PeerJ
type: channel
link: https://peerj.com/articles/
description: Articles published in PeerJ
publisher: PeerJ Inc.
publication name: PeerJ
issn: 2167-8359
items: Intraspecific variability in the filter mesh size of suspension feeding organisms: the case of invasive Ponto-Caspian corophiids (Crustacea: Amphipoda)
items: Historical effective population size of North American hoary bat (Lasiurus cinereus) and challenges to estimating trends in contemporary effective breeding population size from archived samples
items: Student health behavior and academic performance
items: The physiological response of Ectomycorrhizal fungus Lepista sordida to Cd and Cu stress
items: A new fossil mantis shrimp and the convergent evolution of a lobster-like morphotype
items: TP53 mutation and MET amplification in circulating tumor DNA analysis predict disease progression in patients with advanced gastric cancer
items: Predicting migration routes for three species of migratory bats using species distribution models
items: Evaluation potential of PGPR to protect tomato against Fusarium wilt and promote plant growth
items: NGScloud2: optimized bioinformatic analysis using Amazon Web Services
items: https://peerj.com/articles/11242

Intraspecific variability in the filter mesh size of suspension feeding organisms: the case of invasive Ponto-Caspian corophiids (Crustacea: Amphipoda)
type: item
type: AcademicArticle
description: Suspension feeders play pivotal roles in the nutrient cycling of almost all aquatic ecosystems. Since sufficiently large differences in the filter mesh size (FMS) can lead to different food web positions, the inter- and intraspecific variability of this trait might be of community-level importance. The aim of this study was to quantify the range of FMS variation within the three invasive Ponto-Caspian Chelicorophium species based on a large material representing various conditions (1,224 specimens from 40 samples across Central Europe), characterize the components of variation within populations, identify the main factors determining intraspecific differences, and reveal how intraspecific variation affects the FMS overlaps among species. The FMS of the most widespread invader, C. curvispinum, varied within the broadest range (between 2.34–8.28 μm, compared to 2.51–5.97 μm in C. robustum and 1.08–3.23 μm in C. sowinskyi); nevertheless, the contribution of intraspecific plasticity to the invasion success of the species is not evident based on the present study. The within-individual variability of FMS increased with the individual mean of the trait and decreased with body size; however, it showed little differences among samples. The among-individual variation within samples could be partitioned into components related to body size (ontogenetic niche shift/differences among cohorts) and sex (ecological sexual dimorphism) as well as a seemingly random component (individual specialization), varying widely in extent and relative contributions. The FMS of C. curvispinum was significantly larger in the presence of C. sowinskyi than in allopatry, likely reflecting character displacement; however, it did not show further increase when C. robustum was also present. Similar differences could not be observed in C. sowinskyi. The FMS ranges of C. curvispinum and C. robustum never overlapped with that of C. sowinskyi in co-occurrence despite the considerable intraspecific differe…
format: application/pdf
format: text/html
creator: Péter Borza
subject: Ecology
subject: Zoology
subject: Freshwater Biology
description: doi:10.7717/peerj.11245
publisher: PeerJ Inc.
rights: © 2021 Borza
abstract: Suspension feeders play pivotal roles in the nutrient cycling of almost all aquatic ecosystems. Since sufficiently large differences in the filter mesh size (FMS) can lead to different food web positions, the inter- and intraspecific variability of this trait might be of community-level importance. The aim of this study was to quantify the range of FMS variation within the three invasive Ponto-Caspian Chelicorophium species based on a large material representing various conditions (1,224 specimens from 40 samples across Central Europe), characterize the components of variation within populations, identify the main factors determining intraspecific differences, and reveal how intraspecific variation affects the FMS overlaps among species. The FMS of the most widespread invader, C. curvispinum, varied within the broadest range (between 2.34–8.28 μm, compared to 2.51–5.97 μm in C. robustum and 1.08–3.23 μm in C. sowinskyi); nevertheless, the contribution of intraspecific plasticity to the invasion success of the species is not evident based on the present study. The within-individual variability of FMS increased with the individual mean of the trait and decreased with body size; however, it showed little differences among samples. The among-individual variation within samples could be partitioned into components related to body size (ontogenetic niche shift/differences among cohorts) and sex (ecological sexual dimorphism) as well as a seemingly random component (individual specialization), varying widely in extent and relative contributions. The FMS of C. curvispinum was significantly larger in the presence of C. sowinskyi than in allopatry, likely reflecting character displacement; however, it did not show further increase when C. robustum was also present. Similar differences could not be observed in C. sowinskyi. The FMS ranges of C. curvispinum and C. robustum never overlapped with that of C. sowinskyi in co-occurrence despite the considerable intraspecific differe…
bibliographic citation: Borza (2021) Intraspecific variability in the filter mesh size of suspension feeding organisms: the case of invasive Ponto-Caspian corophiids (Crustacea: Amphipoda). PeerJ 9:e11245 https://doi.org/10.7717/peerj.11245
date submitted: 2020-11-09
date accepted: 2021-03-18
issued: 2021-04-19
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Borza
  given name: Péter
doi: 10.7717/peerj.11245
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-04-19
copyright: © 2021 Borza
attribution name: Borza

Historical effective population size of North American hoary bat (Lasiurus cinereus) and challenges to estimating trends in contemporary effective breeding population size from archived samples
type: item
type: AcademicArticle
description: Background Hoary bats (Lasiurus cinereus) are among the bat species most commonly killed by wind turbine strikes in the midwestern United States. The impact of this mortality on species census size is not understood, due in part to the difficulty of estimating population size for this highly migratory and elusive species. Genetic effective population size (Ne) could provide an index of changing census population size if other factors affecting Ne are stable. Methods We used the NeEstimator package to derive effective breeding population size (Nb) estimates for two temporally spaced cohorts: 93 hoary bats collected in 2009–2010 and an additional 93 collected in 2017–2018. We sequenced restriction-site associated polymorphisms and generated a de novo genome assembly to guide the removal of sex-linked and multi-copy loci, as well as identify physically linked markers. Results Analysis of the reference genome with psmc suggested at least a doubling of Ne in the last 100,000 years, likely exceeding Ne = 10,000 in the Holocene. Allele and genotype frequency analyses confirmed that the two cohorts were comparable, although some samples had unusually high or low observed heterozygosities. Additionally, the older cohort had lower mean coverage and greater variability in coverage, and batch effects of sampling locality were observed that were consistent with sample degradation. We therefore excluded samples with low coverage or outlier heterozygosity, as well as loci with sequence coverage far from the mode value, from the final data set. Prior to excluding these outliers, contemporary Nb estimates were significantly higher in the more recent cohort, but this finding was driven by high values for the 2018 sample year and low values for all other years. In the reduced data set, Nb did not differ significantly between cohorts. We found base substitutions to be strongly biased toward cytosine to thymine or the complement, and further partitioning loci by substitution type had a …
format: application/pdf
format: text/html
creator: Robert S. Cornman
creator: Jennifer A. Fike
creator: Sara J. Oyler-McCance
creator: Paul M. Cryan
subject: Conservation Biology
subject: Genetics
subject: Genomics
subject: Molecular Biology
subject: Population Biology
description: doi:10.7717/peerj.11285
publisher: PeerJ Inc.
rights: © 2021 Cornman et al.
abstract: Background Hoary bats (Lasiurus cinereus) are among the bat species most commonly killed by wind turbine strikes in the midwestern United States. The impact of this mortality on species census size is not understood, due in part to the difficulty of estimating population size for this highly migratory and elusive species. Genetic effective population size (Ne) could provide an index of changing census population size if other factors affecting Ne are stable. Methods We used the NeEstimator package to derive effective breeding population size (Nb) estimates for two temporally spaced cohorts: 93 hoary bats collected in 2009–2010 and an additional 93 collected in 2017–2018. We sequenced restriction-site associated polymorphisms and generated a de novo genome assembly to guide the removal of sex-linked and multi-copy loci, as well as identify physically linked markers. Results Analysis of the reference genome with psmc suggested at least a doubling of Ne in the last 100,000 years, likely exceeding Ne = 10,000 in the Holocene. Allele and genotype frequency analyses confirmed that the two cohorts were comparable, although some samples had unusually high or low observed heterozygosities. Additionally, the older cohort had lower mean coverage and greater variability in coverage, and batch effects of sampling locality were observed that were consistent with sample degradation. We therefore excluded samples with low coverage or outlier heterozygosity, as well as loci with sequence coverage far from the mode value, from the final data set. Prior to excluding these outliers, contemporary Nb estimates were significantly higher in the more recent cohort, but this finding was driven by high values for the 2018 sample year and low values for all other years. In the reduced data set, Nb did not differ significantly between cohorts. We found base substitutions to be strongly biased toward cytosine to thymine or the complement, and further partitioning loci by substitution type had a …
bibliographic citation: Cornman et al. (2021) Historical effective population size of North American hoary bat (Lasiurus cinereus) and challenges to estimating trends in contemporary effective breeding population size from archived samples. PeerJ 9:e11285 https://doi.org/10.7717/peerj.11285
date submitted: 2020-11-24
date accepted: 2021-03-25
issued: 2021-04-19
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Cornman
  given name: Robert S.
author list: Agent
  family name: Fike
  given name: Jennifer A.
author list: Agent
  family name: Oyler-McCance
  given name: Sara J.
author list: Agent
  family name: Cryan
  given name: Paul M.
doi: 10.7717/peerj.11285
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-04-19
copyright: ©2021 Cornman et al.
attribution name: Cornman et al.

Student health behavior and academic performance
type: item
type: AcademicArticle
description: Objective To explore the association between health behaviors and habits of university students and academic achievement. Participants Six hundred fourteen undergraduate students at a state university in the United States. Methods Students were invited over a 2-year period to participate in an anonymous online survey that asked questions concerning a wide range of health behaviors and habits; participants were asked to report their current grade point average (GPA). Standard Least Squares Models were used to examine differences in self-reported GPA across the different health behaviors and habits, with individuals as replicates. Results The study found positive associations between breakfast consumption, physical activity, and strength training and self-reported GPA, and negative associations between the hours of sleep per night, hours worked per week, fast food and energy drinks consumption, and use of marijuana, alcohol and electronic vaping products. Conclusions While there is an association for some of the studied health behaviors and habits with self-reported GPA, the effect sizes for these health behaviors were low. The significant effect of vaping on GPA as well as the increased use reported in this study indicates that the topic should be explored further. Furthermore, students should be educated on the potential positive and negative effects of health behavior choices to help them make better choices.
format: application/pdf
format: text/html
creator: Peter R. Reuter
creator: Bridget L. Forster
subject: Epidemiology
subject: Health Policy
subject: Nutrition
subject: Public Health
description: doi:10.7717/peerj.11107
publisher: PeerJ Inc.
rights: © 2021 Reuter and Forster
abstract: Objective To explore the association between health behaviors and habits of university students and academic achievement. Participants Six hundred fourteen undergraduate students at a state university in the United States. Methods Students were invited over a 2-year period to participate in an anonymous online survey that asked questions concerning a wide range of health behaviors and habits; participants were asked to report their current grade point average (GPA). Standard Least Squares Models were used to examine differences in self-reported GPA across the different health behaviors and habits, with individuals as replicates. Results The study found positive associations between breakfast consumption, physical activity, and strength training and self-reported GPA, and negative associations between the hours of sleep per night, hours worked per week, fast food and energy drinks consumption, and use of marijuana, alcohol and electronic vaping products. Conclusions While there is an association for some of the studied health behaviors and habits with self-reported GPA, the effect sizes for these health behaviors were low. The significant effect of vaping on GPA as well as the increased use reported in this study indicates that the topic should be explored further. Furthermore, students should be educated on the potential positive and negative effects of health behavior choices to help them make better choices.
bibliographic citation: Reuter et al. (2021) Student health behavior and academic performance. PeerJ 9:e11107 https://doi.org/10.7717/peerj.11107
date submitted: 2020-09-02
date accepted: 2021-02-23
issued: 2021-04-16
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Reuter
  given name: Peter R.
author list: Agent
  family name: Forster
  given name: Bridget L.
doi: 10.7717/peerj.11107
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-04-16
copyright: © 2021 Reuter and Forster
attribution name: Reuter and Forster

The physiological response of Ectomycorrhizal fungus Lepista sordida to Cd and Cu stress
type: item
type: AcademicArticle
description: Ectomycorrhizal fungi (ECMF) can develop the resistance of host plants to heavy metal stress. However, little is known about the response of ECMF to heavy metal exposure. In this study, the growth and physiological indices of Lepista sordida under Cd and Cu stress were studied. The growth of L. sordida on PDA medium under Cd and Cu stress was observed using scanning electron microscopy (SEM). After the addition of Cd and Cu to the medium, the mycelium started twisting, breaking, sticking together, and even dissolving. In the control group, a good and luxuriant mycelium growth of L. sordida along with the numerous clamp connections was observed. The mycelial biomass decreased with increasing concentrations of heavy metals in a liquid medium. The catalase (CAT), peroxidase (POD), superoxide dismutase (SOD), and ascorbate peroxidase (APX) activities were also investigated, and the results showed that the Cd and Cu treatments caused a significant increase in the antioxidant enzyme activities. The contents of soluble protein, soluble sugar, and free proline in L. sordida were investigated, and it was found that the contents initially increased and then decreased with the increasing concentrations of Cd and Cu. However, the content of malondialdehyde (MDA) increased with the increasing concentrations of Cd and Cu. In conclusion, the present study provides a theoretical basis for the better utilization of Ectomycorrhizal fungal resources for the remediation of soil contaminated with heavy metal.
format: application/pdf
format: text/html
creator: Yin Dachuan
creator: Qi Jinyu
subject: Agricultural Science
subject: Mycology
subject: Plant Science
subject: Soil Science
description: doi:10.7717/peerj.11115
publisher: PeerJ Inc.
rights: © 2021 Dachuan and Jinyu
abstract: Ectomycorrhizal fungi (ECMF) can develop the resistance of host plants to heavy metal stress. However, little is known about the response of ECMF to heavy metal exposure. In this study, the growth and physiological indices of Lepista sordida under Cd and Cu stress were studied. The growth of L. sordida on PDA medium under Cd and Cu stress was observed using scanning electron microscopy (SEM). After the addition of Cd and Cu to the medium, the mycelium started twisting, breaking, sticking together, and even dissolving. In the control group, a good and luxuriant mycelium growth of L. sordida along with the numerous clamp connections was observed. The mycelial biomass decreased with increasing concentrations of heavy metals in a liquid medium. The catalase (CAT), peroxidase (POD), superoxide dismutase (SOD), and ascorbate peroxidase (APX) activities were also investigated, and the results showed that the Cd and Cu treatments caused a significant increase in the antioxidant enzyme activities. The contents of soluble protein, soluble sugar, and free proline in L. sordida were investigated, and it was found that the contents initially increased and then decreased with the increasing concentrations of Cd and Cu. However, the content of malondialdehyde (MDA) increased with the increasing concentrations of Cd and Cu. In conclusion, the present study provides a theoretical basis for the better utilization of Ectomycorrhizal fungal resources for the remediation of soil contaminated with heavy metal.
bibliographic citation: Dachuan et al. (2021) The physiological response of Ectomycorrhizal fungus Lepista sordida to Cd and Cu stress. PeerJ 9:e11115 https://doi.org/10.7717/peerj.11115
date submitted: 2020-12-10
date accepted: 2021-02-24
issued: 2021-04-16
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Dachuan
  given name: Yin
author list: Agent
  family name: Jinyu
  given name: Qi
doi: 10.7717/peerj.11115
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-04-16
copyright: ©2021 Dachuan and Jinyu
attribution name: Dachuan and Jinyu

A new fossil mantis shrimp and the convergent evolution of a lobster-like morphotype
type: item
type: AcademicArticle
description: Eumalacostracan crustaceans all have a more or less stereotypic body organisation in the sense of tagmosis. Originally, this included a head with six segments (ocular segment plus five appendage-bearing segments), a thorax region with eight segments, and a pleon with six segments. Interestingly, despite these restrictions in variability in terms of tagmosis, the morphological diversity within Eumalacostraca is rather high. A group providing representative examples that are commonly known is Decapoda. Decapodan crustaceans include shrimp-like forms, lobster-like forms and crab-like forms. The stem species of Eucarida, the group including Decapoda and Euphausiacea, presumably possessed a rather shrimp-like morphology, quite similar to the stem species of Eumalacostraca. Also two other lineages within Eumalacostraca, namely Hoplocarida (with the mantis shrimps as modern representatives) and Neocarida (with the sister groups Thermosbaenacea and Peracarida) evolved from the shrimp-like body organisation to include a lobster-like one. In this study, we demonstrate that the stepwise evolution towards a lobster morphotype occurred to a certain extent in similar order in these three lineages, Hoplocarida, Eucarida and Peracarida, leading to similar types of derived body organisation. This evolutionary reconstruction is based not only on observations of modern fauna, but especially on exceptionally preserved Mesozoic fossils, including the description of a new species of mantis shrimps bridging the morphological gap between the more ancestral-appearing Carboniferous forms and the more modern-appearing Jurassic forms. With this, Mesozoic eumalacostracans represent an important (if not unique) ‘experimental set-up’ for research on factors leading to convergent evolution, the understanding of which is still one of the puzzling challenges of modern evolutionary theory.
format: application/pdf
format: text/html
creator: Carolin Haug
creator: Joachim T. Haug
subject: Evolutionary Studies
subject: Paleontology
subject: Taxonomy
subject: Zoology
description: doi:10.7717/peerj.11124
publisher: PeerJ Inc.
rights: © 2021 Haug and Haug
abstract: Eumalacostracan crustaceans all have a more or less stereotypic body organisation in the sense of tagmosis. Originally, this included a head with six segments (ocular segment plus five appendage-bearing segments), a thorax region with eight segments, and a pleon with six segments. Interestingly, despite these restrictions in variability in terms of tagmosis, the morphological diversity within Eumalacostraca is rather high. A group providing representative examples that are commonly known is Decapoda. Decapodan crustaceans include shrimp-like forms, lobster-like forms and crab-like forms. The stem species of Eucarida, the group including Decapoda and Euphausiacea, presumably possessed a rather shrimp-like morphology, quite similar to the stem species of Eumalacostraca. Also two other lineages within Eumalacostraca, namely Hoplocarida (with the mantis shrimps as modern representatives) and Neocarida (with the sister groups Thermosbaenacea and Peracarida) evolved from the shrimp-like body organisation to include a lobster-like one. In this study, we demonstrate that the stepwise evolution towards a lobster morphotype occurred to a certain extent in similar order in these three lineages, Hoplocarida, Eucarida and Peracarida, leading to similar types of derived body organisation. This evolutionary reconstruction is based not only on observations of modern fauna, but especially on exceptionally preserved Mesozoic fossils, including the description of a new species of mantis shrimps bridging the morphological gap between the more ancestral-appearing Carboniferous forms and the more modern-appearing Jurassic forms. With this, Mesozoic eumalacostracans represent an important (if not unique) ‘experimental set-up’ for research on factors leading to convergent evolution, the understanding of which is still one of the puzzling challenges of modern evolutionary theory.
bibliographic citation: Haug et al. (2021) A new fossil mantis shrimp and the convergent evolution of a lobster-like morphotype. PeerJ 9:e11124 https://doi.org/10.7717/peerj.11124
date submitted: 2019-08-21
date accepted: 2021-02-26
issued: 2021-04-16
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Haug
  given name: Carolin
author list: Agent
  family name: Haug
  given name: Joachim T.
doi: 10.7717/peerj.11124
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-04-16
copyright: © 2021 Haug and Haug
attribution name: Haug and Haug

TP53 mutation and MET amplification in circulating tumor DNA analysis predict disease progression in patients with advanced gastric cancer
type: item
type: AcademicArticle
description: Background Gastric cancer (GC) is a heterogeneous disease that encompasses various molecular subtypes. The molecular mutation characteristics of circulating tumor DNA (ctDNA) in advanced gastric cancer (AGC), especially the clinical utility of TP53 mutation and MET amplification in ctDNA need to be further explored. Objectives The aim of this study was mainly to assess the clinical utility of TP53 mutation and MET amplification in ctDNA as biomarkers for monitoring disease progression of AGC. Patients and Methods We used multigene NGS-panel technology to study the characteristics of ctDNA gene mutations and screen the key mutant genes in AGC patients. The Kaplan-Meier method was used to calculate the survival probability and log-rank test was used to compare the survival curves of TP53 mutation and MET amplification in ctDNA of AGC patients. The survival time was set from the blood test time to the follow-up time to observe the relationship between the monitoring index and tumor prognosis. Results We performed mutation detection on ctDNA in 23 patients with AGC and identified the top 20 mutant genes. The five most frequently mutated genes were TP53 (55%), EGFR (20%), ERBB2 (20%), MET (15%) and APC (10%). TP53 was the most common mutated gene (55%) and MET had a higher frequency of mutations (15%) in our study. Kaplan-Meier analysis showed that patients with TP53 mutant in ctDNA had shorter overall survival (OS) than these with TP53 wild (P < 0.001). The Allele frequency (AF) of TP53 mutations in patient number 1 was higher in the second time (0.94%) than in the first time (0.36%); the AF of TP53 mutations in patient number 16 was from scratch (0∼0.26%). In addition, the AF of TP53 mutations in patients who survive was relatively low (P = 0.047). Simultaneously, Kaplan-Meier analysis showed that patients with MET amplification also had shorter OS than these with MET without amplification (P < 0.001). Conclusion TP53 and MET are the two common frequently mutant genes …
format: application/pdf
format: text/html
creator: Jia Li
creator: Zhaoyan Li
creator: Yajie Ding
creator: Yan Xu
creator: Xiaohong Zhu
creator: Nida Cao
creator: Chen Huang
creator: Mengmeng Qin
creator: Feng Liu
creator: Aiguang Zhao
subject: Bioinformatics
subject: Molecular Biology
subject: Gastroenterology and Hepatology
subject: Oncology
subject: Medical Genetics
description: doi:10.7717/peerj.11146
publisher: PeerJ Inc.
rights: © 2021 Li et al.
abstract: Background Gastric cancer (GC) is a heterogeneous disease that encompasses various molecular subtypes. The molecular mutation characteristics of circulating tumor DNA (ctDNA) in advanced gastric cancer (AGC), especially the clinical utility of TP53 mutation and MET amplification in ctDNA need to be further explored. Objectives The aim of this study was mainly to assess the clinical utility of TP53 mutation and MET amplification in ctDNA as biomarkers for monitoring disease progression of AGC. Patients and Methods We used multigene NGS-panel technology to study the characteristics of ctDNA gene mutations and screen the key mutant genes in AGC patients. The Kaplan-Meier method was used to calculate the survival probability and log-rank test was used to compare the survival curves of TP53 mutation and MET amplification in ctDNA of AGC patients. The survival time was set from the blood test time to the follow-up time to observe the relationship between the monitoring index and tumor prognosis. Results We performed mutation detection on ctDNA in 23 patients with AGC and identified the top 20 mutant genes. The five most frequently mutated genes were TP53 (55%), EGFR (20%), ERBB2 (20%), MET (15%) and APC (10%). TP53 was the most common mutated gene (55%) and MET had a higher frequency of mutations (15%) in our study. Kaplan-Meier analysis showed that patients with TP53 mutant in ctDNA had shorter overall survival (OS) than these with TP53 wild (P < 0.001). The Allele frequency (AF) of TP53 mutations in patient number 1 was higher in the second time (0.94%) than in the first time (0.36%); the AF of TP53 mutations in patient number 16 was from scratch (0∼0.26%). In addition, the AF of TP53 mutations in patients who survive was relatively low (P = 0.047). Simultaneously, Kaplan-Meier analysis showed that patients with MET amplification also had shorter OS than these with MET without amplification (P < 0.001). Conclusion TP53 and MET are the two common frequently mutant genes …
bibliographic citation: Li et al. (2021) TP53 mutation and MET amplification in circulating tumor DNA analysis predict disease progression in patients with advanced gastric cancer. PeerJ 9:e11146 https://doi.org/10.7717/peerj.11146
date submitted: 2020-10-06
date accepted: 2021-03-03
issued: 2021-04-16
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Li
  given name: Jia
author list: Agent
  family name: Li
  given name: Zhaoyan
author list: Agent
  family name: Ding
  given name: Yajie
author list: Agent
  family name: Xu
  given name: Yan
author list: Agent
  family name: Zhu
  given name: Xiaohong
author list: Agent
  family name: Cao
  given name: Nida
author list: Agent
  family name: Huang
  given name: Chen
author list: Agent
  family name: Qin
  given name: Mengmeng
author list: Agent
  family name: Liu
  given name: Feng
author list: Agent
  family name: Zhao
  given name: Aiguang
doi: 10.7717/peerj.11146
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-04-16
copyright: ©2021 Li et al.
attribution name: Li et al.

Predicting migration routes for three species of migratory bats using species distribution models
type: item
type: AcademicArticle
description: Understanding seasonal variation in the distribution and movement patterns of migratory species is essential to monitoring and conservation efforts. While there are many species of migratory bats in North America, little is known about their seasonal movements. In terms of conservation, this is important because the bat fatalities from wind energy turbines are significant and may fluctuate seasonally. Here we describe seasonally resolved distributions for the three species that are most impacted by wind farms (Lasiurus borealis (eastern red bat), L. cinereus (hoary bat) and Lasionycteris noctivagans (silver-haired bat)) and use these distributions to infer their most likely migratory pathways. To accomplish this, we collected 2,880 occurrence points from the Global Biodiversity Information Facility over five decades in North America to model species distributions on a seasonal basis and used an ensemble approach for modeling distributions. This dataset included 1,129 data points for L. borealis, 917 for L. cinereus and 834 for L. noctivagans. The results suggest that all three species exhibit variation in distributions from north to south depending on season, with each species showing potential migratory pathways during the fall migration that follow linear features. Finally, we describe proposed migratory pathways for these three species that can be used to identify stop-over sites, assess small-scale migration and highlight areas that should be prioritized for actions to reduce the effects of wind farm mortality.
format: application/pdf
format: text/html
creator: Jamin G. Wieringa
creator: Bryan C. Carstens
creator: H Lisle Gibbs
subject: Animal Behavior
subject: Biogeography
subject: Ecology
subject: Zoology
description: doi:10.7717/peerj.11177
publisher: PeerJ Inc.
rights: © 2021 Wieringa et al.
abstract: Understanding seasonal variation in the distribution and movement patterns of migratory species is essential to monitoring and conservation efforts. While there are many species of migratory bats in North America, little is known about their seasonal movements. In terms of conservation, this is important because the bat fatalities from wind energy turbines are significant and may fluctuate seasonally. Here we describe seasonally resolved distributions for the three species that are most impacted by wind farms (Lasiurus borealis (eastern red bat), L. cinereus (hoary bat) and Lasionycteris noctivagans (silver-haired bat)) and use these distributions to infer their most likely migratory pathways. To accomplish this, we collected 2,880 occurrence points from the Global Biodiversity Information Facility over five decades in North America to model species distributions on a seasonal basis and used an ensemble approach for modeling distributions. This dataset included 1,129 data points for L. borealis, 917 for L. cinereus and 834 for L. noctivagans. The results suggest that all three species exhibit variation in distributions from north to south depending on season, with each species showing potential migratory pathways during the fall migration that follow linear features. Finally, we describe proposed migratory pathways for these three species that can be used to identify stop-over sites, assess small-scale migration and highlight areas that should be prioritized for actions to reduce the effects of wind farm mortality.
bibliographic citation: Wieringa et al. (2021) Predicting migration routes for three species of migratory bats using species distribution models. PeerJ 9:e11177 https://doi.org/10.7717/peerj.11177
date submitted: 2020-12-10
date accepted: 2021-03-08
issued: 2021-04-16
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Wieringa
  given name: Jamin G.
author list: Agent
  family name: Carstens
  given name: Bryan C.
author list: Agent
  family name: Gibbs
  given name: H Lisle
doi: 10.7717/peerj.11177
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-04-16
copyright: © 2021 Wieringa et al.
attribution name: Wieringa et al.

Evaluation potential of PGPR to protect tomato against Fusarium wilt and promote plant growth
type: item
type: AcademicArticle
description: Soilborne fungal diseases are most common among vegetable crops and have major implications for crop yield and productivity. Eco-friendly sustainable agriculture practices that can overcome biotic and abiotic stresses are of prime importance. In this study, we evaluated the ability of plant growth-promoting rhizobacterium (PGPR) Bacillus aryabhattai strain SRB02 to control the effects of tomato wilt disease caused by Fusarium oxysporum f. sp. lycopersici (strain KACC40032) and promote plant growth. In vitro bioassays showed significant inhibition of fungal growth by SRB02. Inoculation of susceptible and tolerant tomato cultivars in the presence of SRB02 showed significant protection of the cultivar that was susceptible to infection and promotion of plant growth and biomass production in both of the cultivars. Further analysis of SRB02-treated plants revealed a significantly higher production of amino acids following infection by F. oxysporum. Analysis of plant defense hormones after inoculation by the pathogen revealed a significantly higher accumulation of salicylic acid (SA), with a concomitant reduction in jasmonic acid (JA). These results indicate that B. aryabhattai strain SRB02 reduces the effects of Fusarium wilt disease in tomato by modulating endogenous phytohormones and amino acid levels.
format: application/pdf
format: text/html
creator: Rizwana begum Syed Nabi
creator: Raheem Shahzad
creator: Rupesh Tayade
creator: Muhammad Shahid
creator: Adil Hussain
creator: Muhammad Waqas Ali
creator: Byung-Wook Yun
subject: Agricultural Science
subject: Microbiology
subject: Mycology
subject: Plant Science
subject: Soil Science
description: doi:10.7717/peerj.11194
publisher: PeerJ Inc.
rights: © 2021 Syed Nabi et al.
abstract: Soilborne fungal diseases are most common among vegetable crops and have major implications for crop yield and productivity. Eco-friendly sustainable agriculture practices that can overcome biotic and abiotic stresses are of prime importance. In this study, we evaluated the ability of plant growth-promoting rhizobacterium (PGPR) Bacillus aryabhattai strain SRB02 to control the effects of tomato wilt disease caused by Fusarium oxysporum f. sp. lycopersici (strain KACC40032) and promote plant growth. In vitro bioassays showed significant inhibition of fungal growth by SRB02. Inoculation of susceptible and tolerant tomato cultivars in the presence of SRB02 showed significant protection of the cultivar that was susceptible to infection and promotion of plant growth and biomass production in both of the cultivars. Further analysis of SRB02-treated plants revealed a significantly higher production of amino acids following infection by F. oxysporum. Analysis of plant defense hormones after inoculation by the pathogen revealed a significantly higher accumulation of salicylic acid (SA), with a concomitant reduction in jasmonic acid (JA). These results indicate that B. aryabhattai strain SRB02 reduces the effects of Fusarium wilt disease in tomato by modulating endogenous phytohormones and amino acid levels.
bibliographic citation: Syed Nabi et al. (2021) Evaluation potential of PGPR to protect tomato against Fusarium wilt and promote plant growth. PeerJ 9:e11194 https://doi.org/10.7717/peerj.11194
date submitted: 2020-12-09
date accepted: 2021-03-09
issued: 2021-04-16
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Syed Nabi
  given name: Rizwana begum
author list: Agent
  family name: Shahzad
  given name: Raheem
author list: Agent
  family name: Tayade
  given name: Rupesh
author list: Agent
  family name: Shahid
  given name: Muhammad
author list: Agent
  family name: Hussain
  given name: Adil
author list: Agent
  family name: Ali
  given name: Muhammad Waqas
author list: Agent
  family name: Yun
  given name: Byung-Wook
doi: 10.7717/peerj.11194
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-04-16
copyright: ©2021 Syed Nabi et al.
attribution name: Syed Nabi et al.

NGScloud2: optimized bioinformatic analysis using Amazon Web Services
type: item
type: AcademicArticle
description: Background NGScloud was a bioinformatic system developed to perform de novo RNAseq analysis of non-model species by exploiting the cloud computing capabilities of Amazon Web Services. The rapid changes undergone in the way this cloud computing service operates, along with the continuous release of novel bioinformatic applications to analyze next generation sequencing data, have made the software obsolete. NGScloud2 is an enhanced and expanded version of NGScloud that permits the access to ad hoc cloud computing infrastructure, scaled according to the complexity of each experiment. Methods NGScloud2 presents major technical improvements, such as the possibility of running spot instances and the most updated AWS instances types, that can lead to significant cost savings. As compared to its initial implementation, this improved version updates and includes common applications for de novo RNAseq analysis, and incorporates tools to operate workflows of bioinformatic analysis of reference-based RNAseq, RADseq and functional annotation. NGScloud2 optimizes the access to Amazon’s large computing infrastructures to easily run popular bioinformatic software applications, otherwise inaccessible to non-specialized users lacking suitable hardware infrastructures. Results The correct performance of the pipelines for de novo RNAseq, reference-based RNAseq, RADseq and functional annotation was tested with real experimental data, providing workflow performance estimates and tips to make optimal use of NGScloud2. Further, we provide a qualitative comparison of NGScloud2 vs. the Galaxy framework. NGScloud2 code, instructions for software installation and use are available at https://github.com/GGFHF/NGScloud2. NGScloud2 includes a companion package, NGShelper that contains Python utilities to post-process the output of the pipelines for downstream analysis at https://github.com/GGFHF/NGShelper.
format: application/pdf
format: text/html
creator: Fernando Mora-Márquez
creator: José Luis Vázquez-Poletti
creator: Unai López de Heredia
subject: Bioinformatics
subject: Computational Biology
description: doi:10.7717/peerj.11237
publisher: PeerJ Inc.
rights: © 2021 Mora-Márquez et al.
abstract: Background NGScloud was a bioinformatic system developed to perform de novo RNAseq analysis of non-model species by exploiting the cloud computing capabilities of Amazon Web Services. The rapid changes undergone in the way this cloud computing service operates, along with the continuous release of novel bioinformatic applications to analyze next generation sequencing data, have made the software obsolete. NGScloud2 is an enhanced and expanded version of NGScloud that permits the access to ad hoc cloud computing infrastructure, scaled according to the complexity of each experiment. Methods NGScloud2 presents major technical improvements, such as the possibility of running spot instances and the most updated AWS instances types, that can lead to significant cost savings. As compared to its initial implementation, this improved version updates and includes common applications for de novo RNAseq analysis, and incorporates tools to operate workflows of bioinformatic analysis of reference-based RNAseq, RADseq and functional annotation. NGScloud2 optimizes the access to Amazon’s large computing infrastructures to easily run popular bioinformatic software applications, otherwise inaccessible to non-specialized users lacking suitable hardware infrastructures. Results The correct performance of the pipelines for de novo RNAseq, reference-based RNAseq, RADseq and functional annotation was tested with real experimental data, providing workflow performance estimates and tips to make optimal use of NGScloud2. Further, we provide a qualitative comparison of NGScloud2 vs. the Galaxy framework. NGScloud2 code, instructions for software installation and use are available at https://github.com/GGFHF/NGScloud2. NGScloud2 includes a companion package, NGShelper that contains Python utilities to post-process the output of the pipelines for downstream analysis at https://github.com/GGFHF/NGShelper.
bibliographic citation: Mora-Márquez et al. (2021) NGScloud2: optimized bioinformatic analysis using Amazon Web Services. PeerJ 9:e11237 https://doi.org/10.7717/peerj.11237
date submitted: 2020-12-08
date accepted: 2021-03-17
issued: 2021-04-16
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Mora-Márquez
  given name: Fernando
author list: Agent
  family name: Vázquez-Poletti
  given name: José Luis
author list: Agent
  family name: López de Heredia
  given name: Unai
doi: 10.7717/peerj.11237
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-04-16
copyright: ©2021 Mora-Márquez et al.
attribution name: Mora-Márquez et al.

https://peerj.com/articles/11242
type: item
type: AcademicArticle
title: Antifungal properties of volatile organic compounds produced by Daldinia eschscholtzii MFLUCC 19-0493 isolated from Barleria prionitis leaves against Colletotrichum acutatum and its post-harvest infections on strawberry fruits
description: Fungal endophytes are microorganisms living symbiotically with a host plant. They can produce volatile organic compounds (VOCs) that have antimicrobial activity. This study aimed to isolate endophytic fungi from Barleria prionitis plants grown in Thailand and to investigate the antifungal properties of their VOCs against Colletotrichum acutatum, a causal agent of anthracnose disease on post-harvest strawberry fruits. A total of 34 endophytic fungi were isolated from leaves of B. prionitis. The VOCs produced from each individual isolate were screened for their antifungal activity against C. acutatum using a dual-culture plate method. From this in vitro screening experiment, the VOCs produced by the endophytic isolate BP11 were found to have the highest inhibition percentage (80.3%) against the mycelial growth of C. acutatum. The endophytic isolate BP11 was molecularly identified as Daldinia eschscholtzii MFLUCC 19-0493. This strain was then selected for an in vivo experiment. Results from the in vivo experiment indicated that the VOCs produced by D. eschscholtzii MFLUCC 19-0493 were able to inhibit infections by C. acutatum on organic fresh strawberry fruits with an average inhibition percentage of 72.4%. The quality of the pathogen-inoculated strawberry fruits treated with VOCs produced by D. eschscholtzii MFLUCC 19-0493 was evaluated. Their fruit firmness, total soluble solids, and pH were found to be similar to the untreated strawberry fruits. Solid phase microextraction-gas chromatographic-mass spectrometric analysis of the VOCs produced by D. eschscholtzii MFLUCC 19-0493 led to the detection and identification of 60 compounds. The major compounds were elemicin (23.8%), benzaldehyde dimethyl acetal (8.5%), ethyl sorbate (6.8%), methyl geranate (6.5%), trans-sabinene hydrate (5.4%), and 3,5-dimethyl-4-heptanone (5.1%). Each major compound was tested for its antifungal activity against C. acutatum using the in vitro assay. While all these selected VOCs showed varyi…
format: application/pdf
format: text/html
creator: Sarunpron Khruengsai
creator: Patcharee Pripdeevech
creator: Chutima Tanapichatsakul
creator: Chanin Srisuwannapa
creator: Priya Esilda D’Souza
creator: Parinya Panuwet
subject: Agricultural Science
subject: Biotechnology
subject: Microbiology
subject: Plant Science
description: doi:10.7717/peerj.11242
publisher: PeerJ Inc.
rights: © 2021 Khruengsai et al.
abstract: Fungal endophytes are microorganisms living symbiotically with a host plant. They can produce volatile organic compounds (VOCs) that have antimicrobial activity. This study aimed to isolate endophytic fungi from Barleria prionitis plants grown in Thailand and to investigate the antifungal properties of their VOCs against Colletotrichum acutatum, a causal agent of anthracnose disease on post-harvest strawberry fruits. A total of 34 endophytic fungi were isolated from leaves of B. prionitis. The VOCs produced from each individual isolate were screened for their antifungal activity against C. acutatum using a dual-culture plate method. From this in vitro screening experiment, the VOCs produced by the endophytic isolate BP11 were found to have the highest inhibition percentage (80.3%) against the mycelial growth of C. acutatum. The endophytic isolate BP11 was molecularly identified as Daldinia eschscholtzii MFLUCC 19-0493. This strain was then selected for an in vivo experiment. Results from the in vivo experiment indicated that the VOCs produced by D. eschscholtzii MFLUCC 19-0493 were able to inhibit infections by C. acutatum on organic fresh strawberry fruits with an average inhibition percentage of 72.4%. The quality of the pathogen-inoculated strawberry fruits treated with VOCs produced by D. eschscholtzii MFLUCC 19-0493 was evaluated. Their fruit firmness, total soluble solids, and pH were found to be similar to the untreated strawberry fruits. Solid phase microextraction-gas chromatographic-mass spectrometric analysis of the VOCs produced by D. eschscholtzii MFLUCC 19-0493 led to the detection and identification of 60 compounds. The major compounds were elemicin (23.8%), benzaldehyde dimethyl acetal (8.5%), ethyl sorbate (6.8%), methyl geranate (6.5%), trans-sabinene hydrate (5.4%), and 3,5-dimethyl-4-heptanone (5.1%). Each major compound was tested for its antifungal activity against C. acutatum using the in vitro assay. While all these selected VOCs showed varyi…
bibliographic citation: Khruengsai et al. (2021) Antifungal properties of volatile organic compounds produced by Daldinia eschscholtzii MFLUCC 19-0493 isolated from Barleria prionitis leaves against Colletotrichum acutatum and its post-harvest infections on strawberry fruits. PeerJ 9:e11242 https://doi.org/10.7717/peerj.11242
date submitted: 2020-10-19
date accepted: 2021-03-17
issued: 2021-04-16
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Khruengsai
  given name: Sarunpron
author list: Agent
  family name: Pripdeevech
  given name: Patcharee
author list: Agent
  family name: Tanapichatsakul
  given name: Chutima
author list: Agent
  family name: Srisuwannapa
  given name: Chanin
author list: Agent
  family name: D’Souza
  given name: Priya Esilda
author list: Agent
  family name: Panuwet
  given name: Parinya
doi: 10.7717/peerj.11242
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-04-16
copyright: ©2021 Khruengsai et al.
attribution name: Khruengsai et al.

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