PeerJ
type: channel
link: https://peerj.com/articles/
description: Articles published in PeerJ
publisher: PeerJ Inc.
publication name: PeerJ
issn: 2167-8359
items: Greater reproductive investment, but shorter lifespan, in agrosystem than in natural-habitat toads
items: Factors influencing healthcare provider respondent fatigue answering a globally administered in-app survey
items: Identification and analysis of CYP450 genes from transcriptome of Lonicera japonica and expression analysis of chlorogenic acid biosynthesis related CYP450s
items: Comparison of polybrominated diphenyl ethers (PBDEs) and polychlorinated biphenyls (PCBs) in the serum of hypothyroxinemic and euthyroid dogs
items: The landscape of fear conceptual framework: definition and review of current applications and misuses
items: Habitat suitability—density relationship in an endangered woodland species: the case of the Blue Chaffinch (Fringilla polatzeki)
items: Challenging a bioinformatic tool’s ability to detect microbial contaminants using in silico whole genome sequencing data
items: Adaptations to different habitats in sexual and asexual populations of parasitoid wasps: a meta-analysis
items: The evolutionary history of plant T2/S-type ribonucleases
items: Biochemical and structural characterization of a novel arginine kinase from the spider Polybetes pythagoricus

Greater reproductive investment, but shorter lifespan, in agrosystem than in natural-habitat toads
type: item
type: AcademicArticle
description: Global amphibian decline is due to several factors: habitat loss, anthropization, pollution, emerging diseases, and global warming. Amphibians, with complex life cycles, are particularly susceptible to habitat alterations, and their survival may be impaired in anthropized habitats. Increased mortality is a well-known consequence of anthropization. Life-history theory predicts higher reproductive investment when mortality is increased. In this work, we compared age, body size, and different indicators of reproductive investment, as well as prey availability, in natterjack toads (Epidalea calamita) from agrosystems and adjacent natural pine groves in Southwestern Spain. Mean age was lower in agrosystems than in pine groves, possibly as a consequence of increased mortality due to agrosystem environmental stressors. Remarkably, agrosystem toads were larger despite being younger, suggesting accelerated growth rate. Although we detected no differences in prey availability between habitats, artificial irrigation could shorten aestivation in agrosystems, thus increasing energy trade. Moreover, agrosystem toads exhibited increased indicators of reproductive investment. In the light of life-history theory, agrosystem toads might compensate for lesser reproductive events—due to shorter lives—with a higher reproductive investment in each attempt. Our results show that agrosystems may alter demography, which may have complex consequences on both individual fitness and population stability.
format: application/pdf
format: text/html
creator: Francisco Javier Zamora-Camacho
creator: Mar Comas
subject: Biosphere Interactions
subject: Conservation Biology
subject: Environmental Impacts
subject: Evolutionary Studies
subject: Zoology
description: doi:10.7717/peerj.3791
publisher: PeerJ Inc.
rights: © 2017 Zamora-Camacho and Comas
abstract: Global amphibian decline is due to several factors: habitat loss, anthropization, pollution, emerging diseases, and global warming. Amphibians, with complex life cycles, are particularly susceptible to habitat alterations, and their survival may be impaired in anthropized habitats. Increased mortality is a well-known consequence of anthropization. Life-history theory predicts higher reproductive investment when mortality is increased. In this work, we compared age, body size, and different indicators of reproductive investment, as well as prey availability, in natterjack toads (Epidalea calamita) from agrosystems and adjacent natural pine groves in Southwestern Spain. Mean age was lower in agrosystems than in pine groves, possibly as a consequence of increased mortality due to agrosystem environmental stressors. Remarkably, agrosystem toads were larger despite being younger, suggesting accelerated growth rate. Although we detected no differences in prey availability between habitats, artificial irrigation could shorten aestivation in agrosystems, thus increasing energy trade. Moreover, agrosystem toads exhibited increased indicators of reproductive investment. In the light of life-history theory, agrosystem toads might compensate for lesser reproductive events—due to shorter lives—with a higher reproductive investment in each attempt. Our results show that agrosystems may alter demography, which may have complex consequences on both individual fitness and population stability.
bibliographic citation: Zamora-Camacho et al. (2017) Greater reproductive investment, but shorter lifespan, in agrosystem than in natural-habitat toads. PeerJ 5:e3791 https://doi.org/10.7717/peerj.3791
date submitted: 2017-04-29
date accepted: 2017-08-19
issued: 2017-09-12
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Zamora-Camacho
  given name: Francisco Javier
author list: Agent
  family name: Comas
  given name: Mar
doi: 10.7717/peerj.3791
volume: 5
issn: 2167-8359
publication name: PeerJ
publication date: 2017-09-12
copyright: ©2017 Zamora-Camacho and Comas
attribution name: Zamora-Camacho and Comas

Factors influencing healthcare provider respondent fatigue answering a globally administered in-app survey
type: item
type: AcademicArticle
description: Background Respondent fatigue, also known as survey fatigue, is a common problem in the collection of survey data. Factors that are known to influence respondent fatigue include survey length, survey topic, question complexity, and open-ended question type. There is a great deal of interest in understanding the drivers of physician survey responsiveness due to the value of information received from these practitioners. With the recent explosion of mobile smartphone technology, it has been possible to obtain survey data from users of mobile applications (apps) on a question-by-question basis. The author obtained basic demographic survey data as well as survey data related to an anesthesiology-specific drug called sugammadex and leveraged nonresponse rates to examine factors that influenced respondent fatigue. Methods Primary data were collected between December 2015 and February 2017. Surveys and in-app analytics were collected from global users of a mobile anesthesia calculator app. Key independent variables were user country, healthcare provider role, rating of importance of the app to personal practice, length of time in practice, and frequency of app use. Key dependent variable was the metric of respondent fatigue. Results Provider role and World Bank country income level were predictive of the rate of respondent fatigue for this in-app survey. Importance of the app to the provider and length of time in practice were moderately associated with fatigue. Frequency of app use was not associated. This study focused on a survey with a topic closely related to the subject area of the app. Respondent fatigue rates will likely change dramatically if the topic does not align closely. Discussion Although apps may serve as powerful platforms for data collection, responses rates to in-app surveys may differ on the basis of important respondent characteristics. Studies should be carefully designed to mitigate fatigue as well as powered with the understanding of the respondent…
format: application/pdf
format: text/html
creator: Vikas N. O’Reilly-Shah
subject: Anesthesiology and Pain Management
subject: Global Health
subject: Human-Computer Interaction
subject: Statistics
description: doi:10.7717/peerj.3785
publisher: PeerJ Inc.
rights: © 2017 O’Reilly-Shah
abstract: Background Respondent fatigue, also known as survey fatigue, is a common problem in the collection of survey data. Factors that are known to influence respondent fatigue include survey length, survey topic, question complexity, and open-ended question type. There is a great deal of interest in understanding the drivers of physician survey responsiveness due to the value of information received from these practitioners. With the recent explosion of mobile smartphone technology, it has been possible to obtain survey data from users of mobile applications (apps) on a question-by-question basis. The author obtained basic demographic survey data as well as survey data related to an anesthesiology-specific drug called sugammadex and leveraged nonresponse rates to examine factors that influenced respondent fatigue. Methods Primary data were collected between December 2015 and February 2017. Surveys and in-app analytics were collected from global users of a mobile anesthesia calculator app. Key independent variables were user country, healthcare provider role, rating of importance of the app to personal practice, length of time in practice, and frequency of app use. Key dependent variable was the metric of respondent fatigue. Results Provider role and World Bank country income level were predictive of the rate of respondent fatigue for this in-app survey. Importance of the app to the provider and length of time in practice were moderately associated with fatigue. Frequency of app use was not associated. This study focused on a survey with a topic closely related to the subject area of the app. Respondent fatigue rates will likely change dramatically if the topic does not align closely. Discussion Although apps may serve as powerful platforms for data collection, responses rates to in-app surveys may differ on the basis of important respondent characteristics. Studies should be carefully designed to mitigate fatigue as well as powered with the understanding of the respondent…
bibliographic citation: O’Reilly-Shah (2017) Factors influencing healthcare provider respondent fatigue answering a globally administered in-app survey. PeerJ 5:e3785 https://doi.org/10.7717/peerj.3785
date submitted: 2017-04-19
date accepted: 2017-08-18
issued: 2017-09-12
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: O’Reilly-Shah
  given name: Vikas N.
doi: 10.7717/peerj.3785
volume: 5
issn: 2167-8359
publication name: PeerJ
publication date: 2017-09-12
copyright: ©2017 O’Reilly-Shah
attribution name: O’Reilly-Shah

Identification and analysis of CYP450 genes from transcriptome of Lonicera japonica and expression analysis of chlorogenic acid biosynthesis related CYP450s
type: item
type: AcademicArticle
description: Background Lonicera japonica is an important medicinal plant that has been widely used in traditional Chinese medicine for thousands of years. The pharmacological activities of L. japonica are mainly due to its rich natural active ingredients, most of which are secondary metabolites. CYP450s are a large, complex, and widespread superfamily of proteins that participate in many endogenous and exogenous metabolic reactions, especially secondary metabolism. Here, we identified CYP450s in L. japonica transcriptome and analyzed CYP450s that may be involved in chlorogenic acid (CGA) biosynthesis. Methods The recent availability of L. japonica transcriptome provided opportunity to identify CYP450s in this herb. BLAST based method and HMM based method were used to identify CYP450s in L. japonica transcriptome. Then, phylogenetic analysis, conserved motifs analysis, GO annotation, and KEGG annotation analyses were conducted to characterize the identified CYP450s. qRT-PCR was used to explore expression patterns of five CGA biosynthesis related CYP450s. Results In this study, 151 putative CYP450s with complete cytochrome P450 domain, which belonged to 10 clans, 45 families and 76 subfamilies, were identified in L. japonica transcriptome. Phylogenetic analysis classified these CYP450s into two major branches, A-type (47%) and non-A type (53%). Both types of CYP450s had conserved motifs in L. japonica. The differences of typical motif sequences between A-type and non-A type CYP450s in L. japonica were similar with other plants. GO classification indicated that non-A type CYP450s participated in more molecular functions and biological processes than A-type. KEGG pathway annotation totally assigned 47 CYP450s to 25 KEGG pathways. From these data, we cloned two LjC3Hs (CYP98A subfamily) and three LjC4Hs (CYP73A subfamily) that may be involved in biosynthesis of CGA, the major ingredient for pharmacological activities of L. japonica. qRT-PCR results indicated that two LjC3Hs exhibite…
format: application/pdf
format: text/html
creator: Xiwu Qi
creator: Xu Yu
creator: Daohua Xu
creator: Hailing Fang
creator: Ke Dong
creator: Weilin Li
creator: Chengyuan Liang
subject: Molecular Biology
subject: Plant Science
description: doi:10.7717/peerj.3781
publisher: PeerJ Inc.
rights: © 2017 Qi et al.
abstract: Background Lonicera japonica is an important medicinal plant that has been widely used in traditional Chinese medicine for thousands of years. The pharmacological activities of L. japonica are mainly due to its rich natural active ingredients, most of which are secondary metabolites. CYP450s are a large, complex, and widespread superfamily of proteins that participate in many endogenous and exogenous metabolic reactions, especially secondary metabolism. Here, we identified CYP450s in L. japonica transcriptome and analyzed CYP450s that may be involved in chlorogenic acid (CGA) biosynthesis. Methods The recent availability of L. japonica transcriptome provided opportunity to identify CYP450s in this herb. BLAST based method and HMM based method were used to identify CYP450s in L. japonica transcriptome. Then, phylogenetic analysis, conserved motifs analysis, GO annotation, and KEGG annotation analyses were conducted to characterize the identified CYP450s. qRT-PCR was used to explore expression patterns of five CGA biosynthesis related CYP450s. Results In this study, 151 putative CYP450s with complete cytochrome P450 domain, which belonged to 10 clans, 45 families and 76 subfamilies, were identified in L. japonica transcriptome. Phylogenetic analysis classified these CYP450s into two major branches, A-type (47%) and non-A type (53%). Both types of CYP450s had conserved motifs in L. japonica. The differences of typical motif sequences between A-type and non-A type CYP450s in L. japonica were similar with other plants. GO classification indicated that non-A type CYP450s participated in more molecular functions and biological processes than A-type. KEGG pathway annotation totally assigned 47 CYP450s to 25 KEGG pathways. From these data, we cloned two LjC3Hs (CYP98A subfamily) and three LjC4Hs (CYP73A subfamily) that may be involved in biosynthesis of CGA, the major ingredient for pharmacological activities of L. japonica. qRT-PCR results indicated that two LjC3Hs exhibite…
bibliographic citation: Qi et al. (2017) Identification and analysis of CYP450 genes from transcriptome of Lonicera japonica and expression analysis of chlorogenic acid biosynthesis related CYP450s. PeerJ 5:e3781 https://doi.org/10.7717/peerj.3781
date submitted: 2017-04-21
date accepted: 2017-08-17
issued: 2017-09-12
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Qi
  given name: Xiwu
author list: Agent
  family name: Yu
  given name: Xu
author list: Agent
  family name: Xu
  given name: Daohua
author list: Agent
  family name: Fang
  given name: Hailing
author list: Agent
  family name: Dong
  given name: Ke
author list: Agent
  family name: Li
  given name: Weilin
author list: Agent
  family name: Liang
  given name: Chengyuan
doi: 10.7717/peerj.3781
volume: 5
issn: 2167-8359
publication name: PeerJ
publication date: 2017-09-12
copyright: ©2017 Qi et al.
attribution name: Qi et al.

Comparison of polybrominated diphenyl ethers (PBDEs) and polychlorinated biphenyls (PCBs) in the serum of hypothyroxinemic and euthyroid dogs
type: item
type: AcademicArticle
description: Objective To determine the profile of 14 polybrominated diphenyl ethers (PBDEs) and 23 polychlorinated biphenyls (PCBs) in serum of domestic canines and whether this was predictive of thyroid hormone status. Samples Serum samples were collected from 51 client-owned dogs visiting the University of California Davis William R. Pritchard Veterinary Medical Teaching Hospital during 2012 to 2016 for routine appointments. Fifteen dogs were diagnosed with hypothyroxinemia while 36 were euthyroid. Procedures Concentrations of PBDEs and PCBs in canine serum samples were measured by gas chromatography mass spectrometry. Logistic regression analysis was used to determine the association between the presence/absence of canine hypothyroxinemia and the serum concentration of individual PBDE or PCB congeners. Results The median concentrations of total PBDE and PCB congeners in the hypothyroxinemic group were 660 and 1,371 ng/g lipid, respectively, which were higher than concentrations detected in the control group. However, logistic regression analysis determined that current concentrations of PBDEs and PCBs in canines were not significantly associated with hypothyroxinemia. BDE 183 was the only congener showing near significance (p = 0.068). Conclusions PBDE and PCB congeners were detected in all canine samples confirming ongoing exposure to these pollutants. Because household dogs share the human environment, they may serve as biosentinels of human exposure to these contaminants.
format: application/pdf
format: text/html
creator: Grace Lau
creator: Kyla Walter
creator: Philip Kass
creator: Birgit Puschner
subject: Ecotoxicology
subject: Environmental Contamination and Remediation
subject: Environmental Sciences
subject: Toxicology
subject: Veterinary Medicine
description: doi:10.7717/peerj.3780
publisher: PeerJ Inc.
rights: © 2017 Lau et al.
abstract: Objective To determine the profile of 14 polybrominated diphenyl ethers (PBDEs) and 23 polychlorinated biphenyls (PCBs) in serum of domestic canines and whether this was predictive of thyroid hormone status. Samples Serum samples were collected from 51 client-owned dogs visiting the University of California Davis William R. Pritchard Veterinary Medical Teaching Hospital during 2012 to 2016 for routine appointments. Fifteen dogs were diagnosed with hypothyroxinemia while 36 were euthyroid. Procedures Concentrations of PBDEs and PCBs in canine serum samples were measured by gas chromatography mass spectrometry. Logistic regression analysis was used to determine the association between the presence/absence of canine hypothyroxinemia and the serum concentration of individual PBDE or PCB congeners. Results The median concentrations of total PBDE and PCB congeners in the hypothyroxinemic group were 660 and 1,371 ng/g lipid, respectively, which were higher than concentrations detected in the control group. However, logistic regression analysis determined that current concentrations of PBDEs and PCBs in canines were not significantly associated with hypothyroxinemia. BDE 183 was the only congener showing near significance (p = 0.068). Conclusions PBDE and PCB congeners were detected in all canine samples confirming ongoing exposure to these pollutants. Because household dogs share the human environment, they may serve as biosentinels of human exposure to these contaminants.
bibliographic citation: Lau et al. (2017) Comparison of polybrominated diphenyl ethers (PBDEs) and polychlorinated biphenyls (PCBs) in the serum of hypothyroxinemic and euthyroid dogs. PeerJ 5:e3780 https://doi.org/10.7717/peerj.3780
date submitted: 2017-02-23
date accepted: 2017-08-17
issued: 2017-09-12
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Lau
  given name: Grace
author list: Agent
  family name: Walter
  given name: Kyla
author list: Agent
  family name: Kass
  given name: Philip
author list: Agent
  family name: Puschner
  given name: Birgit
doi: 10.7717/peerj.3780
volume: 5
issn: 2167-8359
publication name: PeerJ
publication date: 2017-09-12
copyright: ©2017 Lau et al.
attribution name: Lau et al.

The landscape of fear conceptual framework: definition and review of current applications and misuses
type: item
type: AcademicArticle
description: Landscapes of Fear (LOF), the spatially explicit distribution of perceived predation risk as seen by a population, is increasingly cited in ecological literature and has become a frequently used “buzz-word”. With the increase in popularity, it became necessary to clarify the definition for the term, suggest boundaries and propose a common framework for its use. The LOF, as a progeny of the “ecology of fear” conceptual framework, defines fear as the strategic manifestation of the cost-benefit analysis of food and safety tradeoffs. In addition to direct predation risk, the LOF is affected by individuals’ energetic-state, inter- and intra-specific competition and is constrained by the evolutionary history of each species. Herein, based on current applications of the LOF conceptual framework, I suggest the future research in this framework will be directed towards: (1) finding applied management uses as a trait defining a population’s habitat-use and habitat-suitability; (2) studying multi-dimensional distribution of risk-assessment through time and space; (3) studying variability between individuals within a population; (4) measuring eco-neurological implications of risk as a feature of environmental heterogeneity and (5) expanding temporal and spatial scales of empirical studies.
format: application/pdf
format: text/html
creator: Sonny S. Bleicher
subject: Animal Behavior
subject: Biodiversity
subject: Conservation Biology
subject: Ecology
subject: Zoology
description: doi:10.7717/peerj.3772
publisher: PeerJ Inc.
rights: © 2017 Bleicher
abstract: Landscapes of Fear (LOF), the spatially explicit distribution of perceived predation risk as seen by a population, is increasingly cited in ecological literature and has become a frequently used “buzz-word”. With the increase in popularity, it became necessary to clarify the definition for the term, suggest boundaries and propose a common framework for its use. The LOF, as a progeny of the “ecology of fear” conceptual framework, defines fear as the strategic manifestation of the cost-benefit analysis of food and safety tradeoffs. In addition to direct predation risk, the LOF is affected by individuals’ energetic-state, inter- and intra-specific competition and is constrained by the evolutionary history of each species. Herein, based on current applications of the LOF conceptual framework, I suggest the future research in this framework will be directed towards: (1) finding applied management uses as a trait defining a population’s habitat-use and habitat-suitability; (2) studying multi-dimensional distribution of risk-assessment through time and space; (3) studying variability between individuals within a population; (4) measuring eco-neurological implications of risk as a feature of environmental heterogeneity and (5) expanding temporal and spatial scales of empirical studies.
bibliographic citation: Bleicher (2017) The landscape of fear conceptual framework: definition and review of current applications and misuses. PeerJ 5:e3772 https://doi.org/10.7717/peerj.3772
date submitted: 2017-02-27
date accepted: 2017-08-16
issued: 2017-09-12
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Bleicher
  given name: Sonny S.
doi: 10.7717/peerj.3772
volume: 5
issn: 2167-8359
publication name: PeerJ
publication date: 2017-09-12
copyright: ©2017 Bleicher
attribution name: Bleicher

Habitat suitability—density relationship in an endangered woodland species: the case of the Blue Chaffinch (Fringilla polatzeki)
type: item
type: AcademicArticle
description: Background Understanding constraints to the distribution of threatened species may help to ascertain whether there are other suitable sectors for reducing the risks associated with species that are recorded in only one protected locality, and to inform about the suitability of other areas for reintroduction or translocation programs. Methods We studied the Gran Canaria blue chaffinch (Fringilla polatzeki), a habitat specialist endemic of the Canary Islands restricted to the pine forest of Inagua, the only area where the species has been naturally present as a regular breeder in the last 25 years. A suitability distribution model using occurrences with demographic relevance (i.e., nest locations of successful breeding attempts analysed using boosted classification trees) was built considering orographic, climatic and habitat structure predictors. By means of a standardized survey program we monitored the yearly abundance of the species in 100 sectors since the declaration of Inagua as a Strict Nature Reserve in 1994. Results The variables with the highest relative importance in blue chaffinch habitat preferences were pine height, tree cover, altitude, and rainfall during the driest trimester (July–September). The observed local abundance of the blue chaffinch in Inagua (survey data) was significantly correlated with habitat suitability derived from modelling the location of successful nesting attempts (using linear and quantile regressions). The outcomes of the habitat suitability model were used to quantify the suitability of other natural, historic, pine forests of Gran Canaria. Tamadaba is the forest with most suitable woodland patches for the species. We estimated a population size of 195–430 blue chaffinches in Inagua since 2011 (95% CI), the smallest population size of a woodland passerine in the Western Palearctic. Discussion Habitat suitability obtained from modelling the location of successful breeding attempts is a good surrogate of the observed local abund…
format: application/pdf
format: text/html
creator: Luis M. Carrascal
creator: Ángel C. Moreno
creator: Alejandro Delgado
creator: Víctor Suárez
creator: Domingo Trujillo
subject: Biogeography
subject: Conservation Biology
subject: Ecology
subject: Zoology
description: doi:10.7717/peerj.3771
publisher: PeerJ Inc.
rights: © 2017 Carrascal et al.
abstract: Background Understanding constraints to the distribution of threatened species may help to ascertain whether there are other suitable sectors for reducing the risks associated with species that are recorded in only one protected locality, and to inform about the suitability of other areas for reintroduction or translocation programs. Methods We studied the Gran Canaria blue chaffinch (Fringilla polatzeki), a habitat specialist endemic of the Canary Islands restricted to the pine forest of Inagua, the only area where the species has been naturally present as a regular breeder in the last 25 years. A suitability distribution model using occurrences with demographic relevance (i.e., nest locations of successful breeding attempts analysed using boosted classification trees) was built considering orographic, climatic and habitat structure predictors. By means of a standardized survey program we monitored the yearly abundance of the species in 100 sectors since the declaration of Inagua as a Strict Nature Reserve in 1994. Results The variables with the highest relative importance in blue chaffinch habitat preferences were pine height, tree cover, altitude, and rainfall during the driest trimester (July–September). The observed local abundance of the blue chaffinch in Inagua (survey data) was significantly correlated with habitat suitability derived from modelling the location of successful nesting attempts (using linear and quantile regressions). The outcomes of the habitat suitability model were used to quantify the suitability of other natural, historic, pine forests of Gran Canaria. Tamadaba is the forest with most suitable woodland patches for the species. We estimated a population size of 195–430 blue chaffinches in Inagua since 2011 (95% CI), the smallest population size of a woodland passerine in the Western Palearctic. Discussion Habitat suitability obtained from modelling the location of successful breeding attempts is a good surrogate of the observed local abund…
bibliographic citation: Carrascal et al. (2017) Habitat suitability—density relationship in an endangered woodland species: the case of the Blue Chaffinch (Fringilla polatzeki). PeerJ 5:e3771 https://doi.org/10.7717/peerj.3771
date submitted: 2017-04-21
date accepted: 2017-08-16
issued: 2017-09-12
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Carrascal
  given name: Luis M.
author list: Agent
  family name: Moreno
  given name: Ángel C.
author list: Agent
  family name: Delgado
  given name: Alejandro
author list: Agent
  family name: Suárez
  given name: Víctor
author list: Agent
  family name: Trujillo
  given name: Domingo
doi: 10.7717/peerj.3771
volume: 5
issn: 2167-8359
publication name: PeerJ
publication date: 2017-09-12
copyright: ©2017 Carrascal et al.
attribution name: Carrascal et al.

Challenging a bioinformatic tool’s ability to detect microbial contaminants using in silico whole genome sequencing data
type: item
type: AcademicArticle
description: High sensitivity methods such as next generation sequencing and polymerase chain reaction (PCR) are adversely impacted by organismal and DNA contaminants. Current methods for detecting contaminants in microbial materials (genomic DNA and cultures) are not sensitive enough and require either a known or culturable contaminant. Whole genome sequencing (WGS) is a promising approach for detecting contaminants due to its sensitivity and lack of need for a priori assumptions about the contaminant. Prior to applying WGS, we must first understand its limitations for detecting contaminants and potential for false positives. Herein we demonstrate and characterize a WGS-based approach to detect organismal contaminants using an existing metagenomic taxonomic classification algorithm. Simulated WGS datasets from ten genera as individuals and binary mixtures of eight organisms at varying ratios were analyzed to evaluate the role of contaminant concentration and taxonomy on detection. For the individual genomes the false positive contaminants reported depended on the genus, with Staphylococcus, Escherichia, and Shigella having the highest proportion of false positives. For nearly all binary mixtures the contaminant was detected in the in-silico datasets at the equivalent of 1 in 1,000 cells, though F. tularensis was not detected in any of the simulated contaminant mixtures and Y. pestis was only detected at the equivalent of one in 10 cells. Once a WGS method for detecting contaminants is characterized, it can be applied to evaluate microbial material purity, in efforts to ensure that contaminants are characterized in microbial materials used to validate pathogen detection assays, generate genome assemblies for database submission, and benchmark sequencing methods.
format: application/pdf
format: text/html
creator: Nathan D. Olson
creator: Justin M. Zook
creator: Jayne B. Morrow
creator: Nancy J. Lin
subject: Bioinformatics
subject: Genomics
subject: Microbiology
description: doi:10.7717/peerj.3729
publisher: PeerJ Inc.
rights: © 2017
abstract: High sensitivity methods such as next generation sequencing and polymerase chain reaction (PCR) are adversely impacted by organismal and DNA contaminants. Current methods for detecting contaminants in microbial materials (genomic DNA and cultures) are not sensitive enough and require either a known or culturable contaminant. Whole genome sequencing (WGS) is a promising approach for detecting contaminants due to its sensitivity and lack of need for a priori assumptions about the contaminant. Prior to applying WGS, we must first understand its limitations for detecting contaminants and potential for false positives. Herein we demonstrate and characterize a WGS-based approach to detect organismal contaminants using an existing metagenomic taxonomic classification algorithm. Simulated WGS datasets from ten genera as individuals and binary mixtures of eight organisms at varying ratios were analyzed to evaluate the role of contaminant concentration and taxonomy on detection. For the individual genomes the false positive contaminants reported depended on the genus, with Staphylococcus, Escherichia, and Shigella having the highest proportion of false positives. For nearly all binary mixtures the contaminant was detected in the in-silico datasets at the equivalent of 1 in 1,000 cells, though F. tularensis was not detected in any of the simulated contaminant mixtures and Y. pestis was only detected at the equivalent of one in 10 cells. Once a WGS method for detecting contaminants is characterized, it can be applied to evaluate microbial material purity, in efforts to ensure that contaminants are characterized in microbial materials used to validate pathogen detection assays, generate genome assemblies for database submission, and benchmark sequencing methods.
bibliographic citation: Olson et al. (2017) Challenging a bioinformatic tool’s ability to detect microbial contaminants using in silico whole genome sequencing data. PeerJ 5:e3729 https://doi.org/10.7717/peerj.3729
date submitted: 2017-04-03
date accepted: 2017-08-02
issued: 2017-09-12
is part of: PeerJ
license: http://creativecommons.org/publicdomain/zero/1.0/
author list: Agent
  family name: Olson
  given name: Nathan D.
author list: Agent
  family name: Zook
  given name: Justin M.
author list: Agent
  family name: Morrow
  given name: Jayne B.
author list: Agent
  family name: Lin
  given name: Nancy J.
doi: 10.7717/peerj.3729
volume: 5
issn: 2167-8359
publication name: PeerJ
publication date: 2017-09-12

Adaptations to different habitats in sexual and asexual populations of parasitoid wasps: a meta-analysis
type: item
type: AcademicArticle
description: Background Coexistence of sexual and asexual populations remains a key question in evolutionary ecology. We address the question how an asexual and a sexual form of the parasitoid Venturia canescens can coexist in southern Europe. We test the hypothesis that both forms are adapted to different habitats within their area of distribution. Sexuals inhabit natural environments that are highly unpredictable, and where density of wasps and their hosts is low and patchily distributed. Asexuals instead are common in anthropic environments (e.g., grain stores) where host outbreaks offer periods when egg-load is the main constraint on reproductive output. Methods We present a meta-analysis of known adaptations to these habitats. Differences in behavior, physiology and life-history traits between sexual and asexual wasps were standardized in term of effect size (Cohen’s d value; Cohen, 1988). Results Seeking consilience from the differences between multiple traits, we found that sexuals invest more in longevity at the expense of egg-load, are more mobile, and display higher plasticity in response to thermal variability than asexual counterparts. Discussion Thus, each form has consistent multiple adaptations to the ecological circumstances in the contrasting environments.
format: application/pdf
format: text/html
creator: Isabelle Amat
creator: Jacques J.M. van Alphen
creator: Alex Kacelnik
creator: Emmanuel Desouhant
creator: Carlos Bernstein
subject: Animal Behavior
subject: Ecology
subject: Entomology
subject: Evolutionary Studies
description: doi:10.7717/peerj.3699
publisher: PeerJ Inc.
rights: © 2017 Amat et al.
abstract: Background Coexistence of sexual and asexual populations remains a key question in evolutionary ecology. We address the question how an asexual and a sexual form of the parasitoid Venturia canescens can coexist in southern Europe. We test the hypothesis that both forms are adapted to different habitats within their area of distribution. Sexuals inhabit natural environments that are highly unpredictable, and where density of wasps and their hosts is low and patchily distributed. Asexuals instead are common in anthropic environments (e.g., grain stores) where host outbreaks offer periods when egg-load is the main constraint on reproductive output. Methods We present a meta-analysis of known adaptations to these habitats. Differences in behavior, physiology and life-history traits between sexual and asexual wasps were standardized in term of effect size (Cohen’s d value; Cohen, 1988). Results Seeking consilience from the differences between multiple traits, we found that sexuals invest more in longevity at the expense of egg-load, are more mobile, and display higher plasticity in response to thermal variability than asexual counterparts. Discussion Thus, each form has consistent multiple adaptations to the ecological circumstances in the contrasting environments.
bibliographic citation: Amat et al. (2017) Adaptations to different habitats in sexual and asexual populations of parasitoid wasps: a meta-analysis. PeerJ 5:e3699 https://doi.org/10.7717/peerj.3699
date submitted: 2017-04-26
date accepted: 2017-07-26
issued: 2017-09-12
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Amat
  given name: Isabelle
author list: Agent
  family name: van Alphen
  given name: Jacques J.M.
author list: Agent
  family name: Kacelnik
  given name: Alex
author list: Agent
  family name: Desouhant
  given name: Emmanuel
author list: Agent
  family name: Bernstein
  given name: Carlos
doi: 10.7717/peerj.3699
volume: 5
issn: 2167-8359
publication name: PeerJ
publication date: 2017-09-12
copyright: ©2017 Amat et al.
attribution name: Amat et al.

The evolutionary history of plant T2/S-type ribonucleases
type: item
type: AcademicArticle
description: A growing number of T2/S-RNases are being discovered in plant genomes. Members of this protein family have a variety of known functions, but the vast majority are still uncharacterized. We present data and analyses of phylogenetic relationships among T2/S-RNases, and pay special attention to the group that contains the female component of the most widespread system of self-incompatibility in flowering plants. The returned emphasis on the initially identified component of this mechanism yields important conjectures about its evolutionary context. First, we find that the clade involved in self-rejection (class III) is found exclusively in core eudicots, while the remaining clades contain members from other vascular plants. Second, certain features, such as intron patterns, isoelectric point, and conserved amino acid regions, help differentiate S-RNases, which are necessary for expression of self-incompatibility, from other T2/S-RNase family members. Third, we devise and present a set of approaches to clarify new S-RNase candidates from existing genome assemblies. We use genomic features to identify putative functional and relictual S-loci in genomes of plants with unknown mechanisms of self-incompatibility. The widespread occurrence of possible relicts suggests that the loss of functional self-incompatibility may leave traces long after the fact, and that this manner of molecular fossil-like data could be an important source of information about the history and distribution of both RNase-based and other mechanisms of self-incompatibility. Finally, we release a public resource intended to aid the search for S-locus RNases, and help provide increasingly detailed information about their taxonomic distribution.
format: application/pdf
format: text/html
creator: Karolis Ramanauskas
creator: Boris Igić
subject: Evolutionary Studies
subject: Genetics
subject: Genomics
subject: Molecular Biology
subject: Plant Science
description: doi:10.7717/peerj.3790
publisher: PeerJ Inc.
rights: © 2017 Ramanauskas and Igić
abstract: A growing number of T2/S-RNases are being discovered in plant genomes. Members of this protein family have a variety of known functions, but the vast majority are still uncharacterized. We present data and analyses of phylogenetic relationships among T2/S-RNases, and pay special attention to the group that contains the female component of the most widespread system of self-incompatibility in flowering plants. The returned emphasis on the initially identified component of this mechanism yields important conjectures about its evolutionary context. First, we find that the clade involved in self-rejection (class III) is found exclusively in core eudicots, while the remaining clades contain members from other vascular plants. Second, certain features, such as intron patterns, isoelectric point, and conserved amino acid regions, help differentiate S-RNases, which are necessary for expression of self-incompatibility, from other T2/S-RNase family members. Third, we devise and present a set of approaches to clarify new S-RNase candidates from existing genome assemblies. We use genomic features to identify putative functional and relictual S-loci in genomes of plants with unknown mechanisms of self-incompatibility. The widespread occurrence of possible relicts suggests that the loss of functional self-incompatibility may leave traces long after the fact, and that this manner of molecular fossil-like data could be an important source of information about the history and distribution of both RNase-based and other mechanisms of self-incompatibility. Finally, we release a public resource intended to aid the search for S-locus RNases, and help provide increasingly detailed information about their taxonomic distribution.
bibliographic citation: Ramanauskas et al. (2017) The evolutionary history of plant T2/S-type ribonucleases. PeerJ 5:e3790 https://doi.org/10.7717/peerj.3790
date submitted: 2017-05-22
date accepted: 2017-08-18
issued: 2017-09-11
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Ramanauskas
  given name: Karolis
author list: Agent
  family name: Igić
  given name: Boris
doi: 10.7717/peerj.3790
volume: 5
issn: 2167-8359
publication name: PeerJ
publication date: 2017-09-11
copyright: ©2017 Ramanauskas and Igić
attribution name: Ramanauskas and Igić

Biochemical and structural characterization of a novel arginine kinase from the spider Polybetes pythagoricus
type: item
type: AcademicArticle
description: Energy buffering systems are key for homeostasis during variations in energy supply. Spiders are the most important predators for insects and therefore key in terrestrial ecosystems. From biomedical interest, spiders are important for their venoms and as a source of potent allergens, such as arginine kinase (AK, EC 2.7.3.3). AK is an enzyme crucial for energy metabolism, keeping the pool of phosphagens in invertebrates, and also an allergen for humans. In this work, we studied AK from the Argentininan spider Polybetes pythagoricus (PpAK), from its complementary DNA to the crystal structure. The PpAK cDNA from muscle was cloned, and it is comprised of 1068 nucleotides that encode a 384-amino acids protein, similar to other invertebrate AKs. The apparent Michaelis-Menten kinetic constant (Km) was 1.7 mM with a kcat of 75 s−1. Two crystal structures are presented, the apoPvAK and PpAK bound to arginine, both in the open conformation with the active site lid (residues 310–320) completely disordered. The guanidino group binding site in the apo structure appears to be organized to accept the arginine substrate. Finally, these results contribute to knowledge of mechanistic details of the function of arginine kinase.
format: application/pdf
format: text/html
creator: Aldana Laino
creator: Alonso A. Lopez-Zavala
creator: Karina D. Garcia-Orozco
creator: Jesus S. Carrasco-Miranda
creator: Marianela Santana
creator: Vivian Stojanoff
creator: Rogerio R. Sotelo-Mundo
creator: Carlos Fernando Garcia
subject: Biochemistry
subject: Biophysics
subject: Zoology
subject: Allergy and Clinical Immunology
description: doi:10.7717/peerj.3787
publisher: PeerJ Inc.
rights: © 2017 Laino et al.
abstract: Energy buffering systems are key for homeostasis during variations in energy supply. Spiders are the most important predators for insects and therefore key in terrestrial ecosystems. From biomedical interest, spiders are important for their venoms and as a source of potent allergens, such as arginine kinase (AK, EC 2.7.3.3). AK is an enzyme crucial for energy metabolism, keeping the pool of phosphagens in invertebrates, and also an allergen for humans. In this work, we studied AK from the Argentininan spider Polybetes pythagoricus (PpAK), from its complementary DNA to the crystal structure. The PpAK cDNA from muscle was cloned, and it is comprised of 1068 nucleotides that encode a 384-amino acids protein, similar to other invertebrate AKs. The apparent Michaelis-Menten kinetic constant (Km) was 1.7 mM with a kcat of 75 s−1. Two crystal structures are presented, the apoPvAK and PpAK bound to arginine, both in the open conformation with the active site lid (residues 310–320) completely disordered. The guanidino group binding site in the apo structure appears to be organized to accept the arginine substrate. Finally, these results contribute to knowledge of mechanistic details of the function of arginine kinase.
bibliographic citation: Laino et al. (2017) Biochemical and structural characterization of a novel arginine kinase from the spider Polybetes pythagoricus. PeerJ 5:e3787 https://doi.org/10.7717/peerj.3787
date submitted: 2017-04-29
date accepted: 2017-08-18
issued: 2017-09-11
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Laino
  given name: Aldana
author list: Agent
  family name: Lopez-Zavala
  given name: Alonso A.
author list: Agent
  family name: Garcia-Orozco
  given name: Karina D.
author list: Agent
  family name: Carrasco-Miranda
  given name: Jesus S.
author list: Agent
  family name: Santana
  given name: Marianela
author list: Agent
  family name: Stojanoff
  given name: Vivian
author list: Agent
  family name: Sotelo-Mundo
  given name: Rogerio R.
author list: Agent
  family name: Garcia
  given name: Carlos Fernando
doi: 10.7717/peerj.3787
volume: 5
issn: 2167-8359
publication name: PeerJ
publication date: 2017-09-11
copyright: ©2017 Laino et al.
attribution name: Laino et al.

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