title: PeerJ
description:  Articles published in PeerJ
link: https://peerj.com/articles/index.rss3?journal=peerj&page=1032
creator: info@peerj.com PeerJ
errorsTo: info@peerj.com PeerJ
language: en

title: The Bacteria Genome Pipeline (BAGEP): an automated, scalable workflow for bacteria genomes with Snakemake
link: https://peerj.com/articles/10121
last-modified: 2020-10-27
description: Next generation sequencing technologies are becoming more accessible and affordable over the years, with entire genome sequences of several pathogens being deciphered in few hours. However, there is the need to analyze multiple genomes within a short time, in order to provide critical information about a pathogen of interest such as drug resistance, mutations and genetic relationship of isolates in an outbreak setting. Many pipelines that currently do this are stand-alone workflows and require huge computational requirements to analyze multiple genomes. We present an automated and scalable pipeline called BAGEP for monomorphic bacteria that performs quality control on FASTQ paired end files, scan reads for contaminants using a taxonomic classifier, maps reads to a reference genome of choice for variant detection, detects antimicrobial resistant (AMR) genes, constructs a phylogenetic tree from core genome alignments and provide interactive short nucleotide polymorphism (SNP) visualization across core genomes in the data set. The objective of our research was to create an easy-to-use pipeline from existing bioinformatics tools that can be deployed on a personal computer. The pipeline was built on the Snakemake framework and utilizes existing tools for each processing step: fastp for quality trimming, snippy for variant calling, Centrifuge for taxonomic classification, Abricate for AMR gene detection, snippy-core for generating whole and core genome alignments, IQ-TREE for phylogenetic tree construction and vcfR for an interactive heatmap visualization which shows SNPs at specific locations across the genomes. BAGEP was successfully tested and validated with Mycobacterium tuberculosis (n = 20) and Salmonella enterica serovar Typhi (n = 20) genomes which are about 4.4 million and 4.8 million base pairs, respectively. Running these test data on a 8 GB RAM, 2.5 GHz quad core laptop took 122 and 61 minutes on respective data sets to complete the analysis. BAGEP is a fast, calls accurate SNPs and an easy to run pipeline that can be executed on a mid-range laptop; it is freely available on: https://github.com/idolawoye/BAGEP.
creator: Idowu B. Olawoye
creator: Simon D.W. Frost
creator: Christian T. Happi
uri: https://doi.org/10.7717/peerj.10121
license: https://creativecommons.org/licenses/by/4.0/
rights: ©2020 Olawoye et al.

title: The size of signal detection and emission organs in a synchronous firefly: sexual dimorphism, allometry and assortative mating
link: https://peerj.com/articles/10127
last-modified: 2020-10-27
description: The size of the organs responsible for emitting and detecting sexual communication signals is a likely target for selection. Communication via bioluminescent signals in synchronous fireflies is a promising model to test hypotheses regarding differences between males and females in the effect of the size of signal emission and detection organs on fitness components. Synchronous firefly species congregate in large numbers during the mating season, displaying bioluminescent signals aimed at potential mates during relatively short nightly periods. Operational sex ratios are male-biased and, thus, the so-called typical sex roles (indiscriminate males and choosy females) are expected to evolve. We studied the synchronous firefly Photinus palaciosi, a species that during the mating season congregates in forests of central Mexico offering a magnificent natural show that attracts numerous tourists. P. palaciosi females have reduced wings (brachyptery) and cannot fly. Our field study tested the hypothesis that the male-biased operational sex ratio and the short daily mating period result in strong male-male competition that selects for males with larger lanterns and larger eyes, and against male mate choice, whereas female-female mate competition is absent and, thus, no selection on lantern or eye size is expected. Even though lantern, eye or body size do not predict the probability of being found in copula for either sex, sexual dimorphism in these features, along with allometric slopes of lantern size and assortative mating in terms of relative lantern size, support not only the hypothesis of intense sexual selection among males, but the possibility of subtle mechanisms of sexual selection among females. Trade-offs between investment in signaling (lanterns) versus detection (eyes) structures, or with pressures different from sexual selection such as those imposed by predators, are also likely to be important in shaping the evolution of sexual signaling in these fireflies.
creator: Tania López-Palafox
creator: Rogelio Macías-Ordóñez
creator: Carlos R. Cordero
uri: https://doi.org/10.7717/peerj.10127
license: https://creativecommons.org/licenses/by/4.0/
rights: © 2020 López-Palafox et al.

title: Integrated transcriptome meta-analysis of pancreatic ductal adenocarcinoma and matched adjacent pancreatic tissues
link: https://peerj.com/articles/10141
last-modified: 2020-10-27
description: A comprehensive meta-analysis of publicly available gene expression microarray data obtained from human-derived pancreatic ductal adenocarcinoma (PDAC) tissues and their histologically matched adjacent tissue samples was performed to provide diagnostic and prognostic biomarkers, and molecular targets for PDAC. An integrative meta-analysis of four submissions (GSE62452, GSE15471, GSE62165, and GSE56560) containing 105 eligible tumor-adjacent tissue pairs revealed 344 differentially over-expressed and 168 repressed genes in PDAC compared to the adjacent-to-tumor samples. The validation analysis using TCGA combined GTEx data confirmed 98.24% of the identified up-regulated and 73.88% of the down-regulated protein-coding genes in PDAC. Pathway enrichment analysis showed that “ECM-receptor interaction”, “PI3K-Akt signaling pathway”, and “focal adhesion” are the most enriched KEGG pathways in PDAC. Protein-protein interaction analysis identified FN1, TIMP1, and MSLN as the most highly ranked hub genes among the DEGs. Transcription factor enrichment analysis revealed that TCF7, CTNNB1, SMAD3, and JUN are significantly activated in PDAC, while SMAD7 is inhibited. The prognostic significance of the identified and validated differentially expressed genes in PDAC was evaluated via survival analysis of TCGA Pan-Cancer pancreatic ductal adenocarcinoma data. The identified candidate prognostic biomarkers were then validated in four external validation datasets (GSE21501, GSE50827, GSE57495, and GSE71729) to further improve reliability. A total of 28 up-regulated genes were found to be significantly correlated with worse overall survival in patients with PDAC. Twenty-one of the identified prognostic genes (ITGB6, LAMC2, KRT7, SERPINB5, IGF2BP3, IL1RN, MPZL2, SFTA2, MET, LAMA3, ARNTL2, SLC2A1, LAMB3, COL17A1, EPSTI1, IL1RAP, AK4, ANXA2, S100A16, KRT19, and GPRC5A) were also found to be significantly correlated with the pathological stages of the disease. The results of this study provided promising prognostic biomarkers that have the potential to differentiate PDAC from both healthy and adjacent-to-tumor pancreatic tissues. Several novel dysregulated genes merit further study as potentially promising candidates for the development of more effective treatment strategies for PDAC.
creator: Sevcan Atay
uri: https://doi.org/10.7717/peerj.10141
license: https://creativecommons.org/licenses/by/4.0/
rights: © 2020 Atay

title: Developing mathematical model for diurnal dynamics of photosynthesis in Saccharum officinarum responsive to different irrigation and silicon application
link: https://peerj.com/articles/10154
last-modified: 2020-10-27
description: In the dynamic era of climate change, agricultural farming systems are facing various unprecedented problems worldwide. Drought stress is one of the serious abiotic stresses that hinder the growth potential and crop productivity. Silicon (Si) can improve crop yield by enhancing the efficiency of inputs and reducing relevant losses. As a quasi-essential element and the 2nd most abundant element in the Earth’s crust, Si is utilized by plants and applied exogenously to combat drought stress and improve plant performance by increasing physiological, cellular and molecular responses. However, the physiological mechanisms that respond to water stress are still not well defined in Saccharum officinarum plants. To the best of our knowledge, the dynamics of photosynthesis responsive to different exogenous Si levels in Saccharum officinarum has not been reported to date. The current experiment was carried out to assess the protective role of Si in plant growth and photosynthetic responses in Saccharum officinarum under water stress conditions. Saccharum officinarum cv. ‘GT 42’ plants were subjected to drought stress conditions (80–75%, 55–50% and 35–30% of soil moisture) after ten weeks of normal growth, followed by the soil irrigation of Si (0, 100, 300 and 500 mg L−1) for 8 weeks. The results indicated that Si addition mitigated the inhibition in Saccharum officinarum growth and photosynthesis, and improved biomass accumulation during water stress. The photosynthetic responses (photosynthesis, transpiration and stomatal conductance) were found down-regulated under water stress, and it was significantly enhanced by Si application. No phytotoxic effects were monitored even at excess (500 mg L−1). Soil irrigation of 300 mg L−1 of Si was more effective as 100 and 500 mg L−1 under water stress condition. It is concluded that the stress in Saccharum officinarum plants applied with Si was alleviated by improving plant fitness, photosynthetic capacity and biomass accumulation as compared with the control. Thus, this study offers new information towards the assessment of growth, biomass accumulation and physiological changes related to water stress with Si application in plants.
creator: Krishan K. Verma
creator: Kai-Chao Wu
creator: Chhedi Lal Verma
creator: Dong-Mei Li
creator: Mukesh Kumar Malviya
creator: Rajesh Kumar Singh
creator: Pratiksha Singh
creator: Gan-Lin Chen
creator: Xiu Peng Song
creator: Yang Rui Li
uri: https://doi.org/10.7717/peerj.10154
license: https://creativecommons.org/licenses/by/4.0/
rights: © 2020 Verma et al.

title: Comparing sediment DNA extraction methods for assessing organic enrichment associated with marine aquaculture
link: https://peerj.com/articles/10231
last-modified: 2020-10-27
description: Marine sediments contain a high diversity of micro- and macro-organisms which are important in the functioning of biogeochemical cycles. Traditionally, anthropogenic perturbation has been investigated by identifying macro-organism responses along gradients. Environmental DNA (eDNA) analyses have recently been advocated as a rapid and cost-effective approach to measuring ecological impacts and efforts are underway to incorporate eDNA tools into monitoring. Before these methods can replace or complement existing methods, robustness and repeatability of each analytical step has to be demonstrated. One area that requires further investigation is the selection of sediment DNA extraction method. Environmental DNA sediment samples were obtained along a disturbance gradient adjacent to a Chinook (Oncorhynchus tshawytscha) salmon farm in Otanerau Bay, New Zealand. DNA was extracted using four extraction kits (Qiagen DNeasy PowerSoil, Qiagen DNeasy PowerSoil Pro, Qiagen RNeasy PowerSoil Total RNA/DNA extraction/elution and Favorgen FavorPrep Soil DNA Isolation Midi Kit) and three sediment volumes (0.25, 2, and 5 g). Prokaryotic and eukaryotic communities were amplified using primers targeting the 16S and 18S ribosomal RNA genes, respectively, and were sequenced on an Illumina MiSeq. Diversity and community composition estimates were obtained from each extraction kit, as well as their relative performance in established metabarcoding biotic indices. Differences were observed in the quality and quantity of the extracted DNA amongst kits with the two Qiagen DNeasy PowerSoil kits performing best. Significant differences were observed in both prokaryotes and eukaryotes (p < 0.001) richness among kits. A small proportion of amplicon sequence variants (ASVs) were shared amongst the kits (~3%) although these shared ASVs accounted for the majority of sequence reads (prokaryotes: 59.9%, eukaryotes: 67.2%). Differences were observed in the richness and relative abundance of taxonomic classes revealed with each kit. Multivariate analysis showed that there was a significant interaction between “distance” from the farm and “kit” in explaining the composition of the communities, with the distance from the farm being a stronger determinant of community composition. Comparison of the kits against the bacterial and eukaryotic metabarcoding biotic index suggested that all kits showed similar patterns along the environmental gradient. Overall, we advocate for the use of Qiagen DNeasy PowerSoil kits for use when characterizing prokaryotic and eukaryotic eDNA from marine farm sediments. We base this conclusion on the higher DNA quality values and richness achieved with these kits compared to the other kits/amounts investigated in this study. The additional advantage of the PowerSoil Kits is that DNA extractions can be performed using an extractor robot, offering additional standardization and reproducibility of results.
creator: John K. Pearman
creator: Nigel B. Keeley
creator: Susanna A. Wood
creator: Olivier Laroche
creator: Anastasija Zaiko
creator: Georgia Thomson-Laing
creator: Laura Biessy
creator: Javier Atalah
creator: Xavier Pochon
uri: https://doi.org/10.7717/peerj.10231
license: https://creativecommons.org/licenses/by/4.0/
rights: © 2020 Pearman et al.

title: Reinstatement of Phascolosoma (Phascolosoma) varians Keferstein, 1865 (Sipuncula: Phascolosomatidae) based on morphological and molecular data
link: https://peerj.com/articles/10238
last-modified: 2020-10-27
description: Phascolosoma (P.) varians, a sipunculan species known from the Greater Caribbean, was designated as a synonym of Phascolosoma (P.) nigrescens, which was originally described from Fiji. Their synonymy was primarily based upon an interpretation that these two species were morphologically indistinguishable. After its designation as a synonym, no further detailed analyses of morphological or molecular characteristics were performed to corroborate the assumed widespread distribution of Phascolosoma (P.) nigrescens. In this study, Phascolosoma (P.) varians is redescribed, and notable differences between this species and its proposed senior synonym are presented. These two species differ in the shape of their hooks, the spatial attachment of nephridia to the body wall, and the morphology of the contractile vessel. Additionally, there is high genetic divergence between nucleotide sequences within their respective cytochrome c oxidase subunit 1 (COI) genes, which supports the morphological data. Herein, the synonymy of Phascolosoma (P.) varians with Phascolosoma (P.) nigrescens is rejected due to morphological and molecular differences. Furthermore, the assumed widespread distribution of Phascolosoma (P.) nigrescens is still considered as questionable.
creator: Itzahi Silva-Morales
uri: https://doi.org/10.7717/peerj.10238
license: https://creativecommons.org/licenses/by/4.0/
rights: © 2020 Silva-Morales

title: An improved modified early warning score that incorporates the abdomen score for identifying multiple traumatic injury severity
link: https://peerj.com/articles/10242
last-modified: 2020-10-27
description: BackgroundRapid identification of trauma severity is essential for the timely triage of multiple trauma patients. Tools such as the modified early warning score (MEWS) are used for determining injury severity. Although the conventional MEWS is a good predictor of mortality, its performance assessing injury severity is moderate. This study hypothesized that adding an injury site severity-related score (e.g., abdomen score) may enhance the capability of the MEWS for identifying severe trauma.MethodTo validate the hypothesis, we propose an improved modified early warning score called MEWS-A, which incorporates an injury site-specific severity-related abdomen score to MEWS. The utility of MEWS and MEWS-A were retrospectively evaluated and compared for identifying trauma severity in adult multiple trauma patients admitted to the emergency department.ResultsWe included 1,230 eligible multiple trauma patients and divided them into minor and severe trauma groups based on the injury severity score. Results of logistic regression and receiver operating characteristic (ROC) curve analyses showed that the MEWS-A had a higher area under the ROC curve (AUC: 0.81 95% CI [0.78–0.83]) than did the MEWS (AUC: 0.77 95% CI [0.74–0.79]), indicating that the MEWS-A is superior to the MEWS in identifying severe trauma. The optimal MEWS-A cut-off score is 4, with a specificity of 0.93 and a sensitivity of 0.54. MEWS-A ≥ 4 can be used as a protocol for decision-making in the emergency department.ConclusionsOur study suggests that while the conventional MEWS is sufficient for predicting mortality risk, adding an injury site-specific score (e.g., abdomen score) can enhance its performance in determining injury severity in multiple trauma patients.
creator: Xiaobin Jiang
uri: https://doi.org/10.7717/peerj.10242
license: https://creativecommons.org/licenses/by/4.0/
rights: ©2020 Jiang

title: Gynomonoecy in a mycoheterotrophic orchid Eulophia zollingeri with autonomous selfing hermaphroditic flowers and putatively outcrossing female flowers
link: https://peerj.com/articles/10272
last-modified: 2020-10-27
description: Most orchid species exhibit an extreme case of hermaphroditism, owing to the fusion of male and female organs into a gynostemium. Exceptions to this rule have only been reported from the subtribes Catasetinae and Satyriinae. Here, I report an additional orchidaceous example whose flowers are not always hermaphroditic. In several Japanese populations of Eulophia zollingeri (Rchb.f.) J.J.Sm, a widespread Asian and Oceanian orchid, some flowers possess both the anther (i.e., anther cap and pollinaria) and stigma, whereas others possess only the stigma. Therefore, pollination experiments, an investigation of floral morphology and observations of floral visitors were conducted to understand the reproductive biology of E. zollingeri in Miyazaki Prefecture, Japan. It was confirmed that E. zollingeri studied here possesses a gynomonoecious reproductive system, a sexual system in which a single plant has both female flowers and hermaphroditic flowers. In addition, hermaphroditic flowers often possess an effective self-pollination system while female flowers could avoid autogamy but suffered from severe pollinator limitation, due to a lack of agamospermy and low insect-mediated pollination. The present study represents the first documented example of gynomonoecy within Orchidaceae. Gynomonoecy in E. zollingeri may be maintained by the tradeoff in reproductive traits between female flowers (with low fruit set but potential outcrossing benefits) and hermaphroditic flowers (with high fruit set but inbreeding depression in selfed offspring). This mixed mating is probably important in mycoheterotrophic E. zollingeri because it occurs in shaded forest understorey with a paucity of pollinators.
creator: Kenji Suetsugu
uri: https://doi.org/10.7717/peerj.10272
license: https://creativecommons.org/licenses/by/4.0/
rights: ©2020 Suetsugu

title: Haiti has more forest than previously reported: land change 2000–2015
link: https://peerj.com/articles/9919
last-modified: 2020-10-26
description: Estimates of forest cover have important political, conservation, and funding implications, but methods vary greatly. Haiti has often been cited as one of the most deforested countries in the world, yet estimates of forest cover range from <1% to 33%. Here, we analyze land change for seven land cover classes (forest, shrub land, agriculture/pasture, plantation, urban/infrastructure, barren land, and water) between 2000 and 2015 using Landsat imagery (30 m resolution) in the Google Earth Engine platform. Forest cover was estimated at 26% in 2000 and 21% in 2015. Although forest cover is declining in Haiti, our quantitative analysis resulted in considerably higher forest cover than what is usually reported by local and international institutions. Our results determined that areas of forest decline were mainly converted to shrubs and mixed agriculture/pasture. An important driver of forest loss and degradation could be the high demand for charcoal, which is the principal source of cooking fuel. Our results differ from other forest cover estimates and forest reports from national and international institutions, most likely due to differences in forest definition, data sources, spatial resolution, and methods. In the case of Haiti, this work demonstrates the need for clear and functional definitions and classification methods to accurately represent land use/cover change. Regardless of how forests are defined, forest cover in Haiti will continue to decline unless corrective actions are taken to protect remaining forest patches. This can serve as a warning of the destructive land use patterns and can help us target efforts for better planning, management, and conservation.
creator: Ose Pauleus
creator: T. Mitchell Aide
uri: https://doi.org/10.7717/peerj.9919
license: https://creativecommons.org/licenses/by/4.0/
rights: © 2020 Pauleus and Aide

title: Effects of changes in isotopic baselines on the evaluation of food web structure using isotopic functional indices
link: https://peerj.com/articles/9999
last-modified: 2020-10-26
description: BackgroundThis study aimed to assess whether ecological inferences from isotopic functional indices (IFIs) are impacted by changes in isotopic baselines in aquatic food webs. We used sudden CO2-outgassing and associated shifts in DIC-δ13C brought by waterfalls as an excellent natural experimental set-up to quantify impacts of changes in algal isotopic baselines on ecological inferences from IFIs.MethodsCarbon (δ13C) and nitrogen (δ15N) stable isotopic ratios of invertebrate communities sharing similar structure were measured at above- and below-waterfall sampling sites from five rivers and streams in Southern Quebec (Canada). For each sampled invertebrate community, the six Laymans IFIs were then calculated in the δ -space (δ13C vs. δ15N).ResultsAs expected, isotopic functional richness indices, measuring the overall extent of community trophic space, were strongly sensitive to changes in isotopic baselines unlike other IFIs. Indeed, other IFIs were calculated based on the distribution of species within δ-space and were not strongly impacted by changes in the vertical or horizontal distribution of specimens in the δ-space. Our results highlighted that IFIs exhibited different sensitivities to changes in isotopic baselines, leading to potential misinterpretations of IFIs in river studies where isotopic baselines generally show high temporal and spatial variabilities. The identification of isotopic baselines and their associated variability, and the use of independent trophic tracers to identify the actual energy pathways through food webs must be a prerequisite to IFIs-based studies to strengthen the reliability of ecological inferences of food web structural properties.
creator: Simon Belle
creator: Gilbert Cabana
uri: https://doi.org/10.7717/peerj.9999
license: https://creativecommons.org/licenses/by/4.0/
rights: ©2020 Belle and Cabana