PeerJ
type: channel
link: https://peerj.com/articles/
description: Articles published in PeerJ
publisher: PeerJ Inc.
publication name: PeerJ
issn: 2167-8359
items: A resource-based game theoretical approach for the paradox of the plankton
items: Effects of social isolation and re-socialization on cognition and ADAR1 (p110) expression in mice
items: Temporal overlaps of feral cats with prey and competitors in primary and human-altered habitats on Bohol Island, Philippines
items: Microbe-ID: an open source toolbox for microbial genotyping and species identification
items: Isolation of an antimicrobial compound produced by bacteria associated with reef-building corals
items: Diet of otters (Lutra lutra) in various habitat types in the Pannonian biogeographical region compared to other regions of Europe
items: Proteomic profiling analysis reveals that glutathione system plays important roles responding to osmotic stress in wheat (Triticum aestivum L.) roots
items: Effects of origin, seasons and storage under different temperatures on germination of Senecio vulgaris (Asteraceae) seeds
items: Selection of a marker gene to construct a reference library for wetland plants, and the application of metabarcoding to analyze the diet of wintering herbivorous waterbirds
items: MOST: a modified MLST typing tool based on short read sequencing

A resource-based game theoretical approach for the paradox of the plankton
type: item
type: AcademicArticle
description: The maintenance of species diversity is a central focus in ecology. It is not rare to observe more species than the number of limiting resources, especially in plankton communities. However, such high species diversity is hard to achieve in theory under the competitive exclusion principles, known as the plankton paradox. Previous studies often focus on the coexistence of predefined species and ignore the fact that species can evolve. We model multi-resource competitions using evolutionary games, where the number of species fluctuates under extinction and the appearance of new species. The interspecific and intraspecific competitions are captured by a dynamical payoff matrix, which has a size of the number of species. The competition strength (payoff entries) is obtained from comparing the capability of species in consuming resources, which can change over time. This allows for the robust coexistence of a large number of species, providing a possible solution to the plankton paradox.
format: application/pdf
format: text/html
creator: Weini Huang
creator: Paulo Roberto de Araujo Campos
creator: Viviane Moraes de Oliveira
creator: Fernando Fagundes Ferrreira
subject: Computational Biology
subject: Evolutionary Studies
description: doi:10.7717/peerj.2329
publisher: PeerJ Inc.
rights: © 2016 Huang et al.
abstract: The maintenance of species diversity is a central focus in ecology. It is not rare to observe more species than the number of limiting resources, especially in plankton communities. However, such high species diversity is hard to achieve in theory under the competitive exclusion principles, known as the plankton paradox. Previous studies often focus on the coexistence of predefined species and ignore the fact that species can evolve. We model multi-resource competitions using evolutionary games, where the number of species fluctuates under extinction and the appearance of new species. The interspecific and intraspecific competitions are captured by a dynamical payoff matrix, which has a size of the number of species. The competition strength (payoff entries) is obtained from comparing the capability of species in consuming resources, which can change over time. This allows for the robust coexistence of a large number of species, providing a possible solution to the plankton paradox.
bibliographic citation: Huang et al. (2016) A resource-based game theoretical approach for the paradox of the plankton. PeerJ 4:e2329 https://doi.org/10.7717/peerj.2329
date submitted: 2016-05-18
date accepted: 2016-07-14
issued: 2016-08-18
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Huang
  given name: Weini
author list: Agent
  family name: de Araujo Campos
  given name: Paulo Roberto
author list: Agent
  family name: Moraes de Oliveira
  given name: Viviane
author list: Agent
  family name: Fagundes Ferrreira
  given name: Fernando
doi: 10.7717/peerj.2329
volume: 4
issn: 2167-8359
publication name: PeerJ
publication date: 2016-08-18
copyright: ©2016 Huang et al.
attribution name: Huang et al.

Effects of social isolation and re-socialization on cognition and ADAR1 (p110) expression in mice
type: item
type: AcademicArticle
description: It has been reported that social isolation stress could be a key factor that leads to cognitive deficit for both humans and rodent models. However, detailed mechanisms are not yet clear. ADAR1 (Adenosine deaminase acting on RNA) is an enzyme involved in RNA editing that has a close relation to cognitive function. We have hypothesized that social isolation stress may impact the expression of ADAR1 in the brain of mice with cognitive deficit. To test our hypothesis, we evaluated the cognition ability of mice isolated for different durations (2, 4, and 8 weeks) using object recognition and object location tests; we also measured ADAR1 expression in hippocampus and cortex using immunohistochemistry and western blot. Our study showed that social isolation stress induced spatial and non-spatial cognition deficits of the tested mice. In addition, social isolation significantly increased both the immunoreactivity and protein expression of ADAR1 (p110) in the hippocampus and frontal cortex. Furthermore, re-socialization could not only recover the cognition deficits, but also bring ADAR1 (p110) immunoreactivity of hippocampus and frontal cortex, as well as ADAR1 (p110) protein expression of hippocampus back to the normal level for the isolated mice in adolescence. In conclusion, social isolation stress significantly increases ADAR1 (p110) expression in the hippocampus and frontal cortex of the mice with cognitive deficit. This finding may open a window to better understand the reasons (e.g., epigenetic change) that are responsible for social isolation-induced cognitive deficit and help the development of novel therapies for the resulted diseases.
format: application/pdf
format: text/html
creator: Wei Chen
creator: Dong An
creator: Hong Xu
creator: Xiaoxin Cheng
creator: Shiwei Wang
creator: Weizhi Yu
creator: Deqin Yu
creator: Dan Zhao
creator: Yiping Sun
creator: Wuguo Deng
creator: Yiyuan Tang
creator: Shengming Yin
subject: Animal Behavior
subject: Biochemistry
subject: Neuroscience
subject: Toxicology
subject: Pharmacology
description: doi:10.7717/peerj.2306
publisher: PeerJ Inc.
rights: © 2016 Chen et al.
abstract: It has been reported that social isolation stress could be a key factor that leads to cognitive deficit for both humans and rodent models. However, detailed mechanisms are not yet clear. ADAR1 (Adenosine deaminase acting on RNA) is an enzyme involved in RNA editing that has a close relation to cognitive function. We have hypothesized that social isolation stress may impact the expression of ADAR1 in the brain of mice with cognitive deficit. To test our hypothesis, we evaluated the cognition ability of mice isolated for different durations (2, 4, and 8 weeks) using object recognition and object location tests; we also measured ADAR1 expression in hippocampus and cortex using immunohistochemistry and western blot. Our study showed that social isolation stress induced spatial and non-spatial cognition deficits of the tested mice. In addition, social isolation significantly increased both the immunoreactivity and protein expression of ADAR1 (p110) in the hippocampus and frontal cortex. Furthermore, re-socialization could not only recover the cognition deficits, but also bring ADAR1 (p110) immunoreactivity of hippocampus and frontal cortex, as well as ADAR1 (p110) protein expression of hippocampus back to the normal level for the isolated mice in adolescence. In conclusion, social isolation stress significantly increases ADAR1 (p110) expression in the hippocampus and frontal cortex of the mice with cognitive deficit. This finding may open a window to better understand the reasons (e.g., epigenetic change) that are responsible for social isolation-induced cognitive deficit and help the development of novel therapies for the resulted diseases.
bibliographic citation: Chen et al. (2016) Effects of social isolation and re-socialization on cognition and ADAR1 (p110) expression in mice. PeerJ 4:e2306 https://doi.org/10.7717/peerj.2306
date submitted: 2016-04-24
date accepted: 2016-07-09
issued: 2016-08-18
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Chen
  given name: Wei
author list: Agent
  family name: An
  given name: Dong
author list: Agent
  family name: Xu
  given name: Hong
author list: Agent
  family name: Cheng
  given name: Xiaoxin
author list: Agent
  family name: Wang
  given name: Shiwei
author list: Agent
  family name: Yu
  given name: Weizhi
author list: Agent
  family name: Yu
  given name: Deqin
author list: Agent
  family name: Zhao
  given name: Dan
author list: Agent
  family name: Sun
  given name: Yiping
author list: Agent
  family name: Deng
  given name: Wuguo
author list: Agent
  family name: Tang
  given name: Yiyuan
author list: Agent
  family name: Yin
  given name: Shengming
doi: 10.7717/peerj.2306
volume: 4
issn: 2167-8359
publication name: PeerJ
publication date: 2016-08-18
copyright: ©2016 Chen et al.
attribution name: Chen et al.

Temporal overlaps of feral cats with prey and competitors in primary and human-altered habitats on Bohol Island, Philippines
type: item
type: AcademicArticle
description: The vertebrate fauna of the Philippines, known for its diversity and high proportion of endemic species, comprises mainly small- to medium-sized forms with a few large exceptions. As with other tropical ecosystems, the major threats to wildlife are habitat loss, hunting and invasive species, of which the feral cat (Felis catus) is considered the most damaging. Our camera-trapping study focused on a terrestrial vertebrate species inventory on Bohol Island and tempo-spatial co-occurrences of feral cats with their prey and competitors. The survey took place in the Rajah Sikatuna Protected Landscape, and we examined the primary rainforest, its border with agricultural land, and rural areas in the vicinity of villages. Altogether, over 2,885 trap days we captured 30 species of vertebrates–10 mammals (including Sus philippensis), 19 birds and one reptile, Varanus cumingi. We trapped 81.8% of expected vertebrates. Based on the number of events, the most frequent native species was the barred rail (Gallirallus torquatus). The highest overlap in diel activity between cats and potential prey was recorded with rodents in rural areas (Δ = 0.62); the lowest was in the same habitat with ground-dwelling birds (Δ = 0.40). Cat activity was not recorded inside the rainforest; in other habitats their diel activity pattern differed. The cats’ activity declined in daylight in the proximity of humans, while it peaked at the transition zone between rainforest and fields. Both rodents and ground-dwelling birds exhibited a shift in activity levels between sites where cats were present or absent. Rodents tend to become active by day in cat-free habitats. No cats’ temporal response to co-occurrences of civets (Paradoxurus hermaphroditus and Viverra tangalunga) was found but cats in diel activity avoided domestic dogs (Canis lupus familiaris). Our first insight into the ecology of this invasive predator in the Philippines revealed an avoidance of homogeneous primary rainforest and a tendency t…
format: application/pdf
format: text/html
creator: Vlastimil Bogdan
creator: Tomáš Jůnek
creator: Pavla Jůnková Vymyslická
subject: Biodiversity
subject: Biosphere Interactions
subject: Conservation Biology
subject: Ecology
subject: Ecosystem Science
description: doi:10.7717/peerj.2288
publisher: PeerJ Inc.
rights: © 2016 Bogdan et al.
abstract: The vertebrate fauna of the Philippines, known for its diversity and high proportion of endemic species, comprises mainly small- to medium-sized forms with a few large exceptions. As with other tropical ecosystems, the major threats to wildlife are habitat loss, hunting and invasive species, of which the feral cat (Felis catus) is considered the most damaging. Our camera-trapping study focused on a terrestrial vertebrate species inventory on Bohol Island and tempo-spatial co-occurrences of feral cats with their prey and competitors. The survey took place in the Rajah Sikatuna Protected Landscape, and we examined the primary rainforest, its border with agricultural land, and rural areas in the vicinity of villages. Altogether, over 2,885 trap days we captured 30 species of vertebrates–10 mammals (including Sus philippensis), 19 birds and one reptile, Varanus cumingi. We trapped 81.8% of expected vertebrates. Based on the number of events, the most frequent native species was the barred rail (Gallirallus torquatus). The highest overlap in diel activity between cats and potential prey was recorded with rodents in rural areas (Δ = 0.62); the lowest was in the same habitat with ground-dwelling birds (Δ = 0.40). Cat activity was not recorded inside the rainforest; in other habitats their diel activity pattern differed. The cats’ activity declined in daylight in the proximity of humans, while it peaked at the transition zone between rainforest and fields. Both rodents and ground-dwelling birds exhibited a shift in activity levels between sites where cats were present or absent. Rodents tend to become active by day in cat-free habitats. No cats’ temporal response to co-occurrences of civets (Paradoxurus hermaphroditus and Viverra tangalunga) was found but cats in diel activity avoided domestic dogs (Canis lupus familiaris). Our first insight into the ecology of this invasive predator in the Philippines revealed an avoidance of homogeneous primary rainforest and a tendency t…
bibliographic citation: Bogdan et al. (2016) Temporal overlaps of feral cats with prey and competitors in primary and human-altered habitats on Bohol Island, Philippines. PeerJ 4:e2288 https://doi.org/10.7717/peerj.2288
date submitted: 2016-02-20
date accepted: 2016-07-05
issued: 2016-08-18
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Bogdan
  given name: Vlastimil
author list: Agent
  family name: Jůnek
  given name: Tomáš
author list: Agent
  family name: Jůnková Vymyslická
  given name: Pavla
doi: 10.7717/peerj.2288
volume: 4
issn: 2167-8359
publication name: PeerJ
publication date: 2016-08-18
copyright: ©2016 Bogdan et al.
attribution name: Bogdan et al.

Microbe-ID: an open source toolbox for microbial genotyping and species identification
type: item
type: AcademicArticle
description: Development of tools to identify species, genotypes, or novel strains of invasive organisms is critical for monitoring emergence and implementing rapid response measures. Molecular markers, although critical to identifying species or genotypes, require bioinformatic tools for analysis. However, user-friendly analytical tools for fast identification are not readily available. To address this need, we created a web-based set of applications called Microbe-ID that allow for customizing a toolbox for rapid species identification and strain genotyping using any genetic markers of choice. Two components of Microbe-ID, named Sequence-ID and Genotype-ID, implement species and genotype identification, respectively. Sequence-ID allows identification of species by using BLAST to query sequences for any locus of interest against a custom reference sequence database. Genotype-ID allows placement of an unknown multilocus marker in either a minimum spanning network or dendrogram with bootstrap support from a user-created reference database. Microbe-ID can be used for identification of any organism based on nucleotide sequences or any molecular marker type and several examples are provided. We created a public website for demonstration purposes called Microbe-ID (microbe-id.org) and provided a working implementation for the genus Phytophthora (phytophthora-id.org). In Phytophthora-ID, the Sequence-ID application allows identification based on ITS or cox spacer sequences. Genotype-ID groups individuals into clonal lineages based on simple sequence repeat (SSR) markers for the two invasive plant pathogen species P. infestans and P. ramorum. All code is open source and available on github and CRAN. Instructions for installation and use are provided at https://github.com/grunwaldlab/Microbe-ID.
format: application/pdf
format: text/html
creator: Javier F. Tabima
creator: Sydney E. Everhart
creator: Meredith M. Larsen
creator: Alexandra J. Weisberg
creator: Zhian N. Kamvar
creator: Matthew A. Tancos
creator: Christine D. Smart
creator: Jeff H. Chang
creator: Niklaus J. Grünwald
subject: Agricultural Science
subject: Bioinformatics
subject: Microbiology
subject: Mycology
subject: Taxonomy
description: doi:10.7717/peerj.2279
publisher: PeerJ Inc.
rights: © 2016 Tabima et al.
abstract: Development of tools to identify species, genotypes, or novel strains of invasive organisms is critical for monitoring emergence and implementing rapid response measures. Molecular markers, although critical to identifying species or genotypes, require bioinformatic tools for analysis. However, user-friendly analytical tools for fast identification are not readily available. To address this need, we created a web-based set of applications called Microbe-ID that allow for customizing a toolbox for rapid species identification and strain genotyping using any genetic markers of choice. Two components of Microbe-ID, named Sequence-ID and Genotype-ID, implement species and genotype identification, respectively. Sequence-ID allows identification of species by using BLAST to query sequences for any locus of interest against a custom reference sequence database. Genotype-ID allows placement of an unknown multilocus marker in either a minimum spanning network or dendrogram with bootstrap support from a user-created reference database. Microbe-ID can be used for identification of any organism based on nucleotide sequences or any molecular marker type and several examples are provided. We created a public website for demonstration purposes called Microbe-ID (microbe-id.org) and provided a working implementation for the genus Phytophthora (phytophthora-id.org). In Phytophthora-ID, the Sequence-ID application allows identification based on ITS or cox spacer sequences. Genotype-ID groups individuals into clonal lineages based on simple sequence repeat (SSR) markers for the two invasive plant pathogen species P. infestans and P. ramorum. All code is open source and available on github and CRAN. Instructions for installation and use are provided at https://github.com/grunwaldlab/Microbe-ID.
bibliographic citation: Tabima et al. (2016) Microbe-ID: an open source toolbox for microbial genotyping and species identification. PeerJ 4:e2279 https://doi.org/10.7717/peerj.2279
date submitted: 2016-04-29
date accepted: 2016-07-02
issued: 2016-08-18
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Tabima
  given name: Javier F.
author list: Agent
  family name: Everhart
  given name: Sydney E.
author list: Agent
  family name: Larsen
  given name: Meredith M.
author list: Agent
  family name: Weisberg
  given name: Alexandra J.
author list: Agent
  family name: Kamvar
  given name: Zhian N.
author list: Agent
  family name: Tancos
  given name: Matthew A.
author list: Agent
  family name: Smart
  given name: Christine D.
author list: Agent
  family name: Chang
  given name: Jeff H.
author list: Agent
  family name: Grünwald
  given name: Niklaus J.
doi: 10.7717/peerj.2279
volume: 4
issn: 2167-8359
publication name: PeerJ
publication date: 2016-08-18
copyright: ©2016 Tabima et al.
attribution name: Tabima et al.

Isolation of an antimicrobial compound produced by bacteria associated with reef-building corals
type: item
type: AcademicArticle
description: Bacterial communities associated with healthy corals produce antimicrobial compounds that inhibit the colonization and growth of invasive microbes and potential pathogens. To date, however, bacteria-derived antimicrobial molecules have not been identified in reef-building corals. Here, we report the isolation of an antimicrobial compound produced by Pseudovibrio sp. P12, a common and abundant coral-associated bacterium. This strain was capable of metabolizing dimethylsulfoniopropionate (DMSP), a sulfur molecule produced in high concentrations by reef-building corals and playing a role in structuring their bacterial communities. Bioassay-guided fractionation coupled with nuclear magnetic resonance (NMR) and mass spectrometry (MS), identified the antimicrobial as tropodithietic acid (TDA), a sulfur-containing compound likely derived from DMSP catabolism. TDA was produced in large quantities by Pseudovibrio sp., and prevented the growth of two previously identified coral pathogens, Vibrio coralliilyticus and V. owensii, at very low concentrations (0.5 μg/mL) in agar diffusion assays. Genome sequencing of Pseudovibrio sp. P12 identified gene homologs likely involved in the metabolism of DMSP and production of TDA. These results provide additional evidence for the integral role of DMSP in structuring coral-associated bacterial communities and underline the potential of these DMSP-metabolizing microbes to contribute to coral disease prevention.
format: application/pdf
format: text/html
creator: Jean-Baptiste Raina
creator: Dianne Tapiolas
creator: Cherie A. Motti
creator: Sylvain Foret
creator: Torsten Seemann
creator: Jan Tebben
creator: Bette L. Willis
creator: David G. Bourne
subject: Marine Biology
subject: Microbiology
description: doi:10.7717/peerj.2275
publisher: PeerJ Inc.
rights: © 2016 Raina et al.
abstract: Bacterial communities associated with healthy corals produce antimicrobial compounds that inhibit the colonization and growth of invasive microbes and potential pathogens. To date, however, bacteria-derived antimicrobial molecules have not been identified in reef-building corals. Here, we report the isolation of an antimicrobial compound produced by Pseudovibrio sp. P12, a common and abundant coral-associated bacterium. This strain was capable of metabolizing dimethylsulfoniopropionate (DMSP), a sulfur molecule produced in high concentrations by reef-building corals and playing a role in structuring their bacterial communities. Bioassay-guided fractionation coupled with nuclear magnetic resonance (NMR) and mass spectrometry (MS), identified the antimicrobial as tropodithietic acid (TDA), a sulfur-containing compound likely derived from DMSP catabolism. TDA was produced in large quantities by Pseudovibrio sp., and prevented the growth of two previously identified coral pathogens, Vibrio coralliilyticus and V. owensii, at very low concentrations (0.5 μg/mL) in agar diffusion assays. Genome sequencing of Pseudovibrio sp. P12 identified gene homologs likely involved in the metabolism of DMSP and production of TDA. These results provide additional evidence for the integral role of DMSP in structuring coral-associated bacterial communities and underline the potential of these DMSP-metabolizing microbes to contribute to coral disease prevention.
bibliographic citation: Raina et al. (2016) Isolation of an antimicrobial compound produced by bacteria associated with reef-building corals. PeerJ 4:e2275 https://doi.org/10.7717/peerj.2275
date submitted: 2016-05-15
date accepted: 2016-07-19
issued: 2016-08-18
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Raina
  given name: Jean-Baptiste
author list: Agent
  family name: Tapiolas
  given name: Dianne
author list: Agent
  family name: Motti
  given name: Cherie A.
author list: Agent
  family name: Foret
  given name: Sylvain
author list: Agent
  family name: Seemann
  given name: Torsten
author list: Agent
  family name: Tebben
  given name: Jan
author list: Agent
  family name: Willis
  given name: Bette L.
author list: Agent
  family name: Bourne
  given name: David G.
doi: 10.7717/peerj.2275
volume: 4
issn: 2167-8359
publication name: PeerJ
publication date: 2016-08-18
copyright: © 2016 Raina et al.
attribution name: Raina et al.

Diet of otters (Lutra lutra) in various habitat types in the Pannonian biogeographical region compared to other regions of Europe
type: item
type: AcademicArticle
description: Knowledge of the effect of habitat type and region on diet and feeding behaviours of a species facilitates a better understanding of factors impacting populations, which contributes to effective conservation management. Using spraint analysis and relative frequency of occurrence data from the literature, we described the dietary patterns of Eurasian otters (Lutra lutra) in 23 study sites within the Pannonian biogeographical region in Hungary. Our results indicated that diet composition varied by habitat type and is therefore context dependant. The differences among habitat types were however lower than expected. We noticed a decline in the fish consumption with a concomitant increase in trophic niche breadth and amphibian consumption in rivers, ponds (fish farms), backwaters, marshes and small watercourses. The main differences in diet were not attributed to the consumption of primary and secondary food types (fish and amphibians), but rather to differences in other, less important food types (mammals, birds). Using hierarchical cluster analysis, rivers and ponds could clearly be separated from other habitat types. We found the main fish diet of otters in most of these areas consisted of small (<100 g), eurytopic, littoral and non-native, mostly invasive species. Dietary studies from 91 sites in six European biogeographical regions showed that fish are consumed most frequently in the Atlantic and Boreal, less in the Continental and Pannonian, and least in the Alpine and Mediterranean regions. Comparative analysis indicated that the Mediterranean region (with frequent crayfish consumption) and Alpine region (frequent amphibian consumption) cluster separate from the other regions.
format: application/pdf
format: text/html
creator: József Lanszki
creator: István Lehoczky
creator: Antoinette Kotze
creator: Michael J. Somers
subject: Animal Behavior
subject: Biodiversity
subject: Biogeography
subject: Conservation Biology
subject: Zoology
description: doi:10.7717/peerj.2266
publisher: PeerJ Inc.
rights: © 2016 Lanszki et al.
abstract: Knowledge of the effect of habitat type and region on diet and feeding behaviours of a species facilitates a better understanding of factors impacting populations, which contributes to effective conservation management. Using spraint analysis and relative frequency of occurrence data from the literature, we described the dietary patterns of Eurasian otters (Lutra lutra) in 23 study sites within the Pannonian biogeographical region in Hungary. Our results indicated that diet composition varied by habitat type and is therefore context dependant. The differences among habitat types were however lower than expected. We noticed a decline in the fish consumption with a concomitant increase in trophic niche breadth and amphibian consumption in rivers, ponds (fish farms), backwaters, marshes and small watercourses. The main differences in diet were not attributed to the consumption of primary and secondary food types (fish and amphibians), but rather to differences in other, less important food types (mammals, birds). Using hierarchical cluster analysis, rivers and ponds could clearly be separated from other habitat types. We found the main fish diet of otters in most of these areas consisted of small (<100 g), eurytopic, littoral and non-native, mostly invasive species. Dietary studies from 91 sites in six European biogeographical regions showed that fish are consumed most frequently in the Atlantic and Boreal, less in the Continental and Pannonian, and least in the Alpine and Mediterranean regions. Comparative analysis indicated that the Mediterranean region (with frequent crayfish consumption) and Alpine region (frequent amphibian consumption) cluster separate from the other regions.
bibliographic citation: Lanszki et al. (2016) Diet of otters (Lutra lutra) in various habitat types in the Pannonian biogeographical region compared to other regions of Europe. PeerJ 4:e2266 https://doi.org/10.7717/peerj.2266
date submitted: 2016-03-26
date accepted: 2016-06-28
issued: 2016-08-18
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Lanszki
  given name: József
author list: Agent
  family name: Lehoczky
  given name: István
author list: Agent
  family name: Kotze
  given name: Antoinette
author list: Agent
  family name: Somers
  given name: Michael J.
doi: 10.7717/peerj.2266
volume: 4
issn: 2167-8359
publication name: PeerJ
publication date: 2016-08-18
copyright: ©2016 Lanszki et al.
attribution name: Lanszki et al.

Proteomic profiling analysis reveals that glutathione system plays important roles responding to osmotic stress in wheat (Triticum aestivum L.) roots
type: item
type: AcademicArticle
description: Wheat is one of the most important crops in the world, and osmotic stress has become one of the main factors affecting wheat production. Understanding the mechanism of the response of wheat to osmotic stress would be greatly significant. In the present study, isobaric tag for relative and absolute quantification (iTRAQ) was used to analyze the changes of protein expression in the wheat roots exposed to different osmotic stresses. A total of 2,228 expressed proteins, including 81 differentially expressed proteins, between osmotic stress and control, were found. The comprehensive analysis of these differentially expressed proteins revealed that osmotic stress increased the variety of expressed proteins and suppressed the quantity of expressed proteins in wheat roots. Furthermore, the proteins for detoxifying and reactive oxygen species scavenging, especially the glutathione system, played important roles in maintaining organism balance in response to osmotic stress in wheat roots. Thus, the present study comprehensively describes the protein expression changes in wheat roots in response to osmotic stress, providing firmer foundation to further study the mechanism of osmotic resistance in wheat.
format: application/pdf
format: text/html
creator: Jianhui Ma
creator: Wen Dong
creator: Daijing Zhang
creator: Xiaolong Gao
creator: Lina Jiang
creator: Yun Shao
creator: Doudou Tong
creator: Chunxi Li
subject: Agricultural Science
subject: Genomics
subject: Plant Science
description: doi:10.7717/peerj.2334
publisher: PeerJ Inc.
rights: © 2016 Ma et al.
abstract: Wheat is one of the most important crops in the world, and osmotic stress has become one of the main factors affecting wheat production. Understanding the mechanism of the response of wheat to osmotic stress would be greatly significant. In the present study, isobaric tag for relative and absolute quantification (iTRAQ) was used to analyze the changes of protein expression in the wheat roots exposed to different osmotic stresses. A total of 2,228 expressed proteins, including 81 differentially expressed proteins, between osmotic stress and control, were found. The comprehensive analysis of these differentially expressed proteins revealed that osmotic stress increased the variety of expressed proteins and suppressed the quantity of expressed proteins in wheat roots. Furthermore, the proteins for detoxifying and reactive oxygen species scavenging, especially the glutathione system, played important roles in maintaining organism balance in response to osmotic stress in wheat roots. Thus, the present study comprehensively describes the protein expression changes in wheat roots in response to osmotic stress, providing firmer foundation to further study the mechanism of osmotic resistance in wheat.
bibliographic citation: Ma et al. (2016) Proteomic profiling analysis reveals that glutathione system plays important roles responding to osmotic stress in wheat (Triticum aestivum L.) roots. PeerJ 4:e2334 https://doi.org/10.7717/peerj.2334
date submitted: 2015-11-16
date accepted: 2016-07-16
issued: 2016-08-17
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Ma
  given name: Jianhui
author list: Agent
  family name: Dong
  given name: Wen
author list: Agent
  family name: Zhang
  given name: Daijing
author list: Agent
  family name: Gao
  given name: Xiaolong
author list: Agent
  family name: Jiang
  given name: Lina
author list: Agent
  family name: Shao
  given name: Yun
author list: Agent
  family name: Tong
  given name: Doudou
author list: Agent
  family name: Li
  given name: Chunxi
doi: 10.7717/peerj.2334
volume: 4
issn: 2167-8359
publication name: PeerJ
publication date: 2016-08-17
copyright: ©2016 Ma et al.
attribution name: Ma et al.

Effects of origin, seasons and storage under different temperatures on germination of Senecio vulgaris (Asteraceae) seeds
type: item
type: AcademicArticle
description: Invasive plants colonize new environments, become pests and cause biodiversity loss, economic loss and health damage. Senecio vulgaris L. (Common groundsel, Asteraceae), a widely distributing cosmopolitan weed in the temperate area, is reported with large populations in the north–eastern and south–western part, but not in southern, central, or north-western parts of China. We studied the germination behavior of S. vulgaris to explain the distribution and the biological invasion of this species in China. We used seeds originating from six native and six invasive populations to conduct germination experiments in a climate chamber and under outdoor condition. When incubated in a climate chamber (15 °C), seeds from the majority of the populations showed >90% germination percentage (GP) and the GP was equal for seeds with a native and invasive origin. The mean germination time (MGT) was significantly different among the populations. Under outdoor conditions, significant effects of origin, storage conditions (stored at 4 °C or ambient room temperature, ca. 27 °C) and seasons (in summer or autumn) were observed on the GP while the MGT was only affected by the season. In autumn, the GP (38.6%) was higher and the MGT was slightly longer than that in summer. In autumn, seeds stored at 4 °C showed higher GP than those stored at ambient room temperature (ca.27 °C), and seeds from invasive populations revealed higher GP than those from native populations. The results implied that the high temperature in summer has a negative impact on the germination and might cause viability loss or secondary dormancy to S. vulgaris seeds. Our study offers a clue to exploring what factor limits the distribution of S. vulgaris in China by explaining why, in the cities in South-East China and central China such as Wuhan, S. vulgaris cannot establish natural and viable populations.
format: application/pdf
format: text/html
creator: Noel Ndihokubwayo
creator: Viet-Thang Nguyen
creator: Dandan Cheng
subject: Biodiversity
subject: Biogeography
subject: Ecology
subject: Plant Science
description: doi:10.7717/peerj.2346
publisher: PeerJ Inc.
rights: © 2016 Ndihokubwayo et al.
abstract: Invasive plants colonize new environments, become pests and cause biodiversity loss, economic loss and health damage. Senecio vulgaris L. (Common groundsel, Asteraceae), a widely distributing cosmopolitan weed in the temperate area, is reported with large populations in the north–eastern and south–western part, but not in southern, central, or north-western parts of China. We studied the germination behavior of S. vulgaris to explain the distribution and the biological invasion of this species in China. We used seeds originating from six native and six invasive populations to conduct germination experiments in a climate chamber and under outdoor condition. When incubated in a climate chamber (15 °C), seeds from the majority of the populations showed >90% germination percentage (GP) and the GP was equal for seeds with a native and invasive origin. The mean germination time (MGT) was significantly different among the populations. Under outdoor conditions, significant effects of origin, storage conditions (stored at 4 °C or ambient room temperature, ca. 27 °C) and seasons (in summer or autumn) were observed on the GP while the MGT was only affected by the season. In autumn, the GP (38.6%) was higher and the MGT was slightly longer than that in summer. In autumn, seeds stored at 4 °C showed higher GP than those stored at ambient room temperature (ca.27 °C), and seeds from invasive populations revealed higher GP than those from native populations. The results implied that the high temperature in summer has a negative impact on the germination and might cause viability loss or secondary dormancy to S. vulgaris seeds. Our study offers a clue to exploring what factor limits the distribution of S. vulgaris in China by explaining why, in the cities in South-East China and central China such as Wuhan, S. vulgaris cannot establish natural and viable populations.
bibliographic citation: Ndihokubwayo et al. (2016) Effects of origin, seasons and storage under different temperatures on germination of Senecio vulgaris (Asteraceae) seeds. PeerJ 4:e2346 https://doi.org/10.7717/peerj.2346
date submitted: 2016-02-03
date accepted: 2016-07-19
issued: 2016-08-17
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Ndihokubwayo
  given name: Noel
author list: Agent
  family name: Nguyen
  given name: Viet-Thang
author list: Agent
  family name: Cheng
  given name: Dandan
doi: 10.7717/peerj.2346
volume: 4
issn: 2167-8359
publication name: PeerJ
publication date: 2016-08-17
copyright: ©2016 Ndihokubwayo et al.
attribution name: Ndihokubwayo et al.

Selection of a marker gene to construct a reference library for wetland plants, and the application of metabarcoding to analyze the diet of wintering herbivorous waterbirds
type: item
type: AcademicArticle
description: Food availability and diet selection are important factors influencing the abundance and distribution of wild waterbirds. In order to better understand changes in waterbird population, it is essential to figure out what they feed on. However, analyzing their diet could be difficult and inefficient using traditional methods such as microhistologic observation. Here, we addressed this gap of knowledge by investigating the diet of greater white-fronted goose Anser albifrons and bean goose Anser fabalis, which are obligate herbivores wintering in China, mostly in the Middle and Lower Yangtze River floodplain. First, we selected a suitable and high-resolution marker gene for wetland plants that these geese would consume during the wintering period. Eight candidate genes were included: rbcL, rpoC1, rpoB, matK, trnH-psbA, trnL (UAA), atpF-atpH, and psbK-psbI. The selection was performed via analysis of representative sequences from NCBI and comparison of amplification efficiency and resolution power of plant samples collected from the wintering area. The trnL gene was chosen at last with c/h primers, and a local plant reference library was constructed with this gene. Then, utilizing DNA metabarcoding, we discovered 15 food items in total from the feces of these birds. Of the 15 unique dietary sequences, 10 could be identified at specie level. As for greater white-fronted goose, 73% of sequences belonged to Poaceae spp., and 26% belonged to Carex spp. In contrast, almost all sequences of bean goose belonged to Carex spp. (99%). Using the same samples, microhistology provided consistent food composition with metabarcoding results for greater white-fronted goose, while 13% of Poaceae was recovered for bean goose. In addition, two other taxa were discovered only through microhistologic analysis. Although most of the identified taxa matched relatively well between the two methods, DNA metabarcoding gave taxonomically more detailed information. Discrepancies were likely due to b…
format: application/pdf
format: text/html
creator: Yuzhan Yang
creator: Aibin Zhan
creator: Lei Cao
creator: Fanjuan Meng
creator: Wenbin Xu
subject: Animal Behavior
subject: Conservation Biology
subject: Ecology
subject: Molecular Biology
subject: Veterinary Medicine
description: doi:10.7717/peerj.2345
publisher: PeerJ Inc.
rights: © 2016 Yang et al.
abstract: Food availability and diet selection are important factors influencing the abundance and distribution of wild waterbirds. In order to better understand changes in waterbird population, it is essential to figure out what they feed on. However, analyzing their diet could be difficult and inefficient using traditional methods such as microhistologic observation. Here, we addressed this gap of knowledge by investigating the diet of greater white-fronted goose Anser albifrons and bean goose Anser fabalis, which are obligate herbivores wintering in China, mostly in the Middle and Lower Yangtze River floodplain. First, we selected a suitable and high-resolution marker gene for wetland plants that these geese would consume during the wintering period. Eight candidate genes were included: rbcL, rpoC1, rpoB, matK, trnH-psbA, trnL (UAA), atpF-atpH, and psbK-psbI. The selection was performed via analysis of representative sequences from NCBI and comparison of amplification efficiency and resolution power of plant samples collected from the wintering area. The trnL gene was chosen at last with c/h primers, and a local plant reference library was constructed with this gene. Then, utilizing DNA metabarcoding, we discovered 15 food items in total from the feces of these birds. Of the 15 unique dietary sequences, 10 could be identified at specie level. As for greater white-fronted goose, 73% of sequences belonged to Poaceae spp., and 26% belonged to Carex spp. In contrast, almost all sequences of bean goose belonged to Carex spp. (99%). Using the same samples, microhistology provided consistent food composition with metabarcoding results for greater white-fronted goose, while 13% of Poaceae was recovered for bean goose. In addition, two other taxa were discovered only through microhistologic analysis. Although most of the identified taxa matched relatively well between the two methods, DNA metabarcoding gave taxonomically more detailed information. Discrepancies were likely due to b…
bibliographic citation: Yang et al. (2016) Selection of a marker gene to construct a reference library for wetland plants, and the application of metabarcoding to analyze the diet of wintering herbivorous waterbirds. PeerJ 4:e2345 https://doi.org/10.7717/peerj.2345
date submitted: 2016-04-12
date accepted: 2016-07-19
issued: 2016-08-17
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Yang
  given name: Yuzhan
author list: Agent
  family name: Zhan
  given name: Aibin
author list: Agent
  family name: Cao
  given name: Lei
author list: Agent
  family name: Meng
  given name: Fanjuan
author list: Agent
  family name: Xu
  given name: Wenbin
doi: 10.7717/peerj.2345
volume: 4
issn: 2167-8359
publication name: PeerJ
publication date: 2016-08-17
copyright: ©2016 Yang et al.
attribution name: Yang et al.

MOST: a modified MLST typing tool based on short read sequencing
type: item
type: AcademicArticle
description: Multilocus sequence typing (MLST) is an effective method to describe bacterial populations. Conventionally, MLST involves Polymerase Chain Reaction (PCR) amplification of housekeeping genes followed by Sanger DNA sequencing. Public Health England (PHE) is in the process of replacing the conventional MLST methodology with a method based on short read sequence data derived from Whole Genome Sequencing (WGS). This paper reports the comparison of the reliability of MLST results derived from WGS data, comparing mapping and assembly-based approaches to conventional methods using 323 bacterial genomes of diverse species. The sensitivity of the two WGS based methods were further investigated with 26 mixed and 29 low coverage genomic data sets from Salmonella enteridis and Streptococcus pneumoniae. Of the 323 samples, 92.9% (n = 300), 97.5% (n = 315) and 99.7% (n = 322) full MLST profiles were derived by the conventional method, assembly- and mapping-based approaches, respectively. The concordance between samples that were typed by conventional (92.9%) and both WGS methods was 100%. From the 55 mixed and low coverage genomes, 89.1% (n = 49) and 67.3% (n = 37) full MLST profiles were derived from the mapping and assembly based approaches, respectively. In conclusion, deriving MLST from WGS data is more sensitive than the conventional method. When comparing WGS based methods, the mapping based approach was the most sensitive. In addition, the mapping based approach described here derives quality metrics, which are difficult to determine quantitatively using conventional and WGS-assembly based approaches.
format: application/pdf
format: text/html
creator: Rediat Tewolde
creator: Timothy Dallman
creator: Ulf Schaefer
creator: Carmen L. Sheppard
creator: Philip Ashton
creator: Bruno Pichon
creator: Matthew Ellington
creator: Craig Swift
creator: Jonathan Green
creator: Anthony Underwood
subject: Bioinformatics
subject: Microbiology
description: doi:10.7717/peerj.2308
publisher: PeerJ Inc.
rights: © 2016 Tewolde et al.
abstract: Multilocus sequence typing (MLST) is an effective method to describe bacterial populations. Conventionally, MLST involves Polymerase Chain Reaction (PCR) amplification of housekeeping genes followed by Sanger DNA sequencing. Public Health England (PHE) is in the process of replacing the conventional MLST methodology with a method based on short read sequence data derived from Whole Genome Sequencing (WGS). This paper reports the comparison of the reliability of MLST results derived from WGS data, comparing mapping and assembly-based approaches to conventional methods using 323 bacterial genomes of diverse species. The sensitivity of the two WGS based methods were further investigated with 26 mixed and 29 low coverage genomic data sets from Salmonella enteridis and Streptococcus pneumoniae. Of the 323 samples, 92.9% (n = 300), 97.5% (n = 315) and 99.7% (n = 322) full MLST profiles were derived by the conventional method, assembly- and mapping-based approaches, respectively. The concordance between samples that were typed by conventional (92.9%) and both WGS methods was 100%. From the 55 mixed and low coverage genomes, 89.1% (n = 49) and 67.3% (n = 37) full MLST profiles were derived from the mapping and assembly based approaches, respectively. In conclusion, deriving MLST from WGS data is more sensitive than the conventional method. When comparing WGS based methods, the mapping based approach was the most sensitive. In addition, the mapping based approach described here derives quality metrics, which are difficult to determine quantitatively using conventional and WGS-assembly based approaches.
bibliographic citation: Tewolde et al. (2016) MOST: a modified MLST typing tool based on short read sequencing. PeerJ 4:e2308 https://doi.org/10.7717/peerj.2308
date submitted: 2016-04-19
date accepted: 2016-07-10
issued: 2016-08-17
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Tewolde
  given name: Rediat
author list: Agent
  family name: Dallman
  given name: Timothy
author list: Agent
  family name: Schaefer
  given name: Ulf
author list: Agent
  family name: Sheppard
  given name: Carmen L.
author list: Agent
  family name: Ashton
  given name: Philip
author list: Agent
  family name: Pichon
  given name: Bruno
author list: Agent
  family name: Ellington
  given name: Matthew
author list: Agent
  family name: Swift
  given name: Craig
author list: Agent
  family name: Green
  given name: Jonathan
author list: Agent
  family name: Underwood
  given name: Anthony
doi: 10.7717/peerj.2308
volume: 4
issn: 2167-8359
publication name: PeerJ
publication date: 2016-08-17
copyright: ©2016 Tewolde et al.
attribution name: Tewolde et al.

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