways for therapeutic targets in head and neck squamous cell carcinoma
description: Tumor suppression by the extracts of Azadirachta indica (neem) works via anti-proliferation, cell cycle arrest, and apoptosis, demonstrated previously using cancer cell lines and live animal models. However, very little is known about the molecular targets and pathways that neem extracts and their associated compounds act through. Here, we address this using a genome-wide functional pooled shRNA screen on head and neck squamous cell carcinoma cell lines treated with crude neem leaf extracts, known for their anti-tumorigenic activity. We analyzed differences in global clonal sizes of the shRNA-infected cells cultured under no treatment and treatment with neem leaf extract conditions, assayed using next-generation sequencing. We found 225 genes affected the cancer cell growth in the shRNA-infected cells treated with neem extract. Pathway enrichment analyses of whole-genome gene expression data from cells temporally treated with neem extract revealed important roles played by the TGF-β pathway and HSF-1-related gene network. Our results indicate that neem extract affects various important molecular signaling pathways in head and neck cancer cells, some of which may be therapeutic targets for this devastating tumor.
format: application/pdf
format: text/html
creator: Neeraja M. Krishnan
creator: Hiroto Katoh
creator: Vinayak Palve
creator: Manisha Pareek
creator: Reiko Sato
creator: Shumpei Ishikawa
creator: Binay Panda
subject: Bioinformatics
subject: Computational Biology
subject: Genomics
subject: Oncology
description: doi:10.7717/peerj.6464
publisher: PeerJ Inc.
rights: © 2019 Krishnan et al.
abstract: Tumor suppression by the extracts of Azadirachta indica (neem) works via anti-proliferation, cell cycle arrest, and apoptosis, demonstrated previously using cancer cell lines and live animal models. However, very little is known about the molecular targets and pathways that neem extracts and their associated compounds act through. Here, we address this using a genome-wide functional pooled shRNA screen on head and neck squamous cell carcinoma cell lines treated with crude neem leaf extracts, known for their anti-tumorigenic activity. We analyzed differences in global clonal sizes of the shRNA-infected cells cultured under no treatment and treatment with neem leaf extract conditions, assayed using next-generation sequencing. We found 225 genes affected the cancer cell growth in the shRNA-infected cells treated with neem extract. Pathway enrichment analyses of whole-genome gene expression data from cells temporally treated with neem extract revealed important roles played by the TGF-β pathway and HSF-1-related gene network. Our results indicate that neem extract affects various important molecular signaling pathways in head and neck cancer cells, some of which may be therapeutic targets for this devastating tumor.
bibliographic citation: Krishnan et al. (2019) Functional genomics screen with pooled shRNA library and gene expression profiling with extracts of Azadirachta indica identify potential pathways for therapeutic targets in head and neck squamous cell carcinoma. PeerJ 7:e6464 https://doi.org/10.7717/peerj.6464
date submitted: 2018-11-22
date accepted: 2019-01-16
issued: 2019-03-01
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Krishnan
  given name: Neeraja M.
author list: Agent
  family name: Katoh
  given name: Hiroto
author list: Agent
  family name: Palve
  given name: Vinayak
author list: Agent
  family name: Pareek
  given name: Manisha
author list: Agent
  family name: Sato
  given name: Reiko
author list: Agent
  family name: Ishikawa
  given name: Shumpei
author list: Agent
  family name: Panda
  given name: Binay
doi: 10.7717/peerj.6464
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-03-01
copyright: ©2019 Krishnan et al.
attribution name: Krishnan et al.

Mitochondrial complex activity in permeabilised cells of chronic fatigue syndrome patients using two cell types
type: item
type: AcademicArticle
description: Abnormalities in mitochondrial function have previously been shown in chronic fatigue syndrome (CFS) patients, implying that mitochondrial dysfunction may contribute to the pathogenesis of disease. This study builds on previous work showing that mitochondrial respiratory parameters are impaired in whole cells from CFS patients by investigating the activity of individual mitochondrial respiratory chain complexes. Two different cell types were used in these studies in order to assess individual complex activity locally in the skeletal muscle (myotubes) (n = 6) and systemically (peripheral blood mononuclear cells (PBMCs)) (control n = 6; CFS n = 13). Complex I, II and IV activity and respiratory activitysupported by fatty acid oxidation and glutaminolysis were measured usingextracellular flux analysis. Cells were permeabilised and combinations of substrates and inhibitors were added throughout the assays to allow states of mitochondrial respiration to be calculated and the activity of specific aspects of respiratory activity to be measured. Results showed there to be no significant differences in individual mitochondrial complex activity or respiratory activity supported by fatty acid oxidation or glutaminolysis between healthy control and CFS cohorts in either skeletal muscle (p ≥ 0.190) or PBMCs (p ≥ 0.065). This is the first study to use extracellular flux analysisto investigate individual mitochondrial complex activity in permeabilised cells in the context of CFS. The lack of difference in complex activity in CFS PBMCs suggests that the previously observed mitochondrial dysfunction in whole PBMCs is due to causes upstream of the mitochondrial respiratory chain.
format: application/pdf
format: text/html
creator: Cara Tomas
creator: Audrey E. Brown
creator: Julia L. Newton
creator: Joanna L. Elson
subject: Biochemistry
subject: Immunology
subject: Neurology
subject: Metabolic Sciences
description: doi:10.7717/peerj.6500
publisher: PeerJ Inc.
rights: © 2019 Tomas et al.
abstract: Abnormalities in mitochondrial function have previously been shown in chronic fatigue syndrome (CFS) patients, implying that mitochondrial dysfunction may contribute to the pathogenesis of disease. This study builds on previous work showing that mitochondrial respiratory parameters are impaired in whole cells from CFS patients by investigating the activity of individual mitochondrial respiratory chain complexes. Two different cell types were used in these studies in order to assess individual complex activity locally in the skeletal muscle (myotubes) (n = 6) and systemically (peripheral blood mononuclear cells (PBMCs)) (control n = 6; CFS n = 13). Complex I, II and IV activity and respiratory activitysupported by fatty acid oxidation and glutaminolysis were measured usingextracellular flux analysis. Cells were permeabilised and combinations of substrates and inhibitors were added throughout the assays to allow states of mitochondrial respiration to be calculated and the activity of specific aspects of respiratory activity to be measured. Results showed there to be no significant differences in individual mitochondrial complex activity or respiratory activity supported by fatty acid oxidation or glutaminolysis between healthy control and CFS cohorts in either skeletal muscle (p ≥ 0.190) or PBMCs (p ≥ 0.065). This is the first study to use extracellular flux analysisto investigate individual mitochondrial complex activity in permeabilised cells in the context of CFS. The lack of difference in complex activity in CFS PBMCs suggests that the previously observed mitochondrial dysfunction in whole PBMCs is due to causes upstream of the mitochondrial respiratory chain.
bibliographic citation: Tomas et al. (2019) Mitochondrial complex activity in permeabilised cells of chronic fatigue syndrome patients using two cell types. PeerJ 7:e6500 https://doi.org/10.7717/peerj.6500
date submitted: 2018-10-18
date accepted: 2019-01-22
issued: 2019-03-01
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Tomas
  given name: Cara
author list: Agent
  family name: Brown
  given name: Audrey E.
author list: Agent
  family name: Newton
  given name: Julia L.
author list: Agent
  family name: Elson
  given name: Joanna L.
doi: 10.7717/peerj.6500
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-03-01
copyright: ©2019 Tomas et al.
attribution name: Tomas et al.

The role of juvenile hormone in regulating reproductive physiology and dominance in Dinoponera quadriceps ants
type: item
type: AcademicArticle
description: Unequal reproductive output among members of the same sex (reproductive skew) is a common phenomenon in a wide range of communally breeding animals. In such species, reproductive dominance is often acquired during antagonistic interactions between group members that establish a reproductive hierarchy in which only a few individuals reproduce. Rank-specific syndromes of behavioural and physiological traits characterize such hierarchies, but how antagonistic behavioural interactions translate into stable rank-specific syndromes remains poorly understood. The pleiotropic nature of hormones makes them prime candidates for generating such syndromes as they physiologically integrate environmental (social) information, and often affect reproduction and behaviour simultaneously. Juvenile hormone (JH) is one of several hormones that occupy such a central regulatory role in insects and has been suggested to regulate reproductive hierarchies in a wide range of social insects including ants. Here we use experimental manipulation to investigate the effect of JH levels on reproductive physiology and social dominance in high-ranked workers of the eusocial ant Dinoponera quadriceps, a species that has secondarily reverted to queenless, simple societies. We show that JH regulated reproductive physiology, with ants in which JH levels were experimentally elevated having more regressed ovaries. In contrast, we found no evidence of JH levels affecting dominance in social interactions. This could indicate that JH and ovary development are decoupled from dominance in this species, however only high-ranked workers were investigated. The results therefore confirm that the regulatory role of JH in reproductive physiology in this ant species is in keeping with its highly eusocial ancestors rather than its secondary reversion to simple societies, but more investigation is needed to disentangle the relationships between hormones, behaviour and hierarchies.
format: application/pdf
format: text/html
creator: Victoria C. Norman
creator: Tobias Pamminger
creator: Fabio Nascimento
creator: William O.H. Hughes
subject: Animal Behavior
subject: Entomology
subject: Evolutionary Studies
subject: Zoology
description: doi:10.7717/peerj.6512
publisher: PeerJ Inc.
rights: © 2019 Norman et al.
abstract: Unequal reproductive output among members of the same sex (reproductive skew) is a common phenomenon in a wide range of communally breeding animals. In such species, reproductive dominance is often acquired during antagonistic interactions between group members that establish a reproductive hierarchy in which only a few individuals reproduce. Rank-specific syndromes of behavioural and physiological traits characterize such hierarchies, but how antagonistic behavioural interactions translate into stable rank-specific syndromes remains poorly understood. The pleiotropic nature of hormones makes them prime candidates for generating such syndromes as they physiologically integrate environmental (social) information, and often affect reproduction and behaviour simultaneously. Juvenile hormone (JH) is one of several hormones that occupy such a central regulatory role in insects and has been suggested to regulate reproductive hierarchies in a wide range of social insects including ants. Here we use experimental manipulation to investigate the effect of JH levels on reproductive physiology and social dominance in high-ranked workers of the eusocial ant Dinoponera quadriceps, a species that has secondarily reverted to queenless, simple societies. We show that JH regulated reproductive physiology, with ants in which JH levels were experimentally elevated having more regressed ovaries. In contrast, we found no evidence of JH levels affecting dominance in social interactions. This could indicate that JH and ovary development are decoupled from dominance in this species, however only high-ranked workers were investigated. The results therefore confirm that the regulatory role of JH in reproductive physiology in this ant species is in keeping with its highly eusocial ancestors rather than its secondary reversion to simple societies, but more investigation is needed to disentangle the relationships between hormones, behaviour and hierarchies.
bibliographic citation: Norman et al. (2019) The role of juvenile hormone in regulating reproductive physiology and dominance in Dinoponera quadriceps ants. PeerJ 7:e6512 https://doi.org/10.7717/peerj.6512
date submitted: 2018-03-26
date accepted: 2019-01-24
issued: 2019-03-01
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Norman
  given name: Victoria C.
author list: Agent
  family name: Pamminger
  given name: Tobias
author list: Agent
  family name: Nascimento
  given name: Fabio
author list: Agent
  family name: Hughes
  given name: William O.H.
doi: 10.7717/peerj.6512
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-03-01
copyright: ©2019 Norman et al.
attribution name: Norman et al.

Synthesis of light-inducible and light-independent anthocyanins regulated by specific genes in grape ‘Marselan’ (V. vinifera L.)
type: item
type: AcademicArticle
description: Anthocyanin is an important parameter for evaluating the quality of wine grapes. However, the effects of different light intensities on anthocyanin synthesis in grape berry skin and its regulation mechanisms are still unclear. In this experiment, clusters of wine grape cv. ‘Marselan’ were bagged using fruit bags with different light transmittance of 50%, 15%, 5%, and 0, designated as treatment A, B, C and D, respectively. Fruits that were not bagged were used as the control, designated as CK. The anthocyanin composition and concentration, as well as gene expression profiles in the berry skin were determined. The results showed that the degree of coloration of the berry skin reduced with the decrease of the light transmittance, and the veraison was postponed for 10 days in D when compared with the CK. Total anthocyanin concentration in the berry skin treated with D decreased by 51.50% compared with CK at the harvest stage. A total of 24 and 21 anthocyanins were detected in CK and D, respectively. Among them, Malvidin-3-O-coumaroylglucoside (trans), which showed a significant positive correlation with the total concentration of anthocyanins at the harvest stage (r = 0.775) and was not detected in D, was presumed to be light-induced anthocyanin. Other anthocyanins which were both synthesized in CK and D were considered to be light-independent anthocyanins. Among them, Malvidin-3-O-coumaroylglucoside (cis) and Malvidin-3-O-acetylglucoside were typical representatives. Remarkably, the synthesis of light-inducible anthocyanins and light-independent anthocyanins were regulated by different candidate structural genes involved in flavonoid biosynthesis pathway and members of MYB and bHLH transcription factors.
format: application/pdf
format: text/html
creator: Zong-Huan Ma
creator: Wen-Fang Li
creator: Juan Mao
creator: Wei Li
creator: Cun-Wu Zuo
creator: Xin Zhao
creator: Mohammed Mujitaba Dawuda
creator: Xing-Yun Shi
creator: Bai-Hong Chen
subject: Bioinformatics
subject: Plant Science
description: doi:10.7717/peerj.6521
publisher: PeerJ Inc.
rights: © 2019 Ma et al.
abstract: Anthocyanin is an important parameter for evaluating the quality of wine grapes. However, the effects of different light intensities on anthocyanin synthesis in grape berry skin and its regulation mechanisms are still unclear. In this experiment, clusters of wine grape cv. ‘Marselan’ were bagged using fruit bags with different light transmittance of 50%, 15%, 5%, and 0, designated as treatment A, B, C and D, respectively. Fruits that were not bagged were used as the control, designated as CK. The anthocyanin composition and concentration, as well as gene expression profiles in the berry skin were determined. The results showed that the degree of coloration of the berry skin reduced with the decrease of the light transmittance, and the veraison was postponed for 10 days in D when compared with the CK. Total anthocyanin concentration in the berry skin treated with D decreased by 51.50% compared with CK at the harvest stage. A total of 24 and 21 anthocyanins were detected in CK and D, respectively. Among them, Malvidin-3-O-coumaroylglucoside (trans), which showed a significant positive correlation with the total concentration of anthocyanins at the harvest stage (r = 0.775) and was not detected in D, was presumed to be light-induced anthocyanin. Other anthocyanins which were both synthesized in CK and D were considered to be light-independent anthocyanins. Among them, Malvidin-3-O-coumaroylglucoside (cis) and Malvidin-3-O-acetylglucoside were typical representatives. Remarkably, the synthesis of light-inducible anthocyanins and light-independent anthocyanins were regulated by different candidate structural genes involved in flavonoid biosynthesis pathway and members of MYB and bHLH transcription factors.
bibliographic citation: Ma et al. (2019) Synthesis of light-inducible and light-independent anthocyanins regulated by specific genes in grape ‘Marselan’ (V. vinifera L.). PeerJ 7:e6521 https://doi.org/10.7717/peerj.6521
date submitted: 2018-12-03
date accepted: 2019-01-24
issued: 2019-03-01
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Ma
  given name: Zong-Huan
author list: Agent
  family name: Li
  given name: Wen-Fang
author list: Agent
  family name: Mao
  given name: Juan
author list: Agent
  family name: Li
  given name: Wei
author list: Agent
  family name: Zuo
  given name: Cun-Wu
author list: Agent
  family name: Zhao
  given name: Xin
author list: Agent
  family name: Dawuda
  given name: Mohammed Mujitaba
author list: Agent
  family name: Shi
  given name: Xing-Yun
author list: Agent
  family name: Chen
  given name: Bai-Hong
doi: 10.7717/peerj.6521
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-03-01
copyright: ©2019 Ma et al.
attribution name: Ma et al.

Comparative transcriptomics of sympatric species of coral reef fishes (genus: Haemulon)
type: item
type: AcademicArticle
description: Background Coral reefs are major hotspots of diversity for marine fishes, yet there is still ongoing debate on the mechanisms that promote divergence in these rich ecosystems. Our understanding of how diversity originates in this environment could be enhanced by investigating the evolutionary dynamics of closely related fishes with overlapping ranges. Here, we focus on grunts of the genus Haemulon, a group of coral reef fishes with 15 species in the Western Atlantic, 11 of which are syntopic. Methods Wild fish samples from three sympatric species of the Caribbean: Haemulon flavolineatum, H. carbonarium and H. macrostomum, were collected while SCUBA diving. RNA was extracted from livers, and the transcriptomes were assembled and annotated to investigate positive selection (Pairwise dN/dS) and patterns of gene expression between the three species. Results Pairwise dN/dS analyses showed evidence of positive selection for genes associated with immune response, cranial morphology and formation of the anterior–posterior axis. Analyses of gene expression revealed that despite their sympatric distribution, H. macrostomum showed upregulation of oxidation-reduction machinery, while there was evidence for activation of immune response in H. carbonarium. Discussion Overall, our analyses suggest closely related grunts show important differences in genes associated with body shape and feeding morphology, a result in-line with previous morphological studies in the group. Further, despite their overlapping distribution they interact with their environment in distinct fashions. This is the largest compendium of genomic information for grunts thus far, representing a valuable resource for future studies in this unique group of coral reef fishes.
format: application/pdf
format: text/html
creator: Moisés A. Bernal
creator: Groves B. Dixon
creator: Mikhail V. Matz
creator: Luiz A. Rocha
subject: Aquaculture, Fisheries and Fish Science
subject: Evolutionary Studies
subject: Genomics
subject: Marine Biology
subject: Molecular Biology
description: doi:10.7717/peerj.6541
publisher: PeerJ Inc.
rights: © 2019 Bernal et al.
abstract: Background Coral reefs are major hotspots of diversity for marine fishes, yet there is still ongoing debate on the mechanisms that promote divergence in these rich ecosystems. Our understanding of how diversity originates in this environment could be enhanced by investigating the evolutionary dynamics of closely related fishes with overlapping ranges. Here, we focus on grunts of the genus Haemulon, a group of coral reef fishes with 15 species in the Western Atlantic, 11 of which are syntopic. Methods Wild fish samples from three sympatric species of the Caribbean: Haemulon flavolineatum, H. carbonarium and H. macrostomum, were collected while SCUBA diving. RNA was extracted from livers, and the transcriptomes were assembled and annotated to investigate positive selection (Pairwise dN/dS) and patterns of gene expression between the three species. Results Pairwise dN/dS analyses showed evidence of positive selection for genes associated with immune response, cranial morphology and formation of the anterior–posterior axis. Analyses of gene expression revealed that despite their sympatric distribution, H. macrostomum showed upregulation of oxidation-reduction machinery, while there was evidence for activation of immune response in H. carbonarium. Discussion Overall, our analyses suggest closely related grunts show important differences in genes associated with body shape and feeding morphology, a result in-line with previous morphological studies in the group. Further, despite their overlapping distribution they interact with their environment in distinct fashions. This is the largest compendium of genomic information for grunts thus far, representing a valuable resource for future studies in this unique group of coral reef fishes.
bibliographic citation: Bernal et al. (2019) Comparative transcriptomics of sympatric species of coral reef fishes (genus: Haemulon). PeerJ 7:e6541 https://doi.org/10.7717/peerj.6541
date submitted: 2018-10-25
date accepted: 2019-01-29
issued: 2019-03-01
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Bernal
  given name: Moisés A.
author list: Agent
  family name: Dixon
  given name: Groves B.
author list: Agent
  family name: Matz
  given name: Mikhail V.
author list: Agent
  family name: Rocha
  given name: Luiz A.
doi: 10.7717/peerj.6541
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-03-01
copyright: © 2019 Bernal et al.
attribution name: Bernal et al.

An interpretable machine learning model for diagnosis of Alzheimer's disease
type: item
type: AcademicArticle
description: We present an interpretable machine learning model for medical diagnosis called sparse high-order interaction model with rejection option (SHIMR). A decision tree explains to a patient the diagnosis with a long rule (i.e., conjunction of many intervals), while SHIMR employs a weighted sum of short rules. Using proteomics data of 151 subjects in the Alzheimer’s Disease Neuroimaging Initiative (ADNI) dataset, SHIMR is shown to be as accurate as other non-interpretable methods (Sensitivity, SN = 0.84 ± 0.1, Specificity, SP = 0.69 ± 0.15 and Area Under the Curve, AUC = 0.86 ± 0.09). For clinical usage, SHIMR has a function to abstain from making any diagnosis when it is not confident enough, so that a medical doctor can choose more accurate but invasive and/or more costly pathologies. The incorporation of a rejection option complements SHIMR in designing a multistage cost-effective diagnosis framework. Using a baseline concentration of cerebrospinal fluid (CSF) and plasma proteins from a common cohort of 141 subjects, SHIMR is shown to be effective in designing a patient-specific cost-effective Alzheimer’s disease (AD) pathology. Thus, interpretability, reliability and having the potential to design a patient-specific multistage cost-effective diagnosis framework can make SHIMR serve as an indispensable tool in the era of precision medicine that can cater to the demand of both doctors and patients, and reduce the overwhelming financial burden of medical diagnosis.
format: application/pdf
format: text/html
creator: Diptesh Das
creator: Junichi Ito
creator: Tadashi Kadowaki
creator: Koji Tsuda
subject: Bioinformatics
subject: Computational Biology
subject: Neuroscience
subject: Cognitive Disorders
subject: Data Mining and Machine Learning
description: doi:10.7717/peerj.6543
publisher: PeerJ Inc.
rights: © 2019 Das et al.
abstract: We present an interpretable machine learning model for medical diagnosis called sparse high-order interaction model with rejection option (SHIMR). A decision tree explains to a patient the diagnosis with a long rule (i.e., conjunction of many intervals), while SHIMR employs a weighted sum of short rules. Using proteomics data of 151 subjects in the Alzheimer’s Disease Neuroimaging Initiative (ADNI) dataset, SHIMR is shown to be as accurate as other non-interpretable methods (Sensitivity, SN = 0.84 ± 0.1, Specificity, SP = 0.69 ± 0.15 and Area Under the Curve, AUC = 0.86 ± 0.09). For clinical usage, SHIMR has a function to abstain from making any diagnosis when it is not confident enough, so that a medical doctor can choose more accurate but invasive and/or more costly pathologies. The incorporation of a rejection option complements SHIMR in designing a multistage cost-effective diagnosis framework. Using a baseline concentration of cerebrospinal fluid (CSF) and plasma proteins from a common cohort of 141 subjects, SHIMR is shown to be effective in designing a patient-specific cost-effective Alzheimer’s disease (AD) pathology. Thus, interpretability, reliability and having the potential to design a patient-specific multistage cost-effective diagnosis framework can make SHIMR serve as an indispensable tool in the era of precision medicine that can cater to the demand of both doctors and patients, and reduce the overwhelming financial burden of medical diagnosis.
bibliographic citation: Das et al. (2019) An interpretable machine learning model for diagnosis of Alzheimer's disease. PeerJ 7:e6543 https://doi.org/10.7717/peerj.6543
date submitted: 2018-10-10
date accepted: 2019-01-30
issued: 2019-03-01
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Das
  given name: Diptesh
author list: Agent
  family name: Ito
  given name: Junichi
author list: Agent
  family name: Kadowaki
  given name: Tadashi
author list: Agent
  family name: Tsuda
  given name: Koji
doi: 10.7717/peerj.6543
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-03-01
copyright: © 2019 Das et al.
attribution name: Das et al.

Use of Next Generation Sequencing to study two cowpox virus outbreaks
type: item
type: AcademicArticle
description: Background Between 2008 and 2011 about 40 cases of human cowpox were reported from Germany and France. Infections had been acquired via close contact to infected, young pet rats. An identical and unique sequence of the hemagglutinin gene was found in various cowpox virus (CPXV) isolates pointing to a common source of infection. In a second CPXV outbreak in cats in a small animal clinic in Germany in 2015, four out of five hospitalized cats showed identical hemagglutinin sequences and thus, a hospital-acquired transmission had been assumed. Next-Generation Sequencing was performed in order to re-investigate the outbreaks, as epidemiological data could not confirm all cases. Methods Homogenates of lesion material from rats, cats and humans were cultivated in cell culture. The genomes of four virus isolates, nine CPXVs from our strain collections and from DNA of three paraffin-embedded lesion materials were determined by Next Generation Sequencing (NGS). For phylogenetic analyses a MAFFT-alignment was generated. A distance matrix based on concatenated SNPs was calculated and plotted as dendrogram using Unweighted Pair Group Method with Arithmetic mean (UPGMA) for visualization. Results Aligning of about 200.000 nucleotides of 8 virus isolates associated with the pet rat outbreak revealed complete identity of six genomes, the remainder two genomes differed in as little as 3 SNPs. When comparing this dataset with four already published CPXV genomes also associated with the pet rat outbreak, again a maximum difference of 3 SNPs was found. The outbreak which lasted from 2008 till 2011 was indeed caused by a single strain which has maintained an extremely high level of clonality over 4 years. Aligning genomic sequences from four cases of feline cowpox revealed 3 identical sequences and one sequence which differed in 65 nucleotides. Although identical hemagglutinin sequences had been obtained from four hospitalized cats, genomic sequencing proved that a hospital-acquired tra…
format: application/pdf
format: text/html
creator: Markus H. Antwerpen
creator: Enrico Georgi
creator: Alexandra Nikolic
creator: Gudrun Zoeller
creator: Peter Wohlsein
creator: Wolfgang Baumgärtner
creator: Christophe Peyrefitte
creator: Remi Charrel
creator: Hermann Meyer
subject: Genomics
subject: Microbiology
subject: Epidemiology
subject: Infectious Diseases
description: doi:10.7717/peerj.6561
publisher: PeerJ Inc.
rights: © 2019 Antwerpen et al.
abstract: Background Between 2008 and 2011 about 40 cases of human cowpox were reported from Germany and France. Infections had been acquired via close contact to infected, young pet rats. An identical and unique sequence of the hemagglutinin gene was found in various cowpox virus (CPXV) isolates pointing to a common source of infection. In a second CPXV outbreak in cats in a small animal clinic in Germany in 2015, four out of five hospitalized cats showed identical hemagglutinin sequences and thus, a hospital-acquired transmission had been assumed. Next-Generation Sequencing was performed in order to re-investigate the outbreaks, as epidemiological data could not confirm all cases. Methods Homogenates of lesion material from rats, cats and humans were cultivated in cell culture. The genomes of four virus isolates, nine CPXVs from our strain collections and from DNA of three paraffin-embedded lesion materials were determined by Next Generation Sequencing (NGS). For phylogenetic analyses a MAFFT-alignment was generated. A distance matrix based on concatenated SNPs was calculated and plotted as dendrogram using Unweighted Pair Group Method with Arithmetic mean (UPGMA) for visualization. Results Aligning of about 200.000 nucleotides of 8 virus isolates associated with the pet rat outbreak revealed complete identity of six genomes, the remainder two genomes differed in as little as 3 SNPs. When comparing this dataset with four already published CPXV genomes also associated with the pet rat outbreak, again a maximum difference of 3 SNPs was found. The outbreak which lasted from 2008 till 2011 was indeed caused by a single strain which has maintained an extremely high level of clonality over 4 years. Aligning genomic sequences from four cases of feline cowpox revealed 3 identical sequences and one sequence which differed in 65 nucleotides. Although identical hemagglutinin sequences had been obtained from four hospitalized cats, genomic sequencing proved that a hospital-acquired tra…
bibliographic citation: Antwerpen et al. (2019) Use of Next Generation Sequencing to study two cowpox virus outbreaks. PeerJ 7:e6561 https://doi.org/10.7717/peerj.6561
date submitted: 2018-11-30
date accepted: 2019-02-03
issued: 2019-03-01
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Antwerpen
  given name: Markus H.
author list: Agent
  family name: Georgi
  given name: Enrico
author list: Agent
  family name: Nikolic
  given name: Alexandra
author list: Agent
  family name: Zoeller
  given name: Gudrun
author list: Agent
  family name: Wohlsein
  given name: Peter
author list: Agent
  family name: Baumgärtner
  given name: Wolfgang
author list: Agent
  family name: Peyrefitte
  given name: Christophe
author list: Agent
  family name: Charrel
  given name: Remi
author list: Agent
  family name: Meyer
  given name: Hermann
doi: 10.7717/peerj.6561
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-03-01
copyright: ©2019 Antwerpen et al.
attribution name: Antwerpen et al.

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