Identification, expression, and phylogenetic analyses of terpenoid biosynthesis-related genes in secondary xylem of loblolly pine (Pinus taeda L.) based on transcriptome analyses
Loblolly pine (Pinus taeda L.) is one of the most important species for oleoresin (a mixture of terpenoids) in South China. The high oleoresin content of loblolly pine is associated with resistance to bark beetles and other economic benefits. In this study, we conducted transcriptome analyses of loblolly pine secondary xylem to gain insight into the genes involved in terpenoid biosynthesis. A total of 372 unigenes were identified as being critical for oleoresin production, including genes for ATP-binding cassette (ABC) transporters, the cytochrome P450 (CYP) protein family, and terpenoid backbone biosynthesis enzymes. Six key genes involved in terpenoid biosynthetic pathways were selected for multiple sequence alignment, conserved motif prediction, and phylogenetic and expression profile analyses. The protein sequences of all six genes exhibited a higher degree of sequence conservation, and upstream genes were relatively more conserved than downstream genes in terpenoid biosynthetic pathways. The N-terminal regions of these sequences were less conserved than the C-terminal ends, as the N-terminals were quite diverse in both length and composition. The phylogenetic analyses revealed that most genes originated from gene duplication after species divergence, and partial genes exhibited incomplete lineage sorting. In addition, the expression profile analyses showed that all six genes exhibited high expression levels during the high-oleoresin-yielding phase.
Mao et al. (2019) Identification, expression, and phylogenetic analyses of terpenoid biosynthesis-related genes in secondary xylem of loblolly pine (Pinus taeda L.) based on transcriptome analyses. PeerJ 7:e6124 https://doi.org/10.7717/peerj.6124
Blood parasites in Passeriformes in central Germany: prevalence and lineage diversity of Haemosporida (Haemoproteus, Plasmodium and Leucocytozoon) in six common songbirds
Background Avian Haemosporida are vector-borne parasites that commonly infect Passeriformes. Molecular analyses revealed a high number of different lineages and lineage specific traits like prevalence and host-specificity, but knowledge of parasite prevalence and lineage diversity in wild birds in Central Germany is still lacking. Results Blood samples from a total of 238 adult and 122 nestling songbirds belonging to six species were investigated for infections with avian haemosporidian genera and lineages (Haemoproteus spp., Plasmodium spp., Leucocytozoon spp.) and Trypanosoma avium using PCR, targeting the parasite mitochondrial cytochrome b gene and 18S ribosomal RNA. In total, the prevalence in adult birds was 31.3% infected with Haemoproteus, 12.5% with Plasmodium and 71.0% with Leucocytozoon (nestlings excluded). None of the tested birds was infected with Trypanosoma avium. Only in two nestling birds, aged 12–17 days, a Leucocytozoon spp. infection was proven. Among 225 successfully sequenced samples, we found four Haemoproteus, three Plasmodium and 19 Leucocytozoon lineages, including two new Leucocytozoon lineages. Furthermore, we report two new host-lineage associations. Conclusions As first study investigating avian haemosporidian parasites in Central Germany, we provide new information on genetic diversity of Haemosporida infecting Passeriformes. We show that even with a small sample size new lineages as well as previously unknown linkages between certain lineages and host species can be detected. This may help to elucidate the diversity of lineages as well as lineage-host-connections of avian Haemosporida.
Schumm et al. (2019) Blood parasites in Passeriformes in central Germany: prevalence and lineage diversity of Haemosporida (Haemoproteus, Plasmodium and Leucocytozoon) in six common songbirds. PeerJ 6:e6259 https://doi.org/10.7717/peerj.6259
GRID-independent molecular descriptor analysis and molecular docking studies to mimic the binding hypothesis of γ-aminobutyric acid transporter 1 (GAT1) inhibitors
Background The γ-aminobutyric acid (GABA) transporter GAT1 is involved in GABA transport across the biological membrane in and out of the synaptic cleft. The efficiency of this Na+ coupled GABA transport is regulated by an electrochemical gradient, which is directed inward under normal conditions. However, in certain pathophysiological situations, including strong depolarization or an imbalance in ion homeostasis, the GABA influx into the cytoplasm is increased by re-uptake transport mechanism. This mechanism may lead to extra removal of extracellular GABA which results in numerous neurological disorders such as epilepsy. Thus, small molecule inhibitors of GABA re-uptake may enhance GABA activity at the synaptic clefts. Methods In the present study, various GRID-independent molecular descriptor (GRIND) models have been developed to shed light on the 3D structural features of human GAT1 (hGAT1) inhibitors using nipecotic acid and N-diarylalkenyl piperidine analogs. Further, a binding hypothesis has been developed for the selected GAT1 antagonists by molecular docking inside the binding cavity of hGAT1 homology model. Results Our results indicate that two hydrogen bond acceptors, one hydrogen bond donor and one hydrophobic region at certain distances from each other play an important role in achieving high inhibitory potency against hGAT1. Our docking results elucidate the importance of the COOH group in hGAT1 antagonists by considering substitution of the COOH group with an isoxazol ring in compound 37, which subsequently leads to a three order of magnitude decrease in biological activity of 37 (IC50 = 38 µM) as compared to compound 1 (IC50 = 0.040 µM). Discussion Our docking results are strengthened by the structure activity relationship of the data series as well as by GRIND models, thus providing a significant structural basis for understanding the binding of antagonists, which may be useful for guiding the design of hGAT1 inhibitors.
Zafar et al. (2019) GRID-independent molecular descriptor analysis and molecular docking studies to mimic the binding hypothesis of γ-aminobutyric acid transporter 1 (GAT1) inhibitors. PeerJ 7:e6283 https://doi.org/10.7717/peerj.6283
Genome-wide identification and expression analysis of new cytokinin metabolic genes in bread wheat (Triticum aestivum L.)
Cytokinins (CKs) are involved in determining the final grain yield in wheat. Multiple gene families are responsible for the controlled production of CKs in plants, including isopentenyl transferases for de novo synthesis, zeatin O-glucosyltransferases for reversible inactivation, β-glucosidases for reactivation, and CK oxidases/dehydrogenases for permanent degradation. Identifying and characterizing the genes of these families is an important step in furthering our understanding of CK metabolism. Using bioinformatics tools, we identified four new TaIPT, four new TaZOG, and 25 new TaGLU genes in common wheat. All of the genes harbored the characteristic conserved domains of their respective gene families. We renamed TaCKX genes on the basis of their true orthologs in rice and maize to remove inconsistencies in the nomenclature. Phylogenetic analysis revealed the early divergence of monocots from dicots, and the gene duplication event after speciation was obvious. Abscisic acid-, auxin-, salicylic acid-, sulfur-, drought- and light-responsive cis-regulatory elements were common to most of the genes under investigation. Expression profiling of CK metabolic gene families was carried out at the seedlings stage in AA genome donor of common wheat. Exogenous application of phytohormones (6-benzylaminopurine, salicylic acid, indole-3-acetic acid, gibberellic acid, and abscisic acid) for 3 h significantly upregulated the transcript levels of all four gene families, suggesting that plants tend to maintain CK stability. A 6-benzylaminopurine-specific maximum fold-change was observed for TuCKX1 and TuCKX3 in root and shoot tissues, respectively; however, the highest expression level was observed in the TuGLU gene family, indicating that the reactivation of the dormant CK isoform is the quickest way to counter external stress. The identification of new CK metabolic genes provides the foundation for their in-depth functional characterization and for elucidating their association with grain yield.
Shoaib et al. (2019) Genome-wide identification and expression analysis of new cytokinin metabolic genes in bread wheat (Triticum aestivum L.). PeerJ 7:e6300 https://doi.org/10.7717/peerj.6300
Transcriptome-wide characterization and functional analysis of MATE transporters in response to aluminum toxicity in Medicago sativa L.
Multidrug and toxic compound extrusion (MATE) transporters contribute to multidrug resistance and play major determinants of aluminum (Al) tolerance in plants. Alfalfa (Medicago sativa L.) is the most extensively cultivated forage crop in the world, yet most alfalfa cultivars are not Al tolerant. The basic knowledge of the MATE transcripts family and the characterisation of specific MATE members involved in alfalfa Al stress remain unclear. In this study, 88 alfalfa MATE (MsMATE) transporters were identified at the whole transcriptome level. Phylogenetic analysis classified them into four subfamilies comprising 11 subgroups. Generally, five kinds of motifs were found in group G1, and most were located at the N-terminus, which might confer these genes with Al detoxification functions. Furthermore, 10 putative Al detoxification-related MsMATE genes were identified and the expression of five genes was significantly increased after Al treatment, indicating that these genes might play important roles in conferring Al tolerance to alfalfa. Considering the limited functional understanding of MATE transcripts in alfalfa, our findings will be valuable for the functional investigation and application of this family in alfalfa.
Min et al. (2019) Transcriptome-wide characterization and functional analysis of MATE transporters in response to aluminum toxicity in Medicago sativa L.. PeerJ 7:e6302 https://doi.org/10.7717/peerj.6302
Recent updates on metabolite composition and medicinal benefits of mangosteen plant
Background Mangosteen (Garcinia mangostana L.) fruit has a unique sweet-sour taste and is rich in beneficial compounds such as xanthones. Mangosteen originally been used in various folk medicines to treat diarrhea, wounds, and fever. More recently, it had been used as a major component in health supplement products for weight loss and for promoting general health. This is perhaps due to its known medicinal benefits, including as anti-oxidant and anti-inflammation. Interestingly, publications related to mangosteen have surged in recent years, suggesting its popularity and usefulness in research laboratories. However, there are still no updated reviews (up to 2018) in this booming research area, particularly on its metabolite composition and medicinal benefits. Method In this review, we have covered recent articles within the years of 2016 to 2018 which focus on several aspects including the latest findings on the compound composition of mangosteen fruit as well as its medicinal usages. Result Mangosteen has been vastly used in medicinal areas including in anti-cancer, anti-microbial, and anti-diabetes treatments. Furthermore, we have also described the benefits of mangosteen extract in protecting various human organs such as liver, skin, joint, eye, neuron, bowel, and cardiovascular tissues against disorders and diseases. Conclusion All in all, this review describes the numerous manipulations of mangosteen extracted compounds in medicinal areas and highlights the current trend of its research. This will be important for future directed research and may allow researchers to tackle the next big challenge in mangosteen study: drug development and human applications.
Aizat et al. (2019) Recent updates on metabolite composition and medicinal benefits of mangosteen plant. PeerJ 7:e6324 https://doi.org/10.7717/peerj.6324
A new species of Escallonia (Escalloniaceae) from the inter-Andean tropical dry forests of Bolivia
Over the last two decades, renewed fieldwork in poorly explored areas of the tropical Andes has dramatically increased the comparative material available to study patterns of inter- and intraspecific variation in tropical plants. In the course of a comprehensive study of the genus Escallonia, we found a group of specimens with decumbent branching, small narrowly elliptic leaves, inflorescences with up to three flowers, and flowers with red petals. This unique combination of traits was not present in any known species of the genus. To evaluate the hypothesis that these specimens belonged to a new species, we assessed whether morphological variation between the putative new species and all currently known Escallonia species was discontinuous. The lack of overlap in tolerance regions for vegetative and reproductive traits combined with differences in habit, habitat, and geographic distribution supported the hypothesis of the new species, which we named Escallonia harrisii. The new species grows in sandstone inter-Andean ridges and cliffs covered with dry forest, mostly on steep slopes between 1,300–2,200 m in southern Bolivia. It is readily distinct in overall leaf and flower morphology from other Escallonia species in the region, even though it does not grow in sympatry with other species. Because E. harrisii is locally common it may not be threated at present, but due to its restricted geographic distribution and the multiple threats of the tropical dry forests it could become potentially vulnerable.
Zapata et al. (2019) A new species of Escallonia (Escalloniaceae) from the inter-Andean tropical dry forests of Bolivia. PeerJ 7:e6328 https://doi.org/10.7717/peerj.6328
Subjective assessment for super recognition: an evaluation of self-report methods in civilian and police participants
Metacognition about face recognition has been much discussed in the psychological literature. In particular, the use of self-report to identify people with prosopagnosia (“face blindness”) has contentiously been debated. However, no study to date has specifically assessed metacognition at the top end of the spectrum. If people with exceptionally proficient face recognition skills (“super-recognizers,” SRs) have greater insight into their abilities, self-report instruments may offer an efficient means of reducing candidate lists in SR screening programs. Here, we developed a “super-recognizer questionnaire” (SRQ), calibrated using a top-end civilian sample (Experiment 1). We examined its effectiveness in identifying SRs in pools of police (Experiment 2) and civilian (Experiment 3) participants, using objective face memory and matching tests. Moderate effect sizes in both samples suggest limited insight into face memory and target-present face matching ability, whereas the only predictor of target-absent matching performance across all samples was the number of years that an officer had been in the police force. Because the SRQ and single-item ratings showed little sensitivity in discriminating SRs from typical perceivers in police officers and civilians, we recommend against the use of self-report instruments in SR screening programs.
Bate et al. (2019) Subjective assessment for super recognition: an evaluation of self-report methods in civilian and police participants. PeerJ 7:e6330 https://doi.org/10.7717/peerj.6330
Maternal temperature exposure impairs emotional and cognitive responses and triggers dysregulation of neurodevelopment genes in fish
Fish are sensitive to temperature, but the intergenerational consequences of maternal exposure to high temperature on offspring behavioural plasticity and underlying mechanisms are unknown. Here we show that a thermal maternal stress induces impaired emotional and cognitive responses in offspring rainbow trout (Oncorhynchus mykiss). Thermal stress in mothers triggered the inhibition of locomotor fear-related responses upon exposure to a novel environment and decreased spatial learning abilities in progeny. Impaired behavioural phenotypes were associated with the dysregulation of several genes known to play major roles in neurodevelopment, including auts2 (autism susceptibility candidate 2), a key gene for neurodevelopment, more specifically neuronal migration and neurite extension, and critical for the acquisition of neurocognitive function. In addition, our analysis revealed the dysregulation of another neurodevelopment gene (dpysl5) as well as genes associated with human cognitive disorders (arv1, plp2). We observed major differences in maternal mRNA abundance in the eggs following maternal exposure to high temperature indicating that some of the observed intergenerational effects are mediated by maternally-inherited mRNAs accumulated in the egg. Together, our observations shed new light on the intergenerational determinism of fish behaviour and associated underlying mechanisms. They also stress the importance of maternal history on fish behavioural plasticity.
Colson et al. (2019) Maternal temperature exposure impairs emotional and cognitive responses and triggers dysregulation of neurodevelopment genes in fish. PeerJ 7:e6338 https://doi.org/10.7717/peerj.6338
Empirical analysis and modeling of Argos Doppler location errors in Romania
Background Advances in wildlife tracking technology have allowed researchers to understand the spatial ecology of many terrestrial and aquatic animal species. Argos Doppler is a technology that is widely used for wildlife tracking owing to the small size and low weight of the Argos transmitters. This allows them to be fitted to small-bodied species. The longer lifespan of the Argos units in comparison to units outfitted with miniaturized global positioning system (GPS) technology has also recommended their use. In practice, large Argos location errors often occur due to communication conditions such as transmitter settings, local environment, and the behavior of the tracked individual. Methods Considering the geographic specificity of errors and the lack of benchmark studies in Eastern Europe, the research objectives were: (1) to evaluate the accuracy of Argos Doppler technology under various environmental conditions in Romania, (2) to investigate the effectiveness of straightforward destructive filters for improving Argos Doppler data quality, and (3) to provide guidelines for processing Argos Doppler wildlife monitoring data. The errors associated with Argos locations in four geographic locations in Romania were assessed during static, low-speed and high-speed tests. The effectiveness of the Douglas Argos distance angle filter algorithm was then evaluated to ascertain its effect on the minimization of localization errors. Results Argos locations received in the tests had larger associated horizontal errors than those indicated by the operator of the Argos system, including under ideal reception conditions. Positional errors were similar to those obtained in other studies outside of Europe. The errors were anisotropic, with larger longitudinal errors for the vast majority of the data. Errors were mostly related to speed of the Argos transmitter at the time of reception, but other factors such as topographical conditions and orientation of antenna at the time of the transmission also contributed to receiving low-quality data. The Douglas Argos filter successfully excluded the largest errors while retaining a large amount of data when the threshold was set to the local scale (two km). Discussion Filter selection requires knowledge about the movement patterns and behavior of the species of interest, and the parametrization of the selected filter typically requires a trial and error approach. Selecting the proper filter reduces the errors while retaining a large amount of data. However, the post-processed data typically includes large positional errors; thus, we recommend incorporating Argos error metrics (e.g., error ellipse) or use complex modeling approaches when working with filtered data.
Spatial and Geographic Information Science
Rozylowicz et al. (2019) Empirical analysis and modeling of Argos Doppler location errors in Romania. PeerJ 7:e6362 https://doi.org/10.7717/peerj.6362
Taxifolin protects rat against myocardial ischemia/reperfusion injury by modulating the mitochondrial apoptosis pathway
Background Taxifolin (TAX), is an active flavonoid, that plays an underlying protective role on the cardiovascular system. This study aimed to evaluate its effect and potential mechanisms on myocardial ischemia/reperfusion (I/R) injury. Methods Healthy rat heart was subjected to I/R using the Langendorff apparatus. Hemodynamic parameters, including heart rate, left ventricular developed pressure (LVDP), maximum/minimum rate of the left ventricular pressure rise (+dp/dtmax and −dp/dtmin) and rate pressure product (RPP) were recorded during the perfusion. Histopathological examination of left ventricular was measured by hematoxylin-eosin (H&E) staining. Creatine kinase-MB (CK-MB) and lactate dehydrogenase (LDH) activities in the effluent perfusion, and the levels of malondialdehyde (MDA), superoxide dismutase (SOD), and glutathione peroxidase (GSH-PX) in the tissue were assayed. Apoptosis related proteins, such as B-cell lymphoma-2 (Bcl-2), Bcl2-associated X (Bax), and cytochrome c (Cyt-c) were also assayed by ELISA. Western blot was employed to determine apoptosis-executive proteins, including caspase 3 and 9. Transferase-mediated dUTP-X nick end labeling assay was performed to evaluate the effect TAX on myocardial apoptosis. Results Taxifolin significantly improved the ventricular functional recovery, as evident by the increase in LVDP, +dp/dtmax, −dp/dtmin and RPP, the levels of SOD, GSH-PX were also increased, but those of LDH, CK-MB, and MDA were decreased. Furthermore, TAX up-regulated the Bcl-2 protein level but down-regulated the levels of Bax, Cyt-c, caspase 3 and 9 protein, thereby inhibits the myocardial apoptosis. Discussion Taxifolin treatment remarkably improved the cardiac function, regulated oxidative stress and attenuated apoptosis. Hence, TAX has a cardioprotective effect against I/R injury by modulating mitochondrial apoptosis pathway.
Tang et al. (2019) Taxifolin protects rat against myocardial ischemia/reperfusion injury by modulating the mitochondrial apoptosis pathway. PeerJ 7:e6383 https://doi.org/10.7717/peerj.6383
Validation of reference genes for gene expression studies in post-harvest leaves of tea plant (Camellia sinensis)
Tea is one of three major non-alcoholic beverages that are popular all around the world. The economic value of tea product largely depends on the post-harvest physiology of tea leaves. The utilization of quantitative reverse transcription polymerase chain reaction is a widely accepted and precise approach to determine the target gene expression of tea plants, and the reliability of results hinges on the selection of suitable reference genes. A few reliable reference genes have been documented using various treatments and different tissues of tea plants, but none has been done on post-harvest leaves during the tea manufacturing process. The present study selected and analyzed 15 candidate reference genes: Cs18SrRNA, CsGADPH, CsACT, CsEF-1α, CsUbi, CsTUA, Cs26SrRNA, CsRuBP, CsCYP, CselF-4α, CsMON1, CsPCS1, CsSAND, CsPPA2, CsTBP. This study made an assessment on the expression stability under two kinds of post-harvest treatment, turn over and withering, using three algorithms—GeNorm, Normfinder, and Bestkeeper. The results indicated that the three commonly used reference genes, CsTUA, Cs18SrRNA, CsRuBP, together with Cs26SrRNA, were the most unstable genes in both the turn over and withering treatments. CsACT, CsEF-1α, CsPPA2, and CsTBP were the top four reference genes in the turn over treatment, while CsTBP, CsPCS1, CsPPA2, CselF-4α, and CsACT were the five best reference genes in the withering group. The expression level of lipoxygenase genes, which were involved in a number of diverse aspects of plant physiology, including wounding, was evaluated to validate the findings. To conclude, we found a basis for the selection of reference genes for accurate transcription normalization in post-harvest leaves of tea plants.
Zhou et al. (2019) Validation of reference genes for gene expression studies in post-harvest leaves of tea plant (Camellia sinensis). PeerJ 7:e6385 https://doi.org/10.7717/peerj.6385
High-resolution maps of Swiss apiaries and their applicability to study spatial distribution of bacterial honey bee brood diseases
Honey bees directly affect and are influenced by their local environment, in terms of food sources, pollinator densities, pathogen and toxin exposure and climate. Currently, there is a lack of studies analyzing these data with Geographic Information Systems (GIS) to investigate spatial relationships with the environment. Particularly for inter-colonial pathogen transmission, it is known that the likelihood of a healthy colony to become infested (e.g., Varroosis) or infected (e.g., American foulbrood—AFB, European foulbrood—EFB) increases with higher colony density. Whether these transmission paths can actually be asserted at apiary level is largely unknown. Here, we unraveled spatial distribution and high-resolution density of apiaries and bacterial honey bee brood diseases in Switzerland based on available GIS data. Switzerland as ‘model country’ offers the unique opportunity to get apiary data since 2010 owing to compulsory registration for every beekeeper. Further, both destructive bee brood diseases (AFB and EFB) are legally notifiable in Switzerland, and EFB has an epizootic character for the last decades. As governmental data sets have to be ameliorated, raw data from the cantonal agricultural or veterinary offices have been included. We found a mean density of 0.56 apiaries per km2, and high resolution spatial analyzes showed strong correlation between density of apiaries and human population density as well as agricultural landscape type. Concerning two bacterial bee brood diseases (AFB, EFB), no significant correlation was detectable with density of apiaries on cantonal level, though a high correlation of EFB cases and apiary density became obvious on higher resolution (district level). Hence, Swiss EFB epizootics seem to have benefited from high apiary densities, promoting the transmission of pathogens by adult bees. The GIS-based method presented here, might also be useful for other bee diseases, anthropogenic or environmental factors affecting bee colonies.
von Büren et al. (2019) High-resolution maps of Swiss apiaries and their applicability to study spatial distribution of bacterial honey bee brood diseases. PeerJ 7:e6393 https://doi.org/10.7717/peerj.6393
Kelpie: generating full-length ‘amplicons’ from whole-metagenome datasets
Introduction Whole-metagenome sequencing can be a rich source of information about the structure and function of entire metagenomic communities, but getting accurate and reliable results from these datasets can be challenging. Analysis of these datasets is founded on the mapping of sequencing reads onto known genomic regions from known organisms, but short reads will often map equally well to multiple regions, and to multiple reference organisms. Assembling metagenomic datasets prior to mapping can generate much longer and more precisely mappable sequences but the presence of closely related organisms and highly conserved regions makes metagenomic assembly challenging, and some regions of particular interest can assemble poorly. One solution to these problems is to use specialised tools, such as Kelpie, that can accurately extract and assemble full-length sequences for defined genomic regions from whole-metagenome datasets. Methods Kelpie is a kMer-based tool that generates full-length amplicon-like sequences from whole-metagenome datasets. It takes a pair of primer sequences and a set of metagenomic reads, and uses a combination of kMer filtering, error correction and assembly techniques to construct sets of full-length inter-primer sequences. Results The effectiveness of Kelpie is demonstrated here through the extraction and assembly of full-length ribosomal marker gene regions, as this allows comparisons with conventional amplicon sequencing and published metagenomic benchmarks. The results show that the Kelpie-generated sequences and community profiles closely match those produced by amplicon sequencing, down to low abundance levels, and running Kelpie on the synthetic CAMI metagenomic benchmarking datasets shows similar high levels of both precision and recall. Conclusions Kelpie can be thought of as being somewhat like an in-silico PCR tool, taking a primer pair and producing the resulting ‘amplicons’ from a whole-metagenome dataset. Marker regions from the 16S rRNA gene were used here as an example because this allowed the overall accuracy of Kelpie to be evaluated through comparisons with other datasets, approaches and benchmarks. Kelpie is not limited to this application though, and can be used to extract and assemble any genomic region present in a whole metagenome dataset, as long as it is bound by a pairs of highly conserved primer sequences.
Greenfield et al. (2019) Kelpie: generating full-length ‘amplicons’ from whole-metagenome datasets. PeerJ 6:e6174 https://doi.org/10.7717/peerj.6174
Urban plums and toads: do fleshy fruits affect the post-metamorphic growth of amphibians?
Background The main aim of the study was to analyse the influence of fleshy fruits (plums) on the post-metamorphic growth and feeding behaviour of the green toad Bufotes viridis. We tested the following two hypotheses: (1) juveniles of the green toad are characterised by faster growth in conditions involving fallen plums Prunus cerasifera due to the associated presence of more varied food such as invertebrates; (2) green toads exhibit more active feeding behaviour in the presence of fleshy fruits. Methods A total of 120 fresh metamorphs of the green toad were randomly assigned to one of four groups: two experimental groups with fleshy plums and two other groups as controls (without fruits). Each group was kept in an enclosure to which wild invertebrates had free access. Each individual toad was measured for snout-vent length (mm) and body mass (g) every other day for 30 days. In order to determine whether fallen plums influence the feeding behaviour of toads, the number of active and hidden (under an artificial shelter) individuals was also noted. Results The results showed that green toads from both enclosures with plums were characterised by more rapid growth than individuals from the control treatments. Simultaneously, in the enclosure with fleshy fruits, greater species richness of wild invertebrates was observed. No differences in active feeding behaviour were noted between control groups and groups with plums. Discussion Fleshy fruits, upon falling, attract many types of invertebrates; thus they may represent good dietary supplements for fresh amphibian metamorphs. Therefore, the presence of fruit trees close to a breeding site might influences the post-metamorphic growth of amphibians, but not their feeding behaviour. The presence of insects associated with fallen fruit seems to favour the occurrence of amphibian populations, which is particularly important, since, due to political and social pressure, numbers of fruit trees are currently being reduced. To our knowledge, no previous study has investigated the potential influence of the presence of fruit trees on the growth and behaviour of anurans.
Kaczmarski et al. (2019) Urban plums and toads: do fleshy fruits affect the post-metamorphic growth of amphibians?. PeerJ 7:e6337 https://doi.org/10.7717/peerj.6337
Spatial variability in soil pH and land use as the main influential factor in the red beds of the Nanxiong Basin, China
Soil pH is the main factor affecting soil nutrient availability and chemical substances in soil. It is of great significance to study the spatial variability of soil pH for the management of soil nutrients and the prediction of soil pollution. In order to explore the causes of spatial variability in soil pH in red-bed areas, the Nanxiong Basin in south China was selected as an example, and soil pH was measured in the topsoil by nested sampling (0–20 cm depth). The spatial variability characteristics of soil pH were analyzed by geostatistics and classical statistical methods, and the main factors influencing spatial variability in soil pH are discussed. The coefficient of variation in the red-bed areas of Nanxiong Basin was 17.18%, indicating moderate variability. Geostatistical analysis showed that the spherical model is the optimal theoretical model for explaining variability in soil pH, which is influenced by both structural and random factors. Analysis of the spatial distribution and pattern showed that soil pH is relatively high in the northeast and southwest, and is lower in the northwest. These results indicate that land use patterns and topographic factors are the main and secondary influencing factors, respectively.
Yan et al. (2019) Spatial variability in soil pH and land use as the main influential factor in the red beds of the Nanxiong Basin, China. PeerJ 7:e6342 https://doi.org/10.7717/peerj.6342
Expression of matrix metalloproteinases to induce the expression of genes associated with apoptosis during corpus luteum development in bovine
Here we investigated the expressions of apoptosis-associated genes known to induce programed cell death through mRNA expressions of two matrix metalloproteinases (MMPs) that are involved in the degradation of collagen and basal membrane in luteal cells cultured in the treatment media. Our results show that the activity of MMP-2 gelatinase was higher in the CL2 and CL1 of luteal phase, was gradually decreased in the CH2 and CH3 of luteal phase. In particular, the expressions of P4-r and survival-associated genes (IGFr, PI3K, AKT, and mTOR) were strongly induced during CL3 stage, whereas the levels of these genes in corpus luteum (CL) were lower during CL2 and CL1 stages. In the cultured lutein cells analyzed, we found that as MMPs increase, genes related to apoptosis (20α-hydroxy steroid dehydrogenase and caspase-3) also increase. In other words, the results for P4-r and survival-related gene expression patterns in the luteal cells were contrary to the MMPs activation results. These results indicate that active MMPs are differentially expressed to induce the expression of genes associated with programed cell death from the degrading luteal cells. Therefore, our results suggest that the MMPs activation may lead to luteal cell development or death.
Kim et al. (2019) Expression of matrix metalloproteinases to induce the expression of genes associated with apoptosis during corpus luteum development in bovine. PeerJ 7:e6344 https://doi.org/10.7717/peerj.6344
Extraordinary centromeres: differences in the meiotic chromosomes of two rock lizards species Darevskia portschinskii and Darevskia raddei
According to the synthesis of 30 years of multidisciplinary studies, parthenogenetic species of rock lizards of genus Darevskia were formed as a result of different combination patterns of interspecific hybridization of the four bisexual parental species: Darevskia raddei, D. mixta, D. valentini, and D. portschinskii. In particular, D. portschinskii and D. raddei are considered as the parental species for the parthenogenetic species D. rostombekowi. Here for the first time, we present the result of comparative immunocytochemical study of primary spermatocyte nuclei spreads from the leptotene to diplotene stages of meiotic prophase I in two species: D. portschinskii and D. raddei. We observed similar chromosome lengths for both synaptonemal complex (SC) karyotypes as well as a similar number of crossing over sites. However, unexpected differences in the number and distribution of anti-centromere antibody (ACA) foci were detected in the SC structure of bivalents of the two species. In all examined D. portschinskii spermatocyte nuclei, one immunostained centromere focus was detected per SC bivalent. In contrast, in almost every studied D. raddei nuclei we identified three to nine SCs with additional immunostained ACA foci per SC bivalent. Thus, the obtained results allow us to identify species-specific karyotype features, previously not been detected using conventional mitotic chromosome analysis. Presumably the additional centromere foci are result of epigenetic chromatin modifications. We assume that this characteristic of the D. raddei karyotype could represent useful marker for the future studies of parthenogenetic species hybrid karyotypes related to D. raddei.
Spangenberg et al. (2019) Extraordinary centromeres: differences in the meiotic chromosomes of two rock lizards species Darevskia portschinskii and Darevskia raddei. PeerJ 7:e6360 https://doi.org/10.7717/peerj.6360
Age-related differences in flexibility in soccer players 8–19 years old
Background Muscle flexibility is a main component of health-related fitness and one of the basic components of fitness for the performance in some sports. Sport and health professionals require the flexibility profile of soccer to define quantitative aims in the training of flexibility. The aim of this study was to identify age-related differences in lower extremity flexibility in youth soccer players. Methods Seventy-two young male soccer players (age: 13.0 ± 3.1 y; body mass: 50.5 ± 15.3 kg; stature 158.2 ± 16.8 cm; BMI: 19.6 ± 2.6 kg/m2) completed this study. Measures of eleven passive hip (hip extension (HE), hip adduction with hip flexed 90°(HAD-HF90°), hip flexion with knee flexed (HF-KF) and extended (HF-KE), hip abduction with hip neutral (HAB) and hip flexed 90°(HAB-HF90°), hip external (HER) and internal (HIR) rotation), knee (knee flexion (KF)) and ankle dorsiflexion (ankle dorsiflexion with knee flexed (ADF-KF) and extended (ADF-KE)) ranges of motion (ROM) were taken. Descriptive statistics were calculated for hip, knee and ankle ROM measured separately by leg (dominant and non-dominant) and age-group (U10, U12, U14, U16 and U19). The data was analysed using a one-way analysis of variance (ANOVA) to examine the interaction of 11 ROM in the different players’ age-group. Results Generally, U10 and/or U12 soccer players obtain the highest mean value in almost all ROM evaluated (U10: HAD-HF [39.6° ± 4.3°], ADF-KE [32.3° ± 4.1°], HER [63.5° ± 5.6°] and HAB-HF90°[64.1° ± 7.5°]; U12: HE [17.7° ± 6.2°], HAB [35.6° ± 3.0], HIR [60.8° ± 4.7°] and KF [133.8° ± 7.1°]). Nonetheless, significant differences between the players’ age-groups are just found in HAD-HF90°(p = .042; ES = .136), HAB (p = .001; ES = .252), HIR (p = .001; ES = .251), HER (p < .001; ES = .321) and HAB-HF90°(p < .001; ES = .376) ROM, showing a progressive and irregular decrease in these ROM until the U19 team. Conclusion The findings of this study reinforce the necessity of prescribing exercises aimed at improving HAD-HF90° ROM in U16, HAB ROM in U14, HIR ROM in U16 and U19, HER ROM in U12 and U19, and HAB-HF90° ROM in U16 and U19 players within everyday soccer training routines.
Cejudo et al. (2019) Age-related differences in flexibility in soccer players 8–19 years old. PeerJ 7:e6236 https://doi.org/10.7717/peerj.6236
Improving the efficiency of the Fukui trap as a capture tool for the invasive European green crab (Carcinus maenas) in Newfoundland, Canada
The European green crab (Carcinus maenas) is a crustacean species native to European and North African coastlines that has become one of the world’s most successful marine invasive species. Targeted fishing programs aimed at removing green crabs from invaded ecosystems commonly use Fukui multi-species marine traps. Improving the efficiency of these traps would improve the ability to respond to green crab invasions. In this study, we developed four distinct trap modifications that were designed to facilitate the successful capture of green crabs, with the goal of improving the performance of the Fukui trap. We tested these modifications in situ during the summer of 2016 at two locations in Placentia Bay, Newfoundland. We discovered that three of our modified Fukui trap designs caught significantly more green crabs than the standard Fukui trap, increasing catch-per-unit-effort (CPUE) by as much as 81%. We conclude that our top-performing modifications have great potential for widespread use with existing Fukui traps that are being used for green crab removal efforts.
Bergshoeff et al. (2019) Improving the efficiency of the Fukui trap as a capture tool for the invasive European green crab (Carcinus maenas) in Newfoundland, Canada. PeerJ 7:e6308 https://doi.org/10.7717/peerj.6308
EGFR deficiency leads to impaired self-renewal and pluripotency of mouse embryonic stem cells
Background Self-renewal and pluripotency are considered as unwavering features of embryonic stem cells (ESCs). How ESCs regulate the self-renewal and differentiation is a central question in development and regenerative medicine research. Epidermal growth factor receptor (EGFR) was identified as a critical regulator in embryonic development, but its role in the maintenance of ESCs is poorly understood. Methods Here, EGFR was disrupted by its specific inhibitor AG1478 in mouse ESCs (mESCs), and its self-renewal and pluripotency were characterized according to their proliferation, expression of pluripotency markers, embryoid body (EB) formation, and mRNA expression patterns. We also used another EGFR inhibitor (gefitinib) and RNA interference assay to rule out the possibility of non-specific effects of AG1478. Results EGFR inhibition by AG1478 treatment in mESCs markedly reduced cell proliferation, caused cell cycle arrest at G0/G1 phase, and altered protein expressions of the cell cycle regulatory genes (CDK2 (decreased 11.3%) and proliferating cell nuclear antigen (decreased 25.2%)). The immunoreactivities and protein expression of pluripotency factors (OCT4 (decreased 26.9%)) also dramatically decreased, while the differentiation related genes (GATA4 (increased 1.6-fold)) were up-regulated in mESCs after EGFR inhibition. Meanwhile, EGFR inhibition in mESCs disrupted EB formation, indicating its impaired pluripotency. Additionally, the effects observed by EGFR inhibition with another inhibitor gefitinib and siRNA were consistent with those observed by AG1478 treatment in mESCs. These effects were manifested in the decreased expression of proliferative and pluripotency-related genes and the increased expression of genes involved in differentiation. Moreover, RNA-seq analysis displayed that transcript profiling was changed significantly after EGFR inhibition by AG1478. A large number of differentially expressed genes were involved in cell cycle, apoptotic process, epigenetic modification, and metabolic process, which were related to self-renewal and pluripotency, confirming that EGFR deficiency impaired self-renewal and pluripotency in mESCs. Conclusions Taken together, our results demonstrated the importance of EGFR in guarding the stemness of mESCs.
Yu et al. (2019) EGFR deficiency leads to impaired self-renewal and pluripotency of mouse embryonic stem cells. PeerJ 7:e6314 https://doi.org/10.7717/peerj.6314
Design, optimization and validation of genes commonly used in expression studies on DMH/AOM rat colon carcinogenesis model
Colorectal cancer (CRC), also known as colon cancer, is the third most common form of cancer worldwide in men and the second in women and is characterized by several genetic alterations, among them the expression of several genes. 1,2-dimethylhydrazine (DMH) and its metabolite azoxymethane (AOM) are procarcinogens commonly used to induce colon cancer in rats (DMH/AOM rat model). This rat model has been used to study changes in mRNA expression in genes involved in this pathological condition. However, a lack of proper detailed PCR primer design in the literature limits the reproducibility of the published data. The present study aims to design, optimize and validate the qPCR, in accordance with the MIQE (Minimum Information for Publication of Quantitative Real-Time PCR Experiments) guidelines, for seventeen genes commonly used in the DMH/AOM rat model of CRC (Apc, Aurka, Bax, Bcl2, β-catenin, Ccnd1, Cdkn1a, Cox2, Gsk3beta, IL-33, iNOs, Nrf2, p53, RelA, Smad4, Tnfα and Vegfa) and two reference genes (Actb or β-actin and B2m). The specificity of all primer pairs was empirically validated on agarose gel, and furthermore, the melting curve inspection was checked as was their efficiency (%) ranging from 90 to 110 with a correlation coefficient of r2 > 0.980. Finally, a pilot study was performed to compare the robustness of two candidate reference genes.
Bars-Cortina et al. (2019) Design, optimization and validation of genes commonly used in expression studies on DMH/AOM rat colon carcinogenesis model. PeerJ 7:e6372 https://doi.org/10.7717/peerj.6372
Designing online species identification tools for biological recording: the impact on data quality and citizen science learning
In recent years, the number and scale of environmental citizen science programmes that involve lay people in scientific research have increased rapidly. Many of these initiatives are concerned with the recording and identification of species, processes which are increasingly mediated through digital interfaces. Here, we address the growing need to understand the particular role of digital identification tools, both in generating scientific data and in supporting learning by lay people engaged in citizen science activities pertaining to biological recording communities. Starting from two well-known identification tools, namely identification keys and field guides, this study focuses on the decision-making and quality of learning processes underlying species identification tasks, by comparing three digital interfaces designed to identify bumblebee species. The three interfaces varied with respect to whether species were directly compared or filtered by matching on visual features; and whether the order of filters was directed by the interface or a user-driven open choice. A concurrent mixed-methods approach was adopted to compare how these different interfaces affected the ability of participants to make correct and quick species identifications, and to better understand how participants learned through using these interfaces. We found that the accuracy of identification and quality of learning were dependent upon the interface type, the difficulty of the specimen on the image being identified and the interaction between interface type and ‘image difficulty’. Specifically, interfaces based on filtering outperformed those based on direct visual comparison across all metrics, and an open choice of filters led to higher accuracy than the interface that directed the filtering. Our results have direct implications for the design of online identification technologies for biological recording, irrespective of whether the goal is to collect higher quality citizen science data, or to support user learning and engagement in these communities of practice.
Sharma et al. (2019) Designing online species identification tools for biological recording: the impact on data quality and citizen science learning. PeerJ 6:e5965 https://doi.org/10.7717/peerj.5965
Breast cancer detection using deep convolutional neural networks and support vector machines
It is important to detect breast cancer as early as possible. In this manuscript, a new methodology for classifying breast cancer using deep learning and some segmentation techniques are introduced. A new computer aided detection (CAD) system is proposed for classifying benign and malignant mass tumors in breast mammography images. In this CAD system, two segmentation approaches are used. The first approach involves determining the region of interest (ROI) manually, while the second approach uses the technique of threshold and region based. The deep convolutional neural network (DCNN) is used for feature extraction. A well-known DCNN architecture named AlexNet is used and is fine-tuned to classify two classes instead of 1,000 classes. The last fully connected (fc) layer is connected to the support vector machine (SVM) classifier to obtain better accuracy. The results are obtained using the following publicly available datasets (1) the digital database for screening mammography (DDSM); and (2) the Curated Breast Imaging Subset of DDSM (CBIS-DDSM). Training on a large number of data gives high accuracy rate. Nevertheless, the biomedical datasets contain a relatively small number of samples due to limited patient volume. Accordingly, data augmentation is a method for increasing the size of the input data by generating new data from the original input data. There are many forms for the data augmentation; the one used here is the rotation. The accuracy of the new-trained DCNN architecture is 71.01% when cropping the ROI manually from the mammogram. The highest area under the curve (AUC) achieved was 0.88 (88%) for the samples obtained from both segmentation techniques. Moreover, when using the samples obtained from the CBIS-DDSM, the accuracy of the DCNN is increased to 73.6%. Consequently, the SVM accuracy becomes 87.2% with an AUC equaling to 0.94 (94%). This is the highest AUC value compared to previous work using the same conditions.
Ragab et al. (2019) Breast cancer detection using deep convolutional neural networks and support vector machines. PeerJ 7:e6201 https://doi.org/10.7717/peerj.6201
A new segmentation algorithm for measuring CBCT images of nasal airway: a pilot study
Background Three-dimensional (3D) modeling of the nasal airway space is becoming increasingly important for assessment in breathing disorders. Processing cone beam computed tomography (CBCT) scans of this region is complicated, however, by the intricate anatomy of the sinuses compared to the simpler nasopharynx. A gold standard for these measures also is lacking. Previous work has shown that software programs can vary in accuracy and reproducibility outcomes of these measurements. This study reports the reproducibility and accuracy of an algorithm, airway segmentor (AS), designed for nasal airway space analysis using a 3D printed anthropomorphic nasal airway model. Methods To test reproducibility, two examiners independently used AS to edit and segment 10 nasal airway CBCT scans. The intra- and inter-examiner reproducibility of the nasal airway volume was evaluated using paired t-tests and intraclass correlation coefficients. For accuracy testing, the CBCT data for pairs of nasal cavities were 3D printed to form hollow shell models. The water-equivalent method was used to calculate the inner volume as the gold standard, and the models were then embedded into a dry human skull as a phantom and subjected to CBCT. AS, along with the software programs MIMICS 19.0 and INVIVO 5, was applied to calculate the inner volume of the models from the CBCT scan of the phantom. The accuracy was reported as a percentage of the gold standard. Results The intra-examiner reproducibility was high, and the inter-examiner reproducibility was clinically acceptable. AS and MIMICS presented accurate volume calculations, while INVIVO 5 significantly overestimated the mockup of the nasal airway volume. Conclusion With the aid of a 3D printing technique, the new algorithm AS was found to be a clinically reliable and accurate tool for the segmentation and reconstruction of the nasal airway space.
Zhang et al. (2019) A new segmentation algorithm for measuring CBCT images of nasal airway: a pilot study. PeerJ 7:e6246 https://doi.org/10.7717/peerj.6246
Genome-wide identification of long non-coding RNAs in tomato plants irradiated by neutrons followed by infection with Tomato yellow leaf curl virus
Long non-coding RNAs (lncRNAs) play an important role in regulating many biological processes. In this study, tomato seeds were first irradiated by neutrons. Eight tomato mutants were then selected and infected by Tomato yellow leaf curl virus (TYLCV). RNA sequencing followed by bioinformatics analyses identified 1,563 tomato lncRNAs. About half of the lncRNAs were derived from intergenic regions, whereas antisense lncRNAs accounted for 35%. There were fewer lncRNAs identified in our study than in other studies identifying tomato lncRNAs. Functional classification of 794 lncRNAs associated with tomato genes showed that many lncRNAs were associated with binding functions required for interactions with other molecules and localized in the cytosol and membrane. In addition, we identified 19 up-regulated and 11 down-regulated tomato lncRNAs by comparing TYLCV infected plants to non-infected plants using previously published data. Based on these results, the lncRNAs identified in this study provide important resources for characterization of tomato lncRNAs in response to TYLCV infection.
Zhou et al. (2019) Genome-wide identification of long non-coding RNAs in tomato plants irradiated by neutrons followed by infection with Tomato yellow leaf curl virus. PeerJ 7:e6286 https://doi.org/10.7717/peerj.6286
Gastric Helicobacter pylori infection perturbs human oral microbiota
Background We investigated the effects of gastric Helicobacter pylori infection on the daytime and overnight human oral microbiota. Methods Twenty four volunteers were recruited. Ten tested positive for H. pylori infection by the Carbon-14 Urea Breath Test, and the rest were negative. Two oral swabs were collected: one immediately after waking up in the morning and before brushing teeth, and another in the evening before teeth-brushing. DNA extract acquired from each swab was subjected to Illumina sequencing of 16S rRNA gene amplicons. The microbial abundance and composition were analysed in relation to H. pylori infection status. Results Helicobacter pylori-positive individuals had significant changes in the alpha and beta diversities in the daytime samples in comparison to those who were H. pylori negative. To identify which taxa could be significantly affected within the cohorts in the daytime, we employed the LEfSe method. When compared against UBT-negative samples, significantly higher abundances were detected in both Pseudomonas and Roseomonas, while Fusobacterium, Solobacterium, Haemophilus and Streptococcus were significantly decreased in the UBT-positive samples. Discussion Our data demonstrated that H. pylori infection affects the human daytime oral microbiota. The hitherto undocumented changes of several bacterial genera due to H. pylori infection require more studies to examine their potential health effects on affected individuals.
Chua et al. (2019) Gastric Helicobacter pylori infection perturbs human oral microbiota. PeerJ 7:e6336 https://doi.org/10.7717/peerj.6336
Optimizing influenza vaccine policies for controlling 2009-like pandemics and regular outbreaks
Background This study examined the effectiveness of various vaccine policies against influenza. The transmission rate was calculated by use of the time-series influenza-like illness case during the year of 2009 and recent epidemics in Taiwan. Methods We developed a stochastic compartmental model to analyze the transmission of influenza, where the population was stratified by location and age group, and the vaccine distribution was considered using the current policy. The simulation study compared the previous vaccine policy and a new policy with expanded coverage and various lengths of the vaccination campaign. The sensitivity analysis investigated different levels of vaccine efficacy to confirm the robustness of the recommended policies. Results Doubling vaccine coverage can decrease the number of infections effectively in the regular epidemic scenario. However, a peak of infections occurs if the duration of implementing vaccination is too long. In the 2009-like pandemic scenario, both increasing vaccine doses and reducing the program’s duration can mitigate infections, although the early outbreak restricts the effectiveness of vaccination programs. Conclusions The finding indicates that only increasing vaccine coverage can reduce influenza infections. To avoid the peak of infections, it is also necessary to execute the vaccination activity immediately. Vaccine efficacy significantly impacts the vaccination policy’s performance. When vaccine efficacy is low, neither increasing vaccination doses nor reducing vaccination timeframe prevents infections. Therefore, the variation in vaccine efficacy should be taken into account when making immunization policies against influenza.
Chen et al. (2019) Optimizing influenza vaccine policies for controlling 2009-like pandemics and regular outbreaks. PeerJ 7:e6340 https://doi.org/10.7717/peerj.6340
A scalable discrete-time survival model for neural networks
There is currently great interest in applying neural networks to prediction tasks in medicine. It is important for predictive models to be able to use survival data, where each patient has a known follow-up time and event/censoring indicator. This avoids information loss when training the model and enables generation of predicted survival curves. In this paper, we describe a discrete-time survival model that is designed to be used with neural networks, which we refer to as Nnet-survival. The model is trained with the maximum likelihood method using mini-batch stochastic gradient descent (SGD). The use of SGD enables rapid convergence and application to large datasets that do not fit in memory. The model is flexible, so that the baseline hazard rate and the effect of the input data on hazard probability can vary with follow-up time. It has been implemented in the Keras deep learning framework, and source code for the model and several examples is available online. We demonstrate the performance of the model on both simulated and real data and compare it to existing models Cox-nnet and Deepsurv.
Gensheimer et al. (2019) A scalable discrete-time survival model for neural networks. PeerJ 7:e6257 https://doi.org/10.7717/peerj.6257
Diatom ecological response to deposition of the 833-850 CE White River Ash (east lobe) ashfall in a small subarctic Canadian lake
A <5 mm thick volcanic ashfall layer associated with the White River Ash (east lobe [WRAe]) originating from the eruption of Mount Churchill, Alaska (833-850 CE; 1,117–1,100 cal BP) was observed in two freeze cores obtained from Pocket Lake (62.5090°N, −114.3719°W), a small subarctic lake located within the city limits of Yellowknife, Northwest Territories, Canada. Here we analyze changes in diatom assemblages to assess impact of tephra deposition on the aquatic biota of a subarctic lake. In a well-dated core constrained by 8 radiocarbon dates, diatom counts were carried out at 1-mm intervals through an interval spanning 1 cm above and below the tephra layer with each 1 mm sub-sample represented about 2 years of deposition. Non-metric Multidimensional Scaling (NMDS) and Stratigraphically Constrained Incremental Sum of Squares (CONISS) analyses were carried out and three distinct diatom assemblages were identified throughout the interval. The lowermost “Pre-WRAe Assemblage (Pre-WRAeA)” was indicative of slightly acidic and eutrophic lacustrine conditions. Winter deposition of the tephra layer drove a subsequent diatom flora shift to the “WRAe Assemblage (WRAeA)” the following spring. The WRAeA contained elevated abundances of taxa associated with oligotrophic, nutrient depleted and slightly more alkaline lake waters. These changes were only apparent in samples within the WRAe containing interval indicating that they were short lived and only sustained for a single year of deposition. Immediately above the WRAe horizon, a third, “Post-WRAe Assemblage (Post-WRAeA)” was observed. This assemblage was initially similar to that of the Pre-WRAeA but gradually became more distinct upwards, likely due to climatic patterns independent of the WRAe event. These results suggest that lacustrine environments are sensitive to perturbations such as deposition of ash fall, but that ecological communities in subarctic systems can also have high resilience and can recover rapidly. If subsampling of the freeze cores was carried out at a more standard resolution (0.5–1 cm) these subtle diatom ecological responses to perturbation associated with the WRAe depositional event would not have been observed. This research illustrates the importance of high-resolution subsampling when studying the environmental impact of geologically “near instantaneous” events such as episodic deposition of ashfalls.
Hutchinson et al. (2019) Diatom ecological response to deposition of the 833-850 CE White River Ash (east lobe) ashfall in a small subarctic Canadian lake. PeerJ 7:e6269 https://doi.org/10.7717/peerj.6269
Convergent origin of the narrowly lanceolate leaf in the genus Aster—with special reference to an unexpected discovery of a new Aster species from East China
Narrowly lanceolate leaves occur frequently in the genus Aster. It was often employed as a distinguishing character in the taxonomy of this genus. The origin of this particular leaf shape, however, has never been investigated using comparative methods. In this study, we reconstructed a comprehensive phylogeny that includes most species of Aster with narrowly lanceolate leaf. We then gathered data on riparian habitats and the presence or absence of narrowly lanceolate leaves, and investigated the evolutionary association between them in a phylogenetic context. Our analysis indicated that the species with narrowly lanceolate leaves are nested in unrelated lineages of the genus Aster, implying that they originated independently several times. Using Pagel’s comparative method of discrete data, we demonstrated a significant correlation between riparian habitats and narrowly lanceolate leaves. We further inferred the sequence of transition of the two characters. This analysis indicated that the sequence of evolution of riparian habitat and narrowly lanceolate leaf form was usually uncertain, but some positive results showed that the occurrence of riparian habitats may not precede the evolution of narrowly lanceolate leaf form. This study provided new insights into the adaptive evolution in a mega-diverse family. In addition, Aster tonglingensis, an unexpected new species with narrowly lanceolate leaves, was discovered and established based on the evidence from morphology, micromorphology and molecular phylogeny.
Zhang et al. (2019) Convergent origin of the narrowly lanceolate leaf in the genus Aster—with special reference to an unexpected discovery of a new Aster species from East China. PeerJ 7:e6288 https://doi.org/10.7717/peerj.6288
Isolation of wheat bran-colonizing and metabolizing species from the human fecal microbiota
Undigestible, insoluble food particles, such as wheat bran, are important dietary constituents that serve as a fermentation substrate for the human gut microbiota. The first step in wheat bran fermentation involves the poorly studied solubilization of fibers from the complex insoluble wheat bran structure. Attachment of bacteria has been suggested to promote the efficient hydrolysis of insoluble substrates, but the mechanisms and drivers of this microbial attachment and colonization, as well as subsequent fermentation remain to be elucidated. We have previously shown that an individually dependent subset of gut bacteria is able to colonize the wheat bran residue. Here, we isolated these bran-attached microorganisms, which can then be used to gain mechanistic insights in future pure culture experiments. Four healthy fecal donors were screened to account for inter-individual differences in gut microbiota composition. A combination of a direct plating and enrichment method resulted in the isolation of a phylogenetically diverse set of species, belonging to the Bacteroidetes, Firmicutes, Proteobacteria and Actinobacteria phyla. A comparison with 16S rRNA gene sequences that were found enriched on wheat bran particles in previous studies, however, showed that the isolates do not yet cover the entire diversity of wheat-bran colonizing species, comprising among others a broad range of Prevotella, Bacteroides and Clostridium cluster XIVa species. We, therefore, suggest several modifications to the experiment set-up to further expand the array of isolated species.
De Paepe et al. (2019) Isolation of wheat bran-colonizing and metabolizing species from the human fecal microbiota. PeerJ 7:e6293 https://doi.org/10.7717/peerj.6293
Prognostic values of GMPS, PR, CD40, and p21 in ovarian cancer
Early detection and prediction of prognosis and treatment responses are all the keys in improving survival of ovarian cancer patients. This study profiled an ovarian cancer progression model to identify prognostic biomarkers for ovarian cancer patients. Mouse ovarian surface epithelial cells (MOSECs) can undergo spontaneous malignant transformation in vitro cell culture. These were used as a model of ovarian cancer progression for alterations in gene expression and signaling detected using the Illumina HiSeq2000 Next-Generation Sequencing platform and bioinformatical analyses. The differential expression of four selected genes was identified using the gene expression profiling interaction analysis (http://gepia.cancer-pku.cn/) and then associated with survival in ovarian cancer patients using the Cancer Genome Atlas dataset and the online Kaplan–Meier Plotter (http://www.kmplot.com) data. The data showed 263 aberrantly expressed genes, including 182 up-regulated and 81 down-regulated genes between the early and late stages of tumor progression in MOSECs. The bioinformatic data revealed four genes (i.e., guanosine 5′-monophosphate synthase (GMPS), progesterone receptor (PR), CD40, and p21 (cyclin-dependent kinase inhibitor 1A)) to play an important role in ovarian cancer progression. Furthermore, the Cancer Genome Atlas dataset validated the differential expression of these four genes, which were associated with prognosis in ovarian cancer patients. In conclusion, this study profiled differentially expressed genes using the ovarian cancer progression model and identified four (i.e., GMPS, PR, CD40, and p21) as prognostic markers for ovarian cancer patients. Future studies of prospective patients could further verify the clinical usefulness of this four-gene signature.
Wang et al. (2019) Prognostic values of GMPS, PR, CD40, and p21 in ovarian cancer. PeerJ 7:e6301 https://doi.org/10.7717/peerj.6301
Impact assessment of high soil CO2 on plant growth and soil environment: a greenhouse study
To ensure the safety of carbon capture and storage (CCS) technology, insight into the potential impacts of CO2 leakage on the ecosystem is necessary. We conducted a greenhouse experiment to investigate the effects of high soil CO2 on plant growth and the soil environment. Treatments comprised 99.99% CO2 injection (CG), 99.99% N2injection (NG), and no injection (BG). NG treatment was employed to differentiate the effects of O2 depletion from those of CO2 enrichment. Soil CO2 and O2 concentrations were maintained at an average of 53% and 11%, respectively, under CG treatment. We verified that high soil CO2 had negative effects on root water absorption, chlorophyll, starch content and total biomass. Soil microbial acid phosphatase activity was affected by CG treatment. These negative effects were attributed to high soil CO2 instead of low O2 or low pH. Our results indicate that high soil CO2 affected the root system, which in turn triggered further changes in aboveground plant tissues and rhizospheric soil water conditions. A conceptual diagram of CO2 toxicity to plants and soil is suggested to act as a useful guideline for impact assessment of CCS technology.
He et al. (2019) Impact assessment of high soil CO2 on plant growth and soil environment: a greenhouse study. PeerJ 7:e6311 https://doi.org/10.7717/peerj.6311
Nonconventional opponents: a review of malaria and leishmaniasis among United States Armed Forces
As the United States military engage with different countries and cultures throughout the world, personnel become exposed to new biospheres as well. There are many infectious pathogens that are not endemic to the US, but two of particular importance are Plasmodium and Leishmania, which respectively cause malaria and leishmaniasis. These parasites are both known to cause significant disease burden in their endemic locales, and thus pose a threat to military travelers. This review introduces readers to basic life cycle and disease mechanisms for each. Local and military epidemiology are described, as are the specific actions taken by the US military for prevention and treatment purposes. Complications of such measures with regard to human health are also discussed, including possible chemical toxicities. Additionally, poor recognition of these diseases upon an individual’s return leading to complications and treatment delays in the United States are examined. Information about canine leishmaniasis, poorly studied relative to its human manifestation, but of importance due to the utilization of dogs in military endeavors is presented. Future implications for the American healthcare system regarding malaria and leishmaniasis are also presented.
Beiter et al. (2019) Nonconventional opponents: a review of malaria and leishmaniasis among United States Armed Forces. PeerJ 7:e6313 https://doi.org/10.7717/peerj.6313
Increased tooth brushing frequency is associated with reduced gingival pocket bacterial diversity in patients with intracranial aneurysms
Objectives The objective of this study was to investigate the association of tooth brushing frequency and bacterial communities of gingival crevicular fluid in patients subjected to preoperative dental examination prior to operative treatment for unruptured intracranial aneurysms. Methods Gingival crevicular fluid samples were taken from their deepest gingival pocket from a series of hospitalized neurosurgical patients undergoing preoperative dental screening (n = 60). The patients were asked whether they brushed their teeth two times a day, once a day, or less than every day. Total bacterial DNA was isolated and the V3–V4 region of the 16S rRNA gene was amplificated. Sequencing was performed with Illumina’s 16S metagenomic sequencing library preparation protocol and data were analyzed with QIIME (1.9.1) and R statistical software (3.3.2). Results Bacterial diversity (Chao1 index) in the crevicular fluid reduced along with reported tooth brushing frequency (p = 0.0002; R2 = 34%; p (adjusted with age and sex) = 0.09; R2 = 11%) showing that patients who reported brushing their teeth twice a day had the lowest bacterial diversity. According to the differential abundant analysis between the tooth brushing groups, tooth brushing associated with two phyla of fusobacteria [p = 0.0001; p = 0.0007], and one bacteroidetes (p = 0.004) by reducing their amounts. Conclusions Tooth brushing may reduce the gingival bacterial diversity and the abundance of periodontal bacteria maintaining oral health and preventing periodontitis, and thus it is highly recommended for neurosurgical patients.
Pyysalo et al. (2019) Increased tooth brushing frequency is associated with reduced gingival pocket bacterial diversity in patients with intracranial aneurysms. PeerJ 7:e6316 https://doi.org/10.7717/peerj.6316
The complete chloroplast genomes of three Betulaceae species: implications for molecular phylogeny and historical biogeography
Background Previous phylogenetic conclusions on the family Betulaceae were based on either morphological characters or traditional single loci, which may indicate some limitations. The chloroplast genome contains rich polymorphism information, which is very suitable for phylogenetic studies. Thus, we sequenced the chloroplast genome sequences of three Betulaceae species and performed multiple analyses to investigate the genome variation, resolve the phylogenetic relationships, and clarify the divergence history. Methods Chloroplast genomes were sequenced using the high-throughput sequencing. A comparative genomic analysis was conducted to examine the global genome variation and screen the hotspots. Three chloroplast partitions were used to reconstruct the phylogenetic relationships using Maximum Likelihood and Bayesian Inference approaches. Then, molecular dating and biogeographic inferences were conducted based on the whole chloroplast genome data. Results Betulaceae chloroplast genomes consisted of a small single-copy region and a large single copy region, and two copies of inverted repeat regions. Nine hotspots can be used as potential DNA barcodes for species delimitation. Phylogenies strongly supported the division of Betulaceae into two subfamilies: Coryloideae and Betuloideae. The phylogenetic position of Ostryopsis davidiana was controversial among different datasets. The divergence time between subfamily Coryloideae and Betuloideae was about 70.49 Mya, and all six extant genera were inferred to have diverged fully by the middle Oligocene. Betulaceae ancestors were probably originated from the ancient Laurasia. Discussions This research elucidates the potential of chloroplast genome sequences in the application of developing molecular markers, studying evolutionary relationships and historical dynamic of Betulaceae.It also reveals the advantages of using chloroplast genome data to illuminate those phylogenies that have not been well solved yet by traditional approaches in other plants.
Yang et al. (2019) The complete chloroplast genomes of three Betulaceae species: implications for molecular phylogeny and historical biogeography. PeerJ 7:e6320 https://doi.org/10.7717/peerj.6320
New material of the ‘microsaur’ Llistrofus from the cave deposits of Richards Spur, Oklahoma and the paleoecology of the Hapsidopareiidae
The Hapsidopareiidae is a group of “microsaurs” characterized by a substantial reduction of several elements in the cheek region that results in a prominent, enlarged temporal emargination. The clade comprises two markedly similar taxa from the early Permian of Oklahoma, Hapsidopareion lepton and Llistrofus pricei, which have been suggested to be synonymous by past workers. Llistrofus was previously known solely from the holotype found near Richards Spur, which consists of a dorsoventrally compressed skull in which the internal structures are difficult to characterize. Here, we present data from two new specimens of Llistrofus. This includes data collected through the use of neutron tomography, which revealed important new details of the palate and the neurocranium. Important questions within “Microsauria” related to the evolutionary transformations that likely occurred as part of the acquisition of the highly modified recumbirostran morphology for a fossorial ecology justify detailed reexamination of less well-studied taxa, such as Llistrofus. Although this study eliminates all but one of the previous features that differentiated Llistrofus and Hapsidopareion, the new data and redescription identify new features that justify the maintained separation of the two hapsidopareiids. Llistrofus possesses some of the adaptations for a fossorial lifestyle that have been identified in recumbirostrans but with a lesser degree of modification (e.g., reduced neurocranial ossification and mandibular modification). Incorporating the new data for Llistrofus into an existing phylogenetic matrix maintains the Hapsidopareiidae’s (Llistrofus + Hapsidopareion) position as the sister group to Recumbirostra. Given its phylogenetic position, we contextualize Llistrofus within the broader “microsaur” framework. Specifically, we propose that Llistrofus may have been fossorial but was probably incapable of active burrowing in the fashion of recumbirostrans, which had more consolidated and reinforced skulls. Llistrofus may represent an earlier stage in the step-wise acquisition of the derived recumbirostran morphology and paleoecology, furthering our understanding of the evolutionary history of “microsaurs.”
Gee et al. (2019) New material of the ‘microsaur’ Llistrofus from the cave deposits of Richards Spur, Oklahoma and the paleoecology of the Hapsidopareiidae. PeerJ 7:e6327 https://doi.org/10.7717/peerj.6327
The dynamics of grooming interactions: maintenance of partner choice and the consequences of demographic variation for female mandrills
A large body of evidence suggests that female Old World monkeys maintain selective long-term grooming interactions with fitness benefits. The last two decades have produced evidence that the regulation of social interactions among primates can be, in part, explained by the Biological Markets theory, with grooming behaviour as the focus of these studies. Grooming facilitates bonding between individuals, constituting an essential part of the regulation of social relationships among female cercopithecids. In contrast to the well-studied baboons (Papio spp), knowledge about the nature of grooming interactions and their regulation is generally lacking for the large, terrestrial species of mandrills (Mandrillus sphinx). We used a combination of social network analysis tools and well-established methods for assessing partner diversity and reciprocity to characterise grooming networks, partner choice and patterns of trade (be groomed, give grooming) among females in a captive group of mandrills, both within and across two separate observation periods. Our results suggest that, even though the relatively stable conditions of captivity allowed the studied females to maintain selective grooming interactions across time, small scale demographic changes affected the grooming dynamics of the group in accordance with the expectations of the Biological Markets theory. In particular, the maturation and consequent integration of a high ranking female into the group’s grooming network from one period to the next resulted in a more pronounced effect of rank on the regulation of grooming interactions. In addition, the influence of the maturation of a dependent infant on the grooming interactions of his mother were evident between periods. Our results also demonstrate that grooming networks are dynamic and that high ranking individuals are not necessarily the most central in grooming networks. Finally, we discuss the potential of social network analysis to identify cases of social exclusion and its consequences for captive management.
Pereira et al. (2019) The dynamics of grooming interactions: maintenance of partner choice and the consequences of demographic variation for female mandrills. PeerJ 7:e6332 https://doi.org/10.7717/peerj.6332
Food-burying behavior in red imported fire ants (Hymenoptera: Formicidae)
The food-burying behavior has been reported in many mammals and birds, but was rarely observed in invertebrates. The red imported fire ants, Solenopsis invicta Buren, is an invasive pest in many areas of the world that usually performing food-burying during the foraging processes. However, the impacted factors and measureable patterns of this behavior is largely unknown. In the present study, food-burying vs food-transport behaviors of Solenopsis invicta were observed under laboratory and field conditions. When starved (no food was provided for 37 days) in the laboratory, food (sausage) was consumed by large numbers of ants, and few burying behaviors were observed. However, when food was provided until satiation of the colonies, food-transport was suppressed and significantly more soil particles were relocated on the food and graph paper square (where the food was placed) when compared with these colonies exposed to starved conditions. Videotapes showed that soil particles (1.47 ± 0.09 mm2) were preferentially placed adjacent to (in contact with) the food items at the beginning; and after the edges were covered, ants transported significantly smaller soil particles (1.13 ± 0.06 mm2) to cover the food. Meanwhile, larger particles (1.96 ± 0.08 mm2) were pulled/dragged around (but not in contact with) the food. Interestingly, only a small number of ants, mainly the small workers, were involved in food-burying, and the ants tended to repeatedly transport soil particles. A total of 12 patterns of particle transport were identified, and soil particles were most frequently picked from the foraging arena and subsequently placed adjacent to the food. In the field, almost all released food was actively transported by Solenopsis invicta workers, and no burying behavior was observed. Our results show that the food-burying behavior of Solenopsis invicta may be associated with the suppressed foraging activity, and the burying task may be carried out by certain groups of workers.
Qin et al. (2019) Food-burying behavior in red imported fire ants (Hymenoptera: Formicidae). PeerJ 7:e6349 https://doi.org/10.7717/peerj.6349
Effects of Salmonella enterica serovar Enteritidis infection on egg production and the immune response of the laying duck Anas platyrhynchos
Persistent colonization of the avian reproductive tract by Salmonella enterica serovar Enteritidis (SE) negatively affects egg production and contaminates the egg. The immune function of the ovary and oviduct is essential for protection from infection and for the production of wholesome eggs. However, the immune response of laying ducks during SE infection is not well-understood. In this study, ducks (Anas platyrhynchos) were infected with SE and were systematically monitored for fecal shedding during a 13-week period. We also assessed bacterial distribution in the reproductive tract and classified infected ducks as resistant or susceptible based on the presence of tissue lesions and on SE isolation from fecal samples. We found that infected animals had persistent, but intermittent, bacterial shedding that resulted in the induction of carrier ducks. Laying rate and egg quality were also decreased after SE infection (P < 0.05). SE readily colonized the stroma, small follicle, isthmus, and vagina in the reproductive tracts of susceptible ducks. Immunoglobulin (IgA, IgG, IgM) levels were higher in susceptible ducks compared with resistant birds (P < 0.05); T-lymphocyte subpopulations (CD3+, CD4+, CD8+) displayed the opposite trend. qRT-PCR analysis was used to examine expression profiles of immune response genes in the reproductive tract of infected ducks. The analysis revealed that immune genes, including toll-like receptors (TLR2, TLR4-5, TLR15, TLR21), NOD-like receptors (NOD1, NLRX1, NLRP12), avian β-defensins (AvβD4-5, AvβD7, AvβD12), cytokines (IL-6, IL-1β, IFN-γ), and MyD88 were markedly upregulated in the reproductive tracts of SE-infected ducks (all P < 0.05); TLR3, TLR7, NLRC3, NLRC5, and TNF-α were significantly downregulated. These results revealed that SE infection promoted lower egg production and quality, and altered the expression of TLRs, NLRs, AvβDs, and cytokine family genes. These findings provide a basis for further investigation of the physiological and immune mechanisms of SE infection in laying ducks.
Zhang et al. (2019) Effects of Salmonella enterica serovar Enteritidis infection on egg production and the immune response of the laying duck Anas platyrhynchos. PeerJ 7:e6359 https://doi.org/10.7717/peerj.6359
Sleeping mattress determinants and evaluation: a biomechanical review and critique
Background Sleeping mattress parameters significantly influence sleeping comfort and health, as reflected by the extensive investigations of sleeping support biomechanics to prevent sleep-related musculoskeletal problems. Methodology Herein, we review the current trends, research methodologies, and determinants of mattress biomechanics research, summarizing evidence published since 2008. In particular, we scrutinize 18 articles dealing with the development of new designs, recommendation criteria, instruments/methods of spine alignment evaluation, and comparative evaluation of different designs. Results The review demonstrated that mattress designs have strived for customization, regional features, and real-time active control to adapt to the biomechanical features of different body builds and postures. However, the suggested threshold or target values for desirable spine alignment and body pressure distribution during sleep cannot yet be justified in view of the lack of sufficient evidence. Conclusions It is necessary to formulate standard objectives and protocols for carrying out mattress evaluation.
Wong et al. (2019) Sleeping mattress determinants and evaluation: a biomechanical review and critique. PeerJ 7:e6364 https://doi.org/10.7717/peerj.6364
Effects of different training modalities on phosphate homeostasis and local vitamin D metabolism in rat bone
Objectives Mechanical loading may be an important factor in the regulation of bone derived hormones involved in phosphate homeostasis. This study investigated the effects of peak power and endurance training on expression levels of fibroblast growth factor 23 (FGF23) and 1α-hydroxylase (CYP27b1) in bone. Methods Thirty-eight rats were assigned to six weeks of training in four groups: peak power (PT), endurance (ET), PT followed by ET (PET) or no training (control). In cortical bone, FGF23 was quantified using immunohistochemistry. mRNA expression levels of proteins involved in phosphate and vitamin D homeostasis were quantified in cortical bone and kidney. C-terminal FGF23, 25-hydroxyvitamin D3, parathyroid hormone (PTH), calcium and phosphate concentrations were measured in plasma or serum. Results Neither FGF23 mRNA and protein expression levels in cortical bone nor FGF23 plasma concentrations differed between the groups. In cortical bone, mRNA expression levels of sclerostin (SOST), dental matrix protein 1 (DMP1), phosphate-regulating gene with homologies to endopeptidases on the X chromosome (PHEX) and matrix extracellular phosphoglycoprotein (MEPE) were lower after PT compared to ET and PET. Expression levels of CYP27b1 and vitamin D receptor (VDR) in tibial bone were decreased after PT compared to ET. In kidney, no differences between groups were observed for mRNA expression levels of CYP27b1, 24-hydroxylase (CYP24), VDR, NaPi-IIa cotransporter (NPT2a) and NaPi-IIc cotransporter (NPT2c). Serum PTH concentrations were higher after PT compared to controls. Conclusion After six weeks, none of the training modalities induced changes in FGF23 expression levels. However, PT might have caused changes in local phosphate regulation within bone compared to ET and PET. CYP27b1 and VDR expression in bone was reduced after PT compared to ET, suggesting high intensity peak power training in this rat model is associated with decreased vitamin D signalling in bone.
Buskermolen et al. (2019) Effects of different training modalities on phosphate homeostasis and local vitamin D metabolism in rat bone. PeerJ 7:e6184 https://doi.org/10.7717/peerj.6184
GPs’ motivation for teaching medical students in a rural area—development of the Motivation for Medical Education Questionnaire (MoME-Q)
Background The establishment of a medical education program in the rural area of Siegen is planned to be the first step against a shortage of physicians in this region. General practitioners (GPs) will be extensively involved in this program as Family Medicine (Allgemeinmedizin) will become a core subject in the curriculum nationwide. Based on this situation we aim to figure out GPs motivation to participate in medical education. For this purpose, we had to construct and test a new questionnaire. Methods A survey was conducted among general practitioners (GPs) in the region of Siegen-Wittgenstein regarding their motivation to participate in medical education. For this purpose, the Motivation for Medical Education Questionnaire (MoME-Q), a 24-item questionnaire, was developed. Structural characteristics of GPs, the Maslach Burnout Inventory (MBI) and the Work Satisfaction Questionnaire (WSQ) were used for validation purposes. Results A representative number of GPs took part in the study (53.8%). Although the majority had no connection to a university (86%), 83% can imagine participating in the education of medical students. The items of the MoME-Q load on two factors (commitment and personal benefit). The confirmatory factor analysis shows a good model fit. Subscales of the MoME-Q were able to differentiate between physicians with and without authorization to train GP residents, between practices with and without a specialized practice nurse, and between physicians with and without previous experience in medical education. The MoME-Q subscale “commitment” correlated significantly with all three subscales of the MBI. Correlations were in the medium range around |.30|. Conclusion The MoME-Q seems to be an appropriate tool to assess motivation to participate in medical education of GPs. In our sample, a large number of GPs was motivated to participate in the education of medical students. Future studies with larger number of GPs should be carried out to validate and confirm our findings. Whether the MoME-Q is also appropriate for other specialties should also be shown in further empirical studies.
Adarkwah et al. (2019) GPs’ motivation for teaching medical students in a rural area—development of the Motivation for Medical Education Questionnaire (MoME-Q). PeerJ 7:e6235 https://doi.org/10.7717/peerj.6235
Intraspecific divergences and phylogeography of Panzerina lanata (Lamiaceae) in northwest China
Climatic fluctuations during the Quaternary significantly affect many species in their intraspecific divergence and population structure across northwest China. In order to investigate the impact of climate change on herbaceous plants, we studied Panzerina lanata (Lamiaceae), a widely distributed species. Sequences of two chloroplast DNA (cpDNA) intergenic spacers (trnH-psbA and rpoB-trnC) and a nuclear ribosomal region (nrDNA, ITS) were generated from 27 populations of Panzerina lanata and resulted in the identification of seven chloroplast haplotypes and thirty-two nuclear haplotypes. We applied AMOVA, neutrality test and mismatch distribution analysis to estimate genetic differentiation and demographic characteristics. The divergence times of the seven cpDNA haplotypes were estimated using BEAST. Our results revealed high levels of genetic diversity (cpDNA: Hcp = 0.6691, HT = 0.673; nrDNA: Hnr = 0.5668, HT = 0.577). High level of genetic differentiation (GST = 0.950) among populations was observed in the cpDNA sequences, while the genetic differentiation values (GST = 0.348) were low in nuclear sequences. AMOVA results revealed major genetic variation among the three groups: northern, central, and eastern group. However, the genetic differentiation in ITS data was not found. The species distribution modeling and demographic analysis indicated that P. lanata had not experienced recent range expansion. The occurrence of divergence between seven cpDNA haplotypes, probably during Pleistocene, coincides with aridification and expansion of the desert across northwest China that resulted in species diversification and habitat fragmentation. In addition, we discovered that the deserts and the Helan Mountains acted as effective geographic barriers that promoting the intraspecific diversity of P. lanata.
Zhao et al. (2019) Intraspecific divergences and phylogeography of Panzerina lanata (Lamiaceae) in northwest China. PeerJ 7:e6264 https://doi.org/10.7717/peerj.6264
Association of TIMP4 gene variants with steroid-induced osteonecrosis of the femoral head in the population of northern China
Background In clinical treatment, the use of steroid hormones is an important etiological factor of non-traumatic osteonecrosis of the femoral head (ONFH) risk. As an endogenous inhibitor of matrix metalloproteinases (MMPs) in the extracellular matrix, the expression of tissue inhibitors of metalloprotease-4 (TIMP4) plays an essential role in cartilage and bone tissue damage and remodeling, vasculitis formation, intravascular thrombosis, and lipid metabolism. Methods This study aimed to detect the association between TIMP4 polymorphism and steroid-induced ONFH. We genotyped seven single-nucleotide polymorphisms (SNPs) in TIMP4 genes and analyzed the association with steroid-induced ONFH from 286 steroid-induced ONFH patients and 309 normal individuals. Results We performed allelic model analysis and found that the minor alleles of five SNPs (rs99365, rs308952, rs3817004, rs2279750, and rs3755724) were associated with decreased steroid-induced ONFH (p = 0.02, p = 0.03, p = 0.04, p = 0.01, p = 0.04, respectively). rs2279750 showed a significant association with decreased risk of steroid-induced ONFH in the Dominant and Log-additive models (p = 0.042, p = 0.028, respectively), and rs9935, rs30892, and rs3817004 were associated with decreased risk in the Log-additive model (p = 0.038, p = 0.044, p = 0.042, respectively). In further stratification analysis, TIMP4 gene variants showed a significant association with steroid-induced ONFH in gender under the genotypes. Haplotype analysis also revealed that “TCAGAC” and “CCGGAA” sequences have protective effect on steroid-induced ONFH. Conclusion Our results indicate that five TIMP4 SNPs (rs99365, rs308952, rs3817004 rs2279750, and rs3755724) are significantly associated with decreased risk of steroid-induced ONFH in the population of northern China.
Wang et al. (2019) Association of TIMP4 gene variants with steroid-induced osteonecrosis of the femoral head in the population of northern China. PeerJ 7:e6270 https://doi.org/10.7717/peerj.6270
Accessible molecular phylogenomics at no cost: obtaining 14 new mitogenomes for the ant subfamily Pseudomyrmecinae from public data
The advent of Next Generation Sequencing has reduced sequencing costs and increased genomic projects from a huge amount of organismal taxa, generating an unprecedented amount of genomic datasets publicly available. Often, only a tiny fraction of outstanding relevance of the genomic data produced by researchers is used in their works. This fact allows the data generated to be recycled in further projects worldwide. The assembly of complete mitogenomes is frequently overlooked though it is useful to understand evolutionary relationships among taxa, especially those presenting poor mtDNA sampling at the level of genera and families. This is exactly the case for ants (Hymenoptera:Formicidae) and more specifically for the subfamily Pseudomyrmecinae, a group of arboreal ants with several cases of convergent coevolution without any complete mitochondrial sequence available. In this work, we assembled, annotated and performed comparative genomics analyses of 14 new complete mitochondria from Pseudomyrmecinae species relying solely on public datasets available from the Sequence Read Archive (SRA). We used all complete mitogenomes available for ants to study the gene order conservation and also to generate two phylogenetic trees using both (i) concatenated set of 13 mitochondrial genes and (ii) the whole mitochondrial sequences. Even though the tree topologies diverged subtly from each other (and from previous studies), our results confirm several known relationships and generate new evidences for sister clade classification inside Pseudomyrmecinae clade. We also performed a synteny analysis for Formicidae and identified possible sites in which nucleotidic insertions happened in mitogenomes of pseudomyrmecine ants. Using a data mining/bioinformatics approach, the current work increased the number of complete mitochondrial genomes available for ants from 15 to 29, demonstrating the unique potential of public databases for mitogenomics studies. The wide applications of mitogenomes in research and presence of mitochondrial data in different public dataset types makes the “no budget mitogenomics” approach ideal for comprehensive molecular studies, especially for subsampled taxa.
Vieira et al. (2019) Accessible molecular phylogenomics at no cost: obtaining 14 new mitogenomes for the ant subfamily Pseudomyrmecinae from public data. PeerJ 7:e6271 https://doi.org/10.7717/peerj.6271
Prioritizing bona fide bacterial small RNAs with machine learning classifiers
Bacterial small (sRNAs) are involved in the control of several cellular processes. Hundreds of putative sRNAs have been identified in many bacterial species through RNA sequencing. The existence of putative sRNAs is usually validated by Northern blot analysis. However, the large amount of novel putative sRNAs reported in the literature makes it impractical to validate each of them in the wet lab. In this work, we applied five machine learning approaches to construct twenty models to discriminate bona fide sRNAs from random genomic sequences in five bacterial species. Sequences were represented using seven features including free energy of their predicted secondary structure, their distances to the closest predicted promoter site and Rho-independent terminator, and their distance to the closest open reading frames (ORFs). To automatically calculate these features, we developed an sRNA Characterization Pipeline (sRNACharP). All seven features used in the classification task contributed positively to the performance of the predictive models. The best performing model obtained a median precision of 100% at 10% recall and of 64% at 40% recall across all five bacterial species, and it outperformed previous published approaches on two benchmark datasets in terms of precision and recall. Our results indicate that even though there is limited sRNA sequence conservation across different bacterial species, there are intrinsic features in the genomic context of sRNAs that are conserved across taxa. We show that these features are utilized by machine learning approaches to learn a species-independent model to prioritize bona fide bacterial sRNAs.
Eppenhof et al. (2019) Prioritizing bona fide bacterial small RNAs with machine learning classifiers. PeerJ 7:e6304 https://doi.org/10.7717/peerj.6304
Dietary analysis of an uncharacteristic population of the Mountain Pygmy-possum (Burramys parvus) in the Kosciuszko National Park, New South Wales, Australia
Background The Mountain Pygmy-possum (Burramys parvus) is a critically endangered marsupial, endemic to alpine regions of southern Australia. We investigated the diet of a recently discovered population of the possum in northern Kosciuszko National Park, NSW, Australia. This new population occurs at elevations well below the once-presumed lower elevation limit of 1,600 m. Goals and Methods Faecal material was analysed to determine if dietary composition differed between individuals in the newly discovered northern population and those in the higher elevation southern population, and to examine how diet was influenced by rainfall in the southern population and seasonal changes in resource availability in the northern population. Results and Discussion The diet of B. parvus in the northern population comprised of arthropods, fruits and seeds. Results indicate the diet of both populations shares most of the same invertebrate orders and plant species. However, in the absence of preferred food types available to the southern population, individuals of the northern population opportunistically consumed different species that were similar to those preferred by individuals in higher altitude populations. Differing rainfall amounts had a significant effect on diet, with years of below average rainfall having a greater percentage composition and diversity of invertebrates. Seasonal variation was also recorded, with the northern population increasing the diversity of invertebrates in their diet during the Autumn months when Bogong Moths (Agrotis infusa) were absent from those sites, raising questions about the possum’s dependence on the species Conclusions Measurable effects of rainfall amount and seasonal variation on the dietary composition suggest that predicted climatic variability will have a significant impact on its diet, potentially impacting its future survival. Findings suggest that it is likely that B. parvus is not restricted by dietary requirements to its current pattern of distribution. This new understanding needs to be considered when formulating future conservation strategies for this critically endangered species.
Hawke et al. (2019) Dietary analysis of an uncharacteristic population of the Mountain Pygmy-possum (Burramys parvus) in the Kosciuszko National Park, New South Wales, Australia. PeerJ 7:e6307 https://doi.org/10.7717/peerj.6307
A turiasaurian sauropod dinosaur from the Early Cretaceous Wealden Supergroup of the United Kingdom
The Jurassic/Cretaceous (J/K) boundary, 145 million years ago, has long been recognised as an extinction event or faunal turnover for sauropod dinosaurs, with many ‘basal’ lineages disappearing. However, recently, a number of ‘extinct’ groups have been recognised in the Early Cretaceous, including diplodocids in Gondwana, and non-titanosauriform macronarians in Laurasia. Turiasauria, a clade of non-neosauropod eusauropods, was originally thought to have been restricted to the Late Jurassic of western Europe. However, its distribution has recently been extended to the Late Jurassic of Tanzania (Tendaguria tanzaniensis), as well as to the Early Cretaceous of the USA (Mierasaurus bobyoungi and Moabosaurus utahensis), demonstrating the survival of another ‘basal’ clade across the J/K boundary. Teeth from the Middle Jurassic–Early Cretaceous of western Europe and North Africa have also tentatively been attributed to turiasaurs, whilst recent phylogenetic analyses recovered Late Jurassic taxa from Argentina and China as further members of Turiasauria. Here, an anterior dorsal centrum and neural arch (both NHMUK 1871) from the Early Cretaceous Wealden Supergroup of the UK are described for the first time. NHMUK 1871 shares several synapomorphies with Turiasauria, especially the turiasaurs Moabosaurus and Tendaguria, including: (1) a strongly dorsoventrally compressed centrum; (2) the retention of prominent epipophyses; and (3) an extremely low, non-bifid neural spine. NHMUK 1871 therefore represents the first postcranial evidence for Turiasauria from European deposits of Early Cretaceous age. Although turiasaurs show clear heterodont dentition, only broad, characteristically ‘heart’-shaped teeth can currently be attributed to Turiasauria with confidence. As such, several putative turiasaur occurrences based on isolated teeth from Europe, as well as the Middle Jurassic and Early Cretaceous of Africa, cannot be confidently referred to Turiasauria. Unequivocal evidence for turiasaurs is therefore restricted to the late Middle Jurassic–Early Cretaceous of western Europe, the Late Jurassic of Tanzania, and the late Early Cretaceous of the USA, although remains from elsewhere might ultimately demonstrate that the group had a near-global distribution.
Mannion (2019) A turiasaurian sauropod dinosaur from the Early Cretaceous Wealden Supergroup of the United Kingdom. PeerJ 7:e6348 https://doi.org/10.7717/peerj.6348
Transcriptome profiling reveals the role of ZBTB38 knock-down in human neuroblastoma
ZBTB38 belongs to the zinc finger protein family and contains the typical BTB domains. As a transcription factor, ZBTB38 is involved in cell regulation, proliferation and apoptosis, whereas, functional deficiency of ZBTB38 induces the human neuroblastoma (NB) cell death potentially. To have some insight into the role of ZBTB38 in NB development, high throughput RNA sequencing was performed using the human NB cell line SH-SY5Y with the deletion of ZBTB38. In the present study, 2,438 differentially expressed genes (DEGs) in ZBTB38−/− SH-SY5Y cells were obtained, 83.5% of which was down-regulated. Functional annotation of the DEGs in the Kyoto Encyclopedia of Genes and Genomes database revealed that most of the identified genes were enriched in the neurotrophin TRK receptor signaling pathway, including PI3K/Akt and MAPK signaling pathway. we also observed that ZBTB38 affects expression of CDK4/6, Cyclin E, MDM2, ATM, ATR, PTEN, Gadd45, and PIGs in the p53 signaling pathway. In addition, ZBTB38 knockdown significantly suppresses the expression of autophagy-related key genes including PIK3C2A and RB1CC1. The present meeting provides evidence to molecular mechanism of ZBTB38 modulating NB development and targeted anti-tumor therapies.
Chen et al. (2019) Transcriptome profiling reveals the role of ZBTB38 knock-down in human neuroblastoma. PeerJ 7:e6352 https://doi.org/10.7717/peerj.6352
Genome-wide characterization and expression analyses of the MYB superfamily genes during developmental stages in Chinese jujube
The MYB transcription factor (TF) superfamily, one of the largest gene superfamilies, regulates a variety of physiological processes in plants. Although many MYB superfamily genes have been identified in plants, the MYB TFs in Chinese jujube (Ziziphus jujuba Mill.) have not been fully identified and characterized. Additionally, the functions of these genes remain unclear. In total, we identified 171 MYB superfamily genes in jujube and divided them into five subfamilies containing 99 genes of the R2R3-MYB subfamily, 58 genes of the MYB-related subfamily, four genes of the R1R2R3-MYB subfamily, one gene of the 4R-MYB subfamily, and nine genes of the atypical MYB subfamily. The 99 R2R3-MYB genes of jujube were divided into 35 groups, C1–C35, and the 58 MYB-related genes were divided into the following groups: the R-R-type, CCA1-like, I-box-binding-like, TBP-like, CPC-like, and Chinese jujube-specific groups. ZjMYB genes in jujube were well supported by additional highly conserved motifs and exon/intron structures. Most R1 repeats of MYB-related proteins comprised the R2 repeat and had highly conserved EED and EEE residue groups in jujube. Three tandem duplicated gene pairs were found on 12 chromosomes in jujube. According to an expression analysis of 126 ZjMYB genes, MYB-related genes played important roles in jujube development and fruit-related biological processes. The total flavonoid content of jujube fruit decreased as ripening progressed. A total of 93 expressed genes were identified in the RNA-sequencing data from jujube fruit, and 56 ZjMYB members presented significant correlations with total flavonoid contents by correlation analysis. Five pairs of paralogous MYB genes within jujube were composed of nine jujube MYB genes. A total of 14 ZjMYB genes had the same homology to the MYB genes of Arabidopsis and peach, indicating that these 14 MYB genes and their orthologs probably existed before the ancestral divergence of the MYB superfamily. We used a synteny analysis of MYB genes between jujube and Arabidopsis to predict that the functions of the ZjMYBs involve flavonoid/phenylpropanoid metabolism, the light signaling pathway, auxin signal transduction, and responses to various abiotic stresses (cold, drought, and salt stresses). Additionally, we speculate that ZjMYB108 is an important TF involved in the flavonoid metabolic pathway. This comprehensive analysis of MYB superfamily genes in jujube lay a solid foundation for future comprehensive analyses of ZjMYB gene functions.
Qing et al. (2019) Genome-wide characterization and expression analyses of the MYB superfamily genes during developmental stages in Chinese jujube. PeerJ 7:e6353 https://doi.org/10.7717/peerj.6353
Exploring wearable sensors as an alternative to marker-based motion capture in the pitching delivery
Background Improvements in data processing, increased understanding of the biomechanical background behind kinetics and kinematics, and technological advancements in inertial measurement unit (IMU) sensors have enabled high precision in the measurement of joint angles and acceleration on human subjects. This has resulted in new devices that reportedly measure joint angles, arm speed, and stresses to the pitching arms of baseball players. This study seeks to validate one such sensor, the MotusBASEBALL unit, with a marker-based motion capture laboratory. Hypothesis We hypothesize that the joint angle measurements (“arm slot” and “shoulder rotation”) of the MotusBASEBALL device will hold a statistically significant level of reliability and accuracy, but that the “arm speed” and “stress” metrics will not be accurate due to limitations in IMU technology. Methods A total of 10 healthy subjects threw five to seven fastballs followed by five to seven breaking pitches (slider or curveball) in the motion capture lab. Subjects wore retroreflective markers and the MotusBASEBALL sensor simultaneously. Results It was found that the arm slot (R = 0.975, P < 0.001), shoulder rotation (R = 0.749, P < 0.001), and stress (R = 0.667, P = 0.001 when compared to elbow torque; R = 0.653, P = 0.002 when compared to shoulder torque) measurements were all significantly correlated with the results from the motion capture lab. Arm speed showed significant correlations to shoulder internal rotation speed (R = 0.668, P = 0.001) and shoulder velocity magnitude (R = 0.659, P = 0.002). For the entire sample, arm slot and shoulder rotation measurements were on a similar scale, or within 5–15% in absolute value, of magnitude to measurements from the motion capture test, averaging eight degrees less (12.9% relative differences) and nine degrees (5.4%) less, respectively. Arm speed had a much larger difference, averaging 3,745 deg/s (80.2%) lower than shoulder internal rotation velocity, and 3,891 deg/s (80.8%) less than the shoulder velocity magnitude. The stress metric was found to be 41 Newton meter (Nm; 38.7%) less when compared to elbow torque, and 42 Nm (39.3%) less when compared to shoulder torque. Despite the differences in magnitude, the correlations were extremely strong, indicating that the MotusBASEBALL sensor had high reliability for casual use. Conclusion This study attempts to validate the use of the MotusBASEBALL for future studies that look at the arm slot, shoulder rotation, arm speed, and stress measurements from the MotusBASEBALL sensor. Excepting elbow extension velocity, all metrics from the MotusBASEBALL unit showed significant correlations to their corresponding metrics from motion capture and while some magnitudes differ substantially and therefore fall short in validity, the link between the metrics is strong enough to indicate reliable casual use. Further research should be done to further investigate the validity and reliability of the arm speed metric.
Boddy et al. (2019) Exploring wearable sensors as an alternative to marker-based motion capture in the pitching delivery. PeerJ 7:e6365 https://doi.org/10.7717/peerj.6365
Reproductive pattern and population dynamics of commercial red swamp crayfish (Procambarus clarkii) from China: implications for sustainable aquaculture management
Background The red swamp crayfish, Procambarus clarkii (Girard, 1852), is one of the most promising freshwater species for aquaculture in China. Understanding its reproductive pattern and population dynamics is crucial for sustainable management, but there is currently a lack of fundamental knowledge of commercial P. clarkii populations. Therefore, the purpose of this study was to investigate the reproductive pattern and population dynamics of commercial P. clarkii throughout the yearly cycle. Methods A total of 2,051 crayfish (1,012 females and 1,039 males) were collected from March 2016 to February 2017 in the area of Selection and Reproduction Center of Crayfish. The reproductive pattern was evaluated by the gonadosomatic index (GSI), hepatosomatic index (HSI), ovarian development and fecundity. Growth, mortality rates and exploitation rate were estimated by electronic length frequency analysis by R package “TropFishR” based on data of cephalothorax length (CTL). Results Our results demonstrated that spawning activities of P. clarkii took place from September to November, with a mean fecundity of 429 ± 9 eggs per female. There were two recruitments yearly, a major one from October to November and a minor one from March to May. With respect to population growth, five growth cohorts were identified for both females and males. Crayfish grew faster but attained smaller asymptotic maximum CTL as indicated by higher growth coefficient (K), growth parameter index (Ø′) and lower asymptotic CTL (Linf). The estimates of total mortality rate (Z), natural mortality rate (M) and fishing mortality rate (F) were 1.93, 1.02, 0.91 year−1 for females and 2.32, 0.93, 1.39 year−1 for males, which showed that the mortality of male crayfish was mainly caused by fishing. The estimates of exploitation rate (E) indicated that male crayfish were overexploited, with the values of 0.47 and 0.60 year−1 for females and males, respectively. Discussion P. clarkii spawned from September to November while two recruitments were observed yearly. We inferred that some eggs, prevented from hatching by low water temperature in winter, were more likely to hatch in the next spring. Moreover, the fishing mortality rate was relatively high for males, which might be related to the males-directed selection during the reproductive period. The higher values of exploitation rate in our study confirmed that males P. clarkii were overexploited and were under high fishing pressure. We thus suggest reducing fishing intensity on immature crayfish and avoid sex selection during the reproductive period to improve the overall sustainability of commercial P. clarkii populations.
Jin et al. (2019) Reproductive pattern and population dynamics of commercial red swamp crayfish (Procambarus clarkii) from China: implications for sustainable aquaculture management. PeerJ 7:e6214 https://doi.org/10.7717/peerj.6214
Temporal whole field sawtooth flicker without a spatial component elicits a myopic shift following optical defocus irrespective of waveform direction in chicks
Purpose Myopia (short-sightedness) is the commonest visual disorder and greatest risk factor for sight threatening secondary pathologies. Myopia and hyperopia can be induced in animal models by rearing with optical lens defocus of opposite sign. The degree of refractive compensation to lens-induced defocus in chicks has been shown to be modified by directionally drifting sawtooth spatio-temporal luminance diamond plaids, with Fast-ON sawtooth spatio-temporal luminance profiles inhibiting the myopic shift in response to negative lenses, and Fast-OFF profiles inhibiting the hyperopic shift in response to positive lenses. What is unknown is whether similar sign-of-defocus dependent results produced by spatio-temporal modulation of sawtooth patterns could be achieved by rearing chicks under whole field low temporal frequency sawtooth luminance profiles at 1 or 4 Hz without a spatial component, or whether such stimuli would indiscriminately elicit a myopic shift such as that previously shown with symmetrical (or near-symmetrical) low frequency flicker across a range of species. Methods Hatchling chicks (n = 166) were reared from days five to nine under one of three defocus conditions (No Lens, +10D lens, or −10D lens) and five light conditions (No Flicker, 1 Hz Fast-ON/Slow-OFF sawtooth flicker, 4 Hz Fast-ON/Slow-OFF sawtooth flicker, 1 Hz Fast-OFF/Slow-ON sawtooth flicker, or 4Hz Fast-OFF/Slow-ON sawtooth flicker). The sawtooth flicker was produced by light emitting diodes (white LEDs, 1.2 –183 Lux), and had no measurable dark phase. Biometrics (refraction and ocular axial dimensions) were measured on day nine. Results Both 1 Hz and 4 Hz Fast-ON and Fast-OFF sawtooth flicker induced an increase in vitreous chamber depth that was greater in the presence of negative compared to positive lens defocus. Both sawtooth profiles at both temporal frequencies inhibited the hyperopic shift in response to +10D lenses, whilst full myopic compensation (or over-compensation) in response to −10D lenses was observed. Conclusions Whole field low temporal frequency Fast-ON and Fast-OFF sawtooth flicker induces a generalized myopic shift, similar to that previously shown for symmetrical sine-wave and square-wave flicker. Our findings highlight that temporal modulation of retinal ON/OFF pathways per se (without a spatial component) is insufficient to produce strong sign-of-defocus dependent effect.
Murphy et al. (2019) Temporal whole field sawtooth flicker without a spatial component elicits a myopic shift following optical defocus irrespective of waveform direction in chicks. PeerJ 7:e6277 https://doi.org/10.7717/peerj.6277
The use of one-stage meta-analytic method based on individual participant data for binary adverse events under the rule of three: a simulation study
Objective In evidence synthesis practice, dealing with binary rare adverse events (AEs) is a challenging problem. The pooled estimates for rare AEs through traditional inverse variance (IV), Mantel-Haenszel (MH), and Yusuf-Peto (Peto) methods are suboptimal, as the biases tend to be large. We proposed the “one-stage” approach based on multilevel variance component logistic regression (MVCL) to handle this problem. Methods We used simulations to generate trials of individual participant data (IPD) with a series of predefined parameters. We compared the performance of the MVCL “one-stage” approach and the five classical methods (fixed/random effect IV, fixed/random effect MH, and Peto) for rare binary AEs under different scenarios, which included different sample size setting rules, effect sizes, between-study heterogeneity, and numbers of studies in each meta-analysis. The percentage bias, mean square error (MSE), coverage probability, and average width of the 95% confidence intervals were used as performance indicators. Results We set 52 scenarios and each scenario was simulated 1,000 times. Under the rule of three (a sample size setting rule to ensure a 95% chance of detecting at least one AE case), the MVCL “one-stage” IPD method had the lowest percentage bias in most of the situations and the bias remained at a very low level (<10%), when compared to IV, MH, and Peto methods. In addition, the MVCL “one-stage” IPD method generally had the lowest MSE and the narrowest average width of 95% confidence intervals. However, it did not show better coverage probability over the other five methods. Conclusions The MVCL “one-stage” IPD meta-analysis is a useful method to handle binary rare events and superior compared to traditional methods under the rule of three. Further meta-analyses may take account of the “one-stage” IPD method for pooling rare event data.
Cheng et al. (2019) The use of one-stage meta-analytic method based on individual participant data for binary adverse events under the rule of three: a simulation study. PeerJ 7:e6295 https://doi.org/10.7717/peerj.6295
GenoDup Pipeline: a tool to detect genome duplication using the dS-based method
Understanding whole genome duplication (WGD), or polyploidy, is fundamental to investigating the origin and diversification of organisms in evolutionary biology. The wealth of genomic data generated by next generation sequencing (NGS) has resulted in an urgent need for handy and accurate tools to detect WGD. Here, I present a useful and user-friendly pipeline called GenoDup for inferring WGD using the dS-based method. I have successfully applied GenoDup to identify WGD in empirical data from both plants and animals. The GenoDup Pipeline provides a reliable and useful tool to infer WGD from NGS data.
Mao (2019) GenoDup Pipeline: a tool to detect genome duplication using the dS-based method. PeerJ 7:e6303 https://doi.org/10.7717/peerj.6303
P-curve accurately rejects evidence for homeopathic ultramolecular dilutions
Background P-curve has been proposed as a statistical test of evidential value. The distributions of sets of statistically significant p-values are tested for skewness. P-curves of true effects are right-skewed, with greater density at lower p-values than higher p-values. Analyses of null effects result in a flat or left-skewed distribution. The accuracy of p-curve has not been tested using published research analyses of a null effect. We examined whether p-curve accurately rejects a set of significant p-values obtained for a nonexistent effect. Methods Homeopathic ultramolecular dilutions are medicinal preparations with active substances diluted beyond Avogadro’s number. Such dilute mixtures are unlikely to contain a single molecule of an active substance. We tested whether p-curve accurately rejects the evidential value of significant results obtained in placebo-controlled clinical trials of homeopathic ultramolecular dilutions. Results P-curve accurately rejected the evidential value of significant results obtained in placebo-controlled clinical trials of ultramolecular dilutions. Robustness testing using alternate p-values yielded similar results. Conclusion Our results suggest that p-curve can accurately detect when sets of statistically significant results lack evidential value.
Reisman et al. (2019) P-curve accurately rejects evidence for homeopathic ultramolecular dilutions. PeerJ 7:e6318 https://doi.org/10.7717/peerj.6318
Comparison of automatic airway analysis function of Invivo5 and Romexis software
Background Visualization and calculation of the airway dimensions are important because an increase of airway resistance may lead to life-threatening emergencies. The visualization and calculation of the airway are possible using radiography technique with their advance software. The aim of this study was to compare and to test the reliability of the measurement of the upper airway volume and minimum area using airway analysis function in two software. Methods The sample consisted of 11 cone-beam computed tomography (CBCT) scans data, evaluated using the Invivo5 (Anatomage) and Romexis (version 3.8.2.R, Planmeca) software which afford image reconstruction, and airway analysis. The measurements were done twice with one week gap between the two measurements. The measurement obtained was analyzed with t-tests and intraclass correlation coefficient (ICC), with confidence intervals (CI) was set at 95%. Results From the analysis, the mean reading of volume and minimum area is not significantly different between Invivo5 and Romexis. Excellent intrarater reliability values were found for the both measurement on both software, with ICC values ranging from 0.940 to 0.998. Discussion The results suggested that both software can be used in further studies to investigate upper airway, thereby contributing to the diagnosis of upper airway obstructions.
Kamaruddin et al. (2019) Comparison of automatic airway analysis function of Invivo5 and Romexis software. PeerJ 7:e6319 https://doi.org/10.7717/peerj.6319
The sensitivity and specificity of methylene blue spray to identify the parathyroid gland during thyroidectomy
Background Hypocalcemia is a common complication of thyroidectomy resulting from an injury to the parathyroid gland. Methylene blue, which is a medication and dye that has been used for more than a century, is safe and readily available. The previous study has found that methylene blue spray on the surgical field is absorbed by the parathyroid gland faster than in the perithyroidal area. This study was aimed to evaluate the diagnostic value of methylene blue spray to identify the parathyroid gland during thyroid lobectomy. Methods Patients who underwent thyroid lobectomy were recruited. After the recurrent laryngeal nerve was identified, methylene blue was sprayed onto the thyroid bed. After 5 min, the thyroid bed was inspected for areas in which the blue color had been rapidly absorbed. Biopsies were conducted for histopathology at both the stained area and the area in which the color had faded. The sensitivity, specificity, positive predictive value (PPV), and negative predictive value (NPV) were calculated. Results A total of 47 patients participated in this study. The sensitivity of methylene blue spray to identify the parathyroid gland during thyroid lobectomy was 92.31% (95% CI [63.97–99.81]) and specificity was 56.79% (95% CI [45.31–67.76]). The PPV was 25.53% (95% CI [20.34–31.53]) and NPV was 97.87% (95% CI [87.39–99.67]). There were no patients with post-operative hypocalcemia, allergic reactions to the methylene blue, or methylene blue toxicity. Conclusion The methylene blue spray could serve as a screening tool for identification of the parathyroid gland.
Piromchai et al. (2019) The sensitivity and specificity of methylene blue spray to identify the parathyroid gland during thyroidectomy. PeerJ 7:e6376 https://doi.org/10.7717/peerj.6376
Shifting faunal baselines through the Quaternary revealed by cave fossils of eastern Australia
Fossils from caves in the Manning Karst Region, New South Wales, Australia have long been known, but until now have never been assessed for their palaeontological significance. Here, we report on late Quaternary faunal records from eight caves in the region. Extinct Pleistocene megafaunal taxa are recognised in two systems and include giant echidnas (Tachyglossidae gen. et sp. indet.), devils (Sarcophilus laniarius), koalas (Phascolarctos stirtoni), marsupial ‘lions’ (Thylacoleo carnifex), and kangaroos (Macropus giganteus titan). Some caves contain skeletal remains of introduced exotics such as sheep and dogs, but also provide a rich record of small-bodied native species including Eastern Bettongs (Bettongia gaimardi), Eastern Chestnut Mice (Pseudomys gracilicaudatus), and White-footed Rabbit Rats (Conilurus albipes). These endemics are either locally extirpated or have suffered total extinction in the historic period. Their skeletal and dental remains were recorded as unmineralised surface specimens in the caves, indicating that they are recent in age. Extant populations have never been recorded locally, thus, their probable loss from the region in historic times had gone unnoticed in the absence of palaeo-evidence. Our findings suggest that the supposed habitat tolerances of such species have been substantially underestimated. It is highly likely that modern populations have suffered niche contraction since the time of European colonisation of the continent. The local extirpations of several species of digging mammal has likely led to decreased functionality of the current ecosystem.
Price et al. (2019) Shifting faunal baselines through the Quaternary revealed by cave fossils of eastern Australia. PeerJ 6:e6099 https://doi.org/10.7717/peerj.6099
Antimicrobial susceptibility and virulence genes of clinical and environmental isolates of Pseudomonas aeruginosa
Background Pseudomonas aeruginosa is ubiquitous, has intrinsic antibiotic resistance mechanisms, and is associated with serious hospital-associated infections. It has evolved from being a burn wound infection into a major nosocomial threat. In this study, we compared and correlated the antimicrobial resistance, virulence traits and clonal relatedness between clinical and fresh water environmental isolates of P. aeruginosa. Methods 219 P. aeruginosa isolates were studied: (a) 105 clinical isolates from 1977 to 1985 (n = 52) and 2015 (n = 53), and (b) 114 environmental isolates from different fresh water sources. All isolates were subjected to ERIC-PCR typing, antimicrobial susceptibility testing and virulence factor genes screening. Results Clinical and environmental isolates of P. aeruginosa were genetically heterogenous, with only four clinical isolates showing 100% identical ERIC-PCR patterns to seven environmental isolates. Most of the clinical and environmental isolates were sensitive to almost all of the antipseudomonal drugs, except for ticarcillin/clavulanic acid. Increased resistant isolates was seen in 2015 compared to that of the archived isolates; four MDR strains were detected and all were retrieved in 2015. All clinical isolates retrieved from 1977 to 1985 were susceptible to ceftazidime and ciprofloxacin; but in comparison, the clinical isolates recovered in 2015 exhibited 9.4% resistance to ceftazidime and 5.7% to ciprofloxacin; a rise in resistance to imipenem (3.8% to 7.5%), piperacillin (9.6% to 11.3%) and amikacin (1.9% to 5.7%) and a slight drop in resistance rates to piperacillin/tazobactam (7.7% to 7.5%), ticarcillin/clavulanic acid (19.2% to 18.9%), meropenem (15.4% to 7.5%), doripenem (11.5% to 7.5%), gentamicin (7.7% to 7.5%) and netilmicin (7.7% to 7.5%). Environmental isolates were resistant to piperacillin/tazobactam (1.8%), ciprofloxacin (1.8%), piperacillin (4.4%) and carbapenems (doripenem 11.4%, meropenem 8.8% and imipenem 2.6%). Both clinical and environmental isolates showed high prevalence of virulence factor genes, but none were detected in 10 (9.5%) clinical and 18 (15.8%) environmental isolates. The exoT gene was not detected in any of the clinical isolates. Resistance to carbapenems (meropenem, doripenem and imipenem), β-lactamase inhibitors (ticarcillin/clavulanic acid and piperacillin/tazobactam), piperacillin, ceftazidime and ciprofloxacin was observed in some of the isolates without virulence factor genes. Five virulence-negative isolates were susceptible to all of the antimicrobials. Only one MDR strain harbored none of the virulence factor genes. Conclusion Over a period of 30 years, a rise in antipseudomonal drug resistance particularly to ceftazidime and ciprofloxacin was observed in two hospitals in Malaysia. The occurrence of resistant environmental isolates from densely populated areas is relevant and gives rise to collective anxiety to the community at large.
Liew et al. (2019) Antimicrobial susceptibility and virulence genes of clinical and environmental isolates of Pseudomonas aeruginosa. PeerJ 7:e6217 https://doi.org/10.7717/peerj.6217
Genome-wide analysis of circular RNAs in goat skin fibroblast cells in response to Orf virus infection
Orf, caused by Orf virus (ORFV), is a globally distributed zoonotic disease responsible for serious economic losses in the agricultural sector. However, the mechanism underlying ORFV infection remains largely unknown. Circular RNAs (circRNAs), a novel type of endogenous non-coding RNAs, play important roles in various pathological processes but their involvement in ORFV infection and host response is unclear. In the current study, whole transcriptome sequencing and small RNA sequencing were performed in ORFV-infected goat skin fibroblast cells and uninfected cells. A total of 151 circRNAs, 341 messenger RNAs (mRNAs), and 56 microRNAs (miRNAs) were differently expressed following ORFV infection. Four circRNAs: circRNA1001, circRNA1684, circRNA3127 and circRNA7880 were validated by qRT-PCR and Sanger sequencing. Gene ontology (GO) analysis indicated that host genes of differently expressed circRNAs were significantly enriched in regulation of inflammatory response, epithelial structure maintenance, positive regulation of cell migration, positive regulation of ubiquitin-protein transferase activity, regulation of ion transmembrane transport, etc. The constructed circRNA-miRNA-mRNA network suggested that circRNAs may function as miRNA sponges indirectly regulating gene expression following ORFV infection. Our study presented the first comprehensive profiles of circRNAs in response to ORFV infection, thus providing new clues for the mechanisms of interactions between ORFV and the host.
Pang et al. (2019) Genome-wide analysis of circular RNAs in goat skin fibroblast cells in response to Orf virus infection. PeerJ 7:e6267 https://doi.org/10.7717/peerj.6267
Effects of dredging on the vegetation in a small lowland river
Background Conventional river engineering operations have a substantial influence on the fluvial ecosystem. Regulation and channelization generally reduce the physical heterogeneity of river beds and banks and the heterogeneity of habitats. They determine the character, diversity and species richness of plant communities. The effect of river regulation on vegetation has been repeatedly investigated, but few studies have been conducted within reaches of previously regulated rivers. The aim of this work is to expand and current knowledge about the impact of dredging on the vegetation of a regulated section of a lowland river. Materials & Methods The study included pre-dredging (1 year before) and post-dredging surveys (results 1 and 2 years after dredging). The vegetation was analysed in terms of species composition, origin of species, life forms, distribution of Grime’s life strategies, and selected ecological factors. The Shannon–Wiener biodiversity index (H) and evenness were also analysed in each year of the study. The impact of dredging on the vascular flora was assessed by ‘before-after-control-impact’ (BACI) analysis. Results The number of species and biodiversity as measured by the Shannon–Wiener index (H) increased in the analysed section of the river valley. However, enrichment of the flora was observed only on the floodplain, on the surface of the deposited dredging material, while the number of species in the river channel decreased, as dredging of the river bed and levelling of the banks had markedly reduced habitat diversity. Although species richness in the second year after the dredging approached the values recorded before the intervention, the absence of particularly species or phytocenoses associated with shallow river banks and sandbars was still observed. The change in habitat conditions and the destruction of the vegetation cover during the dredging enabled penetration by numerous previously unrecorded alien species of plants and apophytes. There was a perceptible increase in the role of therophytes in the flora. It is worth noting that the number of alien species and therophytes declined significantly in the second year after the dredging. Analysis of the proportions of species representing various life strategies showed that previously unrecorded species with the type R (ruderal) life strategy had appeared, representing by pioneer species occurring in frequently disturbed habitats. There was also a marked increase in the share of species representing the mixed C-R (competitive-ruderal) strategy, occurring in habitats with low levels of stress, whose competitive abilities are limited by repeated disturbances. By the second year after the dredging, however, these changes were largely no longer observed. Conclusions Through appropriate maintenance of the regulated river, it can be rapidly recolonized by vegetation after the procedure, but it may lead to the loss of some species and phytocoenoses.
Stępień et al. (2019) Effects of dredging on the vegetation in a small lowland river. PeerJ 7:e6282 https://doi.org/10.7717/peerj.6282
Use of open mobile mapping tool to assess human mobility traceability in rural offline populations with contrasting malaria dynamics
Infectious disease dynamics are affected by human mobility more powerfully than previously thought, and thus reliable traceability data are essential. In rural riverine settings, lack of infrastructure and dense tree coverage deter the implementation of cutting-edge technology to collect human mobility data. To overcome this challenge, this study proposed the use of a novel open mobile mapping tool, GeoODK. This study consists of a purposive sampling of 33 participants in six villages with contrasting patterns of malaria transmission that demonstrates a feasible approach to map human mobility. The self-reported traceability data allowed the construction of the first human mobility framework in rural riverine villages in the Peruvian Amazon. The mobility spectrum in these areas resulted in travel profiles ranging from 2 hours to 19 days; and distances between 10 to 167 km. Most Importantly, occupational-related mobility profiles with the highest displacements (in terms of time and distance) were observed in commercial, logging, and hunting activities. These data are consistent with malaria transmission studies in the area that show villages in watersheds with higher human movement are concurrently those with greater malaria risk. The approach we describe represents a potential tool to gather critical information that can facilitate malaria control activities.
Carrasco-Escobar et al. (2019) Use of open mobile mapping tool to assess human mobility traceability in rural offline populations with contrasting malaria dynamics. PeerJ 7:e6298 https://doi.org/10.7717/peerj.6298
Quantitatively estimating main soil water-soluble salt ions content based on Visible-near infrared wavelength selected using GC, SR and VIP
Soil salinization is the primary obstacle to the sustainable development of agriculture and eco-environment in arid regions. The accurate inversion of the major water-soluble salt ions in the soil using visible-near infrared (VIS-NIR) spectroscopy technique can enhance the effectiveness of saline soil management. However, the accuracy of spectral models of soil salt ions turns out to be affected by high dimensionality and noise information of spectral data. This study aims to improve the model accuracy by optimizing the spectral models based on the exploration of the sensitive spectral intervals of different salt ions. To this end, 120 soil samples were collected from Shahaoqu Irrigation Area in Inner Mongolia, China. After determining the raw reflectance spectrum and content of salt ions in the lab, the spectral data were pre-treated by standard normal variable (SNV). Subsequently the sensitive spectral intervals of each ion were selected using methods of gray correlation (GC), stepwise regression (SR) and variable importance in projection (VIP). Finally, the performance of both models of partial least squares regression (PLSR) and support vector regression (SVR) was investigated on the basis of the sensitive spectral intervals. The results indicated that the model accuracy based on the sensitive spectral intervals selected using different analytical methods turned out to be different: VIP was the highest, SR came next and GC was the lowest. The optimal inversion models of different ions were different. In general, both PLSR and SVR had achieved satisfactory model accuracy, but PLSR outperformed SVR in the forecasting effects. Great difference existed among the optimal inversion accuracy of different ions: the predicative accuracy of Ca2+, Na+, Cl−, Mg2+ and SO42− was very high, that of CO32− was high and K+ was relatively lower, but HCO3− failed to have any predicative power. These findings provide a new approach for the optimization of the spectral model of water-soluble salt ions and improvement of its predicative precision.
Wang et al. (2019) Quantitatively estimating main soil water-soluble salt ions content based on Visible-near infrared wavelength selected using GC, SR and VIP. PeerJ 7:e6310 https://doi.org/10.7717/peerj.6310
Seasonal changes of commercial traits, proximate and fatty acid compositions of the scallop Flexopecten glaber from the Mediterranean Sea (Southern Italy)
This study provides information on biological (gonadosomatic index), commercial quality (condition index and meat yield) and biochemical aspects (proximate composition, fatty acids) of the soft tissues of Flexopecten glaber reared in suspended cages in the Ionian Sea. The results showed that condition index (CI) and meat yield (MY) peaked in December (60 and 30%, respectively) and in April, May and June (from 53 to 60% for CI and from 34 to 36% for MY). Gonadosomatic index showed three main peaks in winter, spring and summer months. Contents of protein 8.18–11.9 g/100 g), lipid (0,.78–1.18 g/100 g) and carbohydrate (1.19–3.30 g/100 g) varied significantly during the study period. Saturated fatty acids was the dominant group, except in December when polyunsaturated fatty acids showed the highest proportion (43% of total FAs). Fatty acids of the n3 group were dominant with docosahexaenoic and eicosapentaenoic acids. Highest n3/n6 ratios were recorded in spring-summer specimens, with values > of 5. The results showed a better nutritional quality of scallops in May, July and December.
Prato et al. (2019) Seasonal changes of commercial traits, proximate and fatty acid compositions of the scallop Flexopecten glaber from the Mediterranean Sea (Southern Italy). PeerJ 7:e5810 https://doi.org/10.7717/peerj.5810
Genetic variability in a Brazilian apple germplasm collection with low chilling requirements
The apple (Malus domestica Borkh) originally evolved to require temperatures below 7.2 °C for the induction of budding and flowering. In Brazil, breeders have overcome the climate barrier and developed the cultivars Anabela, Julieta, Carícia, and Eva, with low chilling requirements and good yield characteristics. These cultivars are grown in many warmer climate countries in South America, Africa, and the Middle East. The apple germplasm collection that originated these cultivars has several genotypes with pedigrees for a low chilling requirement. Knowledge of the variability and genetic relationships among these genotypes may be useful in the development of superior new cultivars. In this work, we first selected the best ISSR (inter-simple sequence repeat) primers for genetic studies in apple, and then we used the selected primers to evaluate the genetic variability of the apple germplasm collection at the Instituto Agronômico do Paraná. The evaluation of 42 ISSR primers in 10 apple genotypes allowed us to select the best nine primers based on the polymorphic information content (PIC) and resolving power (RP) indexes. The primer selection step was robust since the dendrogram obtained with the nine selected primers was the same as the one obtained using all 26 polymorphic primers. Primer selection using PIC and RP indexes allowed us to save about 60% of time and costs in the genetic variability study. The nine ISSR primers showed high levels of genetic variability in the 60 apple genotypes evaluated. The relevance of the primer selection step is discussed from the perspective of saving time and money in germplasm characterization. The high genetic variability and the genetic relationships among the genotypes are discussed from the perspective of the development of new apple cultivars, mainly aiming for a low chilling requirement that can better adapt to current climatic conditions or those that may arise with global warming.
Mariano et al. (2019) Genetic variability in a Brazilian apple germplasm collection with low chilling requirements. PeerJ 6:e6265 https://doi.org/10.7717/peerj.6265
Molecular mechanism of point mutation-induced Monopolar spindle 1 (Mps1/TTK) inhibitor resistance revealed by a comprehensive molecular modeling study
Background Monopolar spindle 1 (Mps1/TTK) is an apical dual-specificity protein kinase in the spindle assembly checkpoint (SAC) that guarantees accurate segregation of chromosomes during mitosis. High levels of Mps1 are found in various types of human malignancies, such as glioblastoma, osteosarcoma, hepatocellular carcinoma, and breast cancer. Several potent inhibitors of Mps1 exist, and exhibit promising activity in many cell cultures and xenograft models. However, resistance due to point mutations in the kinase domain of Mps1 limits the therapeutic effects of these inhibitors. Understanding the detailed resistance mechanism induced by Mps1 point mutations is therefore vital for the development of novel inhibitors against malignancies. Methods In this study, conventional molecular dynamics (MD) simulation and Gaussian accelerated MD (GaMD) simulation were performed to elucidate the resistance mechanisms of Cpd-5, a potent Mps1 inhibitor, induced by the four representative mutations I531M, I598F, C604Y, S611R. Results Our results from conventional MD simulation combined with structural analysis and free energy calculation indicated that the four mutations weaken the binding affinity of Cpd-5 and the major variations in structural were the conformational changes of the P-loop, A-loop and αC-helix. Energetic differences of per-residue between the WT system and the mutant systems indicated the mutations may allosterically regulate the conformational ensemble and the major variations were residues of Ile-663 and Gln-683, which located in the key loops of catalytic loop and A-loop, respectively. The large conformational and energetic differences were further supported by the GaMD simulations. Overall, these obtained molecular mechanisms will aid rational design of novel Mps1 inhibitors to combat inhibitor resistance.
Han et al. (2019) Molecular mechanism of point mutation-induced Monopolar spindle 1 (Mps1/TTK) inhibitor resistance revealed by a comprehensive molecular modeling study. PeerJ 7:e6299 https://doi.org/10.7717/peerj.6299
Photosynthesis, yield and raw material quality of sugarcane injured by multiple pests
Understanding sugarcane (Saccharum spp.) response to multiple pest injury, sugarcane borer (Diatraea saccharalis) and spittlebug (Mahanarva fimbriolata), is essential to make better management decisions. Moreover, the consequences of both pests on the sugarcane raw material quality have not yet been studied. A field experiment was performed in São Paulo State, Brazil, where sugarcane plants were exposed to pests individually or in combination. Plots consisted of a 2-m long row of caged sugarcane plants. Photosynthesis was measured once every 3 months (seasonal measurement). Yield and sugar production were assessed. The measured photosynthesis rate was negatively affected by both borer and spittlebug infestations. Photosynthesis reduction was similar on plants infested by both pests as well as by spittlebug individual infestation. Plants under spittlebug infestation resulted in yield losses and represented 17.6% (individual infestation) and 15.5% (multiple infestations). The sucrose content and the sucrose yield per area were reduced when plants were infested by multiple pests or spittlebug.
Rossato Jr et al. (2019) Photosynthesis, yield and raw material quality of sugarcane injured by multiple pests. PeerJ 7:e6166 https://doi.org/10.7717/peerj.6166
Potential surrogate plants for use in semi-field pesticide risk assessment with Megachile rotundata
Background Current regulatory pesticide risk assessments for bees are based primarily on the honey bee (Apis mellifera) and may not always be protective of solitary bees. To incorporate solitary bees into the risk assessment process, standardized methods to assess the hazard of pesticides under semi-field (Tier II) conditions will be needed. We conducted a series of experiments over 2 years to assess potential surrogate plants and adult release rates for use in semi-field experiments with the alfalfa leafcutting bee (ALB, Megachile rotundata). Methods We compared ALB foraging activity and reproduction on 12 m2 plots of flowering alfalfa (Medicago sativa) and buckwheat (Fagopyrum esculentum) at low (10♀/20♂) and high (20♀/40♂) adult release rates. The following year, we assessed the same endpoints on plots of purple tansy (Phacelia tanacetifolia) at a release rate of 10♀/15♂. Results Although ALB foraging activity was high on buckwheat plots, fewer adults were produced compared to alfalfa plots. On alfalfa, there were no differences in foraging activity, nesting, or reproduction between the low and high release rates. ALB readily foraged from purple tansy flowers, but females avoided purple tansy leaves for leaf cell construction. Discussion Our study suggests that buckwheat alone cannot support ALB during semi-field studies on small plots. For alfalfa, we recommend a maximum release rate of 10♀/20♂ in 12 m2 plots. Further study of higher ALB release rates on purple tansy is warranted. A mixed planting of purple tansy and a plant suitable for leaf piece collection (e.g., buckwheat) may provide favorable conditions for ALB activity and reproduction during semi-field testing.
Frewin et al. (2019) Potential surrogate plants for use in semi-field pesticide risk assessment with Megachile rotundata. PeerJ 6:e6278 https://doi.org/10.7717/peerj.6278
Review of the ant genus Meranoplus Smith, 1853 (Hymenoptera: Formicidae) in the Arabian Peninsula with description of a new species M. mosalahi sp. n. from Oman
The species of Meranoplus Smith, 1853 of the Arabian Peninsula are reviewed based on the worker caste. Two species are recognized, keyed, and illustrated by Scanning Electron Microscope images (SEM), Meranoplus mosalahi and M. pulcher, Sharaf, 2014. Meranoplus mosalahi sp. n. is described from the Dhofar Governorate, Oman based on the worker caste. The new species belongs to the M. magrettii-group and closely resembles M. pulcher Sharaf, 2014 from the Kingdom of Saudi Arabia (KSA), from which it can be distinguished by the bicolored body, the shallowly concave anterior clypeal margin, the absence of well-developed anterior clypeal teeth, the fewer irregular longitudinal cephalic rugae, and the feeble longitudinal rugae on posterior face of petiolar node.
Sharaf et al. (2019) Review of the ant genus Meranoplus Smith, 1853 (Hymenoptera: Formicidae) in the Arabian Peninsula with description of a new species M. mosalahi sp. n. from Oman. PeerJ 7:e6287 https://doi.org/10.7717/peerj.6287
Aetiology of livestock fetal mortality in Mazandaran province, Iran
In the farming industry, the productivity of livestock herds depends on the fertility efficiency of animals. The accurate diagnosis of a broad range of aetiological agents causing fetal death is often difficult. Our aim was to assess the prevalence rates of Toxoplasma gondii, Neospora caninum, and Brucella spp. infections in ruminant abortion using bacteriological culture and molecular techniques in Mazandaran Province, northern Iran. Samples were collected from 70 aborted sheep, goat, and cattle fetuses between September 2014 and December 2015. Necropsy was performed on all the received samples, and brain tissue and abomasal content were obtained from the aborted fetuses. Protozoan infections were detected by specific polymerase chain reaction (PCR) and bacterial agents using bacteriological examinations and PCR assay. Infectious pathogens were detected in 22 out of 70 (31.4%) examined fetuses. Moreover, T. gondii, N. caninum, and B. melitensis were verified in 13 (18.6%), four (5.7%), and two (2.85%) samples, respectively. Our results showed that infection with the mentioned pathogenic agents may lead to fetal mortality, which can be a major cause of economic loss. The listed pathogens could be considered important etiological agents of fetal loss in Mazandaran Province, for which appropriate control measures such as vaccination and biosecurity can be implemented to prevent infection and reduce reproductive loss in livestock farms.
Amouei et al. (2019) Aetiology of livestock fetal mortality in Mazandaran province, Iran. PeerJ 6:e5920 https://doi.org/10.7717/peerj.5920
A large cockroach from the mesosaur-bearing Konservat-Lagerstätte (Mangrullo Formation), Late Paleozoic of Uruguay
Barona arcuata, n.gen et n.sp., a left forewing of a relatively large cockroach of the Order Blattaria, is described from mesosaur-bearing lagoonal shales of the Mangrullo Formation (north-eastern Uruguay). While most of the insect remains recovered from the Mangrullo Formation come from sandy limestones, associated to scarce isolated mesosaur bones and pygocephalomorph crustaceans, the cockroach wing here described was found in the overlaying green to brownish, gray and dark black shales associated to intercalated bentonites and evaporitic gypsum crystals. Barona arcuata shares some features with typical Late Carboniferous taxa such as its general venation pattern and outline of the wing, four main and powerful veins arising close together from near the base of the wing, Sc simple forked, pectinate, reaching the costal border through a long fork, R and M bifurcating and terminating in the wing margin above and below the apex respectively, short and narrow CuA, and the presence of a broad interspace between CuP and AA. Cross venation seems to be absent or it was not preserved. Some characters might relate Barona arcuata to the Late Carboniferous-Early Permian Neothroblattinidae such as the presence of sigmoidal veins in the anal area, a condition not found in any of the remaining representatives of the Palaeozoic Blattaria. Intriguingly, the Uruguayan blattarian also presents a strong similarity with Qilianiblatta namurensis Zhang, Schneider & Hong, 2012 from the Westphalian of China, clearly a smaller taxon that is also difficult to relate to any of the preexistent families. The apparent plesiomorphic venation pattern of the new species which is reminiscent of that present in the oldest known blattarians, is in agreement with a Permo-Carboniferous (Gzhelian-Asselian) age for the Mangrullo Formation also supported by the presence of a macrofloral assemblage dominated by arborescent lepidondendrids and other lycopsids and the pygocephalid-like morphology of the pygocephalomorph crustaceans from the same levels.
Calisto et al. (2019) A large cockroach from the mesosaur-bearing Konservat-Lagerstätte (Mangrullo Formation), Late Paleozoic of Uruguay. PeerJ 7:e6289 https://doi.org/10.7717/peerj.6289
Phylogeography and population genetics of the endemic Malagasy bat, Macronycteris commersoni s.s. (Chiroptera: Hipposideridae)
Macronycteris commersoni (Hipposideridae), a bat species endemic to Madagascar, is widespread across the island and utilizes a range of habitat types including open woodland, degraded habitats, and forested areas from sea level to 1,325 m. Despite being widely distributed, there is evidence that M. commersoni exhibits morphological and bioacoustic variation across its geographical range. We investigated the fine-scale phylogeographic structure of populations in the western half of the island using extensive spatial sampling and sequence data from two mitochondrial DNA regions. Our results indicated several lineages within M. commersoni. Individuals collected from northern Madagascar formed a single monophyletic clade (clade C). A second clade (clade B) included individuals collected from the south-western portion of the island. This second clade displayed more phylogeographical partitioning with differences in mtDNA haplotypes frequency detected between populations collected in different bioclimatic regions. Lineage dispersal, genetic divergence, and timing of expansion events of M. commersoni were probably associated with Pleistocene climate fluctuations. Our data suggest that the northern and the central western regions of Madagascar may have acted as refugia for this species during periods of cooler and drier climate conditions associated with the Pleistocene.
Rakotoarivelo et al. (2019) Phylogeography and population genetics of the endemic Malagasy bat, Macronycteris commersoni s.s. (Chiroptera: Hipposideridae). PeerJ 7:e5866 https://doi.org/10.7717/peerj.5866
Seasonality and trend prediction of scarlet fever incidence in mainland China from 2004 to 2018 using a hybrid SARIMA-NARX model
Background Scarlet fever is recognized as being a major public health issue owing to its increase in notifications in mainland China, and an advanced response based on forecasting techniques is being adopted to tackle this. Here, we construct a new hybrid method incorporating seasonal autoregressive integrated moving average (SARIMA) with a nonlinear autoregressive with external input(NARX) to analyze its seasonality and trend in order to efficiently prevent and control this re-emerging disease. Methods Four statistical models, including a basic SARIMA, basic nonlinear autoregressive (NAR) method, traditional SARIMA-NAR and new SARIMA-NARX hybrid approaches, were developed based on scarlet fever incidence data between January 2004 and July 2018 to evaluate its temporal patterns, and their mimic and predictive capacities were compared to discover the optimal using the mean absolute percentage error, root mean square error, mean error rate, and root mean square percentage error. Results The four preferred models identified were comprised of the SARIMA(0,1,0)(0,1,1)12, NAR with 14 hidden neurons and five delays, SARIMA-NAR with 33 hidden neurons and five delays, and SARIMA-NARX with 16 hidden neurons and 4 delays. Among which presenting the lowest values of the aforementioned indices in both simulation and prediction horizons is the SARIMA-NARX method. Analyses from the data suggested that scarlet fever was a seasonal disease with predominant peaks of summer and winter and a substantial rising trend in the scarlet fever notifications was observed with an acceleration of 9.641% annually, particularly since 2011 with 12.869%, and moreover such a trend will be projected to continue in the coming year. Conclusions The SARIMA-NARX technique has the promising ability to better consider both linearity and non-linearity behind scarlet fever data than the others, which significantly facilitates its prevention and intervention of scarlet fever. Besides, under current trend of ongoing resurgence, specific strategies and countermeasures should be formulated to target scarlet fever.
Wang et al. (2019) Seasonality and trend prediction of scarlet fever incidence in mainland China from 2004 to 2018 using a hybrid SARIMA-NARX model. PeerJ 7:e6165 https://doi.org/10.7717/peerj.6165
Outcomes of hospitalizations with atrial fibrillation-flutter on a weekday versus weekend: an analysis from a 2014 nationwide inpatient sample
Background Patients with atrial fibrillation-flutter (AF) admitted on the weekends were initially reported to have poor outcomes. The primary purpose of this study is to re-evaluate the outcomes for weekend versus weekday AF hospitalization using the 2014 Nationwide Inpatient Sample (NIS). Methods Included hospitalizations were aged above 18 years. The hospitalizations with AF were identified using the international classification of diseases 9 (ICD-9) codes (427.31, 427.32). In-hospital mortality, length of stay (LOS), other co-morbidities, cardioversion procedures, and time to cardioversion were recorded. All analysis was performed using SAS 9.4 statistical software (Cary, North Carolina). Results A total of 453,505 hospitalizations with atrial fibrillation and flutter as primary discharge diagnosis were identified. Among the total hospitalizations with a primary diagnosis of AF, 20.3% were admitted on the weekend. Among the weekend hospitalizations, 0.19% died in hospital compared to 0.74% among those admitted during the week. After adjusting for patient characteristics, hospital characteristics and disease severity, the adjusted odds for in-hospital mortality were not significantly different for weekend vs. weekday hospitalizations (OR = 0.91, 95% CI [0.77–1.11]; p = 0.33). The weekend admissions were associated with significantly lower odds of cardioversion procedures (OR = 0.72, 95% CI [0.69–0.76], P < 0.0001), lower cost of hospitalization (USD 8265.8 on weekends vs. USD 8966.5 on the weekdays, P < 0.001), slightly lower rate of anticoagulation (17.09% on the weekends vs. 18.73% on the weekdays. P < 0.0001), and slightly increased time to cardioversion (1.94 days on the weekend vs. 1.73 days on weekdays, P < 0.0005). The mean length of hospital stay (LOS) was statistically not different in both groups: (3.49 days ± 3.70 (SD) in the weekend group vs. 3.47 days ± 3.50 (SD) in the weekday group, P = 0.42) Discussion The weekend AF hospitalizations did not have a clinically significant difference in mortality and LOS compared to those admitted on a weekday. However, the use of cardioversion procedures and cost of hospitalization was significantly lower on the weekends.
Voruganti et al. (2019) Outcomes of hospitalizations with atrial fibrillation-flutter on a weekday versus weekend: an analysis from a 2014 nationwide inpatient sample. PeerJ 7:e6211 https://doi.org/10.7717/peerj.6211
Extremely low levels of chloroplast genome sequence variability in Astelia pumila (Asteliaceae, Asparagales)
Astelia pumila (G.Forst.) Gaudich. (Asteliaceae, Asparagales) is a major element of West Patagonian cushion peat bog vegetation. With the aim to identify appropriate chloroplast markers for the use in a phylogeographic study, the complete chloroplast genomes of five A. pumila accessions from almost the entire geographical range of the species were assembled and screened for variable positions. The chloroplast genome sequence was obtained via a mapping approach, using Eustrephus latifolius (Asparagaceae) as a reference. The chloroplast genome of A. pumila varies in length from 158,215 bp to 158,221 bp, containing a large single copy region of 85,981–85,983 bp, a small single copy region of 18,182–18,186 bp and two inverted repeats of 27,026 bp. Genome annotation predicted a total of 113 genes, including 30 tRNA and four rRNA genes. Sequence comparisons revealed a very low degree of intraspecific genetic variability, as only 37 variable sites (18 indels, 18 single nucleotide polymorphisms, one 3-bp mutation)—most of them autapomorphies—were found among the five assembled chloroplast genomes. A Maximum Likelihood analysis, based on whole chloroplast genome sequences of several Asparagales accessions representing six of the currently recognized 14 families (sensu APG IV), confirmed the phylogenetic position of A. pumila. The chloroplast genome of A. pumila is the first to be reported for a member of the astelioid clade (14 genera with c. 215 species), a basally branching group within Asparagales.
Pfanzelt et al. (2019) Extremely low levels of chloroplast genome sequence variability in Astelia pumila (Asteliaceae, Asparagales). PeerJ 7:e6244 https://doi.org/10.7717/peerj.6244
Effects of nickel and cobalt on methane production and methanogen abundance and diversity in paddy soil
Background Paddies are an important anthropogenic source of methane emissions to the atmosphere, and they are impacted by heavy metal pollution. Nickel (Ni) and cobalt (Co) pollution might either enhance or mitigate CH4 emission from paddy soils due to the total amounts of metals, bioavailability and functional microbial activity and composition. Methods An incubation experiment was conducted, and different Ni and Co concentrations were added to test the effects of trace metals on methane production in paddy soil. The archaea community structure and the abundance of methanogen functional groups in the paddy soil with added Ni and Co were detected using high-throughput sequencing and quantitative PCR based on the 16S rRNA and mcrA (methyl coenzyme M reductase) genes, respectively. Results The highest methane production rate was 561 mg CH4 kg−1 dry soil d−1 with the addition of 50 mg kg−1 Ni and 684 mg CH4 kg−1 dry soil d−1 with the addition of 25 mg kg−1 Co. Accordingly, the mcrA gene was most abundant in the 50 mg kg−1 Ni addition (3.1 × 106 ± 0.5 × 106 copies g−1 dry soil). The lowest mcrA gene abundance was detected in the 500 mg kg−1 Co addition (9.2× 105 ± 0.4 × 105 copies g−1 dry soil). The dominant methanogens were Methanobacterium, Methanosarcina, Methanocella, Methanomassiliicoccus, Bathyarchaeota, and Rice Cluster I (RC-I), and the relative abundances of these groups were higher than 1% in the Ni and Co treatments. Additionally, the archaeal compositions differed significantly in the soils with various Ni and Co additions. The most abundant Methanococcus spp. represented 51.3% of the composition in the 50 mg kg−1 Ni addition, which was significantly higher than that of the control (12.9% to 17.5%). Discussion Our results indicated that the contamination of soil by Ni and Co significantly affected total methanogens abundance and specific methanogen functional groups. Ni and Co additions to paddy soil promoted methanogenic activity at low concentrations, while they had inhibitory effects at high concentrations. Because paddy soils largely contribute to methane emissions and are increasingly exposed to heavy metal pollution, our results show that future assessments of greenhouse gas flux from paddy soils should take into account the effects of pollution by Ni and Co.
Wang et al. (2019) Effects of nickel and cobalt on methane production and methanogen abundance and diversity in paddy soil. PeerJ 7:e6274 https://doi.org/10.7717/peerj.6274
Evaluation of AAV-DJ vector for retinal gene therapy
Purpose The most common virus vector used in gene therapy research for ophthalmologic diseases is the adeno-associated virus (AAV) vector, which has been used successfully in a number of preclinical and clinical studies. It is important to evaluate novel AAV vectors in animal models for application of clinical gene therapy. The AAV-DJ (type 2/type 8/type 9 chimera) was engineered from shuffling eight different wild-type native viruses. In this study, we investigated the efficiency of gene transfer by AAV-DJ injections into the retina. Methods One microliter of AAV-2-CAGGS-EGFP or AAV-DJ-CAGGS-EGFP vector at a titer of 1.4 × 10e12 vg/ml was injected intravitreally or subretinally in each eye of C57BL/6 mice. We evaluated the transduction characteristics of AAV-2 and -DJ vectors using fluorescence microscopy and electroretinography. Results The results confirmed that AAV-DJ could deeply transfer gene to photoreceptor layer with intravitreal injection and has an efficient gene transfer to various cell types especially the Mueller cells in the retina. Retinal function was not affected by AAV-DJ infection or ectopic EGFP expression. Conclusions The AAV-DJ vector efficiently induces the reporter gene in both the inner and outer murine retina without functional toxicity. These data indicated that the AAV-DJ vector is a useful tool for the gene therapy research targeting retinal disorders.
Katada et al. (2019) Evaluation of AAV-DJ vector for retinal gene therapy. PeerJ 7:e6317 https://doi.org/10.7717/peerj.6317
Putatively asexual chrysophytes have meiotic genes: evidence from transcriptomic data
Chrysophytes are a large group of heterotrophic, phototrophic, or even mixotrophic protists that are abundant in aquatic as well as terrestrial environments. Although much is known about chrysophyte biology and ecology, it is unknown if they are sexual or not. Here we use available transcriptomes of 18 isolates of 15 putatively asexual species to inventory the presence of genes used in meiosis. Since we were able to detect a set of nine meiosis-specific and 29 meiosis-related genes shared by the chrysophytes, we conclude that they are secretively sexual and therefore should be investigated further using genome sequencing to uncover any missed genes from the transcriptomes.
Kraus et al. (2019) Putatively asexual chrysophytes have meiotic genes: evidence from transcriptomic data. PeerJ 6:e5894 https://doi.org/10.7717/peerj.5894
Targeted inactivation of Salmonella Agona metabolic genes by group II introns and in vivo assessment of pathogenicity and anti-tumour activity in mouse model
The fight against cancer has been a never-ending battle. Limitations of conventional therapies include lack of selectivity, poor penetration and highly toxic to the host. Using genetically modified bacteria as a tumour therapy agent has gained the interest of scientist from the past few decades. Low virulence and highly tolerability of Salmonella spp. in animals and humans make it as the most studied pathogen with regards to anti-tumour therapy. The present study aims to construct a genetically modified S. Agona auxotroph as an anti-tumour agent. LeuB and ArgD metabolic genes in ΔSopBΔSopD double knockout S. Agona were successfully knocked out using a Targetron gene knockout system. The knockout was confirmed by colony PCR and the strains were characterized in vitro and in vivo. The knockout of metabolic genes causes significant growth defect in M9 minimal media. Quadruple knockout ΔSopBΔSopDΔLeuBΔArgD (BDLA) exhibited lowest virulence among all of the strains in all parameters including bacterial load, immunity profile and histopathology studies. In vivo anti-tumour study on colorectal tumour bearing-BALB/c mice revealed that all strains of S. Agona were able to suppress the growth of the large solid tumour as compared with negative control and ΔLeuBΔArgD (LA) and BDLA auxotroph showed better efficacy. Interestingly, higher level of tumour growth suppression was noticed in large tumour. However, multiple administration of bacteria dosage did not increase the tumour suppression efficacy. In this study, the virulence of BDLA knockout strain was slightly reduced and tumour growth suppression efficacy was successfully enhanced, which provide a valuable starting point for the development of S. Agona as anti-tumour agent.
Gwee et al. (2019) Targeted inactivation of Salmonella Agona metabolic genes by group II introns and in vivo assessment of pathogenicity and anti-tumour activity in mouse model. PeerJ 7:e5989 https://doi.org/10.7717/peerj.5989
Inverse modelling for predicting both water and nitrate movement in a structured-clay soil (Red Ferrosol)
Soil physical parameter calculation by inverse modelling provides an indirect way of estimating the unsaturated hydraulic properties of soils. However many measurements are needed to provide sufficient data to determine unknown parameters. The objective of this research was to assess the use of unsaturated water flow and solute transport experiments, in horizontal packed soil columns, to estimate the parameters that govern water flow and solute transport. The derived parameters are then used to predict water infiltration and solute migration in a repacked soil wedge. Horizontal columns packed with Red Ferrosol were used in a nitrate diffusion experiment to estimate either three or six parameters of the van Genuchten–Mualem equation while keeping residual and saturated water content, and saturated hydraulic conductivity fixed to independently measured values. These parameters were calculated using the inverse optimisation routines in Hydrus 1D. Nitrate concentrations measured along the horizontal soil columns were used to independently determine the Langmuir adsorption isotherm. The soil hydraulic properties described by the van Genuchten–Mualem equation, and the NO3– adsorption isotherm, were then used to predict water and NO3– distributions from a point-source in two 3D flow scenarios. The use of horizontal columns of repacked soil and inverse modelling to quantify the soil water retention curve was found to be a simple and effective method for determining soil hydraulic properties of Red Ferrosols. These generated parameters supported subsequent testing of interactive flow and reactive transport processes under dynamic flow conditions.
Kirkham et al. (2019) Inverse modelling for predicting both water and nitrate movement in a structured-clay soil (Red Ferrosol). PeerJ 6:e6002 https://doi.org/10.7717/peerj.6002
Growth estimation of the larger foraminifer Heterostegina depressa by means of population dynamics
In Heterostegina depressa, the flagship species of laboratory investigations of larger benthic foraminifera (LBF) since the 70’s, the timing of reproduction, longevity and natural chamber building rates are still understudied. A recently developed method, the natural laboratory (sensu Hohenegger), has been applied on H. depressa populations from Sesoko Jima, NW Okinawa, Japan. An averaged chamber building rate and longevity of H. depressa were calculated based on 17 monthly samplings at fixed stations. All samples were collected at 20 and 50 m water depths using SCUBA. Live populations were dried and investigated by microCT. The monthly frequency distributions of chamber numbers and test diameters have been decomposed in normally distributed components. For each month, mean and standard deviations of the components were used to calculate the maximum chamber number and maximum test diameter. Based on these values, the natural chamber building rate (CBR) or diameter increase rate (DIR) could be estimated using the Michaelis-Menten function. CBR and DIR were inverted to estimate the ‘birthdate’ of all investigated individuals. Based on frequencies of these ‘birthdates’, main reproduction events could be detected and compared to the reproduction timing of other subtropical and tropical LBF taxa. Furthermore, peaks in reproduction could be linked to monsoon wet seasons (=“rainy seasons”) and winter rains.
Eder et al. (2019) Growth estimation of the larger foraminifer Heterostegina depressa by means of population dynamics. PeerJ 6:e6096 https://doi.org/10.7717/peerj.6096
Recognition of species groups of Naupactus Dejean (Coleoptera: Curculionidae) from Argentina and neighboring countries
Naupactus Dejean is the most diverse genus of the tribe Naupactini (Curculionidae: Entiminae), with more than 200 species occurring in South America, of which about 40 range in Argentina and neighboring countries. The Argentinean species treated herein were classified into nine groups having different biogeographic patterns: (1) the groups of Naupactus xanthographus, N. delicatulus and N. auricinctus mainly occur in northeastern Argentina (Misiones province) and reach the highest species diversity in the Atlantic and Parana forests of Brazil; (2) the groups of N. hirtellus, N. cinereidorsum, N. rivulosus and N. tarsalis show the highest species diversity in the Chacoan biogeographic province and also occur in the Yungas, Espinal, Monte, Parana forest (Argentina) and Cerrado (Brazil); (3) the groups of N. leucoloma and N. purpureoviolaceus have the highest species diversity in the Pampean biogeographic province, being also present in adjoining areas, mainly Chaco, Espinal, Monte and Parana forest. We provide descriptions, a dichotomous key, habitus photographs and line drawings of genitalia for the identification of the nine species groups, and a list of the Argentinean species from each group, together with their abbreviated synonymies, updated geographic distributions (including six new country records and several state/province records) and host plant associations. We discuss the characters that allow the separation of the species groups in a geographic distribution context, and provide information on species reassigned to genera other than Naupactus; among these, we transferred N. cephalotes (Hustache) to the tribe Tanymecini, genus Eurymetopellus, establishing the new combination Eurymetopellus cephalotes.
del Río et al. (2019) Recognition of species groups of Naupactus Dejean (Coleoptera: Curculionidae) from Argentina and neighboring countries. PeerJ 6:e6196 https://doi.org/10.7717/peerj.6196
Registered reports: an early example and analysis
The recent ‘replication crisis’ in psychology has focused attention on ways of increasing methodological rigor within the behavioral sciences. Part of this work has involved promoting ‘Registered Reports’, wherein journals peer review papers prior to data collection and publication. Although this approach is usually seen as a relatively recent development, we note that a prototype of this publishing model was initiated in the mid-1970s by parapsychologist Martin Johnson in the European Journal of Parapsychology (EJP). A retrospective and observational comparison of Registered and non-Registered Reports published in the EJP during a seventeen-year period provides circumstantial evidence to suggest that the approach helped to reduce questionable research practices. This paper aims both to bring Johnson’s pioneering work to a wider audience, and to investigate the positive role that Registered Reports may play in helping to promote higher methodological and statistical standards.
Wiseman et al. (2019) Registered reports: an early example and analysis. PeerJ 7:e6232 https://doi.org/10.7717/peerj.6232
Termite mound architecture regulates nest temperature and correlates with species identities of symbiotic fungi
Background Large and complex mounds built by termites of the genus Macrotermes characterize many dry African landscapes, including the savannas, bushlands, and dry forests of the Tsavo Ecosystem in southern Kenya. The termites live in obligate symbiosis with filamentous fungi of the genus Termitomyces. The insects collect dead plant material from their environment and deposit it into their nests where indigestible cell wall compounds are effectively decomposed by the fungus. Above-ground mounds are built to enhance nest ventilation and to maintain nest interior microclimates favorable for fungal growth. Objectives In Tsavo Ecosystem two Macrotermes species associate with three different Termitomyces symbionts, always with a monoculture of one fungal species within each termite nest. As mound architecture differs considerably both between and within termite species we explored potential relationships between nest thermoregulatory strategies and species identity of fungal symbionts. Methods External dimensions were measured from 164 Macrotermes mounds and the cultivated Termitomyces species were identified by sequencing internal transcribed spacer (ITS) region of ribosomal DNA. We also recorded the annual temperature regimes of several termite mounds to determine relations between mound architecture and nest temperatures during different seasons. Results Mound architecture had a major effect on nest temperatures. Relatively cool temperatures were always recorded from large mounds with open ventilation systems, while the internal temperatures of mounds with closed ventilation systems and small mounds with open ventilation systems were consistently higher. The distribution of the three fungal symbionts in different mounds was not random, with one fungal species confined to “hot nests.” Conclusions Our results indicate that different Termitomyces species have different temperature requirements, and that one of the cultivated species is relatively intolerant of low temperatures. The dominant Macrotermes species in our study area can clearly modify its mound architecture to meet the thermal requirements of several different symbionts. However, a treacherous balance seems to exist between symbiont identity and mound architecture, as the maintenance of the thermophilic fungal species obviously requires reduced mound architecture that, in turn, leads to inadequate gas exchange. Hence, our study concludes that while the limited ventilation capacity of small mounds sets strict limits to insect colony growth, in this case, improving nest ventilation would invariable lead to excessively low nest temperatures, with negative consequences to the symbiotic fungus.
Vesala et al. (2019) Termite mound architecture regulates nest temperature and correlates with species identities of symbiotic fungi. PeerJ 6:e6237 https://doi.org/10.7717/peerj.6237
Screening of reference genes in real-time PCR for Radopholus similis
Six candidate reference genes were chosen from the transcriptome database of Radopholus similis using the bioinformatics method, including four conventional reference genes (actin, Eukaryotic translation initiation factor 5A (eIF5A), Tubulin alpha (a-tubulin), ubiquitin (UBI)) and two new candidate reference genes (Ribosomal protein S21 (Rps21) and Serine/threonine protein phosphatase PP1-β catalytic subunit (β-PP1)). In addition, a traditional reference gene 18S ribosomal RNA (18S rRNA) obtained from NCBI databases was also added to the analysis. Real-time PCR was used to detect the expression of seven candidate reference genes in six populations of R. similis and four developmental stages (female, male, larva and egg) of a population. The stability of the expression of candidate genes was evaluated by three software programs, BestKeeper, geNorm and NormFinder. The results showed that eIF5A is the most suitable reference gene for gene functional research of different populations, while both Rps21 and eIF5A are the most suitable reference genes for different developmental stages of a population. Therefore, eIF5A is the best reference gene for studying R. similis. However, one defect of this study is that only seven candidate reference genes were analyzed; ideally, more genes should be tested.
Li et al. (2019) Screening of reference genes in real-time PCR for Radopholus similis. PeerJ 7:e6253 https://doi.org/10.7717/peerj.6253
Foraging habitat choice of White-tailed Tropicbirds revealed by fine-scale GPS tracking and remote sensing
Background The introduction of animal tracking technology has rapidly advanced our understanding of seabird foraging ecology. Tracking data is particularly powerful when combined with oceanographic information derived from satellite remote sensing, allowing insights into the functional mechanisms of marine ecosystems. While this framework has been used extensively over the last two decades, there are still vast ocean regions and many seabird species for which information is scarce, particularly in tropical oceans. Methods In this study we tracked the movement at high GPS recording frequency of 15 White-tailed Tropicbirds (Phaethon lepturus) during chick-rearing from a colony in Fernando de Noronha (offshore of Northeast Brazil). Flight behaviours of travelling and searching for food were derived from GPS data and examined in relation to satellite-sensed oceanographic variables (sea surface temperature, turbidity and chlorophyll-a concentration). Results White-tailed Tropicbirds showed marked preference for clear and warm sea surface waters, which are indicative of low primary productivity but are likely the best habitat for preying upon flying fish. Discussion These findings are consistent with previous studies showing that foraging habitat choices of tropical seabirds may not be driven by primary productivity, as has been widely shown for non-tropical species.
Santos et al. (2019) Foraging habitat choice of White-tailed Tropicbirds revealed by fine-scale GPS tracking and remote sensing. PeerJ 7:e6261 https://doi.org/10.7717/peerj.6261
Effects of table tennis multi-ball training on dynamic posture control
Background Prior to the 2017 table tennis season, each participant performed the anterior, posteromedial, and posterolateral the star excursion balance test (SEBT) reach distances in a randomized order. The aim of this study was to assess the effects of table tennis multi-ball training and dynamic balance on performance measures of the SEBT for the male and female. Methods The limb lengths of the 12 table tennis athletes were measured bilaterally in the study. Besides warm-up end, the data of this study were recorded at a regular interval at approximately 16 min for the entire multi-ball training session, and they were defined as Phase I, Phase II, Phase II, respectively. The Borg rating of perceived exertion (RPE) scale was used to document the degree of physical strain. Results Reaching distances showed a decrease with training progression in all directions. Compared with the male table tennis athletes, the females showed poorer dynamic posture control, particularly when the free limb was considered with the right-leg stance toward posterolateral and posteromedial directions in phase I. Discussion This study suggests that during table tennis multi-ball training the male should have a regulatory protocol to compensate the deficit observed in phase II, but the females should be given the protocol in phase I.
Gu et al. (2019) Effects of table tennis multi-ball training on dynamic posture control. PeerJ 6:e6262 https://doi.org/10.7717/peerj.6262
Individual and flock immunity responses of naïve ducks on smallholder farms after vaccination with H5N1 Avian Influenza vaccine: a study in a province of the Mekong Delta, Vietnam
In Vietnam, vaccination has played a crucial role in the national strategy for the prevention and control of H5 highly pathogenic avian influenza (HPAI). This study aimed to evaluate antibody responses of immunologically naïve domestic ducks to H5N1 avian influenza vaccine currently used in the national mass vaccination program of Vietnam. Blood samples of 166 ducks reared on smallholder farms were individually collected at three sampling time points, namely, right before vaccination, 21 days after primary vaccination, and 21 days after booster vaccination. Vaccine-induced antibody titers of duck sera were measured by the hemagglutination inhibition assay. Temporal differences in mean antibody titers were analyzed using the generalized least-squares method. No sampled ducks showed anti-H5 seropositivity pre-vaccination. The geometric mean titer (GMT) of the vaccinated ducks was 5.30 after primary vaccination, with 80% of the vaccinated ducks showing seropositivity. This result indicates that the immunity of duck flocks met the targets of the national poultry H5N1 HPAI mass vaccination program. GMT and seropositive rates of the ducks were 6.48 and 96.3%, respectively, after booster vaccination, which were significantly higher than those after primary vaccination. Flock-level seroprotection rate significantly increased from 68% to 84.7%, whereas variability in GMT titers decreased from 34.87% to 26.3%. This study provided important information on humoral immune responses of ducks to the currently used H5N1 vaccine under field conditions. Our findings may help guide veterinary authorities in planning effective vaccine protocols for the prevention and control of H5N1 in the target poultry population.
Huynh et al. (2019) Individual and flock immunity responses of naïve ducks on smallholder farms after vaccination with H5N1 Avian Influenza vaccine: a study in a province of the Mekong Delta, Vietnam. PeerJ 7:e6268 https://doi.org/10.7717/peerj.6268
CRISPR/Cas9-mediated deletion of the Wiskott-Aldrich syndrome locus causes actin cytoskeleton disorganization in murine erythroleukemia cells
Wiskott-Aldrich syndrome (WAS) is a recessive X-linked inmmunodeficiency caused by loss-of-function mutations in the gene encoding the WAS protein (WASp). WASp plays an important role in the polymerization of the actin cytoskeleton in hematopoietic cells through activation of the Arp2/3 complex. In a previous study, we found that actin cytoskeleton proteins, including WASp, were silenced in murine erythroleukemia cells defective in differentiation. Here, we designed a CRISPR/Cas9 strategy to delete a 9.5-kb genomic region encompassing the Was gene in the X chromosome of murine erythroleukemia (MEL) cells. We show that Was-deficient MEL cells have a poor organization of the actin cytoskeleton that can be recovered by restoring Was expression. We found that whereas the total amount of actin protein was similar between wild-type and Was knockout MEL cells, the latter exhibited an altered ratio of monomeric G-actin to polymeric F-actin. We also demonstrate that Was overexpression can mediate the activation of Bruton’s tyrosine kinase. Overall, these findings support the role of WASp as a key regulator of F-actin in erythroid cells.
Fernández-Calleja et al. (2019) CRISPR/Cas9-mediated deletion of the Wiskott-Aldrich syndrome locus causes actin cytoskeleton disorganization in murine erythroleukemia cells. PeerJ 7:e6284 https://doi.org/10.7717/peerj.6284
A new virus found in garlic virus complex is a member of possible novel genus of the family Betaflexiviridae (order Tymovirales)
Plant vegetative propagation strategies for agricultural crops cause the accumulation of viruses, resulting in the formation of virus complexes or communities. The cultivation of garlic is based on vegetative propagation and more than 13 virus species from the genera Potyvirus, Allexivirus and Carlavirus have been reported. Aiming for an unbiased identification of viruses from a garlic germplasm collection in Brazil, total RNA from eight garlic cultivars was sequenced by high-throughput sequencing (HTS) technology. Although most viruses found in this study were previously reported, one of them did not belong to any known genera. This putative new virus was found in seven out of eight garlic cultivars and phylogenetic data positioned it as representative of an independent evolutionary lineage within family Betaflexiviridae. This virus has been tentatively named garlic yellow mosaic-associated virus (GYMaV), sharing highest nucleotide identities with African oil palm ringspot virus (genus Robigovirus) and potato virus T (genus Tepovirus) for the replicase gene, and with viruses classified within genus Foveavirus for the coat protein gene. Due to its high frequency in garlic cultivars, GYMaV should be considered in upcoming surveys of pathogens in this crop and in the development of virus-free garlic plants.
Da Silva et al. (2019) A new virus found in garlic virus complex is a member of possible novel genus of the family Betaflexiviridae (order Tymovirales). PeerJ 7:e6285 https://doi.org/10.7717/peerj.6285
The expression of chondrogenesis-related and arthritis-related genes in human ONFH cartilage with different Ficat stages
Background It has been well known that the degeneration of hip articular cartilage with osteonecrosis of the femoral head (ONFH) increases the instability of hip and accelerates the development process of ONFH. A better understanding of the expression of chondrogenesis-related and arthritis-related genes of cartilage along with the progression of ONFH seems to be essential for further insight into the molecular mechanisms of ONFH pathogenesis. Methods We analyzed the differentially expressed gene profile (GSE74089) of human hip articular cartilage with ONFH. The functions and pathway enrichments of differentially expressed genes (DEGs) were analyzed via GO and KEGG analysis. The expression of six selected critical chondrogenesis-related and four arthritis-related genes in eight human hip articular cartilage with femoral neck fracture (FNF) and 26 human hip articular cartilage with different stages ONFH (6 cases of Ficat stage II, 10 cases of Ficat stage III and 10 cases of Ficat stage IV) were detected. Results A total of 2,174 DEGs, including 1,482 up-regulated and 692 down-regulated ones, were obtained in the ONFH cartilage specimens compared to the control group. The GO and KEGG enrichment analysis indicated that the function of these DEGs mainly enriched in extracellular matrix, angiogenesis, antigen processing and presentation. The results showed a significant stepwise up-expression of chondrogenesis-related genes, including MMP13, ASPN, COL1A1, OGN, COL2A1 and BMP2, along with the progression of ONFH. The arthritis-related genes IL1β, IL6 and TNFα were only found up-expressed in Ficat IV stage which indicated that the arthritis-related molecular changes were not significant in the progression of ONFH before Ficat III stage. However, the arthritis-related gene PTGS2 was significant stepwise up-expression along with the progression of ONFH which makes it to be a sensitive arthritis-related biomarker of ONFH. Conclusion Expression changes of six chondrogenesis-related and four arthritis-related genes were found in hip articular cartilage specimens with different ONFH Ficat stages. These findings are expected to a get a further insight into the molecular mechanisms of ONFH progression.
Chen et al. (2019) The expression of chondrogenesis-related and arthritis-related genes in human ONFH cartilage with different Ficat stages. PeerJ 7:e6306 https://doi.org/10.7717/peerj.6306
Influence of light intensity, fertilizing and season on the cirsiliol content, a chemical marker of Leonotis nepetifolia (Lamiaceae)
Background Leonotis nepetifolia (Family Lamiaceae) is a medicinal plant from which the flavonoid cirsiliol with sedative, hypnotic, anti-inflammatory and cytotoxic activity has been extracted. Methods Seedlings were cultivated under different levels of shade in native or fertilized modes. The content of cirsiliol was measured monthly by high-performance liquid chromatography and the total phenolic content by the Folin-Ciocalteu method. Monitoring of growth was carried out with the weekly measurement of height until the stabilization of growth. Results The application of fertilizing and/or shading does not alter significantly the cirsiliol content. However, this content varies throughout the year, reaching the peak production in the summer, independently of the treatment applied. This same profile, with production in the summer, was also verified for phenolic compounds, reaching 58.15 ± 9.35 mg of equivalents of gallic acid per g of extract in the summer, content 1.84 times greater than the content verified in winter (31.56 ± 4.09 mg of gallic acid/g of extract). Although shading and fertilizing had no effect on cirsiliol content, the results also showed a positive influence on the height and biomass of the plant, which can causes a higher yield of extractable material. Discussion Biotic and abiotic stresses are able to increase or decrease the production of secondary metabolites, including phenolic compounds in medicinal plants and, as the stress response is peculiar to each species, cultivation studies become necessary. The present study reports by the first time the influence of shading, fertilizing and seasons in cirsiliol content in L. nepetifolia. Among analyzed variables, the seasons showed a larger influence in expression of cirsiliol and among seasons, our results showed that the summer is the ideal season for collections. In summer, the photoperiod is larger than in other seasons of the year and due to that, the plants need greater protection against the long photoperiod. For this, the plants increase the production of phenolic compounds as observed in this study. Although they do not influence the production of cirsiliol, the shading and nutrients in soil favor growth and leaf area of several plants, explaining, thus, the higher height and biomass obtained.
de Oliveira et al. (2019) Influence of light intensity, fertilizing and season on the cirsiliol content, a chemical marker of Leonotis nepetifolia (Lamiaceae). PeerJ 7:e6187 https://doi.org/10.7717/peerj.6187
Awareness, behavior and attitudes concerning sun exposure among beachgoers in the northern coast of Peru
Background Skin cancer incidence has increased over the last years, becoming a major public health problem. Objective To describe the awareness, behavior and attitudes concerning sun exposure among beachgoers in the northern coast of Peru. Methods We conducted a cross-sectional study in the Pimentel beach, Peru. The “Beach Questionnaire” was used and we surveyed all the beachgoers from 8 a.m. to 4 p.m. and from March 5 to March 19. For the statistical analysis, sun exposure habits, sunburns history, knowledge, attitudes and practices were crossed with sex using the chi2 test. Results We surveyed 410 beachgoers, the most frequent phototype was type III (40.5%). Only the 13.66% of the respondents correctly answered the seven knowledge questions related to sun exposure and skin cancer. Men more frequently agreed that “when they are tanned their clothes looks nicer” (p = 0.048). Likewise, regarding the questions “Sunbathing is relaxing” and “Sunbathing improves my mood”, men agreed or totally agreed with more frequency than women (63.64% vs. 46.15%, p < 0.001; and 61.36% vs 49.15%, p = 0.014, respectively). Regarding sun protection practices, women more frequently used sunshade (p = 0.001) and sunscreen (SPF ≥ 15) (p < 0.001) when compared to the male group. Conclusion Sun exposure is a potentially preventable risk factor for skin cancer. Thus, awareness of the risks of UVR overexposure and adequate sun-protective behaviors and attitudes are essential. Our results, however, are not as favorable as expected. Public health efforts should encourage sun-safety precautions and intervention campaigns should be carried out in recreational settings, such as the beaches.
Toro-Huamanchumo et al. (2019) Awareness, behavior and attitudes concerning sun exposure among beachgoers in the northern coast of Peru. PeerJ 7:e6189 https://doi.org/10.7717/peerj.6189
TGF-beta signalling in bovine mammary gland involution and a comparative assessment of MAC-T and BME-UV1 cells as in vitro models for its study
The goal of the dairy industry is ultimately to increase lactation persistency, which is the length of time during which peak milk yield is sustained. Lactation persistency is determined by the balance of cell apoptosis and cell proliferation; when the balance is skewed toward the latter, this results in greater persistency. Thus, we can potentially increase milk production in dairy cows through manipulating apoptogenic and antiproliferative cellular signaling that occurs in the bovine mammary gland. Transforming growth factor beta 1 (TGFβ1) is an antiproliferative and apoptogenic cytokine that is upregulated during bovine mammary gland involution. Here, we discuss possible applications of TGFβ1 signaling for the purposes of increasing lactation persistency. We also compare the features of mammary alveolar cells expressing SV-40 large T antigen (MAC-T) and bovine mammary epithelial cells-clone UV1 (BME-UV1) cells, two extensively used bovine mammary epithelial cell lines, to assess their appropriateness for the study of TGFβ1 signaling. TGFβ1 induces apoptosis and arrests cell growth in BME-UV1 cells, and this was reported to involve suppression of the somatotropic axis. Conversely, there is no proof that exogenous TGFβ1 induces apoptosis of MAC-T cells. In addition to TGFβ1’s different effects on apoptosis in these cell lines, hormones and growth factors have distinct effects on TGFβ1 secretion and synthesis in MAC-T and BME-UV1 cells as well. MAC-T and BME-UV1 cells may behave differently in response to TGFβ1 due to their contrasting phenotypes; MAC-T cells have a profile indicative of both myoepithelial and luminal populations, while the BME-UV1 cells exclusively contain a luminal-like profile. Depending on the nature of the research question, the use of these cell lines as models to study TGFβ1 signaling should be carefully tailored to the questions asked.
Mitz et al. (2019) TGF-beta signalling in bovine mammary gland involution and a comparative assessment of MAC-T and BME-UV1 cells as in vitro models for its study. PeerJ 6:e6210 https://doi.org/10.7717/peerj.6210
Common garden comparisons confirm inherited differences in sensitivity to climate change between forest tree species
The natural distribution, habitat, growth and evolutionary history of tree species are strongly dependent on ecological and genetic processes in ecosystems subject to fluctuating climatic conditions, but there have been few experimental comparisons of sensitivity between species. We compared the responses of two broadleaved tree species (Fagus sylvatica and Quercus petraea) and two conifer tree species (Pinus sylvestris and Picea abies) to climatic transfers by fitting models containing the same climatic variables. We used published data from European provenance test networks to model the responses of individual populations nested within species. A mixed model approach was applied to develop a response function for tree height over climatic transfer distance, taking into account the climatic conditions at both the seed source and the test location. The two broadleaved species had flat climatic response curves, indicating high levels of plasticity in populations, facilitating adaptation to a broader range of environments, and conferring a high potential for resilience in the face of climatic change. By contrast, the two conifer species had response curves with more pronounced slopes, indicating a lower resilience to climate change. This finding may reflect stronger genetic clines in P. sylvestris and P. abies, which constrain their climate responses to narrower climatic ranges. The response functions had maxima that deviated from the expected maximum productivity in the climate of provenance towards cooler/moister climate conditions, which we interpreted as an adaptation lag. Unilateral, linear regression analyses following transfer to warmer and drier sites confirmed a decline in productivity, predictive of the likely impact of ongoing climate change on forest populations. The responses to mimicked climate change evaluated here are of considerable interest for forestry and ecology, supporting projections of expected performance based on “real-time” field data.
Sáenz-Romero et al. (2019) Common garden comparisons confirm inherited differences in sensitivity to climate change between forest tree species. PeerJ 7:e6213 https://doi.org/10.7717/peerj.6213
The sinemydid turtle Ordosemys from the Lower Cretaceous Mengyin Formation of Shandong, China and its implication for the age of the Luohandong Formation of the Ordos Basin
Chronostratigraphic correlation of terrestrial Early Cretaceous biotas in China is highly problematic due to the lack of marine deposits, few absolute dates, and limited number of index fossils. This often leaves vertebrate faunas as one of the few potential tools for a preliminary biostratigraphy. Taxonomic identity of fragmentary fossils is, however, often uncertain and many faunas are insufficiently sampled. Turtles are one of the most common elements of Early Cretaceous biotas of Asia and their skeleton is frequently preserved more completely than that of other vertebrates- they yet receive little attention from vertebrate paleontologists. We here record the presence of the sinemydid turtle Ordosemys leios from the Lower Cretaceous Mengyin Formation of Shandong Province, China, best known for the first dinosaurs and Mesozoic turtles described from the country. Ordosemys is the third turtle reported from the Mengyin Formation along with Sinemys lens and Sinochelys applanata and the only other formation where Ordosemys is known to co-occur with Sinemys is the Luohandong Formation of the Ordos Basin (Inner Mongolia), the type and so far only horizon of Ordosemys leios. The presence of the crocodyliform Shantungosuchus may further define a fauna that is so far only known from these two formations. The stratigraphic position of the Luohandong Formation is poorly controlled and it has been placed anywhere between the Valanginian and Aptian. Published absolute dates from the Mengyin Formation and the numerous shared vertebrate and invertebrate taxa (now also including turtles) implies a Valanginian—early Hauterivian age for the Luohandong Formation—in contrast to late Hauterivian-Albian as previously proposed using the temporal distribution of Psittacosaurus. The new specimen of Ordosemys leios preserves the only known manus of this species and ecomorphological analysis of limb proportions implies that it was a less capable swimmer compared to Ordosemys liaoxiensis coming from the younger Jehol Biota.
Li et al. (2019) The sinemydid turtle Ordosemys from the Lower Cretaceous Mengyin Formation of Shandong, China and its implication for the age of the Luohandong Formation of the Ordos Basin. PeerJ 7:e6229 https://doi.org/10.7717/peerj.6229
Serverless OpenHealth at data commons scale—traversing the 20 million patient records of New York’s SPARCS dataset in real-time
In a previous report, we explored the serverless OpenHealth approach to the Web as a Global Compute space. That approach relies on the modern browser full stack, and, in particular, its configuration for application assembly by code injection. The opportunity, and need, to expand this approach has since increased markedly, reflecting a wider adoption of Open Data policies by Public Health Agencies. Here, we describe how the serverless scaling challenge can be achieved by the isomorphic mapping between the remote data layer API and a local (client-side, in-browser) operator. This solution is validated with an accompanying interactive web application (bit.ly/loadsparcs) capable of real-time traversal of New York’s 20 million patient records of the Statewide Planning and Research Cooperative System (SPARCS), and is compared with alternative approaches. The results obtained strengthen the argument that the FAIR reproducibility needed for Population Science applications in the age of P4 Medicine is particularly well served by the Web platform.
Almeida et al. (2019) Serverless OpenHealth at data commons scale—traversing the 20 million patient records of New York’s SPARCS dataset in real-time. PeerJ 7:e6230 https://doi.org/10.7717/peerj.6230
Duplicated flavonoid 3’-hydroxylase and flavonoid 3’, 5’-hydroxylase genes in barley genome
Background Anthocyanin compounds playing multiple biological functions can be synthesized in different parts of barley (Hordeum vulgare L.) plant. The diversity of anthocyanin molecules is related with branching the pathway to alternative ways in which dihydroflavonols may be modified either with the help of flavonoid 3′-hydroxylase (F3′H) or flavonoid 3′,5′-hydroxylase (F3′5′H)—the cytochrome P450-dependent monooxygenases. The F3′H and F3′5′H gene families are among the least studied anthocyanin biosynthesis structural genes in barley. The aim of this study was to identify and characterise duplicated copies of the F3′H and F3′5′H genes in the barley genome. Results Four copies of the F3′5′H gene (on chromosomes 4HL, 6HL, 6HS and 7HS) and two copies of the F3′H gene (on chromosomes 1HL and 6HS) were identified in barley genome. These copies have either one or two introns. Amino acid sequences analysis demonstrated the presence of the flavonoid hydroxylase-featured conserved motifs in all copies of the F3′H and F3′5′H genes with the exception of F3′5′H-3 carrying a loss-of-function mutation in a conservative cytochrome P450 domain. It was shown that the divergence between F3′H and F3′5′H genes occurred 129 million years ago (MYA) before the emergence of monocot and dicot plant species. The F3′H copy approximately occurred 80 MYA; the appearance of F3′5′H copies occurred 8, 36 and 91 MYA. qRT-PCR analysis revealed the tissue-specific activity for some copies of the studied genes. The F3′H-1 gene was transcribed in aleurone layer, lemma and pericarp (with an increased level in the coloured pericarp), whereas the F3′H-2 gene was expressed in stems only. The F3′5′H-1 gene was expressed only in the aleurone layer, and in a coloured aleurone its expression was 30-fold higher. The transcriptional activity of F3′5′H-2 was detected in different tissues with significantly higher level in uncoloured genotype in contrast to coloured ones. The F3′5′H-3 gene expressed neither in stems nor in aleurone layer, lemma and pericarp. The F3′5′H-4 gene copy was weakly expressed in all tissues analysed. Conclusion F3′H and F3′5′H-coding genes involved in anthocyanin synthesis in H. vulgare were identified and characterised, from which the copies designated F3′H-1, F3′H-2, F3′5′H-1 and F3′5′H-2 demonstrated tissue-specific expression patterns. Information on these modulators of the anthocyanin biosynthesis pathway can be used in future for manipulation with synthesis of diverse anthocyanin compounds in different parts of barley plant. Finding both the copies with tissue-specific expression and a copy undergoing pseudogenization demonstrated rapid evolutionary events tightly related with functional specialization of the duplicated members of the cytochrome P450-dependent monooxygenases gene families.
Vikhorev et al. (2019) Duplicated flavonoid 3’-hydroxylase and flavonoid 3’, 5’-hydroxylase genes in barley genome. PeerJ 7:e6266 https://doi.org/10.7717/peerj.6266
Opioid distribution trends (2006–2017) in the US Territories
Background The US mainland is experiencing an epidemic of opioid overdoses. Unfortunately, the US Territories (Guam, Puerto Rico, and the Virgin Islands) have often been overlooked in opioid pharmacoepidemiology research. This study examined common prescription opioids over the last decade. Methods The United States Drug Enforcement Administration’s Automation of Reports and Consolidated Orders System (ARCOS) was used to report on ten medical opioids: buprenorphine, codeine, fentanyl, hydrocodone, hydromorphone, meperidine, methadone, morphine, oxycodone, and oxymorphone, by weight from 2006 to 2017. Florida and Hawaii were selected as comparison areas. Results Puerto Rico had the greatest Territorial oral morphine mg equivalent (MME) per capita (421.5) which was significantly higher (p < .005) than the Virgin Islands (139.2) and Guam (118.9) but significantly lower than that of Hawaii (794.6) or Florida (1,509.8). Methadone was the largest opioid by MMEs in 2017 in most municipalities, accounting for 41.1% of the total in the Virgin Islands, 37.9% in Florida, 36.6% in Hawaii but 80.8% in Puerto Rico. Puerto Rico and Florida showed pronounced differences in the distribution patterns by pharmacies, hospitals, and narcotic treatment programs for opioids. Conclusions Continued monitoring of the US Territories is needed to provide a balance between appropriate access to these important agents for cancer related and acute pain while also minimizing diversion and avoiding the opioid epidemic which has adversely impacted the US mainland.
Cabrera et al. (2019) Opioid distribution trends (2006–2017) in the US Territories. PeerJ 7:e6272 https://doi.org/10.7717/peerj.6272
Estimating the incidence and diagnosed proportion of HIV infections in Japan: a statistical modeling study
Background Epidemiological surveillance of HIV infection in Japan involves two technical problems for directly applying a classical backcalculation method, i.e., (i) all AIDS cases are not counted over time and (ii) people diagnosed with HIV have received antiretroviral therapy, extending the incubation period. The present study aimed to address these issues and estimate the HIV incidence and the proportion of diagnosed HIV infections, using a simple statistical model. Methods From among Japanese nationals, yearly incidence data of HIV diagnoses and patients with AIDS who had not previously been diagnosed as HIV positive, from 1985 to 2017, were analyzed. Using the McKendrick partial differential equation, general convolution-like equations were derived, allowing estimation of the HIV incidence and the time-dependent rate of diagnosis. A likelihood-based approach was used to obtain parameter estimates. Results Assuming that the median incubation period was 10.0 years, the cumulative number of HIV infections was estimated to be 29,613 (95% confidence interval (CI): 29,059, 30,167) by the end of 2017, and the proportion of diagnosed HIV infections was estimated at 80.3% (95% CI [78.7%–82.0%]). Allowing the median incubation period to range from 7.5 to 12.3 years, the estimate of the proportion diagnosed can vary from 77% to 84%. Discussion The proportion of diagnosed HIV infections appears to have not yet reached 90% among Japanese nationals. Compared with the peak incidence from 2005–2008, new HIV infections have clearly been in a declining trend; however, there are still more than 1,000 new HIV infections per year in Japan. To increase the diagnosed proportion of HIV infections, it is critical to identify people who have difficulty accessing consultation, testing, and care, and to explore heterogeneous patterns of infection.
Nishiura (2019) Estimating the incidence and diagnosed proportion of HIV infections in Japan: a statistical modeling study. PeerJ 7:e6275 https://doi.org/10.7717/peerj.6275
Identification and characterization of capsule depolymerase Dpo48 from Acinetobacter baumannii phage IME200
Background The emergence of multidrug- or extensively drug-resistant Acinetobacter baumannii has made it difficult to treat and control infections caused by this bacterium. It is urgently necessary to search for alternatives to conventional antibiotics for control of severe A. baumannii infections. In recent years, bacteriophages and their derivatives, such as depolymerases, showed great potential as antibacterial or antivirulence agents against bacterial infections. Nonetheless, unlike broad-spectrum bactericidal antibiotics, phage-encoded depolymerase targets only a limited number of bacterial strains. Therefore, identification of novel depolymerases and evaluation of their ability to control A. baumannii infections is important. Methods A bacteriophage was isolated from hospital sewage using an extensively drug-resistant A. baumannii strain as the host bacterium, and the phage’s plaque morphology and genomic composition were studied. A polysaccharide depolymerase (Dpo48) was expressed and identified, and the effects of pH and temperature on its activity were determined. Besides, a serum killing assay was conducted, and amino acid sequences homologous to those of putative polysaccharide depolymerases were compared. Results Phage IME200 yielded clear plaques surrounded by enlarged halos, with polysaccharide depolymerase activity against the host bacterium. A tail fiber protein with a Pectate_lyase_3 domain was identified as Dpo48 and characterized . Dpo48 was found to degrade the capsule polysaccharide of the bacterial surface, as revealed by Alcian blue staining. Dpo48 manifested stable activity over a broad range of pH (5.0–9.0) and temperatures (20–70 °C). Results from in vitro serum killing assays indicated that 50% serum was sufficient to cause a five log reduction of overnight enzyme-treated bacteria, with serum complement playing an important role in these killing assays. Moreover, Dpo48 had a spectrum of activity exactly the same as its parental phage IME200, which was active against 10 out of 41 A. baumannii strains. Amino acid sequence alignment showed that the putative tail fiber proteins had a relatively short, highly conserved domain in their N-terminal sequences, but their amino acid sequences containing pectate lyase domains, found in the C-terminal regions, were highly diverse. Conclusions Phage-encoded capsule depolymerases may become promising antivirulence agents for preventing and controlling A. baumannii infections.
Liu et al. (2019) Identification and characterization of capsule depolymerase Dpo48 from Acinetobacter baumannii phage IME200. PeerJ 7:e6173 https://doi.org/10.7717/peerj.6173
Application of built-in adjuvants for epitope-based vaccines
Several studies have shown that epitope vaccines exhibit substantial advantages over conventional vaccines. However, epitope vaccines are associated with limited immunity, which can be overcome by conjugating antigenic epitopes with built-in adjuvants (e.g., some carrier proteins or new biomaterials) with special properties, including immunologic specificity, good biosecurity and biocompatibility, and the ability to vastly improve the immune response of epitope vaccines. When designing epitope vaccines, the following types of built-in adjuvants are typically considered: (1) pattern recognition receptor ligands (i.e., toll-like receptors); (2) virus-like particle carrier platforms; (3) bacterial toxin proteins; and (4) novel potential delivery systems (e.g., self-assembled peptide nanoparticles, lipid core peptides, and polymeric or inorganic nanoparticles). This review primarily discusses the current and prospective applications of these built-in adjuvants (i.e., biological carriers) to provide some references for the future design of epitope-based vaccines.
Lei et al. (2019) Application of built-in adjuvants for epitope-based vaccines. PeerJ 6:e6185 https://doi.org/10.7717/peerj.6185
Worldwide co-occurrence analysis of 17 species of the genus Brachypodium using data mining
The co-occurrence of plant species is a fundamental aspect of plant ecology that contributes to understanding ecological processes, including the establishment of ecological communities and its applications in biological conservation. A priori algorithms can be used to measure the co-occurrence of species in a spatial distribution given by coordinates. We used 17 species of the genus Brachypodium, downloaded from the Global Biodiversity Information Facility data repository or obtained from bibliographical sources, to test an algorithm with the spatial points process technique used by Silva et al. (2016), generating association rules for co-occurrence analysis. Brachypodium spp. has emerged as an effective model for monocot species, growing in different environments, latitudes, and elevations; thereby, representing a wide range of biotic and abiotic conditions that may be associated with adaptive natural genetic variation. We created seven datasets of two, three, four, six, seven, 15, and 17 species in order to test the algorithm with four different distances (1, 5, 10, and 20 km). Several measurements (support, confidence, lift, Chi-square, and p-value) were used to evaluate the quality of the results generated by the algorithm. No negative association rules were created in the datasets, while 95 positive co-occurrences rules were found for datasets with six, seven, 15, and 17 species. Using 20 km in the dataset with 17 species, we found 16 positive co-occurrences involving five species, suggesting that these species are coexisting. These findings are corroborated by the results obtained in the dataset with 15 species, where two species with broad range distributions present in the previous dataset are eliminated, obtaining seven positive co-occurrences. We found that B. sylvaticum has co-occurrence relations with several species, such as B. pinnatum, B. rupestre, B. retusum, and B. phoenicoides, due to its wide distribution in Europe, Asia, and north of Africa. We demonstrate the utility of the algorithm implemented for the analysis of co-occurrence of 17 species of the genus Brachypodium, agreeing with distributions existing in nature. Data mining has been applied in the field of biological sciences, where a great amount of complex and noisy data of unseen proportion has been generated in recent years. Particularly, ecological data analysis represents an opportunity to explore and comprehend biological systems with data mining and bioinformatics tools.
Orozco-Arias et al. (2019) Worldwide co-occurrence analysis of 17 species of the genus Brachypodium using data mining. PeerJ 6:e6193 https://doi.org/10.7717/peerj.6193
Combining legacy data with new drone and DGPS mapping to identify the provenance of Plio-Pleistocene fossils from Bolt’s Farm, Cradle of Humankind (South Africa)
Bolt’s Farm is a Plio-Pleistocene fossil site located within the southwestern corner of the UNESCO Hominid Fossil Sites of South Africa World Heritage Site. The site is a complex of active caves and more than 20 palaeokarst deposits or pits, many of which were exposed through the action of lime mining in the early 20th century. The pits represent heavily eroded cave systems, and as such associating the palaeocave sediments within and between the pits is difficult, especially as little geochronological data exists. These pits and the associated lime miner’s rubble were first explored by palaeoanthropologists in the late 1930s, but as yet no hominin material has been recovered. The first systematic mapping was undertaken by Frank Peabody as part of the University of California Africa Expedition (UCAE) in 1947–1948. A redrawn version of the map was not published until 1991 by Basil Cooke and this has subsequently been used and modified by recent researchers. Renewed work in the 2000s used Cooke’s map to try and relocate the original fossil deposits. However, Peabody’s map does not include all the pits and caves, and thus in some cases this was successful, while in others previously sampled pits were inadvertently given new names. This was compounded by the fact that new fossil bearing deposits were discovered in this new phase, causing confusion in associating the 1940s fossils with the deposits from which they originated; as well as associating them with the recently excavated material. To address this, we have used a Geographic Information System (GIS) to compare Peabody’s original map with subsequently published maps. This highlighted transcription errors between maps, most notably the location of Pit 23, an important palaeontological deposit given the recovery of well-preserved primate crania (Parapapio, Cercopithecoides) and partial skeletons of the extinct felid Dinofelis. We conducted the first drone and Differential Global Positioning System (DGPS) survey of Bolt’s Farm. Using legacy data, high-resolution aerial imagery, accurate DGPS survey and GIS, we relocate the original fossil deposits and propose a definitive and transparent naming strategy for Bolt’s Farm, based on the original UCAE Pit numbers. We provide datum points and a new comprehensive, georectified map to facilitate spatially accurate fossil collection for all future work. Additionally, we have collated recently published faunal data with historic fossil data to evaluate the biochronological potential of the various deposits. This suggests that the palaeocave deposits in different pits formed at different times with the occurrence of Equus in some pits implying ages of <2.3 Ma, whereas more primitive suids (Metridiochoerus) hint at a terminal Pliocene age for other deposits. This study highlights that Bolt’s Farm contains rare South African terminal Pliocene fossil deposits and creates a framework for future studies of the deposits and previously excavated material.
Edwards et al. (2019) Combining legacy data with new drone and DGPS mapping to identify the provenance of Plio-Pleistocene fossils from Bolt’s Farm, Cradle of Humankind (South Africa). PeerJ 7:e6202 https://doi.org/10.7717/peerj.6202
Using lidar to assess the development of structural diversity in forests undergoing passive rewilding in temperate Northern Europe
Forested areas are increasing across Europe, driven by both reforestation programs and farmland abandonment. While tree planting remains the standard reforestation strategy, there is increased interest in spontaneous regeneration as a cost-effective method with equal or potentially greater benefits. Furthermore, expanding areas of already established forests are left for passive rewilding to promote biodiversity conservation. Effective and objective methods are needed for monitoring and analyzing the development of forest structure under these management scenarios, with airborne laser scanning (lidar: light detection and ranging) being a promising methodology. Here, we assess the structural characteristics and development of unmanaged forests and 28- to 78-year old spontaneously regenerated forests on former agricultural land, relative to managed forests of similar age in Denmark, using 25 lidar-derived metrics in 10- and 30-m grid cells. We analyzed the lidar-derived cell values in a principal component analysis (PCA) and interpreted the axes ecologically, in conjunction with pairwise tests of median and variance of PCA-values for each forest. Spontaneously regenerated forest in general had increased structural heterogeneity compared to planted and managed forests. Furthermore, structural heterogeneity kept increasing in spontaneously regenerated forest across the maximal 78-year timespan investigated. Natural disturbances showed strong impacts on vegetation structure, leading to both structural homogeneity and heterogeneity. The results illustrate the utility of passive rewilding for generating structurally heterogeneous forested nature areas, and the utility of lidar surveys for monitoring and interpreting structural development of such forests.
Thers et al. (2019) Using lidar to assess the development of structural diversity in forests undergoing passive rewilding in temperate Northern Europe. PeerJ 6:e6219 https://doi.org/10.7717/peerj.6219
Global genomic similarity and core genome sequence diversity of the Streptococcus genus as a toolkit to identify closely related bacterial species in complex environments
Background The Streptococcus genus is relevant to both public health and food safety because of its ability to cause pathogenic infections. It is well-represented (>100 genomes) in publicly available databases. Streptococci are ubiquitous, with multiple sources of isolation, from human pathogens to dairy products. The Streptococcus genus has traditionally been classified by morphology, serum types, the 16S ribosomal RNA (rRNA) gene, and multi-locus sequence types subject to in-depth comparative genomic analysis. Methods Core and pan-genomes described the genomic diversity of 108 strains belonging to 16 Streptococcus species. The core genome nucleotide diversity was calculated and compared to phylogenomic distances within the genus Streptococcus. The core genome was also used as a resource to recruit metagenomic fragment reads from streptococci dominated environments. A conventional 16S rRNA gene phylogeny reconstruction was used as a reference to compare the resulting dendrograms of average nucleotide identity (ANI) and genome similarity score (GSS) dendrograms. Results The core genome, in this work, consists of 404 proteins that are shared by all 108 Streptococcus. The average identity of the pairwise compared core proteins decreases proportionally to GSS lower scores, across species. The GSS dendrogram recovers most of the clades in the 16S rRNA gene phylogeny while distinguishing between 16S polytomies (unresolved nodes). The GSS is a distance metric that can reflect evolutionary history comparing orthologous proteins. Additionally, GSS resulted in the most useful metric for genus and species comparisons, where ANI metrics failed due to false positives when comparing different species. Discussion Understanding of genomic variability and species relatedness is the goal of tools like GSS, which makes use of the maximum pairwise shared orthologous sequences for its calculation. It allows for long evolutionary distances (above species) to be included because of the use of amino acid alignment scores, rather than nucleotides, and normalizing by positive matches. Newly sequenced species and strains could be easily placed into GSS dendrograms to infer overall genomic relatedness. The GSS is not restricted to ubiquitous conservancy of gene features; thus, it reflects the mosaic-structure and dynamism of gene acquisition and loss in bacterial genomes.
Barajas et al. (2019) Global genomic similarity and core genome sequence diversity of the Streptococcus genus as a toolkit to identify closely related bacterial species in complex environments. PeerJ 6:e6233 https://doi.org/10.7717/peerj.6233
Method for the quantitative evaluation of ecosystem services in coastal regions
Wetlands, tidal flats, seaweed beds, and coral reefs are valuable not only as habitats for many species, but also as places where people interact with the sea. Unfortunately, these areas have declined in recent years, so environmental improvement projects to conserve and restore them are being carried out across the world. In this study, we propose a method for quantifying ecosystem services, that is, useful for the proper maintenance and management of artificial tidal flats, a type of environmental improvement project. With this method, a conceptual model of the relationship between each service and related environmental factors in natural and social systems was created, and the relationships between services and environmental factors were clarified. The state of the environmental factors affecting each service was quantified, and the state of those factors was reflected in the evaluation value of the service. As a result, the method can identify which environmental factors need to be improved and if the goal is to increase the value of the targeted tidal flat. The method demonstrates an effective approach in environmental conservation for the restoration and preservation of coastal areas.
Okada et al. (2019) Method for the quantitative evaluation of ecosystem services in coastal regions. PeerJ 6:e6234 https://doi.org/10.7717/peerj.6234
Mantle transcriptome sequencing of Mytilus spp. and identification of putative biomineralization genes
In molluscs, the shell secreted by mantle tissue during the biomineralization process is the first barrier against predators and mechanical damage. Changing environmental conditions, such as ocean acidification, influence shell strength and thus protection of the soft body within. Mussels are marine bivalves with important commercial and ecological value worldwide. Despite this importance, the proteins involved in the biomineralization and pigmentation processes in Mytilus spp. remain unclear, as does taxonomy of Mytilus taxa, though there have been many molecular studies. To further understanding in these areas, this study aimed to characterize and compare mantle transcriptomes of four mussel taxa using next generation sequencing. Mussels representing four taxa, were collected from several localities and RNA from mantle tissue was extracted. RNA sequences obtained were assembled, annotated and potential molecular markers, including simple sequence repeats (SSRs) and single nucleotide polymorphisms (SNPs) were identified. Candidate contigs putatively related to biomineralization and pigmentation processes were then selected and several transcripts were chosen for phylogenetic analyses from the Bivalvia class. Transcriptome comparisons between Mytilus taxa, including gene ontology (GO) enrichment analysis and orthologues identification were performed. Of assembled contigs, 46.57%, 37.28% and 17.53% were annotated using NCBI NR, GO and Kyoto Encyclopedia of Genes and Genomes databases, respectively. Potential SSRs (483) and SNPs (1,497) were identified. Results presented a total of 1,292 contigs putatively involved in biomineralization and melanogenesis. Phylogenetic analyses of α-carbonic anhydrase, chitinase and tyrosinase revealed complex evolutionary history and diversity of these genes, which may be a result of duplication events or adaptation to different environments in mussels and other bivalves. Enrichment analyses revealed GO terms associated with pH and thermal response in Mytilus edulis from the North Sea and M. galloprovincialis from the Mediterranean Sea. The phylogenetic analysis within the genus Mytilus revealed M. californianus and M. coruscus to be genetically more distant from the other taxa: M. trossulus, M. edulis, M. chilensis and M. galloprovincialis. This work represents the first mantle transcriptome comparison between Mytilus taxa and provides contigs putatively involved in biomineralization.
Malachowicz et al. (2019) Mantle transcriptome sequencing of Mytilus spp. and identification of putative biomineralization genes. PeerJ 6:e6245 https://doi.org/10.7717/peerj.6245
Effect of agricultural land-use change on ant dominance hierarchy and food preferences in a temperate oak forest
Background The discovery-dominance trade-off is the inverse relationship between the ability of a species to discover resources and the species’ dominance of those resources; a paradigm used to explain species coexistence in ant communities dependent on similar resources. However, factors such as stress (e.g., temperature) or disturbance (e.g., removal of biomass) associated with the change in land use, can modify this trade-off. Here, we aimed to determine the potential effects of land use change on dominance hierarchy, food preferences and on the discovery-dominance trade-off. Methods An experiment with baits was used to investigate the dominance hierarchies of ant communities in a temperate mountain habitat in central Mexico. We evaluated the dominance index (DI), food preferences and discovery-dominance trade-offs of ants inhabiting two types of vegetation: a native oak forest and agricultural land resulting from agricultural land use and grazing. Results The ant communities in both environments were comprised of three species of ants (Monomorium minimum, Myrmica mexicana, and Camponotus picipes pilosulus), four morphospecies (Pheidole sp.1 and Pheidole sp.2, Temnothorax sp. and Lasius sp.) and one genus (Formica spp.). All Formicidae showed values of intermediate to low DI, and this factor did not seem to be influenced by the change in land use. Ants in the modified vegetation (i.e., agricultural land) were found to be numerically greater. Overall, a higher number of visits were registered to the tuna bait, although the duration of foraging events to the honey baits was longer. However, foraging times were dependent on the species considered: the generalized Myrmicinae, M. minimum, the ant species with highest DI, foraged for longer periods of time in the agricultural land and on the tuna bait. Meanwhile, the cold-climate specialist Formica spp., with a lower DI, foraged for longer periods of time in the oak (although not significant) and on the honey bait. We found little evidence of the discovery-dominance trade-off; instead, we found considerable diversity in the strategies used by the different species to access resources. This range of strategies is well represented by the generalized Myrmicinae M. minimum, the cold-climate specialists Formica spp. and Temnothorax sp., and the rare species, as the cold climate specialist Lasius sp. (insinuators). Conclusions Our evaluation shows that transformation of the original habitat does not appear to affect the hierarchical dominance of the ant communities, but it does affect their food preferences. Species with higher DI values such as the generalized Myrmicinae are more skilled at resource acquisition in modified habitats. Our results suggest that change in land use promotes an increase in the diversity of foraging strategies used by different ant species. This diversity may contribute to resource partitioning which favors coexistence.
Castillo-Guevara et al. (2019) Effect of agricultural land-use change on ant dominance hierarchy and food preferences in a temperate oak forest. PeerJ 7:e6255 https://doi.org/10.7717/peerj.6255
Comparative genomics of 16 Microbacterium spp. that tolerate multiple heavy metals and antibiotics
A total of 16 different strains of Microbacterium spp. were isolated from contaminated soil and enriched on the carcinogen, hexavalent chromium [Cr(VI)]. The majority of the isolates (11 of the 16) were able to tolerate concentrations (0.1 mM) of cobalt, cadmium, and nickel, in addition to Cr(VI) (0.5–20 mM). Interestingly, these bacteria were also able to tolerate three different antibiotics (ranges: ampicillin 0–16 μg ml−1, chloramphenicol 0–24 μg ml−1, and vancomycin 0–24 μg ml−1). To gain genetic insight into these tolerance pathways, the genomes of these isolates were assembled and annotated. The genomes of these isolates not only have some shared genes (core genome) but also have a large amount of variability. The genomes also contained an annotated Cr(VI) reductase (chrR) that could be related to Cr(VI) reduction. Further, various heavy metal tolerance (e.g., Co/Zn/Cd efflux system) and antibiotic resistance genes were identified, which provide insight into the isolates’ ability to tolerate metals and antibiotics. Overall, these isolates showed a wide range of tolerances to heavy metals and antibiotics and genetic diversity, which was likely required of this population to thrive in a contaminated environment.
Environmental Contamination and Remediation
Learman et al. (2019) Comparative genomics of 16 Microbacterium spp. that tolerate multiple heavy metals and antibiotics. PeerJ 6:e6258 https://doi.org/10.7717/peerj.6258
Variation in wild pea (Pisum sativum subsp. elatius) seed dormancy and its relationship to the environment and seed coat traits
Background Seed germination is one of the earliest key events in the plant life cycle. The timing of transition from seed to seedling is an important developmental stage determining the survival of individuals that influences the status of populations and species. Because of wide geographical distribution and occurrence in diverse habitats, wild pea (Pisum sativum subsp. elatius) offers an excellent model to study physical type of seed dormancy in an ecological context. This study addresses the gap in knowledge of association between the seed dormancy, seed properties and environmental factors, experimentally testing oscillating temperature as dormancy release clue. Methods Seeds of 97 pea accessions were subjected to two germination treatments (oscillating temperatures of 25/15 °C and 35/15 °C) over 28 days. Germination pattern was described using B-spline coefficients that aggregate both final germination and germination speed. Relationships between germination pattern and environmental conditions at the site of origin (soil and bioclimatic variables extracted from WorldClim 2.0 and SoilGrids databases) were studied using principal component analysis, redundancy analysis and ecological niche modelling. Seeds were analyzed for the seed coat thickness, seed morphology, weight and content of proanthocyanidins (PA). Results Seed total germination ranged from 0% to 100%. Cluster analysis of germination patterns of seeds under two temperature treatments differentiated the accessions into three groups: (1) non-dormant (28 accessions, mean germination of 92%), (2) dormant at both treatments (29 acc., 15%) and (3) responsive to increasing temperature range (41 acc., with germination change from 15 to 80%). Seed coat thickness differed between groups with dormant and responsive accessions having thicker testa (median 138 and 140 µm) than non-dormant ones (median 84 mm). The total PA content showed to be higher in the seed coat of dormant (mean 2.18 mg g−1) than those of non-dormant (mean 1.77 mg g−1) and responsive accessions (mean 1.87 mg g−1). Each soil and bioclimatic variable and also germination responsivity (representing synthetic variable characterizing germination pattern of seeds) was spatially clustered. However, only one environmental variable (BIO7, i.e., annual temperature range) was significantly related to germination responsivity. Non-dormant and responsive accessions covered almost whole range of BIO7 while dormant accessions are found in the environment with higher annual temperature, smaller temperature variation, seasonality and milder winter. Ecological niche modelling showed a more localized potential distribution of dormant group. Seed dormancy in the wild pea might be part of a bet-hedging mechanism for areas of the Mediterranean basin with more unpredictable water availability in an otherwise seasonal environment. This study provides the framework for analysis of environmental aspects of physical seed dormancy.
Hradilová et al. (2019) Variation in wild pea (Pisum sativum subsp. elatius) seed dormancy and its relationship to the environment and seed coat traits. PeerJ 7:e6263 https://doi.org/10.7717/peerj.6263
The effects of afforestation on soil bacterial communities in temperate grassland are modulated by soil chemical properties
Grassland afforestation dramatically affects the abiotic, biotic, and ecological function properties of the original ecosystems. Interference from afforestation might disrupt the stasis of soil physicochemical properties and the dynamic balance of microbiota. Some studies have suggested low sensitivity of soil properties and bacterial community to afforestation, but the apparent lack of a significant relationship is probably due to the confounding effects of the generalist habitat and rare bacterial communities. In this study, soil chemical and prokaryotic properties in a 30-year-old Mongolia pine (Pinus sylvestris var. mongolica Litv.) afforested region and adjacent grassland in Inner Mongolia were classified and quantified. Our results indicate that the high richness of rare microbes accounts for the alpha-diversity of the soil microbiome. Few OTUs of generalist (core bacteria) and habitat-specialist bacteria are present. However, the high abundance of this small number of OTUs governs the beta-diversity of the grassland and afforested land bacterial communities. Afforestation has changed the soil chemical properties, thus indirectly affecting the soil bacterial composition rather than richness. The contents of soil P, Ca2+, and Fe3+ account for differentially abundant OTUs such as Planctomycetes and subsequent changes in the ecologically functional potential of soil bacterial communities due to grassland afforestation. We conclude that grassland afforestation has changed the chemical properties and composition of the soil and ecological functions of the soil bacterial community and that these effects of afforestation on the microbiome have been modulated by changes in soil chemical properties.
Wu et al. (2019) The effects of afforestation on soil bacterial communities in temperate grassland are modulated by soil chemical properties. PeerJ 7:e6147 https://doi.org/10.7717/peerj.6147
Effects of Trichoderma seedling treatment with System of Rice Intensification management and with conventional management of transplanted rice
Many benefits of Trichoderma inoculation for improving crop production have been documented, including growth and yield enhancement and the alleviation of biotic and abiotic stresses. However, because rice is usually cultivated under continuous flooding that creates anaerobic soil conditions, this limits the benefits of these beneficial fungi. Cultivating rice with the methods of the System of Rice Intensification (SRI) provides rice plants with a more favorable environment for their colonization by beneficial microbes in the soil because the soil is more aerobic under SRI management and contains more organic matter. This study evaluated the effects of Trichoderma inoculation of rice plants under SRI management compared with transplanted and flooded rice plants, considering also the effects of different means of fertilization and different varieties in rice. Experiments were conducted in 2015 and 2016 under the tropical climate of Nepal’s western terai (plains) during both the rainy season (July to November) and the dry season (March to July). The results indicated significantly better performance (P = 0.01) associated with Trichoderma inoculation for both seasons and for both systems of crop management in terms of grain yield and other growth-contributing factors, compared to non-inoculated rice cropping. Relatively higher effects on grain yield were recorded also with organic compared to inorganic fertilization; for unimproved (heirloom) varieties compared with improved varieties; and from SRI vs. conventional flooded crop management. The yield increase with Trichoderma treatments across all trials was 31% higher than in untreated plots (4.9 vs 4.5 mt ha−1). With Trichoderma treatment, yields compared with non-treated plots were 24% higher with organic SRI (6.38 vs 5.13 mt ha−1) and 52% higher with non-organic SRI (6.38 vs 3.53 mt ha−1). With regard to varietal differences, under SRI management Trichoderma inoculation of the improved variety Sukhadhan-3 led to 26% higher yield (6.35 vs 5.04 mt ha−1), and with the heirloom variety Tilkidhan, yield was 41% higher (6.29 vs 4.45 mt ha−1). Economic analysis indicated that expanding the organic cultivation of local landraces under SRI management should be profitable for farmers where such rice has a good market price due to its premium quality and high demand and when SRI enhances yield. These varieties’ present low yields can be significantly increased by integrating Trichoderma bio-inoculation with SRI cultural methods. Other recent research has shown that such inoculation can be managed profitably by farmers themselves.
Khadka et al. (2019) Effects of Trichoderma seedling treatment with System of Rice Intensification management and with conventional management of transplanted rice. PeerJ 7:e5877 https://doi.org/10.7717/peerj.5877
A miniature inverted-repeat transposable element, AddIn-MITE, located inside a WD40 gene is conserved in Andropogoneae grasses
Miniature inverted-repeat transposable elements (MITEs) have been associated with genic regions in plant genomes and may play important roles in the regulation of nearby genes via recruitment of small RNAs (sRNA) to the MITEs loci. We identified eight families of MITEs in the sugarcane genome assembly with MITE-Hunter pipeline. These sequences were found to be upstream, downstream or inserted into 67 genic regions in the genome. The position of the most abundant MITE (Stowaway-like) in genic regions, which we call AddIn-MITE, was confirmed in a WD40 gene. The analysis of four monocot species showed conservation of the AddIn-MITE sequence, with a large number of copies in their genomes. We also investigated the conservation of the AddIn-MITE’ position in the WD40 genes from sorghum, maize and, in sugarcane cultivars and wild Saccharum species. In all analyzed plants, AddIn-MITE has located in WD40 intronic region. Furthermore, the role of AddIn-MITE-related sRNA in WD40 genic region was investigated. We found sRNAs preferentially mapped to the AddIn-MITE than to other regions in the WD40 gene in sugarcane. In addition, the analysis of the small RNA distribution patterns in the WD40 gene and the structure of AddIn-MITE, suggests that the MITE region is a proto-miRNA locus in sugarcane. Together, these data provide insights into the AddIn-MITE role in Andropogoneae grasses.
Grativol et al. (2019) A miniature inverted-repeat transposable element, AddIn-MITE, located inside a WD40 gene is conserved in Andropogoneae grasses. PeerJ 7:e6080 https://doi.org/10.7717/peerj.6080
Diverse and variable virus communities in wild plant populations revealed by metagenomic tools
Wild plant populations may harbour a myriad of unknown viruses. As the majority of research efforts have targeted economically important plant species, the diversity and prevalence of viruses in the wild has remained largely unknown. However, the recent shift towards metagenomics-based sequencing methodologies, especially those targeting small RNAs, is finally enabling virus discovery from wild hosts. Understanding this diversity of potentially pathogenic microbes in the wild can offer insights into the components of natural biodiversity that promotes long-term coexistence between hosts and parasites in nature, and help predict when and where risks of disease emergence are highest. Here, we used small RNA deep sequencing to identify viruses in Plantago lanceolata populations, and to understand the variation in their prevalence and distribution across the Åland Islands, South-West Finland. By subsequent design of PCR primers, we screened the five most common viruses from two sets of P. lanceolata plants: 164 plants collected from 12 populations irrespective of symptoms, and 90 plants collected from five populations showing conspicuous viral symptoms. In addition to the previously reported species Plantago lanceolata latent virus (PlLV), we found four potentially novel virus species belonging to Caulimovirus, Betapartitivirus, Enamovirus, and Closterovirus genera. Our results show that virus prevalence and diversity varied among the sampled host populations. In six of the virus infected populations only a single virus species was detected, while five of the populations supported between two to five of the studied virus species. In 20% of the infected plants, viruses occurred as coinfections. When the relationship between conspicuous viral symptoms and virus infection was investigated, we found that plants showing symptoms were usually infected (84%), but virus infections were also detected from asymptomatic plants (44%). Jointly, these results reveal a diverse virus community with newly developed tools and protocols that offer exciting opportunities for future studies on the eco-evolutionary dynamics of viruses infecting plants in the wild.
Susi et al. (2019) Diverse and variable virus communities in wild plant populations revealed by metagenomic tools. PeerJ 7:e6140 https://doi.org/10.7717/peerj.6140
Life history responses of two ephemeral plant species to increased precipitation and nitrogen in the Gurbantunggut Desert
Precipitation change and nitrogen deposition are not only hot topics of current global change but also the main environmental factors affecting plant growth in desert ecosystems. Thus, we performed an experiment of increased precipitation, nitrogen, and precipitation plus nitrogen on the ephemeral annual species Nepeta micrantha and Eremopyrum distans in the Gurbantunggut Desert. We aimed to determine the life history responses of N. micrantha and E. distans to environment changes, and the germination percentage of the offspring (seeds) was also tested in the laboratory. The results showed that increased nitrogen and precipitation plus nitrogen increased the growth of both plant species, whereas increased precipitation inhibited the growth of N. micrantha but increased the growth of E. distans. This differential response of these two species to precipitation and nitrogen also affected the germination of their offspring. In response to increased nitrogen and precipitation plus nitrogen, the germination percentage of the offspring produced by two species decreased in conjunction with the plants exhibiting high reproduction, which may prevent overcrowding during the following year; however, the N. micrantha plants produced more nondormant offspring in conjunction with low reproduction under relatively greater amounts of precipitation, and N. micrantha offspring could occupy their habitat via rapid germination in suitable environments. Therefore, with increased precipitation and nitrogen deposition, these differences in offspring dormancy may affect their ecological niche in the community.
Chen et al. (2019) Life history responses of two ephemeral plant species to increased precipitation and nitrogen in the Gurbantunggut Desert. PeerJ 7:e6158 https://doi.org/10.7717/peerj.6158
Impact of inter- and intra-individual variation, sample storage and sampling fraction on human stool microbial community profiles
Stools are commonly used as proxies for studying human gut microbial communities as sample collection is straightforward, cheap and non-invasive. In large-scale human population surveys, however, sample integrity becomes an issue as it is not logistically feasible for researchers to personally collect stools from every participant. Instead, participants are usually given guidelines on sample packaging and storage, and asked to deliver their stools to a centralised facility. Here, we tested a number of delivery conditions (temperature, duration and addition of preservative medium) and assessed their effects on stool microbial community composition using 16S rRNA gene amplicon sequencing. The largest source of variability in stool community composition was attributable to inter-individual differences regardless of delivery condition. Although the relative effect of delivery condition on community composition was small compared to inter-individual variability (1.6% vs. 60.5%, permutational multivariate analysis of variance [PERMANOVA]) and temporal variation within subjects over 10 weeks (5.2%), shifts in microbial taxa associated with delivery conditions were non-systematic and subject-specific. These findings indicated that it is not possible to model or accurately predict shifts in stool community composition associated with sampling logistics. Based on our findings, we recommend delivery of fresh, preservative-free stool samples to laboratories within 2 hr either at ambient or chilled temperatures to minimise perturbations to microbial community composition. In addition, subsamples from different fractions of the same stool displayed a small (3.3% vs. 72.6% inter-individual variation, PERMANOVA) but significant effect on community composition. Collection of larger sample volumes for homogenisation is recommended.
Yeoh et al. (2019) Impact of inter- and intra-individual variation, sample storage and sampling fraction on human stool microbial community profiles. PeerJ 7:e6172 https://doi.org/10.7717/peerj.6172
Artificial liver research output and citations from 2004 to 2017: a bibliometric analysis
Background Researches on artificial livers greatly contribute to the clinical treatments for liver failure. This study aimed to evaluate the research output of artificial livers and citations from 2004 to 2017 through a bibliometric analysis. Methods A list of included articles on artificial livers were generated after a comprehensive search of the Web of Science Core Collection (from 2004 to 2017) with the following basic information: number of publications, citations, publication year, country of origin, authors and authorship, funding source, journals, institutions, keywords, and research area. Results A total of 968 included articles ranged from 47 citations to 394 citations with a fluctuation. The publications were distributed in 12 countries, led by China (n = 212) and the US (n = 207). There were strong correlations of the number of citations with authors (r2 = 0.133, p < 0.001), and countries (r2 = 0.275, p < 0.001), while no correlations of the number of citations with the years since publication (r2 = 0.016, p = 0.216), and funding (r2 < 0.001, p = 0.770) were identified. Keyword analysis demonstrated that with the specific change of “acute liver failure,” decrease in “bioartificial livers” and “hepatocyte,” and increase in “tissue engineering” were identified. The top 53 cited keyword and keyword plus (including some duplicates counts) were identified, led by bioartificial liver (405 citations) and hepatocyte (248 citations). The top 50 cited keywords bursts were mainly “Blood” (2004–2008), “hepatocyte like cell” (2008–2015), and “tissue engineering” (2014–2017). All keywords could be classified into four categories: bioartificial livers (57.40%), blood purification (25.00%), clinical (14.81%), and other artificial organs (2.78%). Discussion This study shows the process and tendency of artificial liver research with a comprehensive analysis on artificial livers. However, although it seems that the future of artificial livers seems brighter for hepatocyte transplantation, the systems of artificial livers now are inclined on focusing on blood purification, plasma exchange, etc.
Li et al. (2019) Artificial liver research output and citations from 2004 to 2017: a bibliometric analysis. PeerJ 6:e6178 https://doi.org/10.7717/peerj.6178
Non-H3 CDR template selection in antibody modeling through machine learning
Antibodies are proteins generated by the adaptive immune system to recognize and counteract a plethora of pathogens through specific binding. This adaptive binding is mediated by structural diversity in the six complementary determining region (CDR) loops (H1, H2, H3, L1, L2 and L3), which also makes accurate structural modeling of CDRs challenging. Both homology and de novo modeling approaches have been used; to date, the former has achieved greater accuracy for the non-H3 loops. The homology modeling of non-H3 CDRs is more accurate because non-H3 CDR loops of the same length and type can be grouped into a few structural clusters. Most antibody-modeling suites utilize homology modeling for the non-H3 CDRs, differing only in the alignment algorithm and how/if they utilize structural clusters. While RosettaAntibody and SAbPred do not explicitly assign query CDR sequences to clusters, two other approaches, PIGS and Kotai Antibody Builder, utilize sequence-based rules to assign CDR sequences to clusters. While the manually curated sequence rules can identify better structural templates, because their curation requires extensive literature search and human effort, they lag behind the deposition of new antibody structures and are infrequently updated. In this study, we propose a machine learning approach (Gradient Boosting Machine [GBM]) to learn the structural clusters of non-H3 CDRs from sequence alone. The GBM method simplifies feature selection and can easily integrate new data, compared to manual sequence rule curation. We compare the classification results using the GBM method to that of RosettaAntibody in a 3-repeat 10-fold cross-validation (CV) scheme on the cluster-annotated antibody database PyIgClassify and we observe an improvement in the classification accuracy of the concerned loops from 84.5% ± 0.24% to 88.16% ± 0.056%. The GBM models reduce the errors in specific cluster membership misclassifications when the involved clusters have relatively abundant data. Based on the factors identified, we suggest methods that can enrich structural classes with sparse data to further improve prediction accuracy in future studies.
Long et al. (2019) Non-H3 CDR template selection in antibody modeling through machine learning. PeerJ 7:e6179 https://doi.org/10.7717/peerj.6179
Genetic diversity and its conservation implications of Vitex rotundifolia (Lamiaceae) populations in East Asia
Vitex rotundifolia is an important coastal and medicinal plant, and is recorded in the List of the Important Wild Plants for Conservation in China and Japan. However, an effective conservation strategy is lacking. In the present study, the genetic diversity and population structure were analyzed using phylogeographical methods based on the trnH-psbA and trnG-trnS intergenic spacers of the chloroplast DNA (cpDNA) sequences from 157 individuals from 25 sampling sites for V. rotundifolia and V. trifolia plus the internal transcribed spacer (ITS) of the nuclear ribosomal DNA (nrDNA) sequences of 177 individuals from 27 sampling sites. The results showed that V. rotundifolia and V. trifolia had eight cpDNA and two nrDNA haplotypes, respectively, and the V. rotundifolia has a low level of genetic diversity (haplotype diversity hd,cp = 0.360, hd,nr = 0.440), a more pronounced genetic differentiation among populations (population differentiation at the species level (GST) = 0.201, population differentiation at the allele level (NST) = 0.462), and an insignificantly different phylogeographical structure (NST > GST, P > 0.05). In addition, haplotype network analyses indicated that V. rotundifolia and V. trifolia have distinct haplotypes. Divergence dating based on BEAST software analyses showed that most cpDNA clades diverged in the late Pleistocene era. Demographic analysis indicated that V. rotundifolia underwent a rapid demographic expansion. Some scientific strategies are suggested for resource conservation of V. rotundifolia based on its genetic diversity and population structure.
Sun et al. (2019) Genetic diversity and its conservation implications of Vitex rotundifolia (Lamiaceae) populations in East Asia. PeerJ 7:e6194 https://doi.org/10.7717/peerj.6194
Local fishermen’s perceptions of the usefulness of artificial reef ecosystem services in Portugal
Proponents of artificial reef (AR) deployment are often motivated by the usefulness of such structures. The usefulness of ARs is related to their capability of providing ecosystem services/additional functions. We present two distinct Portuguese AR case studies: (1) The Nazaré reef off the central coast of Portugal and (2) the Oura reef off the Algarve coast. Semi-structured interviews were conducted with local fishermen in the fishing towns of Nazaré and Quarteira pre-and post-AR deployment. The main focus of the interviews was to understand fishermen’s perception of AR usefulness (or lack thereof) in terms of nine ecosystem services/additional functions potentially provided by the ARs. We tested the null hypothesis that ARs do not provide additional ecosystem services/additional functions. When queried pre-AR deployment, fishermen indicated that ARs are most likely to provide three ecosystem services: “habitat and refuge,” “biodiversity preservation” and “food production.” Fishermen had similar perceptions post-deployment. For the Nazaré reef, fishermen tended to have a positive or neutral perception of ecosystem services/additional functions being provided by ARs. For the Oura reef, fishermen tended to have a mostly neutral perception of AR ecosystem services; however, there were also some positive and other negative perceptions. It was difficult for stakeholders to conceptualize some of the ecosystem services/additional functions provided by ARs prior to actively using them. As a result, some stakeholders changed their perception of the ecosystem services/additional functions after using the structures. These results indicate that stakeholders likely need to perceive ARs as useful in order for them to provide their support for AR installation. Likewise, their support is often needed to justify the use of public funds to install ARs, therefore making it imperative for resource managers to undertake similar interviews with fishermen when considering the use of ARs in other areas.
Ramos et al. (2019) Local fishermen’s perceptions of the usefulness of artificial reef ecosystem services in Portugal. PeerJ 6:e6206 https://doi.org/10.7717/peerj.6206
Anuran diversity indicates that Caatinga relictual Neotropical forests are more related to the Atlantic Forest than to the Amazon
The relationships among the morphoclimatic domains of South America have been a major biogeographical issue of recent years. Palynological, geological and phytogeographical data suggest that the Amazon Forest and the Atlantic Forest were connected during part of the Tertiary and Quaternary periods. This study uses amphibians as model organisms to investigate whether relict northeastern forests are a transition between the Amazon Forest and the Atlantic Forest. We compiled matrices of species composition for four different phytogeographic formations and “Brejos de Altitude,” and analyzed them using clustering methods and Cladistic Analysis of Distributions and Endemism. Our results indicate that the anurofauna of these northeastern forest relicts is most similar in composition to the areas of the Atlantic Forest included in this study, and most dissimilar to the Amazon Forest, which leads us to affirm that events of biotic exchange were more frequent within the Atlantic Forest areas.
Castro et al. (2019) Anuran diversity indicates that Caatinga relictual Neotropical forests are more related to the Atlantic Forest than to the Amazon. PeerJ 6:e6208 https://doi.org/10.7717/peerj.6208
Immunohistochemical analysis of cyclin A expression in Wilms tumor
Background Cyclin A overexpression is found in a variety of human tumors and correlates with unfavorable outcome. We analyzed immunohistochemical expression of cyclin A in Wilms tumor (WT) in relation to clinicopathological characteristics, preoperative chemotherapy (PrOpChTh), and overall survival (OS). Methods This retrospective study involved 43 patients who underwent nephrectomy from January 1996 to October 2010. Tumor stage and histological subtype were determined by revised Societé International d’Oncologie Pediatrique protocol, based on histological components/alterations caused by PrOpChTh, within the prognostic group of low, intermediate and high risk, and with criteria for anaplasia. The regressive/necrotic changes in total tumor mass of primary tumor and the proportion of epithelial, blastemal, and stromal components in the remaining viable tumor tissue were also determined. Cyclin A expression was evaluated by immunohistochemistry using a polyclonal rabbit, antihuman antibody (H-432). Results Cyclin A overexpression was found in 34.3% of WTs, with higher frequency in tumors with epithelial (31.3%) and blastemal (37.1%) components than those with stromal component (17.7%). Regarding histological type, cyclin A overexpression was found most often in focal anaplasia (100%), stromal (60%), and diffuse anaplastic (66.7) WTs. The overexpression was also more frequent in stages 3 and 4 (77.8% and 66.7%, respectively) compared to tumors in stages 1 and 2 (13.3% and 12.5%, respectively; p = 0.004) in all components, as well as in blastemal component in stages 3 and 4 (77.8% and 66.7%, respectively) vs. stages 1 and 2 (13.3% and 25%, respectively, p = 0.009). Cyclin A overexpression in all components was 66.7% in WTs with metastasis and 31.3% in WTs without metastasis (p = 0.265, Fisher test). Log-rank testing revealed differences of OS regarding stage (p = 0.000), prognostic groups (p = 0.001), and cyclin A expression in blastemal component (p = 0.025). After univariate analysis, tumor stage (p = 0.001), prognostic group (p = 0.004), and cyclin A expression in blastemal component (p = 0.042) were significant prognostic factors for OS; however, after multivariate analysis, none of these factors were confirmed as independent predictors of survival. Discussion This study showed that cyclin A overexpression might be associated with the development and progression of WT with anaplasia. Also, cyclin A overexpression was more often observed in advanced stages (3 and 4) of WT, in the group of high-risk WTs, and in focal and diffuse anaplasia WTs. There was no relation of cyclin A overexpression and metastatic ability of WT. Although this study has not confirmed the prognostic value of cyclin A overexpression, its association with unfavorable prognosis should be further evaluated.
Radojević-Škodrić et al. (2019) Immunohistochemical analysis of cyclin A expression in Wilms tumor. PeerJ 6:e6212 https://doi.org/10.7717/peerj.6212
Detection and variability analyses of CRISPR-like loci in the H. pylori genome
Helicobacter pylori is a human pathogenic bacterium with a high genomic plasticity. Although the functional CRISPR-Cas system has not been found in its genome, CRISPR-like loci have been recently identified. In this work, 53 genomes from different geographical areas are analyzed for the search and analysis of variability of this type of structure. We confirm the presence of a locus that was previously described in the VlpC gene in al lgenomes, and we characterize new CRISPR-like loci in other genomic locations. By studying the variability and gene location of these loci, the evolution and the possible roles of these sequences are discussed. Additionally, the usefulness of this type of sequences as a phylogenetic marker has been demonstrated, associating the different strains by geographical area.
García-Zea et al. (2019) Detection and variability analyses of CRISPR-like loci in the H. pylori genome. PeerJ 7:e6221 https://doi.org/10.7717/peerj.6221
Grazing by large savanna herbivores indirectly alters ant diversity and promotes resource monopolisation
In savannas, grazing is an important disturbance that modifies the grass layer structure and composition. Habitat structural complexity influences species diversity and assemblage functioning. By using a combination of natural sites and manipulated experiments, we explored how habitat structure (grazing lawns and adjacent bunch grass) affects ant diversity and foraging behaviour, specifically the efficiency of resource acquisition, resource monopolisation and ant body size. We found that in the natural sites there was no difference in the amount of time ants took to locate resources, but in the manipulated experiments, ants were faster at locating resources and were more abundant in the simple treatments than in the more complex treatments. Ant body size was only affected by the manipulated experiments, with smaller ants found in the more complex treatments. In both the grazing lawn and bunch grass habitats there were differences in assemblage patterns of ants discovering resources and those dominating them. Seasonality, which was predicted to affect the speed at which ants discovered resources and the intensity of resource monopolisation, also played a role. We show that ants in winter monopolised more baits and discovered resources at a slower rate, but only at certain times within the experiment. Grazing in conjunction with season thus had a significant effect on ant diversity and foraging behaviour, with dominant ants promoted where habitat complexity was simplified when temperatures were low. Our results indicate that structural complexity plays a major role in determining ant assemblage structure and function in African savannas.
Purdon et al. (2019) Grazing by large savanna herbivores indirectly alters ant diversity and promotes resource monopolisation. PeerJ 7:e6226 https://doi.org/10.7717/peerj.6226
Individual tree crown delineation and tree species classification with hyperspectral and LiDAR data
An international data science challenge, called National Ecological Observatory Network—National Institute of Standards and Technology data science evaluation, was set up in autumn 2017 with the goal to improve the use of remote sensing data in ecological applications. The competition was divided into three tasks: (1) individual tree crown (ITC) delineation, for identifying the location and size of individual trees; (2) alignment between field surveyed trees and ITCs delineated on remote sensing data; and (3) tree species classification. In this paper, the methods and results of team Fondazione Edmund Mach (FEM) are presented. The ITC delineation (Task 1 of the challenge) was done using a region growing method applied to a near-infrared band of the hyperspectral images. The optimization of the parameters of the delineation algorithm was done in a supervised way on the basis of the Jaccard score using the training set provided by the organizers. The alignment (Task 2) between the delineated ITCs and the field surveyed trees was done using the Euclidean distance among the position, the height, and the crown radius of the ITCs and the field surveyed trees. The classification (Task 3) was performed using a support vector machine classifier applied to a selection of the hyperspectral bands and the canopy height model. The selection of the bands was done using the sequential forward floating selection method and the Jeffries Matusita distance. The results of the three tasks were very promising: team FEM ranked first in the data science competition in Task 1 and 2, and second in Task 3. The Jaccard score of the delineated crowns was 0.3402, and the results showed that the proposed approach delineated both small and large crowns. The alignment was correctly done for all the test samples. The classification results were good (overall accuracy of 88.1%, kappa accuracy of 75.7%, and mean class accuracy of 61.5%), although the accuracy was biased toward the most represented species.
Dalponte et al. (2019) Individual tree crown delineation and tree species classification with hyperspectral and LiDAR data. PeerJ 6:e6227 https://doi.org/10.7717/peerj.6227
Label-free quantitative proteomic analysis reveals potential biomarkers for early healing in cutaneous leishmaniasis
Background Leishmaniasis is a parasitic disease caused by more than 20 species of the Leishmania genus. The disease is globally distributed and is endemic in 97 countries and three territories in the tropical and subtropical regions. The efficacy of the current treatments is becoming increasingly low either due to incomplete treatment or resistant parasites. Failure of treatment is frequent, and therefore, the search for early biomarkers of therapeutic response in cutaneous leishmaniasis (CL) is urgently needed. Objective The aim of this study was to compare the proteomic profiles in patients with CL before and after 7 days of treatment and identify early biomarkers of curative response. Methods Four patients with a parasitological diagnosis of leishmaniasis with confirmation of species by PCR-RFLP were recruited. All patients had a single lesion, and a protein from the middle of the ulcer was quantified by liquid chromatography and mass spectrometry. Results A total of 12 proteins showed differential expression in the comparative LC-electrospray ionization MS/MS (LC-ESI-MS/MS) triplicate analysis. Seven of them were up-regulated and five of them were down-regulated. Calcium binding proteins A2, A8, and A9 and hemoglobin subunits alpha-2 and delta showed high correlation with epidermis development and immune response. Conclusion We identified changes in the profiles of proteins that had a positive therapeutic response to the treatment. The proteins identified with differential expression are related to the reduction of inflammation and increased tissue repair. These proteins can be useful as biomarkers for early monitoring of therapeutic response in CL.
Montoya et al. (2019) Label-free quantitative proteomic analysis reveals potential biomarkers for early healing in cutaneous leishmaniasis. PeerJ 6:e6228 https://doi.org/10.7717/peerj.6228
Assigning confidence scores to homoeologs using fuzzy logic
In polyploid genomes, homoeologs are a specific subtype of homologs, and can be thought of as orthologs between subgenomes. In Orthologous MAtrix, we infer homoeologs in three polyploid plant species: upland cotton (Gossypium hirsutum), rapeseed (Brassica napus), and bread wheat (Triticum aestivum). While we can typically recognize the features of a “good” homoeolog prediction (a consistent evolutionary distance, high synteny, and a one-to-one relationship), none of them is a hard-fast criterion. We devised a novel fuzzy logic-based method to assign confidence scores to each pair of predicted homoeologs. We inferred homoeolog pairs and used the new and improved method to assign confidence scores, which ranged from 0 to 100. Most confidence scores were between 70 and 100, but the distribution varied between genomes. The new confidence scores show an improvement over our previous method and were manually evaluated using a subset from various confidence ranges.
Glover et al. (2019) Assigning confidence scores to homoeologs using fuzzy logic. PeerJ 6:e6231 https://doi.org/10.7717/peerj.6231
Characterizing ecomorphological patterns in hyenids: a multivariate approach using postcanine dentition
We analyze the multivariate pattern of lower and upper cheek dentition for the family Hyaenidae along its evolutionary history. A total of 11,698 individual measurements of lengths and widths for the main postcanine teeth were collected for 54 extinct and three extant species of this family and analyzed by means of principal component analyses. Our results indicate that the functional aspects are better reflected by lower cheek dentition as a result of mosaic evolution. The multivariate structure captured by the three first principal components correspond to different adaptive strategies. The two first components characterize the main groups of ecomorphs, while hunting species separate from scavengers along the third axis. In the context of Hyaenidae, the post-canine cheek dentition of Parahyaena brunnea and Hyaena hyaena shows an extreme degree of specialization in scavenging.
Coca-Ortega et al. (2019) Characterizing ecomorphological patterns in hyenids: a multivariate approach using postcanine dentition. PeerJ 6:e6238 https://doi.org/10.7717/peerj.6238
Use of a leaf chlorophyll content index to improve the prediction of above-ground biomass and productivity
Improving the accuracy of predicting plant productivity is a key element in planning nutrient management strategies to ensure a balance between nutrient supply and demand under climate change. A calculation based on intercepted photosynthetically active radiation is an effective and relatively reliable way to determine the climate impact on a crop above-ground biomass (AGB). This research shows that using variations in a chlorophyll content index (CCI) in a mathematical function could effectively obtain good statistical diagnostic results between simulated and observed crop biomass. In this study, the leaf CCI, which is used as a biochemical photosynthetic component and calibration parameter, increased simulation accuracy across the growing stages during 2016–2017. This calculation improves the accuracy of prediction and modelling of crops under specific agroecosystems, and it may also improve projections of AGB for a variety of other crops.
Liu et al. (2019) Use of a leaf chlorophyll content index to improve the prediction of above-ground biomass and productivity. PeerJ 6:e6240 https://doi.org/10.7717/peerj.6240
Genome-wide identification and expression analysis of the MYB transcription factor in moso bamboo (Phyllostachys edulis)
The MYB family, one of the largest transcription factor (TF) families in the plant kingdom, plays vital roles in cell formation, morphogenesis and signal transduction, as well as responses to biotic and abiotic stresses. However, the underlying function of bamboo MYB TFs remains unclear. To gain insight into the status of these proteins, a total of 85 PeMYBs, which were further divided into 11 subgroups, were identified in moso bamboo (Phyllostachys edulis) by using a genome-wide search strategy. Gene structure analysis showed that PeMYBs were significantly different, with exon numbers varying from 4 to 13. Phylogenetic analysis indicated that PeMYBs clustered into 27 clades, of which the function of 18 clades has been predicted. In addition, almost all of the PeMYBs were differently expressed in leaves, panicles, rhizomes and shoots based on RNA-seq data. Furthermore, qRT-PCR analysis showed that 12 PeMYBs related to the biosynthesis and deposition of the secondary cell wall (SCW) were constitutively expressed, and their transcript abundance levels have changed significantly with increasing height of the bamboo shoots, for which the degree of lignification continuously increased. This result indicated that these PeMYBs might play fundamental roles in SCW thickening and bamboo shoot lignification. The present comprehensive and systematic study on the members of the MYB family provided a reference and solid foundation for further functional analysis of MYB TFs in moso bamboo.
Yang et al. (2019) Genome-wide identification and expression analysis of the MYB transcription factor in moso bamboo (Phyllostachys edulis). PeerJ 6:e6242 https://doi.org/10.7717/peerj.6242
Differential expression of the glucose transporter gene glcH in response to glucose and light in marine picocyanobacteria
Background Our team discovered that Prochlorococcus can take up glucose, in a process that changes the transcriptional pattern of several genes involved in glucose metabolization. We have also shown that glcH encodes a very high affinity glucose transporter, and that glucose is taken up by natural Prochlorococcus populations. We demonstrated that the kinetic parameters of glucose uptake show significant diversity in different Prochlorococcus and Synechococcus strains. Here, we tested whether the transcriptional response of glcH to several glucose concentrations and light conditions was also different depending on the studied strain. Methods Cultures were grown in the light, supplemented with five different glucose concentrations or subjected to darkness, and cells harvested after 24 h of treatment. qRT-PCR was used to determine glcH expression in four Prochlorococcus and two Synechococcus strains. Results In all studied strains glcH was expressed in the absence of glucose, and it increased upon glucose addition to cultures. The changes differed depending on the strain, both in the magnitude and in the way cells responded to the tested glucose concentrations. Unlike the other strains, Synechococcus BL107 showed the maximum glucose uptake at 5 nM glucose. Darkness induced a strong decrease in glcH expression, especially remarkable in Prochlorococcus MIT9313. Discussion Our results suggest that marine picocyanobacteria are actively monitoring the availability of glucose, to upregulate glcH expression in order to exploit the presence of sugars in the environment. The diverse responses observed in different strains suggest that the transcriptional regulation of glucose uptake has been adjusted by evolutive selection. Darkness promotes a strong decrease in glcH expression in all studied strains, which fits with previous results on glucose uptake in Prochlorococcus. Overall, this work reinforces the importance of mixotrophy for marine picocyanobacteria.
Moreno-Cabezuelo et al. (2019) Differential expression of the glucose transporter gene glcH in response to glucose and light in marine picocyanobacteria. PeerJ 6:e6248 https://doi.org/10.7717/peerj.6248
Different revegetation types alter soil physical-chemical characteristics and fungal community in the Baishilazi Nature Reserve
The effects of different revegetation types on soil physical–chemical characteristics and fungal community diversity and composition of soils sampled from five different revegetation types (JM, Juglans mandshurica; QM, Quercus mongolica; conifer-broadleaf forest (CB); LG, Larix gmelinii; PK, Pinus koraiensis) in the Baishilazi Nature Reserve were determined. Soil fungal communities were assessed employing ITS rRNA Illunima Miseq high-throughput sequencing. Responses of the soil fungi community to soil environmental factors were assessed through canonical correspondence analysis (CCA) and Pearson correlation analysis. The coniferous forests (L. gmelinii, P. koraiensis) and CB had reduced soil total carbon (C), total nitrogen (N), and available nitrogen (AN) values compared with the broadleaf forest (J. mandshurica, Q. mongolica). The average fungus diversity according to the Shannon, ACE, Chao1, and Simpson index were increased in the J. mandshurica site. Basidiomycota, Ascomycota, Zygomycota, and Rozellomycota were the dominant fungal taxa in this region. The phylum Basidiomycota was dominant in the Q. mongolica, CB, L. gmelinii, and P. koraiensis sites, while Ascomycota was the dominant phylum in the J. mandshurica site. The clear differentiation of fungal communities and the clustering in the heatmap and in non-metric multidimensional scaling plot showed that broadleaf forests, CB, and coniferous forests harbored different fungal communities. The results of the CCA showed that soil environmental factors, such as soil pH, total C, total N, AN, and available phosphorus (P) greatly influenced the fungal community structure. Based on our results, the different responses of the soil fungal communities to the different revegetation types largely dependent on different forest types and soil physicochemical characteristic in Baishilazi Nature Reserve.
Deng et al. (2019) Different revegetation types alter soil physical-chemical characteristics and fungal community in the Baishilazi Nature Reserve. PeerJ 6:e6251 https://doi.org/10.7717/peerj.6251
The way people behave in traffic is not always optimal from the road safety perspective: drivers exceed speed limits, misjudge speeds or distances, tailgate other road users or fail to perceive them. Such behaviors are commonly investigated using self-report-based latent variable models, and conceptualized as reflections of violation- and error-proneness. However, attributing dangerous behavior to stable properties of individuals may not be the optimal way of improving traffic safety, whereas investigating direct relationships between traffic behaviors offers a fruitful way forward. Network models of driver behavior and background factors influencing behavior were constructed using a large UK sample of novice drivers. The models show how individual violations, such as speeding, are related to and may contribute to individual errors such as tailgating and braking to avoid an accident. In addition, a network model of the background factors and driver behaviors was constructed. Finally, a model predicting crashes based on prior behavior was built and tested in separate datasets. This contribution helps to bridge a gap between experimental/theoretical studies and self-report-based studies in traffic research: the former have recognized the importance of focusing on relationships between individual driver behaviors, while network analysis offers a way to do so for self-report studies.
Mattsson (2019) Network models of driver behavior. PeerJ 6:e6119 https://doi.org/10.7717/peerj.6119
cRegions—a tool for detecting conserved cis-elements in multiple sequence alignment of diverged coding sequences
Identifying cis-acting elements and understanding regulatory mechanisms of a gene is crucial to fully understand the molecular biology of an organism. In general, it is difficult to identify previously uncharacterised cis-acting elements with an unknown consensus sequence. The task is especially problematic with viruses containing regions of limited or no similarity to other previously characterised sequences. Fortunately, the fast increase in the number of sequenced genomes allows us to detect some of these elusive cis-elements. In this work, we introduce a web-based tool called cRegions. It was developed to identify regions within a protein-coding sequence where the conservation in the amino acid sequence is caused by the conservation in the nucleotide sequence. The cRegion can be the first step in discovering novel cis-acting sequences from diverged protein-coding genes. The results can be used as a basis for future experimental analysis. We applied cRegions on the non-structural and structural polyproteins of alphaviruses as an example and successfully detected all known cis-acting elements. In this publication and in previous work, we have shown that cRegions is able to detect a wide variety of functional elements in DNA and RNA viruses. These functional elements include splice sites, stem-loops, overlapping reading frames, internal promoters, ribosome frameshifting signals and other embedded elements with yet unknown function. The cRegions web tool is available at http://bioinfo.ut.ee/cRegions/.
Puustusmaa et al. (2019) cRegions—a tool for detecting conserved cis-elements in multiple sequence alignment of diverged coding sequences. PeerJ 6:e6176 https://doi.org/10.7717/peerj.6176
Optimization of a pretreatment and hydrolysis process for the efficient recovery of recycled sugars and unknown compounds from agricultural sweet sorghum bagasse stem pith solid waste
Background Sweet sorghum bagasse (SSB), comprising both a dermal layer and pith, is a solid waste generated by agricultural activities. Open burning was previously used to treat agricultural solid waste but is harmful to the environment and human health. Recent reports showed that certain techniques can convert this agricultural waste into valuable products. While SSB has been considered an attractive raw material for sugar extraction and the production of value-added products, the pith root in the SSB can be difficult to process. Therefore, it is necessary to pretreat bagasse before conventional hydrolysis. Methods A thorough analysis and comparison of various pretreatment methods were conducted based on physicochemical and microscopic approaches. The responses of agricultural SSB stem pith with different particle sizes to pretreatment temperature, acid and alkali concentration and enzyme dosage were investigated to determine the optimal pretreatment. The integrated methods are beneficial to the utilization of carbohydrate-based and unknown compounds in agricultural solid waste. Results Acid (1.5−4.5%, v/v) and alkali (5−8%, w/v) reagents were used to collect cellulose from different meshes of pith at 25–100 °C. The results showed that the use of 100 mesh pith soaked in 8% (w/v) NaOH solution at 100 °C resulted in 32.47% ± 0.01% solid recovery. Follow-up fermentation with 3% (v/v) acid and 6.5% (w/v) alkali at 50 °C for enzymolysis was performed with the optimal enzyme ratio. An analysis of the surface topography and porosity before and after pretreatment showed that both the pore size of the pith and the amount of exposed cellulose increased as the mesh size increased. Interestingly, various compounds, including 42 compounds previously known to be present and 13 compounds not previously known to be present, were detected in the pretreatment liquid, while 10 types of monosaccharides, including D-glucose, D-xylose and D-arabinose, were found in the enzymatic solution. The total monosaccharide content of the pith was 149.48 ± 0.3 mg/g dry matter. Discussion An integrated technique for obtaining value-added products from sweet sorghum pith is presented in this work. Based on this technique, lignin and hemicellulose were effectively broken down, amorphous cellulose was obtained and all sugars in the sweet sorghum pith were hydrolysed into monosaccharides. A total of 42 compounds previously found in these materials, including alcohol, ester, acid, alkene, aldehyde ketone, alkene, phenolic and benzene ring compounds, were detected in the pretreatment pith. In addition, several compounds that had not been previously observed in these materials were found in the pretreatment solution. These findings will improve the transformation of lignocellulosic biomass into sugar to create a high-value-added coproduct during the integrated process and to maximize the potential utilization of agricultural waste in current biorefinery processing.
Jiang et al. (2019) Optimization of a pretreatment and hydrolysis process for the efficient recovery of recycled sugars and unknown compounds from agricultural sweet sorghum bagasse stem pith solid waste. PeerJ 6:e6186 https://doi.org/10.7717/peerj.6186
Checklist to the Elatostema (Urticaceae) of Vietnam including 19 new records, ten new combinations, two new names and four new synonyms
Elatostema (Urticaceae) comprises several hundred herbaceous species distributed in tropical and subtropical Africa, Asia, Australia and Oceania. The greatest species richness occurs on limestone karst in Southeast Asia. Taxonomic revisions of Elatostema are largely out of date and contradict each other with respect to the delimitation of Elatostema and Pellionia. Most herbaria in SE Asia and worldwide contain significant amounts of unidentified material. As part of a broader revision of Elatostema in SE Asia, we present an updated checklist for Vietnam based on field visits, a review of specimens in herbaria worldwide, a review of type material and nomenclature. We recognize 77 taxa (75 species and two infraspecific taxa) of Elatostema in Vietnam, 23 of which were previously ascribed to Pellionia. Nineteen of these are new records for the country, i.e., E. attenuatoides, E. austrosinense, E. backeri, E. brunneinerve, E. crassiusculum, E. crenatum, E. fengshanense, E. glochidioides, E. malacotrichum, E. nanchuanense, E. oblongifolium, E. obtusum, E. oppositum, E. pergameneum, E. prunifolium, E. pseudolongipes, E. pycnodontum, E. salvinioides and E. xichouense. We place E. baviensis in synonymy of E. platyphyllum, E. colaniae in synonymy of E. myrtillus, P. macroceras in synonymy of E. hookerianum, and P. tetramera in synonymy of E. dissectum for the first time. Fourteen taxa (18% of all the recognized taxa) are endemic to Vietnam, which makes Elatostema one of the richest genera for endemic species in this country; this level of endemism is comparable to levels observed in Orchidaceae. Our checklist suggests that the highest diversity and endemism of Elatostema occurs in northern Vietnam, and that there is the greatest floristic similarity of northern Vietnam to SW China. The relationship among floristic regions is also investigated. We could find no records of Elatostema for 33 out of 63 provincial units of Vietnam, including all the southernmost provinces. We propose that further studies on the diversity of Elatostema in central and southern Vietnam are severely needed.
Fu et al. (2019) Checklist to the Elatostema (Urticaceae) of Vietnam including 19 new records, ten new combinations, two new names and four new synonyms. PeerJ 7:e6188 https://doi.org/10.7717/peerj.6188
Forest floor temperature and greenness link significantly to canopy attributes in South Africa’s fragmented coastal forests
Tropical landscapes are changing rapidly due to changes in land use and land management. Being able to predict and monitor land use change impacts on species for conservation or food security concerns requires the use of habitat quality metrics, that are consistent, can be mapped using above-ground sensor data and are relevant for species performance. Here, we focus on ground surface temperature (Thermalground) and ground vegetation greenness (NDVIdown) as potentially suitable metrics of habitat quality. Both have been linked to species demography and community structure in the literature. We test whether they can be measured consistently from the ground and whether they can be up-scaled indirectly using canopy structure maps (Leaf Area Index, LAI, and Fractional vegetation cover, FCover) developed from Landsat remote sensing data. We measured Thermalground and NDVIdown across habitats differing in tree cover (natural grassland to forest edges to forests and tree plantations) in the human-modified coastal forested landscapes of Kwa-Zulua Natal, South Africa. We show that both metrics decline significantly with increasing canopy closure and leaf area, implying a potential pathway for upscaling both metrics using canopy structure maps derived using earth observation. Specifically, our findings suggest that opening forest canopies by 20% or decreasing forest canopy LAI by one unit would result in increases of Thermalground by 1.2 °C across the range of observations studied. NDVIdown appears to decline by 0.1 in response to an increase in canopy LAI by 1 unit and declines nonlinearly with canopy closure. Accounting for micro-scale variation in temperature and resources is seen as essential to improve biodiversity impact predictions. Our study suggests that mapping ground surface temperature and ground vegetation greenness utilising remotely sensed canopy cover maps could provide a useful tool for mapping habitat quality metrics that matter to species. However, this approach will be constrained by the predictive capacity of models used to map field-derived forest canopy attributes. Furthermore, sampling efforts are needed to capture spatial and temporal variation in Thermalground within and across days and seasons to validate the transferability of our findings. Finally, whilst our approach shows that surface temperature and ground vegetation greenness might be suitable habitat quality metric used in biodiversity monitoring, the next step requires that we map demographic traits of species of different threat status onto maps of these metrics in landscapes differing in disturbance and management histories. The derived understanding could then be exploited for targeted landscape restoration that benefits biodiversity conservation at the landscape scale.
Pfeifer et al. (2019) Forest floor temperature and greenness link significantly to canopy attributes in South Africa’s fragmented coastal forests. PeerJ 7:e6190 https://doi.org/10.7717/peerj.6190
Native bluegill influence the foraging and aggressive behavior of invasive mosquitofish
Two fish species that are common invaders of aquatic ecosystems world-wide are Gambusia affinis and G. holbrooki, commonly known as mosquitofish. In North America, introduced G. affinis are thought to have contributed to the population decline of several native fish species. Sunfish (family Centrarchidae) naturally occur across much of North American, thus mosquitofish and sunfish are likely to come into contact and interact more frequently as mosquitofish spread. However, the nature of this interaction is not well known. We used a lab experiment to explore whether and how the aggressive and foraging behaviors of G. affinis might be influenced by a representative and ubiquitous native centrarchid (Lepomis macrochirus; bluegill sunfish), a species with juveniles that inhabit littoral habitats also preferred by mosquitofish. The experiment partnered an individual male or female mosquitofish (focal fish) with a juvenile bluegill, or a same- or opposite-sex conspecific, filmed these one-to-one interactions, and quantified foraging and aggressive actions for the focal mosquitofish. We found that juvenile bluegill affect foraging in male mosquitofish, resulting in lower percent of handling attempts and handling time in which the male consumed a food item. The presence of juvenile bluegill also led to a reduction in the number of aggressive acts by mosquitofish compared to aggression levels when focal mosquitofish were with conspecifics. In nature, when mosquitofish encounter juvenile bluegill in littoral habitats, our results suggest that the foraging and aggressive behaviors of mosquitofish will be modified, especially for males. This mechanism may influence the rate or geographic extent of the spread of mosquitofish into North American waterbodies.
Clemmer et al. (2019) Native bluegill influence the foraging and aggressive behavior of invasive mosquitofish. PeerJ 7:e6203 https://doi.org/10.7717/peerj.6203
Different ecological processes determined the alpha and beta components of taxonomic, functional, and phylogenetic diversity for plant communities in dryland regions of Northwest China
Drylands account for more than 30% of China’s terrestrial area, while the ecological drivers of taxonomic (TD), functional (FD) and phylogenetic (PD) diversity in dryland regions have not been explored simultaneously. Therefore, we selected 36 plots of desert and 32 plots of grassland (10 × 10 m) from a typical dryland region of northwest China. We calculated the alpha and beta components of TD, FD and PD for 68 dryland plant communities using Rao quadratic entropy index, which included 233 plant species. Redundancy analyses and variation partitioning analyses were used to explore the relative influence of environmental and spatial factors on the above three facets of diversity, at the alpha and beta scales. We found that soil, climate, topography and spatial structures (principal coordinates of neighbor matrices) were significantly correlated with TD, FD and PD at both alpha and beta scales, implying that these diversity patterns are shaped by contemporary environment and spatial processes together. However, we also found that alpha diversity was predominantly regulated by spatial structure, whereas beta diversity was largely determined by environmental variables. Among environmental factors, TD was most strongly correlated with climatic factors at the alpha scale, while with soil factors at the beta scale. FD was only significantly correlated with soil factors at the alpha scale, but with altitude, soil and climatic factors at the beta scale. In contrast, PD was more strongly correlated with altitude at the alpha scale, but with soil factors at the beta scale. Environment and space explained a smaller portion of variance in PD than in TD and FD. These results provide robust evidence that the ecological drivers of biodiversity differ among different scales and facets of diversity. Future research that focuses on the comparisons among TD, FD and PD would likely provide new insights into elucidating the underlying community assembly.
Wang et al. (2019) Different ecological processes determined the alpha and beta components of taxonomic, functional, and phylogenetic diversity for plant communities in dryland regions of Northwest China. PeerJ 6:e6220 https://doi.org/10.7717/peerj.6220
Aridity and land use negatively influence a dominant species' upper critical thermal limits
Understanding the physiological tolerances of ectotherms, such as thermal limits, is important in predicting biotic responses to climate change. However, it is even more important to examine these impacts alongside those from other landscape changes: such as the reduction of native vegetation cover, landscape fragmentation and changes in land use intensity (LUI). Here, we integrate the observed thermal limits of the dominant and ubiquitous meat ant Iridomyrmex purpureus across climate (aridity), land cover and land use gradients spanning 270 km in length and 840 m in altitude across northern New South Wales, Australia. Meat ants were chosen for study as they are ecosystem engineers and changes in their populations may result in a cascade of changes in the populations of other species. When we assessed critical thermal maximum temperatures (CTmax) of meat ants in relation to the environmental gradients we found little influence of climate (aridity) but that CTmax decreased as LUI increased. We found no overall correlation between CTmax and CTmin. We did however find that tolerance to warming was lower for ants sampled from more arid locations. Our findings suggest that as LUI and aridification increase, the physiological resilience of I. purpureus will decline. A reduction in physiological resilience may lead to a reduction in the ecosystem service provision that these populations provide throughout their distribution.
Andrew et al. (2019) Aridity and land use negatively influence a dominant species' upper critical thermal limits. PeerJ 6:e6252 https://doi.org/10.7717/peerj.6252
MicroRNA-705 regulates the differentiation of mouse mandible bone marrow mesenchymal stem cells
The craniofacial skeleton is the foundation of most stomatological treatments, including prosthodontics and maxillofacial surgery. Although histologically similar to the appendicular skeleton, the craniofacial skeleton manifests many unique properties in response to external stimuli and signals. However, the mandibular or maxillary bone marrow mesenchyme, which is the intrinsic foundation of the functions of craniofacial skeleton, has not been well studied, and its homeostasis mechanism remains elusive. Osteoporosis is a systemic disease that affects all skeletons and is characterized by bone mass loss. Osteoporotic bone marrow mesenchymal stem cells (BMMSCs) exhibit disturbed homeostasis and distorted lineage commitment. Many reports have shown that microRNAs (miRNAs) play important roles in regulating MSCs homeostasis. Here, to obtain a better understanding of mandibular bone marrow MSCs homeostasis, we isolated and cultured mandible marrow MSCs from mouse mandibles. Using miR-705 mimics and an inhibitor, we demonstrated that miR-705 played a vital role in shifting the mandibular MSCs lineage commitment in vitro. Utilizing an osteoporosis mouse model, we demonstrated that MSCs from ovariectomized (OVX) mouse mandibular bone marrow exhibited impaired osteogenic and excessive adipogenic differentiation. miR-705 was found overexpressed in OVX mandibular MSCs. The knock down of miR-705 in vitro partially attenuated the differentiation disorder of the OVX mandibular MSCs by upregulating the expression of osteogenic marker genes but suppressing adipogenic genes. Taken together, our findings provide a better understanding of the homeostasis mechanism of mandibular BMMSCs and a novel potential therapeutic target for treating mandibular osteoporosis.
Yang et al. (2019) MicroRNA-705 regulates the differentiation of mouse mandible bone marrow mesenchymal stem cells. PeerJ 7:e6279 https://doi.org/10.7717/peerj.6279
Influence of substrate types and morphological traits on movement behavior in a toad and newt species
Background Inter-patch movements may lead to genetic mixing, decreasing both inbreeding and population extinction risks, and is hence a crucial aspect of amphibian meta-population dynamics. Traveling through heterogeneous landscapes might be particularly risky for amphibians. Understanding how these species perceive their environment and how they move in heterogeneous habitats is an essential step in explaining metapopulation dynamics and can be important for predicting species’ responses to climate change and for conservation policy and management. Methods Using an experimental approach, the present study focused on the movement behavior (crossing speed and number of stops) on different substrates mimicking landscape components (human-made and natural substrates) in two amphibian species contrasting in locomotion mode: the common toad (Bufo bufo), a hopping and burrowing anuran and the marbled newt (Triturus marmoratus), a walking salamander. We tested the hypothesis that species reaction to substrate is dependent on specific ecological requirements or locomotion modes because of morphological and behavioral differences. Results In both species, substrate type influenced individual crossing speed, with individuals moving faster on soil than on concrete substrate. We also demonstrated that long-legged individuals moved faster than individuals with short legs. In both species, the number of stops was higher in females than in males. In common toads, the number of stops did not vary between substrates tested, whereas in marbled newts the number of stops was higher on concrete than on soil substrate. Discussion We highlighted that concrete substrate (mimicking roads) negatively affect the crossing speed of both studied species, with an effect potentially higher in marbled newts. Our findings corroborate negative effects of such heterogeneous landscapes on movement behavior of two amphibian species, which may have implications for the dynamics of metapopulations.
Trochet et al. (2019) Influence of substrate types and morphological traits on movement behavior in a toad and newt species. PeerJ 6:e6053 https://doi.org/10.7717/peerj.6053
Amelioration of drought effects in wheat and cucumber by the combined application of super absorbent polymer and potential biofertilizer
Biofertilizer is a good substitute for chemical fertilizer in sustainable agriculture, but its effects are often hindered by drought stress. Super absorbent polymer (SAP), showing good capacity of water absorption and retention, can increase soil moisture. However, limited information is available about the efficiency of biofertilizer amended with SAP. This study was conducted to investigate the effects of synergistic application of SAP and biofertilizers (Paenibacillus beijingensis BJ-18 and Bacillus sp. L-56) on plant growth, including wheat and cucumber. Potted soil was treated with different fertilizer combinations (SAP, BJ-18 biofertilizer, L-56 biofertilizer, BJ-18 + SAP, L-56 + SAP), and pot experiment was carried out to explore its effects on viability of inoculants, seed germination rate, plant physiological and biochemical parameters, and expression pattern of stress-related genes under drought condition. At day 29 after sowing, the highest viability of strain P. beijingensis BJ-18 (264 copies ng−1 gDNA) was observed in BJ-18 + SAP treatment group of wheat rhizosphere soil, while that of strain Bacillus sp. L-56 (331 copies ng−1 gDNA) was observed in the L-56 + SAP treatment group of cucumber rhizosphere soil. In addition, both biofertilizers amended with SAP could promote germination rate of seeds (wheat and cucumber), plant growth, soil fertility (urease, sucrose, and dehydrogenase activities). Quantitative real-time PCR analysis showed that biofertilizer + SAP significantly down-regulated the expression levels of genes involved in ROS scavenging (TaCAT, CsCAT, TaAPX, and CsAPX2), ethylene biosynthesis (TaACO2, CsACO1, and CsACS1), stress response (TaDHN3, TaLEA, and CsLEA11), salicylic acid (TaPR1-1a and CsPR1-1a), and transcription activation (TaNAC2D and CsNAC35) in plants under drought stress. These results suggest that SAP addition in biofertilizer is a good tactic for enhancing the efficiency of biofertilizer, which is beneficial for plants in response to drought stress. To the best of our knowledge, this is the first report about the effect of synergistic use of biofertilizer and SAP on plant growth under drought stress.
Li et al. (2019) Amelioration of drought effects in wheat and cucumber by the combined application of super absorbent polymer and potential biofertilizer. PeerJ 7:e6073 https://doi.org/10.7717/peerj.6073
Post-mortem detection of six human herpesviruses (HSV-1, HSV-2, VZV, EBV, CMV, HHV-6) in trigeminal and facial nerve ganglia by PCR
Background Among over 100 types of Herpesviridae viruses, eight can infect humans: herpes simplex viruses (HSV-1, HSV-2), varicella zoster virus (VZV), cytomegalovirus (CMV), Epstein-Barr virus (EBV), and human herpesviruses 6, 7, and 8 (HHV-6, HHV-7, HHV-8). After initial infection, the viruses remain latent for the lifetime of the host. The aim of this study was to determine the distribution of six different herpesviruses: HSV-1, HSV-2, VZV, EBV, CMV, and HHV-6 in trigeminal and facial nerve ganglia among a random group of Polish population. Methods The studied group consisted of 47 individuals (40 male, seven female); mean age of 47.4 ± 16.5 years) who died of independent causes (suicide, traffic accident, and poisoning, among others). Bilateral trigeminal and facial nerve ganglia of each cadaver were collected during the autopsy. Herpesviruses were detected using multiplex polymerase chain reaction technique. Results Herpesviruses were found in trigeminal and/or facial ganglia in 30/47 (63.8%) of cadavers. HHV-6 was the most prevalent of the herpesviruses and was found in nearly half of cadavers (n = 22; 46.8%), followed by HSV-1 (n = 7; 14.9%), VZV (n = 4; 8.5%), EBV (n = 4; 8.5%), HSV-2 (n = 2; 4.3%), and CMV (n = 1; 2.1%). Facial nerve ganglia (n = 23; 48.9%) were more often infected than trigeminal ganglia (n = 13; 27.7%). Discussion The results of this study have revealed a common presence of the herpesviruses in trigeminal and facial nerve ganglia among a random group of Polish population. Furthermore, the data also demonstrate simultaneous infection of the ganglia with different herpesviruses. This study has contributed to the knowledge of prevalence and localization of herpesviruses in different structures of the nervous system.
Ptaszyńska-Sarosiek et al. (2019) Post-mortem detection of six human herpesviruses (HSV-1, HSV-2, VZV, EBV, CMV, HHV-6) in trigeminal and facial nerve ganglia by PCR. PeerJ 6:e6095 https://doi.org/10.7717/peerj.6095
The gut microbiome correlates with conspecific aggression in a small population of rescued dogs (Canis familiaris)
Aggression is a serious behavioral disorder in domestic dogs that endangers both dogs and humans. The underlying causes of canine aggression are poorly resolved and require illumination to ensure effective therapy. Recent research links the compositional diversity of the gut microbiome to behavioral and psychological regulation in other mammals, such as mice and humans. Given these observations, we hypothesized that the composition of the canine gut microbiome could associate with aggression. We analyzed fecal microbiome samples collected from a small population of pit bull type dogs seized from a dogfighting organization. This population included 21 dogs that displayed conspecific aggressive behaviors and 10 that did not. Beta-diversity analyses support an association between gut microbiome structure and dog aggression. Additionally, we used a phylogenetic approach to resolve specific clades of gut bacteria that stratify aggressive and non-aggressive dogs, including clades within Lactobacillus, Dorea, Blautia, Turicibacter, and Bacteroides. Several of these taxa have been implicated in modulating mammalian behavior as well as gastrointestinal disease states. Although sample size limits this study, our findings indicate that gut microorganisms are linked to dog aggression and point to an aggression-associated physiological state that interacts with the gut microbiome. These results also indicate that the gut microbiome may be useful for diagnosing aggressive behaviors prior to their manifestation and potentially discerning cryptic etiologies of aggression.
Kirchoff et al. (2019) The gut microbiome correlates with conspecific aggression in a small population of rescued dogs (Canis familiaris). PeerJ 7:e6103 https://doi.org/10.7717/peerj.6103
Efficient generation of human primordial germ cell-like cells from pluripotent stem cells in a methylcellulose-based 3D system at large scale
Background The mechanisms underlying human germ cell development and infertility remain largely unknown due to bioethical issues and the shortage of experimental materials. Therefore, an effective in vitro induction system of human primordial germ-like cells (hPGCLCs) from human pluripotent stem cells (hPSC) is in high demand. The current strategies used for the generation of hPGCLCs are not only costly but also difficult to perform at a large scale, thereby posing barriers to further research. In this study, we attempted to solve these problems by providing a new 3D culture system for hPGCLC differentiation. Methods The efficiency and relative yield of a methylcellulose (MC)-based 3D hPGCLC induction system were first compared with that of a conventional U96 system. Then, we examined the gene expression of germ cell marker genes and the key epigenetic modifications of the EpCAM-/INTEGRINα6-high cells from the 3D MC induction system and the U96 system via quantitative PCR and immunofluorescence. Finally, the reliability of the MC-based 3D hPGCLC induction system was evaluated via the generation of induced pluripotent stem cells (iPSCs) from the testicular cells of one patient with obstructive azoospermia (OA) and followed by the subsequent differentiation of iPSCs into the germ cell lineage. Results In the present study, we demonstrated that the 3D MC induction system combined with low-cell attachment plates facilitated the generation of hPGCLCs at a large scale. We found that the hPGCLCs generated via the MC system shared similar characteristics to that via the U96 system in terms of the gene expression profiles, germ cell-specific markers, epigenetic modification states and cellular states. In addition, hPGCLCs from iPSCs derived from one OA patient were generated with high efficiency via the present 3D MC induction system. Discussion The in vitro induction of hPGCLCs from human embryonic stem cells (hESCs)/human induced pluripotent stem cells (hiPSCs) has significant implications in exploring the underlying mechanisms of the origin and specification of hPGCs and the epigenetic programming of the human germ line as well as treating male infertility. Here, we developed a simple and efficient 3D induction system to generate hPGCLCs from hESCs/hiPSCs at a large scale, which facilitated the study of human germ cell development and stem cell-based reproductive medicine.
Wang et al. (2019) Efficient generation of human primordial germ cell-like cells from pluripotent stem cells in a methylcellulose-based 3D system at large scale. PeerJ 6:e6143 https://doi.org/10.7717/peerj.6143
Changes in bone density and bone quality caused by single fasting for 96 hours in rats
Background Young women occasionally engage in dietary restrictions accompanied by fasting for the purpose of losing weight, but such restrictions have various effects on body functions. The recent increase in the number of people suffering from osteoporosis has become a major social problem mainly in industrialized countries.Therefore, we think it is important to understand the effects of fasting on bone vulnerability, especially to bone quality. Methods Animals used male Wister rats weighing 130 g (6 weeks of age), and were divided into a control group (n = 5) and a fasting group (n = 6). The experimental period was 14 days, the control group had ad libitum food throughout the experimental period, the fasted group was fasted for 4 days, and than, had ad libitum food for 10 days. In this study, parameters related to bone fragility due to three-dimensional bone architecture were determined on Contrast enhanced micro-CT images of the lumbar spine and were used as a method for the evaluation of bone quality. In addition, a time-course observation of each individual was carried out during the fasting period and later upon resuming food intake. Cross-sectional images of all vertebrae were obtained from radiographic computed tomography and were analyzed by using Latheta software ver. 3.0 (Hitachi-Aloka Medical, Nagasaki, Japan). The region of interest that was misrecognized in each cross-sectional image was made consistent with the anatomical structure by carrying out corrections manually and by identifying the cortical bone areas and cancellous bone areas. Results Our findings showed that while single fasting for 96 h did not cause any major change in the macroscopic morphology of bone, it caused a marked decrease in bone density. In addition, the minimum cross-sectional moment, which indicated the “strength against bending” as well as the polar moment that indicated the “strength against torsion” were both lower than in non-fasted rats. Further, after resumption of feeding, bone mineral content in the fasting group recovered rapidly and starting at day 4 after resumption of feeding, there was no difference with the control group. On the other hand, the values of the minimum cross-sectional moment and polar moment did not recover, and the difference with the control group increased during the feeding period. Discussion On the basis of this study, the authors estimate that the fasting-induced decrease in bone minimum cross-sectional moment and polar moment may have been due to changes affecting some factors involved in bone quality, and thus could be useful as a parameter in future studies aimed at elucidating bone quality. At least, in the case where bone change accompanied with a change in macroscopic distribution of mineral components occurs, the values of minimum cross-sectional moment and polar moment are considered to be bone parameters that will provide valuable information to elucidate bone quality.
Hisatomi et al. (2019) Changes in bone density and bone quality caused by single fasting for 96 hours in rats. PeerJ 6:e6161 https://doi.org/10.7717/peerj.6161
Microbiota variations in Culex nigripalpus disease vector mosquito of West Nile virus and Saint Louis Encephalitis from different geographic origins
Although mosquito microbiota are known to influence reproduction, nutrition, disease transmission, and pesticide resistance, the relationship between host-associated microbial community composition and geographical location is poorly understood. To begin addressing this knowledge gap, we characterized microbiota associated with adult females of Culex nigripalpus mosquito vectors of Saint Louis Encephalitis and West Nile viruses sampled from three locations in Florida (Vero Beach, Palmetto Inland, and Palmetto Coast). High-throughput sequencing of PCR-amplified 16S rRNA genes demonstrated significant differences among microbial communities of mosquitoes sampled from the three locations. Mosquitoes from Vero Beach (east coast Florida) were dominated by uncultivated Asaia sp. (Alphaproteobacteria), whereas microbiota associated with mosquitoes collected from two mosquito populations at Palmetto (west coast Florida) sites were dominated by uncultured Spironema culicis (Spirochaetes), Salinisphaera hydrothermalis (Gammaproteobacteria), Spiroplasma (Mollicutes), uncultured Enterobacteriaceae, Candidatus Megaira (Alphaproteobacteria; Rickettsiae), and Zymobacter (Gammaproteobacteria). The variation in taxonomic profiles of Cx. nigripalpus gut microbial communities, especially with respect to dominating taxa, is a potentially critical factor in understanding disease transmission and mosquito susceptibility to insecticides among different mosquito populations.
Duguma et al. (2019) Microbiota variations in Culex nigripalpus disease vector mosquito of West Nile virus and Saint Louis Encephalitis from different geographic origins. PeerJ 6:e6168 https://doi.org/10.7717/peerj.6168
Whole-genome comparisons of Penicillium spp. reveals secondary metabolic gene clusters and candidate genes associated with fungal aggressiveness during apple fruit decay
Blue mold is a postharvest rot of pomaceous fruits caused by Penicillium expansum and a number of other Penicillium species. The genome of the highly aggressive P. expansum strain R19 was re-sequenced and analyzed together with the genome of the less aggressive P. solitum strain RS1. Whole genome scale similarities and differences were examined. A phylogenetic analysis of P. expansum, P. solitum, and several closely related Penicillium species revealed that the two pathogens isolated from decayed apple with blue mold symptoms are not each other’s closest relatives. Among a total of 10,560 and 10,672 protein coding sequences respectively, a comparative genomics analysis revealed 41 genes in P. expansum R19 and 43 genes in P. solitum RS1 that are unique to these two species. These genes may be associated with pome fruit–fungal interactions, subsequent decay processes, and mycotoxin accumulation. An intact patulin gene cluster consisting of 15 biosynthetic genes was identified in the patulin producing P. expansum strain R19, while only a remnant, seven-gene cluster was identified in the patulin-deficient P. solitum strain. However, P. solitum contained a large number of additional secondary metabolite gene clusters, indicating that this species has the potential capacity to produce an array of known as well as not-yet-identified products of possible toxicological or biotechnological interest.
Wu et al. (2019) Whole-genome comparisons of Penicillium spp. reveals secondary metabolic gene clusters and candidate genes associated with fungal aggressiveness during apple fruit decay. PeerJ 7:e6170 https://doi.org/10.7717/peerj.6170
Social network analysis for the assessment of pig, cattle and buffalo movement in Xayabouli, Lao PDR
The aim of this study is to understand the role that the movement patterns of pigs, cattle and buffalo play in the spread of foot-and-mouth disease (FMD). A cross-sectional survey consisting of a questionnaire was used in a hotspot area for FMD: Xayabouli Province, Lao People’s Democratic Republic. A total of 189 respondents were interviewed. We found that the key players in this network were people who were involved with more than one species of animal or occupation (multipurpose occupational node), which represents the highest number of activities of animals moved off the holding (shown with the highest out-degree centrality) and a high likelihood of being an intermediary between others (shown with the highest betweenness centrality). Moreover, the results show that the animals moved to and away from each node had few connections. Some nodes (such as traders) always received animals from the same group of cattle owners at different times. The subgroup connection within this network has many weak components, which means a connection in this network shows that some people can be reached by others, but most people were not. In this way, the number of connections present in the network was low when we defined the proportion of observed connections with all possible connections (density). These findings indicate that the network might not be busy; only one type of node is dominant which enables increased control of disease spread. We recommend that the relevant authorities implement control measures regarding the key players, which is the best way to effectively control the spread of infectious diseases.
Poolkhet et al. (2019) Social network analysis for the assessment of pig, cattle and buffalo movement in Xayabouli, Lao PDR. PeerJ 6:e6177 https://doi.org/10.7717/peerj.6177
A public database for the new MLST scheme for Treponema pallidum subsp. pallidum: surveillance and epidemiology of the causative agent of syphilis
Treponema pallidum subsp. pallidum is the causative agent of syphilis, a sexually transmitted disease with worldwide prevalence. Several different molecular typing schemes are currently available for this pathogen. To enable population biology studies of the syphilis agent and for epidemiological surveillance at the global scale, a harmonized typing tool needs to be introduced. Recently, we published a new multi-locus sequence typing (MLST) with the potential to significantly enhance the epidemiological data in several aspects (e.g., distinguishing genetically different clades of syphilis, subtyping inside these clades, and finally, distinguishing different subspecies of non-cultivable pathogenic treponemes). In this short report, we introduce the PubMLST database for treponemal DNA data storage and for assignments of allelic profiles and sequencing types. Moreover, we have summarized epidemiological data of all treponemal strains (n = 358) with available DNA sequences in typing loci and found several association between genetic groups and characteristics of patients. This study proposes the establishment of a single MLST of T. p. pallidum and encourages researchers and public health communities to use this PubMLST database as a universal tool for molecular typing studies of the syphilis pathogen.
Grillova et al. (2019) A public database for the new MLST scheme for Treponema pallidum subsp. pallidum: surveillance and epidemiology of the causative agent of syphilis. PeerJ 6:e6182 https://doi.org/10.7717/peerj.6182
MLPA is a practical and complementary alternative to CMA for diagnostic testing in patients with autism spectrum disorders and identifying new candidate CNVs associated with autism
Background Autism spectrum disorder (ASD) is a complex heterogeneous developmental disease with a significant genetic background that is frequently caused by rare copy number variants (CNVs). Microarray-based whole-genome approaches for CNV detection are widely accepted. However, the clinical significance of most CNV is poorly understood, so results obtained using such methods are sometimes ambiguous. We therefore evaluated a targeted approach based on multiplex ligation-dependent probe amplification (MLPA) using selected probemixes to detect clinically relevant variants for diagnostic testing of ASD patients. We compare the reliability and efficiency of this test to those of chromosomal microarray analysis (CMA) and other tests available to our laboratory. In addition, we identify new candidate genes for ASD identified in a cohort of ASD-diagnosed patients. Method We describe the use of MLPA, CMA, and karyotyping to detect CNV in 92 ASD patients and evaluate their clinical significance. Result Pathogenic and likely pathogenic mutations were identified by CMA in eight (8.07% of the studied cohort) and 12 (13.04%) ASD patients, respectively, and in eight (8.07%) and four (4.35%) patients, respectively, by MLPA. The detected mutations include the 22q13.3 deletion, which was attributed to ring chromosome 22 formation based on karyotyping. CMA revealed a total of 91 rare CNV in 55 patients: eight pathogenic, 15 designated variants of unknown significance (VOUS)—likely pathogenic, 10 VOUS—uncertain, and 58 VOUS—likely benign or benign. MLPA revealed 18 CNV in 18 individuals: eight pathogenic, four designated as VOUS—likely pathogenic, and six designated as VOUS—likely benign/benign. Rare CNVs were detected in 17 (58.62%) out of 29 females and 38 (60.32%) out of 63 males in the cohort. Two genes, DOCK8 and PARK2, were found to be overlapped by CNV designated pathogenic, VOUS—likely pathogenic, or VOUS—uncertain in multiple patients. Moreover, the studied ASD cohort exhibited significant (p < 0.05) enrichment of duplications encompassing DOCK8. Conclusion Multiplex ligation-dependent probe amplification and CMA yielded concordant results for 12 patients bearing CNV designated pathogenic or VOUS—likely pathogenic. Unambiguous diagnoses were achieved for eight patients (corresponding to 8.7% of the total studied population) by both MLPA and CMA, for one (1.09%) patient by karyotyping, and for one (1.09%) patient by FRAXA testing. MLPA and CMA thus achieved identical reliability with respect to clinically relevant findings. As such, MLPA could be useful as a fast and inexpensive test in patients with syndromic autism. The detection rate of potentially pathogenic variants (VOUS—likely pathogenic) achieved by CMA was higher than that for MLPA (13.04% vs. 4.35%). However, there was no corresponding difference in the rate of unambiguous diagnoses of ASD patients. In addition, the results obtained suggest that DOCK8 may play a role in the etiology of ASD.
Capkova et al. (2019) MLPA is a practical and complementary alternative to CMA for diagnostic testing in patients with autism spectrum disorders and identifying new candidate CNVs associated with autism. PeerJ 6:e6183 https://doi.org/10.7717/peerj.6183
First record of Phyllorhiza sp. (Cnidaria: Scyphozoa) in a Chinese coastal aquaculture pond
Background It has been suggested that aquaculture ponds on the Chinese coast could act as breeding grounds for scyphozoans. Here, we present the first record of the scyphomedusa Phyllorhiza sp. in an aquaculture pond on the coast of the southern Yellow Sea, based on a combination of morphological characteristics and mitochondrial 16S DNA sequence data. Methods A field survey was performed on June 29, 2017 in a pond used for culturing the shrimp Penaeus japonicus, located in the southern Yellow Sea, China. Jellyfish specimens were collected for morphological and genetic analysis. The morphological characters of the jellyfish specimens were compared to taxonomic literature. Additionally, phylogenetic analysis of the mitochondrial 16S fragments of these specimens were also conducted. Results These specimens had the following morphological characters: hemispherical umbrella without scapulets; J-shaped oral arms; a single larger terminal club on each arm; bluish colored with a slightly expanded white tip; and mouthlets present only in the lower half to one-third of each arm. These morphological features of the medusae indicated that the specimens found in the shrimp culture ponds belong to the genus Phyllorhiza Agassiz, 1862, but did not match with the description of any of the known species of the genus Phyllorhiza. Phylogenetic analyses of the mtDNA 16S regions revealed that these specimens, together with Phyllorhiza sp. from Malaysian coastal waters, belong to a sister group of Phyllorhiza punctata. Juveniles and ephyrae of Phyllorhiza sp. were observed in the aquaculture pond. The mean density of Phyllorhiza sp. medusa in the surface water within the pond was estimated to be 0.05 individuals/m2. Discussion Based on our observations of the gross morphology and molecular data, we state that the specimens collected in the aquaculture pond can be identified as Phyllorhiza sp. This is the first record of Phyllorhiza sp. in Chinese seas. Large scale dispersal through ballast water or the expansion of jellyfish aquarium exhibitions are possible pathways of invasion, but this needs to be confirmed in further studies.
Dong et al. (2019) First record of Phyllorhiza sp. (Cnidaria: Scyphozoa) in a Chinese coastal aquaculture pond. PeerJ 7:e6191 https://doi.org/10.7717/peerj.6191
Climatic niche evolution in the viviparous Sceloporus torquatus group (Squamata: Phrynosomatidae)
The cold-climate hypothesis maintains that viviparity arose as a means to prevent increased egg mortality in nests owing to low temperatures, and this hypothesis represents the primary and most strongly supported explanation for the evolution of viviparity in reptiles. In this regard, certain authors have stated that viviparous species will exhibit speciation via climatic niche conservatism, with similar climatic niches being observed in allopatric sister species. However, this prediction remains to be tested with bioclimatic variables relevant to each viviparous group. In the present study, we examined climatic niche evolution in a group of North American viviparous lizards to determine whether their diversification is linked to phylogenetic niche conservatism (PNC). We evaluated the phylogenetic signal and trait evolution of individual bioclimatic variables and principal component (PC) scores of a PC analysis, along with reconstructions of ancestral climate tolerances. The results suggest that diversification of the Sceloporus torquatus group species is associated with both niche differentiation and PNC. Furthermore, we did not observe PNC across nearly all bioclimatic variables and in PC2 and PC3. However, in Precipitation Seasonality (Bio15), in Precipitation of Coldest Quarter (Bio19) and in PC1 (weakly associated with variability of temperature), we did observe PNC. Additionally, variation of the scores along the phylogeny and Pagel’s delta (δ) >1 of PC3 suggests a fast, recent evolution to dry conditions in the clade that sustains S. serrifer.
Martínez-Méndez et al. (2019) Climatic niche evolution in the viviparous Sceloporus torquatus group (Squamata: Phrynosomatidae). PeerJ 6:e6192 https://doi.org/10.7717/peerj.6192
Carabid community structure in northern China grassland ecosystems: Effects of local habitat on species richness, species composition and functional diversity
Background Most carabid beetles are particularly sensitive to local habitat characteristics. Although in China grasslands account for more than 40% of the national land, their biodiversity is still poorly known. The aim of this paper is to identify the main environmental characteristics influencing carabid diversity in different types of grassland in northern China. Methods We investigated the influence of vegetation (plant biomass, cover, density, height and species richness), soil (bulk density, above ground litter, moisture and temperature) and climate (humidity, precipitation and temperature) on carabid community structure (species richness, species composition and functional diversity—measured as body size, movement and total diversity) in three types of grasslands: desert, typical and meadow steppes. We used Canonical correspondence analysis to investigate the role of habitat characteristics on species composition and eigenvector spatial filtering to investigate the responses of species richness and functional diversities. Results We found that carabid community structure was strongly influenced by local habitat characteristics and particularly by climatic factors. Carabids in the desert steppe showed the lowest richness and functional diversities. Climate predictors (temperature, precipitation and humidity) had positive effects on carabid species richness at both regional and ecosystem levels, with difference among ecosystems. Plant diversity had a positive influence on carabid richness at the regional level. Soil compaction and temperature were negatively related to species richness at regional level. Climatic factors positively influenced functional diversities, whereas soil temperature had negative effects. Soil moisture and temperature were the most important drivers of species composition at regional level, whereas the relative importance of the various environmental parameters varied among ecosystems. Discussion Carabid responses to environmental characteristics varied among grassland types, which warns against generalizations and indicates that management programs should be considered at grassland scale. Carabid community structure is strongly influenced by climatic factors, and can therefore be particularly sensitive to ongoing climate change.
Tsafack et al. (2019) Carabid community structure in northern China grassland ecosystems: Effects of local habitat on species richness, species composition and functional diversity. PeerJ 6:e6197 https://doi.org/10.7717/peerj.6197
Fluoxetine-induced alteration of murine gut microbial community structure: evidence for a microbial endocrinology-based mechanism of action responsible for fluoxetine-induced side effects
Background Depression and major depressive disorder affect 25% of the population. First line treatment utilizing selective serotonin reuptake inhibitors (SSRIs) have met with limited success due to well-recognized negative side effects which include weight gain or loss. This inability to control unwanted side effects often result in patients stopping their antidepressant medications. The mechanisms underlying the failure of SSRIs are incompletely understood. Methods Male CF-1 mice (5 weeks of age, N = 10 per group) were per orally administered fluoxetine (20 mg per kg body weight) or diluent daily for 29 days. During this time fecal specimens were collected at three defined time points (0, 15 and 29 days). At the conclusion of the 29-day dosing regimen, animals were subjected to two behavioral assessments. For bacterial identification of the microbiota, 16S rRNA gene sequencing was performed on 60 fecal specimens (three specimens per mouse time course, N = 20 mice) using Illumina MiSeq. Analysis of community sequence data was done using mothur and LEfSe bioinformatic software packages. Results Daily per oral administration of fluoxetine for 29 days to male mice resulted in a significant, time dependent, alteration in microbial communities accompanying changes in body weight. The calculated species richness and diversity indicators of the murine fecal microbial communities were inconsistent and not significantly different between the groups. Among the phylotypes decreased in abundance due to fluoxetine administration were Lactobacillus johnsonii and Bacteroidales S24-7 which belong to phyla associated with regulation of body mass. The observed changes in body weight due to fluoxetine administration mimicked the dramatic shifts in weight gain/loss that has been observed in humans. Further, at the conclusion of the 29-day dosing regimen fluoxetine-dosed animals evidenced a mild anxiogenic-like behavior. Discussion We report that the most widely used antidepressant, fluoxetine, which is an SSRI-type drug, results in the selective depletion of gut microbiota, specifically the Lactobacilli which are involved in the regulation of body weight. Concomitantly, fluoxetine administration increases the abundance of phylotypes related to dysbiosis. Since Lactobacilli have been previously shown to possess a known biogenic amine transporter that regulates the uptake of fluoxetine, it is proposed that a microbial endocrinology-based mechanistic pathway is responsible for the ability of SSRIs to selectively negatively impact beneficial microbiota. The results of this study therefore suggest that the negative clinical side effects due to fluoxetine administration may be due to alterations in gut microbiota. Further, the data also suggests that supplementation of bacterial genera directly affected by fluoxetine administration may prove useful in ameliorating some of the well-known side effects of chronic fluoxetine administration such as weight alterations.
Lyte et al. (2019) Fluoxetine-induced alteration of murine gut microbial community structure: evidence for a microbial endocrinology-based mechanism of action responsible for fluoxetine-induced side effects. PeerJ 7:e6199 https://doi.org/10.7717/peerj.6199
Survival under anthropogenic impact: the response of dragonflies (Odonata), beetles (Coleoptera) and caddisflies (Trichoptera) to environmental disturbances in a two-way industrial canal system (central Poland)
Ecological metrics and assemblages of three orders of aquatic insects (Odonata, Coleoptera and Trichoptera—OCT) in an industrial canal system affected by dredging were studied. Five sites (a river as a control site and canals) along the Vistula River in Central Poland were sampled during six sampling periods (2011 and 2013). Canonical correspondence analyses (CCA) was used to assess the influence of environmental variables on the distribution of 54 insect species in the following system of habitats—a river feeding the canals, river-fed inlet canals and outlet canals with cooling waters. Additionally, before and after control impact (BACI) was used to test for the impact of canal dredging in 2011 on the insect response metrics. Non-metric multidimensional scaling analysis differentiated insect assemblages of the three habitats and similarity percentage (SIMPER) indicated the species most responsible for the faunistic dissimilarities. Temperature was found to be a key factor governing the presence of insects in the outlet canals with cooling water. CCAs revealed that electrolytic conductivity (EC) and salinity had the greatest influence on the OCT fauna in the river and the inlet canals, whilst it was the dissolved oxygen and the level of development of aquatic plants that proved most important in the outlet canals. Modified ANOVAs showed that dredging significantly affected the mean species richness and the dominance in the canals. The changes in OCT species composition were highly informative. The comparison between tolerance patterns of the OCT orders against the five parameters (temperature, EC, total dissolved solids (TDS), pH and current) revealed that caddisflies are the most sensitive group, followed by Coleoptera while Odonata proved the most resistant. Dragonflies have the greatest potential to serve as bioindicators of industrially heated waters. The OCT fauna responded specifically to different environmental factors and stressors, it is strongly recommended to track the responses on different levels, not only metrics, but above all, species.
Buczyńska et al. (2019) Survival under anthropogenic impact: the response of dragonflies (Odonata), beetles (Coleoptera) and caddisflies (Trichoptera) to environmental disturbances in a two-way industrial canal system (central Poland). PeerJ 6:e6215 https://doi.org/10.7717/peerj.6215
Didymin improves UV irradiation resistance in C. elegans
Didymin, a type of flavono-o-glycoside compound naturally present in citrus fruits, has been reported to be an effective anticancer agent. However, its effects on stress resistance are unclear. In this study, we treated Caenorhabditis elegans with didymin at several concentrations. We found that didymin reduced the effects of UV stressor on nematodes by decreasing reactive oxygen species levels and increasing superoxide dismutase (SOD) activity. Furthermore, we found that specific didymin-treated mutant nematodes daf-16(mu86) & daf-2(e1370), daf-16(mu86), akt-1(ok525), akt-2(ok393), and age-1(hx546) were susceptible to UV irradiation, whereas daf-2(e1371) was resistant to UV irradiation. In addition, we found that didymin not only promoted DAF-16 to transfer from cytoplasm to nucleus, but also increased both protein and mRNA expression levels of SOD-3 and HSP-16.2 after UV irradiation. Our results show that didymin affects UV irradiation resistance and it may act on daf-2 to regulate downstream genes through the insulin/IGF-1-like signaling pathway.
Zhou et al. (2019) Didymin improves UV irradiation resistance in C. elegans. PeerJ 6:e6218 https://doi.org/10.7717/peerj.6218
Descriptive anatomy of the largest known specimen of Protoichthyosaurus prostaxalis (Reptilia: Ichthyosauria) including computed tomography and digital reconstruction of a three-dimensional skull
Ichthyosaur fossils are abundant in Lower Jurassic sediments with nine genera found in the UK. In this paper, we describe the partial skeleton of a large ichthyosaur from the Lower Jurassic (lower Sinemurian) of Warwickshire, England, which was conserved and rearticulated to form the centrepiece of a new permanent gallery at the Thinktank, Birmingham Science Museum in 2015. The unusual three-dimensional preservation of the specimen permitted computed tomography (CT) scanning of individual braincase elements as well as the entire reassembled skull. This represents one of the first times that medical imaging and three-dimensional reconstruction methods have been applied to a large skull of a marine reptile. Data from these scans provide new anatomical information, such as the presence of branching vascular canals within the premaxilla and dentary, and an undescribed dorsal (quadrate) wing of the pterygoid hidden within matrix. Scanning also revealed areas of the skull that had been modelled in wood, clay and other materials after the specimen’s initial discovery, highlighting the utility of applying advanced imaging techniques to historical specimens. Additionally, the CT data served as the basis for a new three-dimensional reconstruction of the skull, in which minor damage was repaired and the preserved bones digitally rearticulated. Thus, for the first time a digital reconstruction of the skull and mandible of a large marine reptile skull is available. Museum records show the specimen was originally identified as an example of Ichthyosaurus communis but we identify this specimen as Protoichthyosaurus prostaxalis. The specimen features a skull nearly twice as long as any previously described specimen of P. prostaxalis, representing an individual with an estimated total body length between 3.2 and 4 m.
Lomax et al. (2019) Descriptive anatomy of the largest known specimen of Protoichthyosaurus prostaxalis (Reptilia: Ichthyosauria) including computed tomography and digital reconstruction of a three-dimensional skull. PeerJ 7:e6112 https://doi.org/10.7717/peerj.6112
Another choice for measuring tree photosynthesis in vitro
Background In the case of tall trees in the field or in rugged terrain where an instrument cannot be placed operationally, beveling is a popular method used to measure in vitro photosynthesis. However, some studies and our own research have shown that net photosynthesis values measured in vitro are generally significantly lower than values measured in situ. Methods To develop a more accurate and applicable method for in vitro determination of photosynthesis, we evaluated five different methods for preparing detached tree branches to measure photosynthesis and gas exchange in vitro (beveling, cracking, splitting, girdling, and immersion in salicylic acid solution). Ten common tree-species were used. Results By comparing light response curves and water-status data, we found that (1) it is possible, to some extent, to substitute in vitro measurement of photosynthetic characteristics of tree species for in situ measurement, provided a suitable treatment is employed; (2) the beveling method is likely to underestimate photosynthetic potential of some trees; (3) after cracking application, most detached branches effectively continued to absorb water; and (4) measurements obtained using detached tree-branches processed by the cracking method were closer to those obtained in situ in intact trees; (5) some tree species (Diospyros kaki, Eriobotrya japonica) appeared to be particularly sensitive to the cracking method, and their in-vitro maximum net photosynthesis rate (Pmax) was significantly less than the in-situ value (P < 0.05). Discussion Our findings provide a methodological support for comprehensive and accurate measurement of plant functional traits. The use of the cracking method contributes to feasibility and reliability of the measurement of photosynthetic parameters in tall trees, thus providing more accurate photosynthetic parameters for the analysis of trade-off strategies at the leaf level.
Meng et al. (2019) Another choice for measuring tree photosynthesis in vitro. PeerJ 7:e5933 https://doi.org/10.7717/peerj.5933
The effect of cycling hypoxia on MCF-7 cancer stem cells and the impact of their microenvironment on angiogenesis using human umbilical vein endothelial cells (HUVECs) as a model
Background Breast cancer is the most common type of cancer among females. Hypoxia mediates cancer hallmarks and results from reduced oxygen level due to irregularities in tumor vascularization or when the tumor size prevents oxygen diffusion and triggers angiogenesis to compensate for low oxygen. Cancer stem cells (CSCs) are a rare subpopulation, able to self-renew and to give rise to tumor-initiating cells. It is proposed that CSCs’ secretions help to recruit endothelial cells via angiogenic factors to establish tumor vascularization. In the tumor microenvironment, the effect of hypoxia on CSCs and the impact of their secretions on triggering angiogenesis and tumor vascularization remain questionable. In this study, three-dimensional (3D) CSCs derived from MCF-7 were directly exposed to repetitive long-term cycles of hypoxia to assess its effect on CSCs and then to evaluate the role of the hypoxic CSCs’ (CSCsHYP) secretions in angiogenesis using (HUVECs) as a model for tumor neovascularization response. Methods CSCs derived from MCF-7 cell-line were expanded under repetitive, strictly optimized, long-term/continuous and intermittent hypoxic shots for almost four months to assess hypoxic effect on CSCs, sorted based on CD44+/CD24− biomarkers. Hypoxic phenotype of CSCsHYP was evaluated by assessing the acquired chemoresistance using MTT assay and elevated stemness properties were assessed by flow cytometry. To evaluate the effect of the secretions from CSCsHYP on angiogenesis, HUVECs were exposed to CSCsHYP conditioned-medium (CdM)—in which CSCs had been previously grown—to mimic the tumor microenvironment and to assess the effect of the secretions from CSCsHYP on the HUVECs’ capability of tube formation, migration and wound healing. Additionally, co-culture of CSCsHYP with HUVECs was performed. Results CSCsHYP acquired higher chemoresistance, increased stemness properties and obtained greater propagation, migration, and wound healing capacities, when compared to CSCs in normoxic condition (CSCsNOR). HUVECs’ tube formation and migration abilities were mediated by hypoxic (CSCs) conditioned media (CdM). Discussion This study demonstrates that chemoresistant and migrational properties of CSCs are enhanced under hypoxia to a certain extent. The microenvironment of CSCsHYP contributes to tumor angiogenesis and migration. Hypoxia is a key player in tumor angiogenesis mediated by CSCs.
Alhawarat et al. (2019) The effect of cycling hypoxia on MCF-7 cancer stem cells and the impact of their microenvironment on angiogenesis using human umbilical vein endothelial cells (HUVECs) as a model. PeerJ 7:e5990 https://doi.org/10.7717/peerj.5990
Simultaneous rapid detection of Hantaan virus and Seoul virus using RT-LAMP in rats
Background Hemorrhagic fever with renal syndrome is in most cases caused by the Hantaan virus (HTNV) and Seoul virus (SEOV). To develop and apply reverse transcription loop-mediated isothermal amplification (RT-LAMP) to detect HTNV and SEOV simultaneously, which was faster, more cost effective, and easier to perform as the target gene amplified rapidly. In this article an assay based on LAMP is demonstrated, which only employs such apparatus as a water bath or a heat block. Methods A chromogenic method using the calcein/Mn2+ complex and real-time turbidity monitoring method were used to assess reaction progress of the reaction, and the specificity of the RT-LAMP-based assay was assessed by detecting cDNAs/cRNAs generated from Coxsackievirus A16, Influenza virus, lymphocytic choriomeningitis virus, mouse poxvirus, rotavirus, mouse hepatitis virus. In addition, 23 clinical specimens were used to determine the agreement between the RT-LAMP assay with reverse transcriptase polymerase chain reaction (RT-PCR) and immunofluorescence (IFT) method. Results The detection limit of RT-LAMP to HNTV and SEOV was as low as 10 copies/μL with optimized reaction conditions, which was much more sensitive than the RT-PCR method (100–1,000 copies/μL). At the same time, the detection results of 23 clinical specimens have also illustrated the agreement between this the RT-LAMP assay with RT-PCR and IFT. Discussion This RT-LAMP assay could be used to perform simultaneous and rapid detection of HTNV and SEOV to the clinical specimens.
Sui et al. (2019) Simultaneous rapid detection of Hantaan virus and Seoul virus using RT-LAMP in rats. PeerJ 6:e6068 https://doi.org/10.7717/peerj.6068
Advances in cultivation, wastewater treatment application, bioactive components of Caulerpa lentillifera and their biotechnological applications
The edible seaweed Caulerpa lentillifera, a powerful natural food source that is rich in protein, minerals, dietary fibers, vitamins, saturated fatty acids and unsaturated fatty acids, has been mass cultured in some Asian countries and has been the focus of researchers in recent years. Here, the operational conditions of its culture, application in wastewater treatment, and bioactive components are summarized and comparatively analyzed. Based on previous studies, salinity, nutrient concentrations, irradiance and temperature are stress factors for algal growth. Moreover, dried Caulerpa lentillifera seaweed is efficient in the biosorption of heavy metals and cationic dyes in wastewater, and fresh seaweed can be introduced as a biofilter in aquaculture system treatment. In addition, among the rich bioactive compounds in Caulerpa lentillifera, the phenolic compounds show the potential ability for regulating glucose metabolism in vivo. Polysaccharides and oligosaccharides exhibit anticoagulant, immunomodulatory effects and cancer-preventing activity. Siphonaxanthin is a compound with attractive novel functions in cancer-preventing activity and lipogenesis-inhibiting effects. Furthermore, the antioxidant activity of siphonaxanthin extracted from Caulerpa lentillifera could be stronger than that of astaxanthin. This review offers an overview of studies of Caulerpa lentillifera addressing various aspects including cultivation, wastewater treatment and biological active components which may provide valuable information for the cultivation and utilization of this green alga.
Chen et al. (2019) Advances in cultivation, wastewater treatment application, bioactive components of Caulerpa lentillifera and their biotechnological applications. PeerJ 7:e6118 https://doi.org/10.7717/peerj.6118
Defensin-like peptides in wheat analyzed by whole-transcriptome sequencing: a focus on structural diversity and role in induced resistance
Antimicrobial peptides (AMPs) are the main components of the plant innate immune system. Defensins represent the most important AMP family involved in defense and non-defense functions. In this work, global RNA sequencing and de novo transcriptome assembly were performed to explore the diversity of defensin-like (DEFL) genes in the wheat Triticum kiharae and to study their role in induced resistance (IR) mediated by the elicitor metabolites of a non-pathogenic strain FS-94 of Fusarium sambucinum. Using a combination of two pipelines for DEFL mining in transcriptome data sets, as many as 143 DEFL genes were identified in T. kiharae, the vast majority of them represent novel genes. According to the number of cysteine residues and the cysteine motif, wheat DEFLs were classified into ten groups. Classical defensins with a characteristic 8-Cys motif assigned to group 1 DEFLs represent the most abundant group comprising 52 family members. DEFLs with a characteristic 4-Cys motif CX{3,5}CX{8,17}CX{4,6}C named group 4 DEFLs previously found only in legumes were discovered in wheat. Within DEFL groups, subgroups of similar sequences originated by duplication events were isolated. Variation among DEFLs within subgroups is due to amino acid substitutions and insertions/deletions of amino acid sequences. To identify IR-related DEFL genes, transcriptional changes in DEFL gene expression during elicitor-mediated IR were monitored. Transcriptional diversity of DEFL genes in wheat seedlings in response to the fungus Fusarium oxysporum, FS-94 elicitors, and the combination of both (elicitors + fungus) was demonstrated, with specific sets of up- and down-regulated DEFL genes. DEFL expression profiling allowed us to gain insight into the mode of action of the elicitors from F. sambucinum. We discovered that the elicitors up-regulated a set of 24 DEFL genes. After challenge inoculation with F. oxysporum, another set of 22 DEFLs showed enhanced expression in IR-displaying seedlings. These DEFLs, in concert with other defense molecules, are suggested to determine enhanced resistance of elicitor-pretreated wheat seedlings. In addition to providing a better understanding of the mode of action of the elicitors from FS-94 in controlling diseases, up-regulated IR-specific DEFL genes represent novel candidates for genetic transformation of plants and development of pathogen-resistant crops.
Odintsova et al. (2019) Defensin-like peptides in wheat analyzed by whole-transcriptome sequencing: a focus on structural diversity and role in induced resistance. PeerJ 7:e6125 https://doi.org/10.7717/peerj.6125
Direct and indirect parental exposure to endocrine disruptors and elevated temperature influences gene expression across generations in a euryhaline model fish
Aquatic organisms inhabiting polluted waterways face numerous adverse effects, including physiological disruption by endocrine disrupting compounds (EDCs). Little is known about how the temperatures associated with global climate change may influence the response of organisms exposed to EDCs, and the effects that these combined stressors may have on molecular endpoints such as gene expression. We exposed Menidia beryllina (inland silversides) to environmentally relevant concentrations (1 ng/L) of two estrogenic EDCs (bifenthrin and 17α-ethinylestradiol; EE2) at 22 °C and 28 °C. We conducted this experiment over multiple generations to better understand the potential effects to chronically exposed populations in the wild. We exposed adult parental fish (F0) for 14 days prior to spawning of the next generation. F1 larvae were then exposed from fertilization until 21 days post hatch (dph) before being transferred to clean water tanks. F1 larvae were reared to adulthood, then spawned in clean water to test for further effects of parental exposure on offspring (F2 generation). Gene expression was quantified by performing qPCR on F0 and F1 gonads, as well as F1 and F2 larvae. We did not detect any significant differences in the expression of genes measured in the parental or F1 adult gonads. We found that the 28 °C EE2 treatment significantly decreased the expression of nearly all genes measured in the F1 larvae. This pattern was transferred to the F2 generation for expression of the follicle-stimulating hormone receptor (FSHR) gene. Expression of 17β-hydroxysteroid dehydrogenase (17β-HSD) and G protein-coupled receptor 30 (GPR30) revealed changes not measured in the previous generation. Effects of the bifenthrin treatments were not observed until the F2 generation, which were exposed to the chemicals indirectly as germ cells. Our results indicate that effects of EDCs and their interactions with abiotic factors, may not be adequately represented by singular generation testing. These findings will contribute to the determination of the risk of EDC contamination to organisms inhabiting contaminated waterways under changing temperature regimes.
DeCourten et al. (2019) Direct and indirect parental exposure to endocrine disruptors and elevated temperature influences gene expression across generations in a euryhaline model fish. PeerJ 7:e6156 https://doi.org/10.7717/peerj.6156
High tempo music prolongs high intensity exercise
Music has been shown to reduce rating of perceived exertion, increase exercise enjoyment and enhance exercise performance, mainly in low-moderate intensity exercises. However, the effects of music are less conclusive with high-intensity activities. The purpose of this with-participant design study was to compare the effects of high tempo music (130 bpm) to a no-music condition during repeated high intensity cycling bouts (80% of peak power output (PPO)) on the following measures: time to exercise end-point, rating of perceived exertion (RPE), heart rate (HR), breathing frequency, ventilatory kinetics and blood lactate (BL). Under the music condition, participants exercised 10.7% longer (p = 0.035; Effect size (ES) = 0.28) (increase of 1 min) and had higher HR (4%; p = 0.043; ES = 0.25), breathing frequency (11.6%; p < 0.001; ES = 0.57), and RER (7% at TTF; p = 0.021; ES = 1.1) during exercise, as measured at the exercise end-point. Trivial differences were observed between conditions in RPE and other ventilatory kinetics during exercise. Interestingly, 5 min post-exercise termination, HR recovery was 13.0% faster following the music condition (p < 0.05) despite that music was not played during this period. These results strengthen the notion that music can alter the association between central motor drive, central cardiovascular command and perceived exertion, and contribute to prolonged exercise durations at higher intensities along with a quicken HR recovery.
Maddigan et al. (2019) High tempo music prolongs high intensity exercise. PeerJ 6:e6164 https://doi.org/10.7717/peerj.6164
hdac4 mediates perichondral ossification and pharyngeal skeleton development in the zebrafish
Background Histone deacetylases (HDACs) are epigenetic factors that function to repress gene transcription by removing acetyl groups from the N-terminal of histone lysines. Histone deacetylase 4 (HDAC4), a class IIa HDAC, has previously been shown to regulate the process of endochondral ossification in mice via repression of Myocyte enhancer factor 2c (MEF2C), a transcriptional activator of Runx2, which in turn promotes chondrocyte maturation and production of bone by osteoblasts. Methods & Materials In this study, we generated two zebrafish lines with mutations in hdac4 using CRISPR/Cas9 and analyzed mutants for skeletal phenotypes and expression of genes known to be affected by Hdac4 expression. Results Lines have insertions causing a frameshift in a proximal exon of hdac4 and a premature stop codon. Mutations are predicted to result in aberrant protein sequence and a truncated protein, eliminating the Mef2c binding domain and Hdac domain. Zygotic mutants from two separate lines show a significant increase in ossification of pharyngeal ceratohyal cartilages at 7 days post fertilization (dpf) (p < 0.01, p < 0.001). At 4 dpf, mutant larvae have a significant increase of expression of runx2a and runx2b in the ceratohyal cartilage (p < 0.05 and p < 0.01, respectively). A subset of maternal-zygotic (mz) mutant and heterozygote larvae (40%) have dramatically increased ossification at 7 dpf compared to zygotic mutants, including formation of a premature anguloarticular bone and mineralization of the first and second ceratobranchial cartilages and symplectic cartilages, which normally does not occur until fish are approximately 10 or 12 dpf. Some maternal-zygotic mutants and heterozygotes show loss of pharyngeal first arch elements (25.9% and 10.2%, respectively) and neurocranium defects (30.8% and 15.2%, respectively). Analysis of RNA-seq mRNA transcript levels and in situ hybridizations from zygotic stages to 75–90% epiboly indicates that hdac4 is highly expressed in early embryos, but diminishes by late epiboly, becoming expressed again in larval stages. Discussion Loss of function of hdac4 in zebrafish is associated with increased expression of runx2a and runx2b targets indicating that a role for hdac4 in zebrafish is to repress activation of ossification of cartilage. These findings are consistent with observations of precocious cartilage ossification in Hdac4 mutant mice, demonstrating that the function of Hdac4 in skeletal development is conserved among vertebrates. Expression of hdac4 mRNA in embryos younger than 256–512 cells indicates that there is a maternal contribution of hdac4 to the early embryo. The increase in ossification and profound loss of first pharyngeal arch elements and anterior neurocranium in a subset of maternal-zygotic mutant and heterozygote larvae suggests that maternal hdac4 functions in cartilage ossification and development of cranial neural crest-derived structures.
DeLaurier et al. (2019) hdac4 mediates perichondral ossification and pharyngeal skeleton development in the zebrafish. PeerJ 7:e6167 https://doi.org/10.7717/peerj.6167
The origin of exotic pet sugar gliders (Petaurus breviceps) kept in the United States of America
The demand for exotic non-domesticated animals kept as pets in the United States of America (USA) is increasing the exportation rates of these species from their native ranges. Often, illegal harvesting of these species is used to boost captive-bred numbers and meet this demand. One such species, the sugar glider (Petaurus breviceps), endemic to Australia and New Guinea is a popular domestic pet due to its small size and “cute” demeanour. Despite a legal avenue for trade existing in Indonesia, concerns have been raised that sugar gliders may be entering the USA from other parts of their native range where exportation is prohibited such as Australia, Papua New Guinea and the surrounding Indonesian islands. We compared previously published DNA sequences from across the native range of sugar gliders with samples collected from domestically kept sugar gliders within the USA to determine provenance and gene flow between source and introduced populations. Here we show that as predicted, the USA sugar glider population originates from West Papua, Indonesia with no illegal harvesting from other native areas such as Papua New Guinea or Australia evident in the samples tested within this study.
Campbell et al. (2019) The origin of exotic pet sugar gliders (Petaurus breviceps) kept in the United States of America. PeerJ 7:e6180 https://doi.org/10.7717/peerj.6180
Hardly habitual: chimpanzees and gorillas show flexibility in their motor responses when presented with a causally-clear task
In contrast to reports of wild primates, studies of captive primates’ flexibility often reveal conservatism: individuals are unable to switch to new and more efficient strategies when task demands change. We propose that such conservatism might be a result of task design and hypothesize that conservatism might be linked to primates’ lack of causal understanding in relation to experimental apparatuses. We investigated if chimpanzees (Pan troglodytes) and western lowland gorillas (Gorilla gorilla gorilla) would show greater flexibility when presented with a causally-clear task. We presented six chimpanzees and seven gorillas with a clear tube from which they had to remove straws to release a reward. To first evaluate the apes’ causal understanding, we recorded the efficiency with which the apes solved the task (i.e., whether they only removed straws below the reward, ignoring redundant ones above it). To further explore how they solved the task, we also recorded the order in which they removed the straws, which allowed us to determine if habitual action sequences emerged. All apes spontaneously solved the task in their first trial and across repeated trials the majority of their solutions were efficient (median = 90.9%), demonstrating their understanding of the puzzle. There was individual variation in the consistency of straw removal patterns exhibited by the apes, but no ape developed an exclusive habit in the order with which they removed the straws, further indicating their causal understanding of the task. Next, we presented the apes with a new configuration of the same task that required the apes to remove fewer straws to obtain the reward. All apes switched to a more efficient straw removal sequence even though their previously-successful, but now less-efficient, solution remained available. We theorize that because the apes understood the causality of the task, they did not form habits and were not conservative.
Jacobson et al. (2019) Hardly habitual: chimpanzees and gorillas show flexibility in their motor responses when presented with a causally-clear task. PeerJ 7:e6195 https://doi.org/10.7717/peerj.6195
Inhibition of MEK1/2 and GSK3 (2i system) affects blastocyst quality and early differentiation of porcine parthenotes
Inhibition of both MEK1/2 and glycogen synthase kinase-3 (GSK3; 2i system) facilitates the maintenance of naïve stemness for embryonic stem cells in various mammalian species. However, the effect of the inhibition of the 2i system on porcine early embryogenesis is unknown. We investigated the effect of the 2i system on early embryo development, expression of pluripotency-related genes, and epigenetic modifications. Inhibition of MEK1/2 (by PD0325901) and/or GSK3 (by CHIR99021) did not alter the developmental potential of porcine parthenogenetic embryos, but improved blastocyst quality, as judged by the blastocyst cell number, diameter, and reduction in the number of apoptotic cells. The expression levels of octamer-binding transcription factor 4 and SOX2, the primary transcription factors that maintain embryonic pluripotency, were significantly increased by 2i treatments. Epigenetic modification-related gene expression was altered upon 2i treatment. The collective results indicate that the 2i system in porcine embryos improved embryo developmental potential and blastocyst quality by regulating epigenetic modifications and pluripotency-related gene expression.
Kwon et al. (2019) Inhibition of MEK1/2 and GSK3 (2i system) affects blastocyst quality and early differentiation of porcine parthenotes. PeerJ 6:e5840 https://doi.org/10.7717/peerj.5840
Ocean acidification alters morphology of all otolith types in Clark’s anemonefish (Amphiprion clarkii)
Ocean acidification, the ongoing decline of surface ocean pH and [CO ${}_{3}^{2-}$ 3 2 − ] due to absorption of surplus atmospheric CO2, has far-reaching consequences for marine biota, especially calcifiers. Among these are teleost fishes, which internally calcify otoliths, critical elements of the inner ear and vestibular system. There is evidence in the literature that ocean acidification increases otolith size and alters shape, perhaps impacting otic mechanics and thus sensory perception. Here, larval Clark’s anemonefish, Amphiprion clarkii (Bennett, 1830), were reared in various seawater pCO2/pH treatments analogous to future ocean scenarios. At the onset of metamorphosis, all otoliths were removed from each individual fish and analyzed for treatment effects on morphometrics including area, perimeter, and circularity; scanning electron microscopy was used to screen for evidence of treatment effects on lateral development, surface roughness, and vaterite replacement. The results corroborate those of other experiments with other taxa that observed otolith growth with elevated pCO2, and provide evidence that lateral development and surface roughness increased as well. Both sagittae exhibited increasing area, perimeter, lateral development, and roughness; left lapilli exhibited increasing area and perimeter while right lapilli exhibited increasing lateral development and roughness; and left asterisci exhibited increasing perimeter, roughness, and ellipticity with increasing pCO2. Right lapilli and left asterisci were only impacted by the most extreme pCO2 treatment, suggesting they are resilient to any conditions short of aragonite undersaturation, while all other impacted otoliths responded to lower concentrations. Finally, fish settlement competency at 10 dph was dramatically reduced, and fish standard length marginally reduced with increasing pCO2. Increasing abnormality and asymmetry of otoliths may impact inner ear function by altering otolith-maculae interactions.
Holmberg et al. (2019) Ocean acidification alters morphology of all otolith types in Clark’s anemonefish (Amphiprion clarkii). PeerJ 7:e6152 https://doi.org/10.7717/peerj.6152
Relationship between physical and cognitive performance in community dwelling, ethnically diverse older adults: a cross-sectional study
Background Regular exercise training stimulates physiological adaptations to improve physical performance, reduce chronic disease risk, and slow age-related cognitive decline. Since the physiological mechanisms responsible for aging-associated cognitive decline are not yet fully understood, and training-induced physiological adaptations responsible for performance measure improvements are specific to the type (aerobic vs. strength) and intensity of training, studies are needed to assess the relationships between physical performance measures and cognitive performance in older adults. These results could be used to guide exercise prescriptions with the goal of improving age-related cognitive performance. The purpose of this study was to investigate the relationship between physical performance measures and cognitive performance in a population of community dwelling, ethnically diverse older adults. Methods The cognitive performance of ninety independent, community dwelling participants (69 female, 21 male), aged 75 ± 9.5 years (mean ± SD) was measured with the Modified Mini-Mental State Test (3MS), Trailmaking Tests A and B (TMT A & B), and the Animal Naming test. Sociodemographic (age, sex, ethnicity, medication use, years of education) and anthropometric data were collected, physical activity was assessed with the Physical Activity Scale for the Elderly (PASE), peak hand-grip strength, distance walked in the 6MWT, and heart rate pre-, during, and up to 5 min. post- 6MWT were measured. Forward stepwise multiple regression analyses were performed with each cognitive measure as a dependent variable. Results and Discussion Controlling for sociodemographic covariates, peak heart rate during the 6MWT (6MWT HRPEAK) was positively correlated with performance in the 3MS (p < 0.017), and TMT A (p < 0.001) and B (p < 0.029). Controlling for sociodemographic covariates, PASE was positively (p = 0.001), and β-blocker use negatively (p = 0.035), correlated with performance on the Animal Naming test. Also, controlling for sociodemographic covariates, PASE was positively correlated with performance on the TMT A (p = 0.017). Here we show that higher peak heart rate during the 6MWT is positively correlated with cognitive performance in a population of community dwelling, ethnically diverse older adults (ages 60–95 years). Conclusion Higher peak heart rate during the 6MWT was found to be independently and positively correlated with cognitive function in community-dwelling older adults. Although additional work is needed, these results are promising and suggest that physicians, exercise professionals, and/or fitness/fall prevention programs may use peak heart rate during the 6MWT to easily monitor exercise intensity to support cognitive health.
Sherwood et al. (2019) Relationship between physical and cognitive performance in community dwelling, ethnically diverse older adults: a cross-sectional study. PeerJ 7:e6159 https://doi.org/10.7717/peerj.6159
Diversity analysis of the rhizospheric and endophytic bacterial communities of Senecio vulgaris L. (Asteraceae) in an invasive range
Increasing evidence has confirmed the importance of plant-associated bacteria for plant growth and productivity, and thus it is hypothesized that interactions between bacteria and alien plants might play an important role in plant invasions. However, the diversity of the bacterial communities associated with invasive plants is poorly understood. We therefore investigated the diversity of rhizospheric and endophytic bacteria associated with the invasive annual plant Senecio vulgaris L. (Asteraceae) based on 16S rRNA gene data obtained from 57 samples of four Senecio vulgaris populations in a subtropical mountainous area in central China. Significant differences in diversity were observed between plant compartments. Specifically, the rhizosphere harbored many more bacterial operational taxonomic units and showed higher alpha diversity than the leaf and root endospheres. The relative abundance profiles of the bacterial community composition differed substantially between the compartments and populations, especially at the phylum and family levels. However, the top five phyla (Proteobacteria, Firmicutes, Bacteroidetes, Actinobacteria, and Acidobacteria) accounted for more than 90% of all the bacterial communities. Moreover, similar endophytic communities with a shared core set of bacteria were observed from different Senecio vulgaris populations. Heavy-metal-resistant, phosphate-solubilizing bacteria (Brevundimonas diminuta), nitrogen-fixing bacteria (Rhizobium leguminosarum), and cold-resistant bacteria (Exiguobacterium sibiricum) were present in the endosphere at relatively high abundance. This study, which reveals the structure of bacterial communities and their putative function in invasive Senecio vulgaris plants, is the first step in investigating the role of plant–bacteria interactions in the invasion of this species in China.
Cheng et al. (2019) Diversity analysis of the rhizospheric and endophytic bacterial communities of Senecio vulgaris L. (Asteraceae) in an invasive range. PeerJ 6:e6162 https://doi.org/10.7717/peerj.6162
Intestinal parasitic infection alters bacterial gut microbiota in children
The study of the burden that parasites can exert upon the bacterial gut microbiota was restricted by the available technologies and their costs. Currently, next-generation sequencing coupled with traditional methodologies allows the study of eukaryotic parasites (protozoa and helminths) and its effects on the human bacterial gut microbiota diversity. This diversity can be altered by a variety of factors such as age, diet, genetics and parasitic infections among others. The disturbances of the gut microbiota have been associated with a variety of illnesses. Children population in developing countries, are especially susceptible to parasitic infections because of the lack of proper sanitation and undernutrition, allowing both, the thriving of intestinal parasites and profound alteration of the gut microbiota. In this work, we have sampled the stool of 23 children from four different children’s care-centers in Medellin, Colombia, and we have identified the eukaryotic parasites by traditional and molecular methodologies coupled with microbial profiling using 16S rDNA sequencing. This mixed methodology approach has allowed us to establish an interesting relationship between Giardia intestinalis and helminth infection, having both effects upon the bacterial gut microbiota enterotypes, causing a switch from a type I to a type II enterotype upon infection.
Toro-Londono et al. (2019) Intestinal parasitic infection alters bacterial gut microbiota in children. PeerJ 7:e6200 https://doi.org/10.7717/peerj.6200
Phylogeny of Paleozoic limbed vertebrates reassessed through revision and expansion of the largest published relevant data matrix
The largest published phylogenetic analysis of early limbed vertebrates (Ruta M, Coates MI. 2007. Journal of Systematic Palaeontology 5:69–122) recovered, for example, Seymouriamorpha, Diadectomorpha and (in some trees) Caudata as paraphyletic and found the “temnospondyl hypothesis” on the origin of Lissamphibia (TH) to be more parsimonious than the “lepospondyl hypothesis” (LH)—though only, as we show, by one step. We report 4,200 misscored cells, over half of them due to typographic and similar accidental errors. Further, some characters were duplicated; some had only one described state; for one, most taxa were scored after presumed relatives. Even potentially continuous characters were unordered, the effects of ontogeny were not sufficiently taken into account, and data published after 2001 were mostly excluded. After these issues are improved—we document and justify all changes to the matrix—but no characters are added, we find (Analysis R1) much longer trees with, for example, monophyletic Caudata, Diadectomorpha and (in some trees) Seymouriamorpha; Ichthyostega either crownward or rootward of Acanthostega; and Anthracosauria either crownward or rootward of Temnospondyli. The LH is nine steps shorter than the TH (R2; constrained) and 12 steps shorter than the “polyphyly hypothesis” (PH—R3; constrained). Brachydectes (Lysorophia) is not found next to Lissamphibia; instead, a large clade that includes the adelogyrinids, urocordylid “nectrideans” and aïstopods occupies that position. As expected from the taxon/character ratio, most bootstrap values are low. Adding 56 terminal taxa to the original 102 increases the resolution (and decreases most bootstrap values). The added taxa range in completeness from complete articulated skeletons to an incomplete lower jaw. Even though the lissamphibian-like temnospondyls Gerobatrachus, Micropholis and Tungussogyrinus and the extremely peramorphic salamander Chelotriton are added, the difference between LH (R4; unconstrained) and TH (R5) rises to 10 steps, that between LH and PH (R6) to 15; the TH also requires several more regains of lost bones than the LH. Casineria, in which we tentatively identify a postbranchial lamina, emerges rather far from amniote origins in a gephyrostegid-chroniosuchian grade. Bayesian inference (Analysis EB, settings as in R4) mostly agrees with R4. High posterior probabilities are found for Lissamphibia (1.00) and the LH (0.92); however, many branches remain weakly supported, and most are short, as expected from the small character sample. We discuss phylogeny, approaches to coding, methods of phylogenetics (Bayesian inference vs. equally weighted vs. reweighted parsimony), some character complexes (e.g. preaxial/postaxial polarity in limb development), and prospects for further improvement of this matrix. Even in its revised state, the matrix cannot provide a robust assessment of the phylogeny of early limbed vertebrates. Sufficient improvement will be laborious—but not difficult.
Marjanović et al. (2019) Phylogeny of Paleozoic limbed vertebrates reassessed through revision and expansion of the largest published relevant data matrix. PeerJ 6:e5565 https://doi.org/10.7717/peerj.5565
Changes in interleukin-27 levels in patients with acute coronary syndrome and their clinical significance
Background This study evaluated changes in interleukin (IL)-27 levels in patients with acute coronary syndrome (ACS) and their influence on Th1, Th2, and Th17 cells. Methods Serum levels of IL-27, IL-4, IL-17, and interferon (IFN)-γ in healthy subjects as well as patients with ACS, including stable angina pectoris (SA), unstable angina pectoris (UA), and acute myocardial infarction (AMI), were determined using an enzyme-linked immunosorbent assay. The proportions of Th1, Th2, and Th17 cells among peripheral blood mononuclear cells (PBMCs), were measured using flow cytometry, after incubation with phorbol myristate acetate (PMA) for 4 h. The proportions of Th1 and Th17 cells among PBMCs in AMI and UA were detected after stimulation with IL-27 or PMA + IL-27 for 4, 8, and 12 h. Results Serum levels of IL-27 in patients with AMI and UA were significantly lower than those in SA and control groups, while serum levels of IL-17 and IFN-γ in AMI and UA groups were dramatically increased compared to those in SA and healthy control groups. However, there were no statistically significant differences in serum IL-4. The proportions of Th1 and Th17 cells among PBMCs were statistically significantly higher in the AMI and UA groups than those in the SA and control groups, while there was no statistically significant difference in the proportion of Th2 cells among different groups. For patients with AMI and UA, the effect of co-stimulation of PBMCs with PMA and IL-27 was not significantly different from that of PMA single stimulation, while PMA + IL-27 co-stimulation lowered the Th17 cell proportion significantly compared to PMA single stimulation. Discussion Compared to SA patients and healthy controls, patients with ACS (AMI + UA) had lower serum levels of IL-27 and higher proportions of PBMC Th1 and Th17 cells, which could be attributed to the inhibitory effects of IL-27 on the proliferation of Th17 cells. These results indicated that IL-27 could be a novel therapeutic target in ACS patients.
Zhang et al. (2019) Changes in interleukin-27 levels in patients with acute coronary syndrome and their clinical significance. PeerJ 7:e5652 https://doi.org/10.7717/peerj.5652
Spiculous skeleton formation in the freshwater sponge Ephydatia fluviatilis under hypergravity conditions
Successful dispersal of freshwater sponges depends on the formation of dormant sponge bodies (gemmules) under adverse conditions. Gemmule formation allows the sponge to overcome critical environmental conditions, for example, desiccation or freezing, and to re-establish as a fully developed sponge when conditions are more favorable. A key process in sponge development from hatched gemmules is the construction of the silica skeleton. Silica spicules form the structural support for the three-dimensional filtration system the sponge uses to filter food particles from ambient water. We studied the effect of different hypergravity forces (1, 2.5, 5, 10, and 20 × g for 48 h)—as measure for environmental stress—on the ability of developing sponges to set-up their spiculous skeleton. Additionally, we assessed whether the addition of nutrients (i.e., dissolved 13C- and 15N-labeled amino acids) compensates for this stress. Our results show that freshwater sponges can withstand prolonged periods of hypergravity exposure and successfully set-up their skeleton, even after 48 h under 20 × g. Developing sponges were found to take up and assimilate dissolved food before forming a functional filtering system. However, fed and non-fed sponges showed no differences in skeleton formation and relative surface area growth, suggesting that the gemmules’ intrinsic energy fulfills the processes of skeleton construction. Additionally, non-fed sponges formed oscula significantly more often than fed sponges, especially under higher g-forces. This suggests that the eventual formation of a filtration system might be stimulated by food deprivation and environmentally stressful conditions. These findings indicate that the process of spiculous skeleton formation is energy-efficient and highly resilient. The uptake of dissolved food substances by freshwater sponges may contribute to the cycling of dissolved organic matter in freshwater ecosystems where sponges are abundant.
Bart et al. (2019) Spiculous skeleton formation in the freshwater sponge Ephydatia fluviatilis under hypergravity conditions. PeerJ 6:e6055 https://doi.org/10.7717/peerj.6055
Temperature-mediated feeding between spring-associated and riverine-associated congeners, with implications for community segregation
Freshwater fish communities segregate along water temperature gradients attributed in part to temperature-mediated physiological processes that affect species fitness. In spring complexes of southwest USA, spring complexes with narrow range of water temperatures are dominated by a community of fishes (i.e., spring-associated fishes), whereas riverine habitats with wide-range of water temperatures are dominated by a different community of fishes (i.e., riverine-associated fishes). The purpose of this study was to test a prediction of the concept that temperature-mediated species performance is a mechanism in maintaining community segregation. We predicted that a spring-associated fish (Largespring Gambusia Gambusia geiseri) would feed first and more often in a pairing with a riverine-associated fish (Western Mosquitofish G. affinis) at an average spring temperature (23 °C) and that the riverine-associated fish would feed first and more often in a pairing with the spring-associated fish at a warm riverine temperature (30 °C). Among four trails consisting of 30 pairings, at the spring complex temperature (23 °C), Largespring Gambusia had a greater number of first feeds (mean ± 1 SD, 5.0 ± 0.82) than Western Mosquitofish (2.5 ± 1.73) and had greater mean number of total feeds (1.9 ± 0.31) than Western Mosquitofish (0.81 ± 0.70). At the riverine environment temperature (30 °C), Western Mosquitofish had a greater number of first feeds (5.25 ± 1.71) than Largespring Gambusia (2.5 ± 1.73) and had greater mean number of total feeds (2.78 ± 1.05) than Largespring Gambusia (0.94 ± 0.68). Our findings suggest that temperature-mediated species performance could be maintaining segregation between the two fish communities. This study benefits our understanding of distributional patterns and improves threat assessments of stenothermal aquatic organisms.
Craig et al. (2019) Temperature-mediated feeding between spring-associated and riverine-associated congeners, with implications for community segregation. PeerJ 6:e6144 https://doi.org/10.7717/peerj.6144
Using the wax moth larva Galleria mellonella infection model to detect emerging bacterial pathogens
Climate change, changing farming practices, social and demographic changes and rising levels of antibiotic resistance are likely to lead to future increases in opportunistic bacterial infections that are more difficult to treat. Uncovering the prevalence and identity of pathogenic bacteria in the environment is key to assessing transmission risks. We describe the first use of the Wax moth larva Galleria mellonella, a well-established model for the mammalian innate immune system, to selectively enrich and characterize pathogens from coastal environments in the South West of the UK. Whole-genome sequencing of highly virulent isolates revealed amongst others a Proteus mirabilis strain carrying the Salmonella SGI1 genomic island not reported from the UK before and the recently described species Vibrio injenensis hitherto only reported from human patients in Korea. Our novel method has the power to detect bacterial pathogens in the environment that potentially pose a serious risk to public health.
Hernandez et al. (2019) Using the wax moth larva Galleria mellonella infection model to detect emerging bacterial pathogens. PeerJ 6:e6150 https://doi.org/10.7717/peerj.6150
Role of the larval feeding morphology and digestive enzyme activity in the early development of the polychaete Boccardia wellingtonensis
In marine invertebrates, the modes of development at early stages are related to the type and capacity of larval feeding to achieve growth. Therefore, studying the factors that determine larval feeding strategies can help to understand the diversity of life histories and evolution of marine invertebrates. The polychaete Boccardia wellingtonensis is a poecilogonous species that encapsulates and incubates its offspring. This species produces two types of larvae: (1) larvae that do not feed within the capsule and hatch as planktotrophic larvae (indirect development), and (2) adelphophagic larvae that feed on nurse eggs and other larvae inside the capsule to hatch as advanced larvae or juveniles (direct development). Otherwise, the larval types are indistinguishable at the same stage of development. The non-apparent morphological differences between both types of larvae suggest that other factors are influencing their feeding behavior. This work studied the potential role of the activity of 19 digestive enzymes on the different feeding capacities of planktotrophic and adelphophagic larvae of B. wellingtonensis. Also, differences in larval feeding structures and the larval capacity to feed from intracapsular fluid were evaluated by electron and fluorescence microscopy. Results showed that both types of larvae present similar feeding structures and had the capacity to ingest intracapsular fluid protein. Adelphophagic larvae showed overall the highest activities of digestive enzymes. Significant differences between larval types were observed in nine enzymes related to the use of internal and external nutritional sources. Given that larval feeding is closely related to larval development in species with encapsulation, this work supports that the study of the digestive enzymatic machinery of larvae may contribute to understanding the evolution of developmental modes.
Doherty-Weason et al. (2019) Role of the larval feeding morphology and digestive enzyme activity in the early development of the polychaete Boccardia wellingtonensis. PeerJ 7:e6151 https://doi.org/10.7717/peerj.6151
Secreted Frizzled-related protein 4 inhibits the regeneration of hair follicles
Secreted Frizzled-related Protein 4 (sFRP4) belongs to Wnt inhibitors. Previously, we reported that sFRP4 inhibited the differentiation of melanocyte. Here, by using of immunostaining, we showed that sFRP4 is expressed in both human and mouse hair follicles, especially in the outer root sheath and inner root sheath. To reveal the role of sFRP4 in hair follicle growth and hair cycle, we induced synchronized hair cycle in the dorsal skin of mice by depilation, and injected sFRP4 intradermally into the skin. By hematoxylin and eosin staining, we found that the regeneration of hair follicles was inhibited by sFRP4. However, the structure of hair follicles remained complete. Compared with phosphate buffer saline-treated hair follicles, the sFRP4-treated hair follicles still had the same expression pattern of keratins. Our findings reveal that sFRP4 inhibits but not blocks the regeneration of hair follicles, and supply a potential therapeutic application to treat hair follicle regeneration disorders.
Guo et al. (2019) Secreted Frizzled-related protein 4 inhibits the regeneration of hair follicles. PeerJ 6:e6153 https://doi.org/10.7717/peerj.6153
Primulina anisocymosa (Gesneriaceae), a new species with a unique inflorescence structure from Guangdong, China
A new Primulina species from Guangdong, China with an unusual inflorescence is described here. Primulina anisocymosa is vegetatively most similar to P. bobaiensis. It can be distinguished from all species within Primulina morphologically by its unique zigzag monochasial cyme and infructescence. To confirm the phylogenetic relationships and generic placement of this species, not only morphological anatomical features but also chromosome and DNA sequence data were examined and analysed here. Two samples from different populations identified as Primulina anisocymosa are monophyletic and were nested in a monophyletic clade within Primulina with high branch support. The somatic chromosome number of the new species is also reported (2n = 36), supporting its placement in the genus.
Hong et al. (2019) Primulina anisocymosa (Gesneriaceae), a new species with a unique inflorescence structure from Guangdong, China. PeerJ 7:e6157 https://doi.org/10.7717/peerj.6157
Identifying accurate metagenome and amplicon software via a meta-analysis of sequence to taxonomy benchmarking studies
Metagenomic and meta-barcode DNA sequencing has rapidly become a widely-used technique for investigating a range of questions, particularly related to health and environmental monitoring. There has also been a proliferation of bioinformatic tools for analysing metagenomic and amplicon datasets, which makes selecting adequate tools a significant challenge. A number of benchmark studies have been undertaken; however, these can present conflicting results. In order to address this issue we have applied a robust Z-score ranking procedure and a network meta-analysis method to identify software tools that are consistently accurate for mapping DNA sequences to taxonomic hierarchies. Based upon these results we have identified some tools and computational strategies that produce robust predictions.
Gardner et al. (2019) Identifying accurate metagenome and amplicon software via a meta-analysis of sequence to taxonomy benchmarking studies. PeerJ 7:e6160 https://doi.org/10.7717/peerj.6160
Long-term effects of straw and straw-derived biochar on soil aggregation and fungal community in a rice–wheat rotation system
Background Soil aggregation is fundamental for soil functioning and agricultural productivity. Aggregate formation depends on microbial activity influencing the production of exudates and hyphae, which in turn act as binding materials. Fungi are also important for improving soil quality and promoting plant growth in a symbiotic manner. There is a scarcity of findings comparing the long-term impacts of different yearly double-crop straw return modes (e.g., straw return to the field and straw-derived biochar return to the field) on soil aggregation and fungal community structure in rice–wheat rotation systems. Methods The effects of 6-year continuous straw and straw-derived biochar amendment on soil physicochemical properties and the fungal community were evaluated in an intensively managed crop rotation system (rice–wheat). Soil samples of different aggregates (macroaggregates, microaggregates, and silt clay) from four different fertilization regimes (control, CK; traditional inorganic fertilization, CF; straw returned to field, CS; straw-derived biochar addition, CB) were obtained, and Illumina MiSeq sequencing analysis of the fungal internal transcribed spacer gene was performed. Results Compared to CF, CS and CB enhanced soil organic carbon, total nitrogen, and aggregation in 0–20 and 20–40 cm soil, with CB exhibiting a stronger effect. Additionally, agrowaste addition increased the mean weight diameter and the geometric diameter and decreased the fractal dimension (p < 0.05). Principal coordinates analysis indicated that fertilization management affected fungal community structure and aggregation distribution. In addition, CS increased fungal community richness and diversity, compared to CK, CB decreased these aspects. Ascomycota, unclassified_k_Fungi, and Basidiomycota were the dominant phyla in all soil samples. At the genus level, CB clearly increased fungi decomposing biosolids (Articulospora in macroaggregates in 0–20 cm soil and Neurospora in macroaggregates in 20–40 cm soil); decreased pathogenic fungi (Monographella in macroaggregates and Gibberella in microaggregates in 0–20 cm soil) and CO2-emission-related fungi (Pyrenochaetopsis in microaggregates and silt clay in 0–40 cm soil) (p < 0.05). Straw and biochar with inorganic fertilizer counteracted some of the adverse effects of the inorganic fertilizer with biochar showing better effects than straw.
Bai et al. (2019) Long-term effects of straw and straw-derived biochar on soil aggregation and fungal community in a rice–wheat rotation system. PeerJ 6:e6171 https://doi.org/10.7717/peerj.6171
Functional polymorphisms of the APOA1/C3/A4/A5-ZPR1-BUD13 gene cluster are associated with dyslipidemia in a sex-specific pattern
Background Dyslipidemia contributes to the risk of many diseases, including stroke, cardiovascular disease and metabolic-related diseases. Previous studies have indicated that single nucleotide polymorphisms (SNPs) are associated with different levels of serum lipid. Therefore, this study explored the relationship between the APOA1/C3/A4/A5-ZPR1-BUD13 gene cluster gene polymorphisms and dyslipidemia in the total sample population and stratified by genders in a northeast Chinese population. Methods A total of 3,850 participants from Jilin Province, China, were enrolled in our study, and their serum lipid levels were measured. Six functional SNPs (APOA1 rs5072, APOC3 rs5128, APOA4 rs5104, APOA5 rs651821, ZPR1 rs2075294 and BUD13 rs10488698) were genotyped using polymerase chain reaction and MALDI-TOF-MS. Logistic regression analysis was performed to explore the relationship of APOA1/C3/A4/A5-ZPR1-BUD13 gene cluster gene polymorphisms with dyslipidemia. Linkage disequilibrium and haplotype analyses were performed with the SNPStats program and Haploview software. Results All SNPs conformed to Hardy–Weinberg equilibrium. Logistic regression analysis revealed that rs5072, rs5128 and rs651821 were associated with hypertriglyceridemia, rs5104 and rs651821 were associated with low-HDL cholesterolemia in overall group. rs651821 was associated with hypertriglyceridemia and low-HDL cholesterolemia in both the male and female group. However, among females, rs5072 was observed to be associated with hypertriglyceridemia. Haplotype analysis showed that haplotypes TGCCGC and CAGCGC were associated with dyslipidemia in the overall, male and female groups. Conclusion SNPs in the APOA1/C3/A4/A5-ZPR1-BUD13 gene cluster were associated with dyslipidemia. Furthermore, the association of APOA1 rs5072 in this gene cluster with dyslipidemia differed between genders; thus, additional studies are needed to confirm this conclusion, and the mechanisms underlying these results warrant further exploration.
Bai et al. (2019) Functional polymorphisms of the APOA1/C3/A4/A5-ZPR1-BUD13 gene cluster are associated with dyslipidemia in a sex-specific pattern. PeerJ 6:e6175 https://doi.org/10.7717/peerj.6175
A Tournaisian (earliest Carboniferous) conglomerate-preserved non-marine faunal assemblage and its environmental and sedimentological context
A conglomerate bed from the Tournaisian Ballagan Formation of Scotland preserves a rich array of vertebrate and other nonmarine fossils providing an insight into the wider ecosystem and paleoenvironment that existed during this pivotal stage of Earth history. It challenges hypotheses of a long-lasting post-extinction trough following the end-Devonian extinction event. The fauna recovered includes a wide size range of tetrapods, rhizodonts, and dipnoans, from tiny juveniles or small-bodied taxa up to large adults, and more than one taxon of each group is likely. Some fauna, such as actinopterygians and chondrichthyans, are rare as macrofauna but are better represented in the microfossil assemblage. The fauna provides evidence of the largest Carboniferous lungfish ever found. The specimens are preserved in a localized, poorly-sorted conglomerate which was deposited in the deepest part of a river channel, the youngest of a group of channels. In addition to the fossils (micro- and macro-), the conglomerate includes locally-derived clasts of paleosols and other distinctive elements of the surrounding floodplains. Charcoal fragments represent small woody axes and possible larger trunk tissue from arborescent pteridosperms. Preservation of the fossils indicates some aerial exposure prior to transport, with abrasion from rolling. The findings presented here contrast with other published trends in vertebrate size that are used to interpret a reduction in maximum sizes during the Tournaisian. The richness of the fauna runs counter to the assumption of a depauperate nonmarine fauna following the end-Devonian Hangenberg event, and charcoal content highlights the occurrence of fire, with the requisite levels of atmospheric oxygen during that stage.
Clack et al. (2019) A Tournaisian (earliest Carboniferous) conglomerate-preserved non-marine faunal assemblage and its environmental and sedimentological context. PeerJ 6:e5972 https://doi.org/10.7717/peerj.5972
Steroidal glycoalkaloids from Solanum nigrum target cytoskeletal proteins: an in silico analysis
Background Solanum nigrum (black nightshade; S. nigrum), a member of family Solanaceae, has been endowed with a heterogeneous array of secondary metabolites of which the steroidal glycoalkaloids (SGAs) and steroidal saponins (SS) have vast potential to serve as anticancer agents. Since there has been much controversy regarding safety of use of glycoalkaloids as anticancer agents, this area has remained more or less unexplored. Cytoskeletal proteins like actin play an important role in maintaining cell shape, synchronizing cell division, cell motility, etc. and along with their accessory proteins may also serve as important therapeutic targets for potential anticancer candidates. In the present study, glycoalkaloids and saponins from S. nigrum were screened for their interaction and binding affinity to cytoskeletal proteins, using molecular docking. Methods Bioactivity score and Prediction of Activity Spectra for Substances (PASS) analysis were performed using softwares Molinspiration and Osiris Data Explorer respectively, to assess the feasibility of selected phytoconstituents as potential drug candidates. The results were compared with two standard reference drugs doxorubicin hydrochloride (anticancer) and tetracycline (antibiotic). Multivariate data obtained were analyzed using principal component analysis (PCA). Results Docking analysis revealed that the binding affinities of the phytoconstituents towards the target cytoskeletal proteins decreased in the order coronin>villin>ezrin>vimentin>gelsolin>thymosin>cofilin. Glycoalkaloid solasonine displayed the greatest binding affinity towards the target proteins followed by alpha-solanine whereas amongst the saponins, nigrumnin-I showed maximum binding affinity. PASS Analysis of the selected phytoconstituents revealed 1 to 3 violations of Lipinski’s parameters indicating the need for modification of their structure-activity relationship (SAR) for improvement of their bioactivity and bioavailability. Glycoalkaloids and saponins all had bioactivity scores between −5.0 and 0.0 with respect to various receptor proteins and target enzymes. Solanidine, solasodine and solamargine had positive values of druglikeness which indicated that these compounds have the potential for development into future anticancer drugs. Toxicity potential evaluation revealed that glycoalkaloids and saponins had no toxicity, tumorigenicity or irritant effect(s). SAR analysis revealed that the number, type and location of sugar or the substitution of hydroxyl group on alkaloid backbone had an effect on the activity and that the presence of α-L-rhamnopyranose sugar at C-2 was critical for a compound to exhibit anticancer activity. Conclusion The present study revealed some cytoskeletal target(s) for S. nigrum phytoconstituents by docking analysis that have not been previously reported and thus warrant further investigations both in vitro and in vivo.
Ahmad (2019) Steroidal glycoalkaloids from Solanum nigrum target cytoskeletal proteins: an in silico analysis. PeerJ 7:e6012 https://doi.org/10.7717/peerj.6012
The existence and evolution of morphotypes in Anolis lizards: coexistence patterns, not adaptive radiations, distinguish mainland and island faunas
The evolution of distinct ecologies and correlated morphologies (“ecomorphs,” in combination) among similar species allows sympatric occupation of diverse microhabitats. Particular ecomorphs may evolve repeatedly, that is, convergently, as separate lineages arrive at similar solutions. Caribbean Anolis lizards (anoles) are a classic ecomorph system, particularly well-studied for the diverse morphotypes resulting from adaptive radiations. But few studies have analyzed the equally species-diverse mainland Anolis. Here, we use clustering analyses of nine traits for 336 species of Anolis to objectively identify morphological groups (morphotypes). We analyze the presence of recovered morphotypes on mainland and islands in general and relative to the composition of 76 mainland and 91 island anole assemblages. We test for evolutionary convergence of morphotypes within and between mainland and island environments by mapping our recovered morphotypes onto recent phylogenetic estimates and by analyzing four of our measured traits using program SURFACE. We find that particular morphotypes tend to be restricted to either mainland or island environments. Morphotype diversity and convergence are not concentrated within either island or mainland environments. Morphotype content of assemblages differs between mainland and island areas, with island assemblages displaying greater numbers of morphotypes than mainland assemblages. Taken with recent research, these results suggest a restructuring of one of the classic adaptive radiation stories and a reconsideration of research concerning island–mainland faunal differences. Island radiations of anoles are unexceptional relative to mainland radiations with regard to species count, rates of speciation and phenotypic evolution, morphotype diversity, and rates of convergence. But local island assemblage appear to be more diverse than mainland assemblages. The explanation for this assemblage disparity may reside in one of the classic hypothesized island–mainland environmental differences (i.e., greater numbers of predators/competitors/environmental complexity on the mainland). Similarity between mainland and island anole radiations may indicate exceptional evolution in the anole clade overall or ordinary evolution in an extraordinarily studied clade.
Poe et al. (2019) The existence and evolution of morphotypes in Anolis lizards: coexistence patterns, not adaptive radiations, distinguish mainland and island faunas. PeerJ 6:e6040 https://doi.org/10.7717/peerj.6040
Isolation and identification of marine strains of Stenotrophomona maltophilia with high chitinolytic activity
Chitin is the second most abundant organic compound in nature and represents a rich carbon and nitrogen source that is primarily transformed by bacterial communities. Bacteria capable of gradually hydrolyzing chitin into N-acetylglucosamine monomers can have applications in the transformation of residues from shrimp and other crustaceans. The objective of the present study was to isolate, characterize and identify microorganisms with high chitinolytic activity. These microorganisms were isolated and characterized based on macro- and microscopic morphological traits. Strains were selected on colloidal chitin agar medium primarily based on a hydrolysis halo larger than 2 mm and a growing phase no longer than 6 days. Secondary selection consisted of semi-quantitative evaluation of chitinolytic activity with a drop dilution assay. From the above, ten strains were selected. Then, strain-specific activity was evaluated. The B4 strain showed the highest specific activity, which was 6,677.07 U/mg protein. Molecular identification indicated that the isolated strains belong to the species Stenotrophomonas maltophilia.
Salas-Ovilla et al. (2019) Isolation and identification of marine strains of Stenotrophomona maltophilia with high chitinolytic activity. PeerJ 7:e6102 https://doi.org/10.7717/peerj.6102
The role of Central American barriers in shaping the evolutionary history of the northernmost glassfrog, Hyalinobatrachium fleischmanni (Anura: Centrolenidae)
The complex geological history of Central America has been useful for understanding the processes influencing the distribution and diversity of multiple groups of organisms. Anurans are an excellent choice for such studies because they typically exhibit site fidelity and reduced movement. The objective of this work was to identify the impact of recognized geographic barriers on the genetic structure, phylogeographic patterns and divergence times of a wide-ranging amphibian species, Hyalinobatrachium fleischmanni. We amplified three mitochondrial regions, two coding (COI and ND1) and one ribosomal (16S), in samples collected from the coasts of Veracruz and Guerrero in Mexico to the humid forests of Chocó in Ecuador. We examined the biogeographic history of the species through spatial clustering analyses (Geneland and sPCA), Bayesian and maximum likelihood reconstructions, and spatiotemporal diffusion analysis. Our data suggest a Central American origin of H. fleischmanni and two posterior independent dispersals towards North and South American regions. The first clade comprises individuals from Colombia, Ecuador, Panama and the sister species Hyalinobatrachium tatayoi; this clade shows little structure, despite the presence of the Andes mountain range and the long distances between sampling sites. The second clade consists of individuals from Costa Rica, Nicaragua, and eastern Honduras with no apparent structure. The third clade includes individuals from western Honduras, Guatemala, and Mexico and displays deep population structure. Herein, we synthesize the impact of known geographic areas that act as barriers to glassfrog dispersal and demonstrated their effect of differentiating H. fleischmanni into three markedly isolated clades. The observed genetic structure is associated with an initial dispersal event from Central America followed by vicariance that likely occurred during the Pliocene. The southern samples are characterized by a very recent population expansion, likely related to sea-level and climatic oscillations during the Pleistocene, whereas the structure of the northern clade has probably been driven by dispersal through the Isthmus of Tehuantepec and isolation by the Motagua–Polochic–Jocotán fault system and the Mexican highlands.
Mendoza et al. (2019) The role of Central American barriers in shaping the evolutionary history of the northernmost glassfrog, Hyalinobatrachium fleischmanni (Anura: Centrolenidae). PeerJ 7:e6115 https://doi.org/10.7717/peerj.6115
Comparison of non-magnetic and magnetic beads multiplex assay for assessment of Plasmodium falciparum antibodies
Background New reagents have emerged allowing researchers to assess a growing number of vaccine-associated immune parameters. Multiplex immunoassay(s) are emerging as efficient high-throughput assays in malaria serology. Currently, commercial vendors market several bead reagents for cytometric bead assays (CBA) but relative performances are not well published. We have compared two types of bead-based multiplex assays to measure relative antibody levels to malarial antigens. Methods Assays for the measurement of antibodies to five Plasmodium falciparum vaccine candidates using non-magnetic and magnetic fluorescent microspheres were compared for their performances with a Bio-Plex200 instrument. Mean fluorescence intensity (MFI) was determined from individuals from western Kenya and compared to known positive and negative control plasma samples. Results P. falciparum recombinant antigens were successfully coupled to both non-magnetic and magnetic beads in multiplex assays. MFIs between the two bead types were comparable for all antigens tested. Bead recovery was superior with magnetic beads for all antigens. MFI values of stored non-magnetic coupled beads did not differ from freshly coupled beads, though they showed higher levels of bead aggregation. Discussion Magnetic and non-magnetic beads performed similarly in P. falciparum antibody assays. Magnetic beads were more expensive, but had higher bead recovery, were more convenient to use, and provided rapid and easy protocol manipulation. Magnetic beads are a suitable alternative to non-magnetic beads in malarial antibody serology.
Ondigo et al. (2019) Comparison of non-magnetic and magnetic beads multiplex assay for assessment of Plasmodium falciparum antibodies. PeerJ 7:e6120 https://doi.org/10.7717/peerj.6120
Analysis of the complete genome sequence of a marine-derived strain Streptomyces sp. S063 CGMCC 14582 reveals its biosynthetic potential to produce novel anti-complement agents and peptides
Genome sequences of marine streptomycetes are valuable for the discovery of useful enzymes and bioactive compounds by genome mining. However, publicly available complete genome sequences of marine streptomycetes are still limited. Here, we present the complete genome sequence of a marine streptomycete Streptomyces sp. S063 CGMCC 14582. Species delineation based on the pairwise digital DNA-DNA hybridization and genome comparison ANI (average nucleotide identity) value showed that Streptomyces sp. S063 CGMCC 14582 possesses a unique genome that is clearly different from all of the other available genomes. Bioactivity tests showed that Streptomyces sp. S063 CGMCC 14582 produces metabolites with anti-complement activities, which are useful for treatment of numerous diseases that arise from inappropriate activation of the human complement system. Analysis of the genome reveals no biosynthetic gene cluster (BGC) which shows even low similarity to that of the known anti-complement agents was detected in the genome, indicating that Streptomyces sp. S063 CGMCC 14582 may produce novel anti-complement agents of microbial origin. Four BGCs which are potentially involved in biosynthesis of non-ribosomal peptides were disrupted, but no decrease of anti-complement activities was observed, suggesting that these four BGCs are not involved in biosynthesis of the anti-complement agents. In addition, LC-MS/MS analysis and subsequent alignment through the Global Natural Products Social Molecular Networking (GNPS) platform led to the detection of novel peptides produced by the strain. Streptomyces sp. S063 CGMCC 14582 grows rapidly and is salt tolerant, which benefits efficient secondary metabolite production via seawater-based fermentation. Our results indicate that Streptomyces sp. S063 has great potential to produce novel bioactive compounds, and also is a good host for heterologous production of useful secondary metabolites for drug discovery.
Chen et al. (2019) Analysis of the complete genome sequence of a marine-derived strain Streptomyces sp. S063 CGMCC 14582 reveals its biosynthetic potential to produce novel anti-complement agents and peptides. PeerJ 7:e6122 https://doi.org/10.7717/peerj.6122
Toxicity of TiO2, SiO2, ZnO, CuO, Au and Ag engineered nanoparticles on hatching and early nauplii of Artemia sp.
The potential of environmental release enhances with increased commercial applications of the nanomaterials. In this work, a simple and efficient test to estimate the acute toxicity of nanoparticles is carried out on Artemia species and their hatching rates. We have tested six different engineered nanoparticles (silver, gold, copper oxide, zinc oxide, TiO2 and SiO2 nanoparticles) and three soluble salts (CuSO4, ZnSO4 and AgNO3) on Artemia sp. The physicochemical properties of the nanoparticles involved in this study were analyzed in normal water and marine water. Hydrated and bleached Artemia cysts were allowed to hatch in continuously aerated, filtered sterile salt water containing nanoparticles; hatching of viable nauplii and total hatchlings have been recorded. In parallel, standard Artemia toxicity test was conducted on the nauplii monitoring the viability. In hatching experiments, a reduction in hatching rate was observed along with mortality of newly hatched nauplii. The results of the hatching experiment and of the standard Artemia test showed a good correlation. The toxicity of the nanoparticles was compared and the order of toxicity was estimated as Ag>CuO>ZnO>Au>TiO2>SiO2. The study thus suggests that the hatching test itself is a reliable assay for determining the toxicity of nanomaterials.
Rekulapally et al. (2019) Toxicity of TiO2, SiO2, ZnO, CuO, Au and Ag engineered nanoparticles on hatching and early nauplii of Artemia sp.. PeerJ 6:e6138 https://doi.org/10.7717/peerj.6138
Fully automated sequence alignment methods are comparable to, and much faster than, traditional methods in large data sets: an example with hepatitis B virus
Aligning sequences for phylogenetic analysis (multiple sequence alignment; MSA) is an important, but increasingly computationally expensive step with the recent surge in DNA sequence data. Much of this sequence data is publicly available, but can be extremely fragmentary (i.e., a combination of full genomes and genomic fragments), which can compound the computational issues related to MSA. Traditionally, alignments are produced with automated algorithms and then checked and/or corrected “by eye” prior to phylogenetic inference. However, this manual curation is inefficient at the data scales required of modern phylogenetics and results in alignments that are not reproducible. Recently, methods have been developed for fully automating alignments of large data sets, but it is unclear if these methods produce alignments that result in compatible phylogenies when compared to more traditional alignment approaches that combined automated and manual methods. Here we use approximately 33,000 publicly available sequences from the hepatitis B virus (HBV), a globally distributed and rapidly evolving virus, to compare different alignment approaches. Using one data set comprised exclusively of whole genomes and a second that also included sequence fragments, we compared three MSA methods: (1) a purely automated approach using traditional software, (2) an automated approach including by eye manual editing, and (3) more recent fully automated approaches. To understand how these methods affect phylogenetic results, we compared resulting tree topologies based on these different alignment methods using multiple metrics. We further determined if the monophyly of existing HBV genotypes was supported in phylogenies estimated from each alignment type and under different statistical support thresholds. Traditional and fully automated alignments produced similar HBV phylogenies. Although there was variability between branch support thresholds, allowing lower support thresholds tended to result in more differences among trees. Therefore, differences between the trees could be best explained by phylogenetic uncertainty unrelated to the MSA method used. Nevertheless, automated alignment approaches did not require human intervention and were therefore considerably less time-intensive than traditional approaches. Because of this, we conclude that fully automated algorithms for MSA are fully compatible with older methods even in extremely difficult to align data sets. Additionally, we found that most HBV diagnostic genotypes did not correspond to evolutionarily-sound groups, regardless of alignment type and support threshold. This suggests there may be errors in genotype classification in the database or that HBV genotypes may need a revision.
Catanach et al. (2019) Fully automated sequence alignment methods are comparable to, and much faster than, traditional methods in large data sets: an example with hepatitis B virus. PeerJ 7:e6142 https://doi.org/10.7717/peerj.6142
Otolith microchemistry and diadromy in Patagonian river fishes
Coastal habitats in Chile are hypothesized to support a number of diadromous fish species. The objective of this study was to document migratory life histories of native galaxiids and introduced salmonids from a wide latitudinal range in Chilean Patagonia (39–48°S). Otolith microchemistry data were analysed using a recursive partitioning approach to test for diadromy. Based on annular analysis of Sr:Ca ratios, a diadromous life history was suggested for populations of native Aplochiton taeniatus, A. marinus, and Galaxias maculatus. Lifetime residency in freshwater was suggested for populations of A. zebra and G. platei. Among introduced salmonids, populations of Oncorhynchus tshawytscha and O. kisutch exhibited patterns consistent with anadromy, whereas the screened population of O. mykiss appeared restricted to freshwater. Salmo trutta exhibited variable patterns suggesting freshwater residency and possibly anadromy in one case. The capacity and geographic scope of hydropower development is increasing and may disrupt migratory routes of diadromous fishes. Identification of diadromous species is a critical first step for preventing their loss due to hydropower development.
Alò et al. (2019) Otolith microchemistry and diadromy in Patagonian river fishes. PeerJ 7:e6149 https://doi.org/10.7717/peerj.6149
Polyphasic evaluation of key cyanobacteria in biocrusts from the most arid region in Europe
Cyanobacteria are key microbes in topsoil communities that have important roles in preventing soil erosion, carbon and nitrogen fixation, and influencing soil hydrology. However, little is known regarding the identity and distribution of the microbial components in the photosynthetic assemblages that form a cohesive biological soil crust (biocrust) in drylands of Europe. In this study, we investigated the cyanobacterial species colonizing biocrusts in three representative dryland ecosystems from the most arid region in Europe (SE Spain) that are characterized by different soil conditions. Isolated cyanobacterial cultures were identified by a polyphasic approach, including 16S rRNA gene sequencing, phylogenetic relationship determination, and morphological and ecological habitat assessments. Three well-differentiated groups were identified: heterocystous-cyanobacteria (Nostoc commune, Nostoc calcicola, Tolypothrix distorta and Scytonema hyalinum), which play an important role in N and C cycling in soil; nonheterocystous bundle-forming cyanobacteria (Microcoleus steenstrupii, Trichocoleus desertorum, and Schizothrix cf. calcicola); and narrow filamentous cyanobacteria (Leptolyngbya frigida and Oculatella kazantipica), all of which are essential genera for initial biocrust formation. The results of this study contribute to our understanding of cyanobacterial species composition in biocrusts from important and understudied European habitats, such as the Mediterranean Basin, a hotspot of biodiversity, where these species are keystone pioneer organisms.
Roncero-Ramos et al. (2019) Polyphasic evaluation of key cyanobacteria in biocrusts from the most arid region in Europe. PeerJ 7:e6169 https://doi.org/10.7717/peerj.6169