PeerJ
type: channel
link: https://peerj.com/articles/
description: Articles published in PeerJ
publisher: PeerJ Inc.
publication name: PeerJ
issn: 2167-8359
items: Transcriptome analysis of Pseudomonas aeruginosa PAO1 grown at both body and elevated temperatures
items: Gall-ID: tools for genotyping gall-causing phytopathogenic bacteria
items: Genetic diversity of pomegranate germplasm collection from Spain determined by fruit, seed, leaf and flower characteristics
items: Enhanced functional connectivity properties of human brains during in-situ nature experience
items: fluff: exploratory analysis and visualization of high-throughput sequencing data
items: Advances in global sensitivity analyses of demographic-based species distribution models to address uncertainties in dynamic landscapes
items: Data mining in conservation research using Latin and vernacular species names
items: Effects of 16S rDNA sampling on estimates of the number of endosymbiont lineages in sucking lice
items: The diagnostic accuracy of acute phase proteins and proinflammatory cytokines in sheep with pneumonic pasteurellosis
items: Preferred temperature and thermal breadth of birds wintering in peninsular Spain: the limited effect of temperature on species distribution

Transcriptome analysis of Pseudomonas aeruginosa PAO1 grown at both body and elevated temperatures
type: item
type: AcademicArticle
description: Functional genomics research can give us valuable insights into bacterial gene function. RNA Sequencing (RNA-seq) can generate information on transcript abundance in bacteria following abiotic stress treatments. In this study, we used the RNA-seq technique to study the transcriptomes of the opportunistic nosocomial pathogen Pseudomonas aeruginosa PAO1 following heat shock. Samples were grown at both the human body temperature (37 °C) and an arbitrarily-selected temperature of 46 °C. In this work using RNA-seq, we identified 133 genes that are differentially expressed at 46 °C compared to the human body temperature. Our work identifies some key P. aeruginosa PAO1 genes whose products have importance in both environmental adaptation as well as in vivo infection in febrile hosts. More importantly, our transcriptomic results show that many genes are only expressed when subjected to heat shock. Because the RNA-seq can generate high throughput gene expression profiles, our work reveals many unanticipated genes with further work to be done exploring such genes products.
format: application/pdf
format: text/html
creator: Kok-Gan Chan
creator: Kumutha Priya
creator: Chien-Yi Chang
creator: Ahmad Yamin Abdul Rahman
creator: Kok Keng Tee
creator: Wai-Fong Yin
subject: Bioinformatics
subject: Genomics
subject: Microbiology
description: doi:10.7717/peerj.2223
publisher: PeerJ Inc.
rights: © 2016 Chan et al.
abstract: Functional genomics research can give us valuable insights into bacterial gene function. RNA Sequencing (RNA-seq) can generate information on transcript abundance in bacteria following abiotic stress treatments. In this study, we used the RNA-seq technique to study the transcriptomes of the opportunistic nosocomial pathogen Pseudomonas aeruginosa PAO1 following heat shock. Samples were grown at both the human body temperature (37 °C) and an arbitrarily-selected temperature of 46 °C. In this work using RNA-seq, we identified 133 genes that are differentially expressed at 46 °C compared to the human body temperature. Our work identifies some key P. aeruginosa PAO1 genes whose products have importance in both environmental adaptation as well as in vivo infection in febrile hosts. More importantly, our transcriptomic results show that many genes are only expressed when subjected to heat shock. Because the RNA-seq can generate high throughput gene expression profiles, our work reveals many unanticipated genes with further work to be done exploring such genes products.
bibliographic citation: Chan et al. (2016) Transcriptome analysis of Pseudomonas aeruginosa PAO1 grown at both body and elevated temperatures. PeerJ 4:e2223 https://doi.org/10.7717/peerj.2223
date submitted: 2016-01-19
date accepted: 2016-06-15
issued: 2016-07-19
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Chan
  given name: Kok-Gan
author list: Agent
  family name: Priya
  given name: Kumutha
author list: Agent
  family name: Chang
  given name: Chien-Yi
author list: Agent
  family name: Abdul Rahman
  given name: Ahmad Yamin
author list: Agent
  family name: Tee
  given name: Kok Keng
author list: Agent
  family name: Yin
  given name: Wai-Fong
doi: 10.7717/peerj.2223
volume: 4
issn: 2167-8359
publication name: PeerJ
publication date: 2016-07-19
copyright: © 2016 Chan et al.
attribution name: Chan et al.

Gall-ID: tools for genotyping gall-causing phytopathogenic bacteria
type: item
type: AcademicArticle
description: Understanding the population structure and genetic diversity of plant pathogens, as well as the effect of agricultural practices on pathogen evolution, is important for disease management. Developments in molecular methods have contributed to increase the resolution for accurate pathogen identification, but those based on analysis of DNA sequences can be less straightforward to use. To address this, we developed Gall-ID, a web-based platform that uses DNA sequence information from 16S rDNA, multilocus sequence analysis and whole genome sequences to group disease-associated bacteria to their taxonomic units. Gall-ID was developed with a particular focus on gall-forming bacteria belonging to Agrobacterium, Pseudomonas savastanoi, Pantoea agglomerans, and Rhodococcus. Members of these groups of bacteria cause growth deformation of plants, and some are capable of infecting many species of field, orchard, and nursery crops. Gall-ID also enables the use of high-throughput sequencing reads to search for evidence for homologs of characterized virulence genes, and provides downloadable software pipelines for automating multilocus sequence analysis, analyzing genome sequences for average nucleotide identity, and constructing core genome phylogenies. Lastly, additional databases were included in Gall-ID to help determine the identity of other plant pathogenic bacteria that may be in microbial communities associated with galls or causative agents in other diseased tissues of plants. The URL for Gall-ID is http://gall-id.cgrb.oregonstate.edu/.
format: application/pdf
format: text/html
creator: Edward W. Davis II
creator: Alexandra J. Weisberg
creator: Javier F. Tabima
creator: Niklaus J. Grunwald
creator: Jeff H. Chang
subject: Agricultural Science
subject: Bioinformatics
subject: Genomics
subject: Microbiology
subject: Taxonomy
description: doi:10.7717/peerj.2222
publisher: PeerJ Inc.
rights: © 2016 Davis II et al.
abstract: Understanding the population structure and genetic diversity of plant pathogens, as well as the effect of agricultural practices on pathogen evolution, is important for disease management. Developments in molecular methods have contributed to increase the resolution for accurate pathogen identification, but those based on analysis of DNA sequences can be less straightforward to use. To address this, we developed Gall-ID, a web-based platform that uses DNA sequence information from 16S rDNA, multilocus sequence analysis and whole genome sequences to group disease-associated bacteria to their taxonomic units. Gall-ID was developed with a particular focus on gall-forming bacteria belonging to Agrobacterium, Pseudomonas savastanoi, Pantoea agglomerans, and Rhodococcus. Members of these groups of bacteria cause growth deformation of plants, and some are capable of infecting many species of field, orchard, and nursery crops. Gall-ID also enables the use of high-throughput sequencing reads to search for evidence for homologs of characterized virulence genes, and provides downloadable software pipelines for automating multilocus sequence analysis, analyzing genome sequences for average nucleotide identity, and constructing core genome phylogenies. Lastly, additional databases were included in Gall-ID to help determine the identity of other plant pathogenic bacteria that may be in microbial communities associated with galls or causative agents in other diseased tissues of plants. The URL for Gall-ID is http://gall-id.cgrb.oregonstate.edu/.
bibliographic citation: Davis II et al. (2016) Gall-ID: tools for genotyping gall-causing phytopathogenic bacteria. PeerJ 4:e2222 https://doi.org/10.7717/peerj.2222
date submitted: 2016-04-29
date accepted: 2016-06-15
issued: 2016-07-19
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Davis II
  given name: Edward W.
author list: Agent
  family name: Weisberg
  given name: Alexandra J.
author list: Agent
  family name: Tabima
  given name: Javier F.
author list: Agent
  family name: Grunwald
  given name: Niklaus J.
author list: Agent
  family name: Chang
  given name: Jeff H.
doi: 10.7717/peerj.2222
volume: 4
issn: 2167-8359
publication name: PeerJ
publication date: 2016-07-19
copyright: ©2016 Davis II et al.
attribution name: Davis II et al.

Genetic diversity of pomegranate germplasm collection from Spain determined by fruit, seed, leaf and flower characteristics
type: item
type: AcademicArticle
description: Background. Miguel Hernandez University (Spain) created a germplasm bank of the varieties of pomegranate from different Southeastern Spain localities in order to preserve the crop’s wide genetic diversity. Once this collection was established, the next step was to characterize the phenotype of these varieties to determine the phenotypic variability that existed among all the different pomegranate genotypes, and to understand the degree of polymorphism of the morphometric characteristics among varieties. Methods. Fifty-three pomegranate (Punica granatum L.) accessions were studied in order to determine their degree of polymorphism and to detect similarities in their genotypes. Thirty-one morphometric characteristics were measured in fruits, arils, seeds, leaves and flowers, as well as juice characteristics including content, pH, titratable acidity, total soluble solids and maturity index. ANOVA, principal component analysis, and cluster analysis showed that there was a considerable phenotypic diversity (and presumably genetic). Results. The cluster analysis produced a dendrogram with four main clusters. The dissimilarity level ranged from 1 to 25, indicating that there were varieties that were either very similar or very different from each other, with varieties from the same geographical areas being more closely related. Within each varietal group, different degrees of similarity were found, although there were no accessions that were identical. These results highlight the crop’s great genetic diversity, which can be explained not only by their different geographical origins, but also to the fact that these are native plants that have not come from genetic improvement programs. The geographic origin could be, in the cases where no exchanges of plant material took place, a key criterion for cultivar clustering. Conclusions. As a result of the present study, we can conclude that among all the parameters analyzed, those related to fruit and seed size as well as the jui…
format: application/pdf
format: text/html
creator: Juan J. Martinez-Nicolas
creator: Pablo Melgarejo
creator: Pilar Legua
creator: Francisco Garcia-Sanchez
creator: Francisca Hernández
subject: Agricultural Science
subject: Biodiversity
subject: Plant Science
description: doi:10.7717/peerj.2214
publisher: PeerJ Inc.
rights: © 2016 Martinez-Nicolas et al.
abstract: Background. Miguel Hernandez University (Spain) created a germplasm bank of the varieties of pomegranate from different Southeastern Spain localities in order to preserve the crop’s wide genetic diversity. Once this collection was established, the next step was to characterize the phenotype of these varieties to determine the phenotypic variability that existed among all the different pomegranate genotypes, and to understand the degree of polymorphism of the morphometric characteristics among varieties. Methods. Fifty-three pomegranate (Punica granatum L.) accessions were studied in order to determine their degree of polymorphism and to detect similarities in their genotypes. Thirty-one morphometric characteristics were measured in fruits, arils, seeds, leaves and flowers, as well as juice characteristics including content, pH, titratable acidity, total soluble solids and maturity index. ANOVA, principal component analysis, and cluster analysis showed that there was a considerable phenotypic diversity (and presumably genetic). Results. The cluster analysis produced a dendrogram with four main clusters. The dissimilarity level ranged from 1 to 25, indicating that there were varieties that were either very similar or very different from each other, with varieties from the same geographical areas being more closely related. Within each varietal group, different degrees of similarity were found, although there were no accessions that were identical. These results highlight the crop’s great genetic diversity, which can be explained not only by their different geographical origins, but also to the fact that these are native plants that have not come from genetic improvement programs. The geographic origin could be, in the cases where no exchanges of plant material took place, a key criterion for cultivar clustering. Conclusions. As a result of the present study, we can conclude that among all the parameters analyzed, those related to fruit and seed size as well as the jui…
bibliographic citation: Martinez-Nicolas et al. (2016) Genetic diversity of pomegranate germplasm collection from Spain determined by fruit, seed, leaf and flower characteristics. PeerJ 4:e2214 https://doi.org/10.7717/peerj.2214
date submitted: 2016-02-20
date accepted: 2016-06-14
issued: 2016-07-19
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Martinez-Nicolas
  given name: Juan J.
author list: Agent
  family name: Melgarejo
  given name: Pablo
author list: Agent
  family name: Legua
  given name: Pilar
author list: Agent
  family name: Garcia-Sanchez
  given name: Francisco
author list: Agent
  family name: Hernández
  given name: Francisca
doi: 10.7717/peerj.2214
volume: 4
issn: 2167-8359
publication name: PeerJ
publication date: 2016-07-19
copyright: ©2016 Martinez-Nicolas et al.
attribution name: Martinez-Nicolas et al.

Enhanced functional connectivity properties of human brains during in-situ nature experience
type: item
type: AcademicArticle
description: In this study, we investigated the impacts of in-situ nature and urban exposure on human brain activities and their dynamics. We randomly assigned 32 healthy right-handed college students (mean age = 20.6 years, SD = 1.6; 16 males) to a 20 min in-situ sitting exposure in either a nature (n = 16) or urban environment (n = 16) and measured their Electroencephalography (EEG) signals. Analyses revealed that a brief in-situ restorative nature experience may induce more efficient and stronger brain connectivity with enhanced small-world properties compared with a stressful urban experience. The enhanced small-world properties were found to be correlated with “coherent” experience measured by Perceived Restorativeness Scale (PRS). Exposure to nature also induces stronger long-term correlated activity across different brain regions with a right lateralization. These findings may advance our understanding of the functional activities during in-situ environmental exposures and imply that a nature or nature-like environment may potentially benefit cognitive processes and mental well-being.
format: application/pdf
format: text/html
creator: Zheng Chen
creator: Yujia He
creator: Yuguo Yu
subject: Computational Biology
subject: Neuroscience
description: doi:10.7717/peerj.2210
publisher: PeerJ Inc.
rights: © 2016 Chen et al.
abstract: In this study, we investigated the impacts of in-situ nature and urban exposure on human brain activities and their dynamics. We randomly assigned 32 healthy right-handed college students (mean age = 20.6 years, SD = 1.6; 16 males) to a 20 min in-situ sitting exposure in either a nature (n = 16) or urban environment (n = 16) and measured their Electroencephalography (EEG) signals. Analyses revealed that a brief in-situ restorative nature experience may induce more efficient and stronger brain connectivity with enhanced small-world properties compared with a stressful urban experience. The enhanced small-world properties were found to be correlated with “coherent” experience measured by Perceived Restorativeness Scale (PRS). Exposure to nature also induces stronger long-term correlated activity across different brain regions with a right lateralization. These findings may advance our understanding of the functional activities during in-situ environmental exposures and imply that a nature or nature-like environment may potentially benefit cognitive processes and mental well-being.
bibliographic citation: Chen et al. (2016) Enhanced functional connectivity properties of human brains during in-situ nature experience. PeerJ 4:e2210 https://doi.org/10.7717/peerj.2210
date submitted: 2016-03-10
date accepted: 2016-06-13
issued: 2016-07-19
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Chen
  given name: Zheng
author list: Agent
  family name: He
  given name: Yujia
author list: Agent
  family name: Yu
  given name: Yuguo
doi: 10.7717/peerj.2210
volume: 4
issn: 2167-8359
publication name: PeerJ
publication date: 2016-07-19
copyright: © 2016 Chen et al.
attribution name: Chen et al.

fluff: exploratory analysis and visualization of high-throughput sequencing data
type: item
type: AcademicArticle
description: Summary. In this article we describe fluff, a software package that allows for simple exploration, clustering and visualization of high-throughput sequencing data mapped to a reference genome. The package contains three command-line tools to generate publication-quality figures in an uncomplicated manner using sensible defaults. Genome-wide data can be aggregated, clustered and visualized in a heatmap, according to different clustering methods. This includes a predefined setting to identify dynamic clusters between different conditions or developmental stages. Alternatively, clustered data can be visualized in a bandplot. Finally, fluff includes a tool to generate genomic profiles. As command-line tools, the fluff programs can easily be integrated into standard analysis pipelines. The installation is straightforward and documentation is available at http://fluff.readthedocs.org. Availability. fluff is implemented in Python and runs on Linux. The source code is freely available for download at https://github.com/simonvh/fluff.
format: application/pdf
format: text/html
creator: Georgios Georgiou
creator: Simon J. van Heeringen
subject: Bioinformatics
subject: Computational Biology
subject: Genomics
description: doi:10.7717/peerj.2209
publisher: PeerJ Inc.
rights: © 2016 Georgiou and Van Heeringen
abstract: Summary. In this article we describe fluff, a software package that allows for simple exploration, clustering and visualization of high-throughput sequencing data mapped to a reference genome. The package contains three command-line tools to generate publication-quality figures in an uncomplicated manner using sensible defaults. Genome-wide data can be aggregated, clustered and visualized in a heatmap, according to different clustering methods. This includes a predefined setting to identify dynamic clusters between different conditions or developmental stages. Alternatively, clustered data can be visualized in a bandplot. Finally, fluff includes a tool to generate genomic profiles. As command-line tools, the fluff programs can easily be integrated into standard analysis pipelines. The installation is straightforward and documentation is available at http://fluff.readthedocs.org. Availability. fluff is implemented in Python and runs on Linux. The source code is freely available for download at https://github.com/simonvh/fluff.
bibliographic citation: Georgiou et al. (2016) fluff: exploratory analysis and visualization of high-throughput sequencing data. PeerJ 4:e2209 https://doi.org/10.7717/peerj.2209
date submitted: 2016-04-07
date accepted: 2016-06-13
issued: 2016-07-19
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Georgiou
  given name: Georgios
author list: Agent
  family name: van Heeringen
  given name: Simon J.
doi: 10.7717/peerj.2209
volume: 4
issn: 2167-8359
publication name: PeerJ
publication date: 2016-07-19
copyright: ©2016 Georgiou and Van Heeringen
attribution name: Georgiou and Van Heeringen

Advances in global sensitivity analyses of demographic-based species distribution models to address uncertainties in dynamic landscapes
type: item
type: AcademicArticle
description: Developing a rigorous understanding of multiple global threats to species persistence requires the use of integrated modeling methods that capture processes which influence species distributions. Species distribution models (SDMs) coupled with population dynamics models can incorporate relationships between changing environments and demographics and are increasingly used to quantify relative extinction risks associated with climate and land-use changes. Despite their appeal, uncertainties associated with complex models can undermine their usefulness for advancing predictive ecology and informing conservation management decisions. We developed a computationally-efficient and freely available tool (GRIP 2.0) that implements and automates a global sensitivity analysis of coupled SDM-population dynamics models for comparing the relative influence of demographic parameters and habitat attributes on predicted extinction risk. Advances over previous global sensitivity analyses include the ability to vary habitat suitability across gradients, as well as habitat amount and configuration of spatially-explicit suitability maps of real and simulated landscapes. Using GRIP 2.0, we carried out a multi-model global sensitivity analysis of a coupled SDM-population dynamics model of whitebark pine (Pinus albicaulis) in Mount Rainier National Park as a case study and quantified the relative influence of input parameters and their interactions on model predictions. Our results differed from the one-at-time analyses used in the original study, and we found that the most influential parameters included the total amount of suitable habitat within the landscape, survival rates, and effects of a prevalent disease, white pine blister rust. Strong interactions between habitat amount and survival rates of older trees suggests the importance of habitat in mediating the negative influences of white pine blister rust. Our results underscore the importance of considering habitat attributes along …
format: application/pdf
format: text/html
creator: Ilona Naujokaitis-Lewis
creator: Janelle M.R. Curtis
subject: Biogeography
subject: Conservation Biology
subject: Ecology
subject: Ecosystem Science
subject: Environmental Sciences
description: doi:10.7717/peerj.2204
publisher: PeerJ Inc.
rights: © 2016 Naujokaitis-Lewis and Curtis
abstract: Developing a rigorous understanding of multiple global threats to species persistence requires the use of integrated modeling methods that capture processes which influence species distributions. Species distribution models (SDMs) coupled with population dynamics models can incorporate relationships between changing environments and demographics and are increasingly used to quantify relative extinction risks associated with climate and land-use changes. Despite their appeal, uncertainties associated with complex models can undermine their usefulness for advancing predictive ecology and informing conservation management decisions. We developed a computationally-efficient and freely available tool (GRIP 2.0) that implements and automates a global sensitivity analysis of coupled SDM-population dynamics models for comparing the relative influence of demographic parameters and habitat attributes on predicted extinction risk. Advances over previous global sensitivity analyses include the ability to vary habitat suitability across gradients, as well as habitat amount and configuration of spatially-explicit suitability maps of real and simulated landscapes. Using GRIP 2.0, we carried out a multi-model global sensitivity analysis of a coupled SDM-population dynamics model of whitebark pine (Pinus albicaulis) in Mount Rainier National Park as a case study and quantified the relative influence of input parameters and their interactions on model predictions. Our results differed from the one-at-time analyses used in the original study, and we found that the most influential parameters included the total amount of suitable habitat within the landscape, survival rates, and effects of a prevalent disease, white pine blister rust. Strong interactions between habitat amount and survival rates of older trees suggests the importance of habitat in mediating the negative influences of white pine blister rust. Our results underscore the importance of considering habitat attributes along …
bibliographic citation: Naujokaitis-Lewis et al. (2016) Advances in global sensitivity analyses of demographic-based species distribution models to address uncertainties in dynamic landscapes. PeerJ 4:e2204 https://doi.org/10.7717/peerj.2204
date submitted: 2015-12-11
date accepted: 2016-06-11
issued: 2016-07-19
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Naujokaitis-Lewis
  given name: Ilona
author list: Agent
  family name: Curtis
  given name: Janelle M.R.
doi: 10.7717/peerj.2204
volume: 4
issn: 2167-8359
publication name: PeerJ
publication date: 2016-07-19
copyright: ©2016 Naujokaitis-Lewis and Curtis
attribution name: Naujokaitis-Lewis and Curtis

Data mining in conservation research using Latin and vernacular species names
type: item
type: AcademicArticle
description: In conservation science, assessments of trends and priorities for actions often focus on species as the management unit. Studies on species coverage in online media are commonly conducted by using species vernacular names. However, the use of species vernacular names for web-based data search is problematic due to the high risk of mismatches in results. While the use of Latin names may produce more consistent results, it is uncertain whether a search using Latin names will produce unbiased results as compared to vernacular names. We assessed the potential of Latin names to be used as an alternative to vernacular names for the data mining within the field of conservation science. By using Latin and vernacular names, we searched for species from four species groups: diurnal birds of prey, Carnivora, Primates and marine mammals. We assessed the relationship of the results obtained within different online sources, such as Internet pages, newspapers and social media networks. Results indicated that the search results based on Latin and vernacular names were highly correlated, and confirmed that one may be used as an alternative for the other. We also demonstrated the potential of the number of images posted on the Internet to be used as an indication of the public attention towards different species.
format: application/pdf
format: text/html
creator: Ivan Jarić
creator: Franck Courchamp
creator: Jörn Gessner
creator: David L. Roberts
subject: Biodiversity
subject: Conservation Biology
subject: Environmental Sciences
subject: Human-Computer Interaction
description: doi:10.7717/peerj.2202
publisher: PeerJ Inc.
rights: © 2016 Jarić et al.
abstract: In conservation science, assessments of trends and priorities for actions often focus on species as the management unit. Studies on species coverage in online media are commonly conducted by using species vernacular names. However, the use of species vernacular names for web-based data search is problematic due to the high risk of mismatches in results. While the use of Latin names may produce more consistent results, it is uncertain whether a search using Latin names will produce unbiased results as compared to vernacular names. We assessed the potential of Latin names to be used as an alternative to vernacular names for the data mining within the field of conservation science. By using Latin and vernacular names, we searched for species from four species groups: diurnal birds of prey, Carnivora, Primates and marine mammals. We assessed the relationship of the results obtained within different online sources, such as Internet pages, newspapers and social media networks. Results indicated that the search results based on Latin and vernacular names were highly correlated, and confirmed that one may be used as an alternative for the other. We also demonstrated the potential of the number of images posted on the Internet to be used as an indication of the public attention towards different species.
bibliographic citation: Jarić et al. (2016) Data mining in conservation research using Latin and vernacular species names. PeerJ 4:e2202 https://doi.org/10.7717/peerj.2202
date submitted: 2016-03-17
date accepted: 2016-06-10
issued: 2016-07-19
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Jarić
  given name: Ivan
author list: Agent
  family name: Courchamp
  given name: Franck
author list: Agent
  family name: Gessner
  given name: Jörn
author list: Agent
  family name: Roberts
  given name: David L.
doi: 10.7717/peerj.2202
volume: 4
issn: 2167-8359
publication name: PeerJ
publication date: 2016-07-19
copyright: ©2016 Jarić et al.
attribution name: Jarić et al.

Effects of 16S rDNA sampling on estimates of the number of endosymbiont lineages in sucking lice
type: item
type: AcademicArticle
description: Phylogenetic trees can reveal the origins of endosymbiotic lineages of bacteria and detect patterns of co-evolution with their hosts. Although taxon sampling can greatly affect phylogenetic and co-evolutionary inference, most hypotheses of endosymbiont relationships are based on few available bacterial sequences. Here we examined how different sampling strategies of Gammaproteobacteria sequences affect estimates of the number of endosymbiont lineages in parasitic sucking lice (Insecta: Phthirapatera: Anoplura). We estimated the number of louse endosymbiont lineages using both newly obtained and previously sequenced 16S rDNA bacterial sequences and more than 42,000 16S rDNA sequences from other Gammaproteobacteria. We also performed parametric and nonparametric bootstrapping experiments to examine the effects of phylogenetic error and uncertainty on these estimates. Sampling of 16S rDNA sequences affects the estimates of endosymbiont diversity in sucking lice until we reach a threshold of genetic diversity, the size of which depends on the sampling strategy. Sampling by maximizing the diversity of 16S rDNA sequences is more efficient than randomly sampling available 16S rDNA sequences. Although simulation results validate estimates of multiple endosymbiont lineages in sucking lice, the bootstrap results suggest that the precise number of endosymbiont origins is still uncertain.
format: application/pdf
format: text/html
creator: Julie M. Allen
creator: J. Gordon Burleigh
creator: Jessica E. Light
creator: David L. Reed
subject: Biodiversity
subject: Bioinformatics
subject: Evolutionary Studies
description: doi:10.7717/peerj.2187
publisher: PeerJ Inc.
rights: © 2016 Allen et al.
abstract: Phylogenetic trees can reveal the origins of endosymbiotic lineages of bacteria and detect patterns of co-evolution with their hosts. Although taxon sampling can greatly affect phylogenetic and co-evolutionary inference, most hypotheses of endosymbiont relationships are based on few available bacterial sequences. Here we examined how different sampling strategies of Gammaproteobacteria sequences affect estimates of the number of endosymbiont lineages in parasitic sucking lice (Insecta: Phthirapatera: Anoplura). We estimated the number of louse endosymbiont lineages using both newly obtained and previously sequenced 16S rDNA bacterial sequences and more than 42,000 16S rDNA sequences from other Gammaproteobacteria. We also performed parametric and nonparametric bootstrapping experiments to examine the effects of phylogenetic error and uncertainty on these estimates. Sampling of 16S rDNA sequences affects the estimates of endosymbiont diversity in sucking lice until we reach a threshold of genetic diversity, the size of which depends on the sampling strategy. Sampling by maximizing the diversity of 16S rDNA sequences is more efficient than randomly sampling available 16S rDNA sequences. Although simulation results validate estimates of multiple endosymbiont lineages in sucking lice, the bootstrap results suggest that the precise number of endosymbiont origins is still uncertain.
bibliographic citation: Allen et al. (2016) Effects of 16S rDNA sampling on estimates of the number of endosymbiont lineages in sucking lice. PeerJ 4:e2187 https://doi.org/10.7717/peerj.2187
date submitted: 2015-10-26
date accepted: 2016-06-07
issued: 2016-07-19
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Allen
  given name: Julie M.
author list: Agent
  family name: Burleigh
  given name: J. Gordon
author list: Agent
  family name: Light
  given name: Jessica E.
author list: Agent
  family name: Reed
  given name: David L.
doi: 10.7717/peerj.2187
volume: 4
issn: 2167-8359
publication name: PeerJ
publication date: 2016-07-19
copyright: ©2016 Allen et al.
attribution name: Allen et al.

The diagnostic accuracy of acute phase proteins and proinflammatory cytokines in sheep with pneumonic pasteurellosis
type: item
type: AcademicArticle
description: The goal of this study was to assess the diagnostic accuracy of acute phase proteins and proinflammatory cytokines in sheep with pneumonic pasteurellosis. Blood samples were collected from 56 sheep (36 naturally infected with Pasteurella multocida and 20 healthy controls) belonging to one farm in Eastern region, Saudi Arabia. Serum samples were evaluated for acute phase proteins (Haptoglobin (Hp), serum amyloid A (SAA) and fibrinogen (Fb)), and the proinflammatory cytokines (interleukins (IL-1α, IL-1β, and IL-6), tumor necrosis factor-alpha (TNF-α), and interferon-gamma (IFN-ϒ)). Additionally, nasopharyngeal swabs and bronchoalveolar lavages were collected from all animals for bacteriological examinations. Receiver operating characteristic curve was used to assess the diagnostic performance of each parameter. All parameters showed moderate to high degree of positive correlation with case-control status. There was no significant difference in the area under the curve (AUC) among acute phase proteins; however, both Hp and SAA showed better sensitivity and specificity than Fb. The proinflammatory cytokines (IL1-α, IL1-β, and IL6) showed similar and highly accurate diagnostic performance (AUC > 0.9), whereas IFN-ϒ was moderately accurate (AUC = 0.79). In conclusion, this study confirms the value of acute phase proteins and cytokines as diagnostic biomarkers of naturally occuring pneumonic pasteurellosis in sheep.
format: application/pdf
format: text/html
creator: Wael M. El-Deeb
creator: Ahmed M. Elmoslemany
subject: Agricultural Science
subject: Microbiology
subject: Veterinary Medicine
description: doi:10.7717/peerj.2161
publisher: PeerJ Inc.
rights: © 2016 El-Deeb and Elmoslemany
abstract: The goal of this study was to assess the diagnostic accuracy of acute phase proteins and proinflammatory cytokines in sheep with pneumonic pasteurellosis. Blood samples were collected from 56 sheep (36 naturally infected with Pasteurella multocida and 20 healthy controls) belonging to one farm in Eastern region, Saudi Arabia. Serum samples were evaluated for acute phase proteins (Haptoglobin (Hp), serum amyloid A (SAA) and fibrinogen (Fb)), and the proinflammatory cytokines (interleukins (IL-1α, IL-1β, and IL-6), tumor necrosis factor-alpha (TNF-α), and interferon-gamma (IFN-ϒ)). Additionally, nasopharyngeal swabs and bronchoalveolar lavages were collected from all animals for bacteriological examinations. Receiver operating characteristic curve was used to assess the diagnostic performance of each parameter. All parameters showed moderate to high degree of positive correlation with case-control status. There was no significant difference in the area under the curve (AUC) among acute phase proteins; however, both Hp and SAA showed better sensitivity and specificity than Fb. The proinflammatory cytokines (IL1-α, IL1-β, and IL6) showed similar and highly accurate diagnostic performance (AUC > 0.9), whereas IFN-ϒ was moderately accurate (AUC = 0.79). In conclusion, this study confirms the value of acute phase proteins and cytokines as diagnostic biomarkers of naturally occuring pneumonic pasteurellosis in sheep.
bibliographic citation: El-Deeb et al. (2016) The diagnostic accuracy of acute phase proteins and proinflammatory cytokines in sheep with pneumonic pasteurellosis. PeerJ 4:e2161 https://doi.org/10.7717/peerj.2161
date submitted: 2016-03-02
date accepted: 2016-06-01
issued: 2016-07-19
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: El-Deeb
  given name: Wael M.
author list: Agent
  family name: Elmoslemany
  given name: Ahmed M.
doi: 10.7717/peerj.2161
volume: 4
issn: 2167-8359
publication name: PeerJ
publication date: 2016-07-19
copyright: ©2016 El-Deeb and Elmoslemany
attribution name: El-Deeb and Elmoslemany

Preferred temperature and thermal breadth of birds wintering in peninsular Spain: the limited effect of temperature on species distribution
type: item
type: AcademicArticle
description: Background. The availability of environmental energy, as measured by temperature, is expected to limit the abundance and distribution of endotherms wintering at temperate latitudes. A prediction of this hypothesis is that birds should attain their highest abundances in warmer areas. However, there may be a spatial mismatch between species preferred habitats and species preferred temperatures, so some species might end-up wintering in sub-optimal thermal environments. Methods. We model the influence of minimum winter temperature on the relative abundance of 106 terrestrial bird species wintering in peninsular Spain, at 10 ×10 km2 resolution, using 95%-quantile regressions. We analyze general trends across species on the shape of the response curves, the environmental preferred temperature (at which the species abundance is maximized), the mean temperature in the area of distribution and the thermal breadth (area under the abundance-temperature curve). Results. Temperature explains a low proportion of variation in abundance. The most significant effect is on limiting the maximum potential abundance of species. Considering this upper-limit response, there is a large interspecific variability on the thermal preferences and specialization of species. Overall, there is a preponderance of positive relationships between species abundance and temperature; on average, species attain their maximum abundances in areas 1.9 °C warmer than the average temperature available in peninsular Spain. The mean temperature in the area of distribution is lower than the thermal preferences of the species. Discussion. Many species prefer the warmest areas to overwinter, which suggests that temperature imposes important restrictions to birds wintering in the Iberian Peninsula. However, one third of species overwinter in locations colder than their thermal preferences, probably reflecting the interaction between habitat and thermal requirements. There is a high inter-specific variation in the v…
format: application/pdf
format: text/html
creator: Luis M. Carrascal
creator: Sara Villén-Pérez
creator: David Palomino
subject: Animal Behavior
subject: Biodiversity
subject: Biogeography
subject: Ecology
subject: Zoology
description: doi:10.7717/peerj.2156
publisher: PeerJ Inc.
rights: © 2016 Carrascal et al.
abstract: Background. The availability of environmental energy, as measured by temperature, is expected to limit the abundance and distribution of endotherms wintering at temperate latitudes. A prediction of this hypothesis is that birds should attain their highest abundances in warmer areas. However, there may be a spatial mismatch between species preferred habitats and species preferred temperatures, so some species might end-up wintering in sub-optimal thermal environments. Methods. We model the influence of minimum winter temperature on the relative abundance of 106 terrestrial bird species wintering in peninsular Spain, at 10 ×10 km2 resolution, using 95%-quantile regressions. We analyze general trends across species on the shape of the response curves, the environmental preferred temperature (at which the species abundance is maximized), the mean temperature in the area of distribution and the thermal breadth (area under the abundance-temperature curve). Results. Temperature explains a low proportion of variation in abundance. The most significant effect is on limiting the maximum potential abundance of species. Considering this upper-limit response, there is a large interspecific variability on the thermal preferences and specialization of species. Overall, there is a preponderance of positive relationships between species abundance and temperature; on average, species attain their maximum abundances in areas 1.9 °C warmer than the average temperature available in peninsular Spain. The mean temperature in the area of distribution is lower than the thermal preferences of the species. Discussion. Many species prefer the warmest areas to overwinter, which suggests that temperature imposes important restrictions to birds wintering in the Iberian Peninsula. However, one third of species overwinter in locations colder than their thermal preferences, probably reflecting the interaction between habitat and thermal requirements. There is a high inter-specific variation in the v…
bibliographic citation: Carrascal et al. (2016) Preferred temperature and thermal breadth of birds wintering in peninsular Spain: the limited effect of temperature on species distribution. PeerJ 4:e2156 https://doi.org/10.7717/peerj.2156
date submitted: 2016-03-17
date accepted: 2016-05-31
issued: 2016-07-19
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: Villén-Pérez
  given name: Sara
author list: Agent
  family name: Palomino
  given name: David
doi: 10.7717/peerj.2156
volume: 4
issn: 2167-8359
publication name: PeerJ
publication date: 2016-07-19
copyright: ©2016 Carrascal et al.
attribution name: Carrascal et al.

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