PeerJ
type: channel
link: https://peerj.com/articles/
description: Articles published in PeerJ
publisher: PeerJ Inc.
publication name: PeerJ
issn: 2167-8359
items: Genetic signatures of ecological diversity along an urbanization gradient
items: Comparative cephalopod shell strength and the role of septum morphology on stress distribution
items: Characterization of novel bacteriophage phiC119 capable of lysing multidrug-resistant Shiga toxin-producing Escherichia coli O157:H7
items: Effect of fragmentation on the Costa Rican dry forest avifauna
items: Distinctive personality profiles of fibromyalgia and chronic fatigue syndrome patients
items: Mischievous responding in Internet Gaming Disorder research
items: Decoupling social status and status certainty effects on health in macaques: a network approach
items: Microbial diversity of extreme habitats in human homes
items: Talk the talk and walk the walk. Evaluation of autonomy in aging and Alzheimer disease by simulating instrumental activities of daily living: the S-IADL
items: Spatial heterogeneity of physicochemical properties explains differences in microbial composition in arid soils from Cuatro Cienegas, Mexico

Genetic signatures of ecological diversity along an urbanization gradient
type: item
type: AcademicArticle
description: Despite decades of work in environmental science and ecology, estimating human influences on ecosystems remains challenging. This is partly due to complex chains of causation among ecosystem elements, exacerbated by the difficulty of collecting biological data at sufficient spatial, temporal, and taxonomic scales. Here, we demonstrate the utility of environmental DNA (eDNA) for quantifying associations between human land use and changes in an adjacent ecosystem. We analyze metazoan eDNA sequences from water sampled in nearshore marine eelgrass communities and assess the relationship between these ecological communities and the degree of urbanization in the surrounding watershed. Counter to conventional wisdom, we find strongly increasing richness and decreasing beta diversity with greater urbanization, and similar trends in the diversity of life histories with urbanization. We also find evidence that urbanization influences nearshore communities at local (hundreds of meters) rather than regional (tens of km) scales. Given that different survey methods sample different components of an ecosystem, we then discuss the advantages of eDNA—which we use here to detect hundreds of taxa simultaneously—as a complement to traditional ecological sampling, particularly in the context of broad ecological assessments where exhaustive manual sampling is impractical. Genetic data are a powerful means of uncovering human-ecosystem interactions that might otherwise remain hidden; nevertheless, no sampling method reveals the whole of a biological community.
format: application/pdf
format: text/html
creator: Ryan P. Kelly
creator: James L. O’Donnell
creator: Natalie C. Lowell
creator: Andrew O. Shelton
creator: Jameal F. Samhouri
creator: Shannon M. Hennessey
creator: Blake E. Feist
creator: Gregory D. Williams
subject: Biodiversity
subject: Biosphere Interactions
subject: Ecology
subject: Environmental Sciences
description: doi:10.7717/peerj.2444
publisher: PeerJ Inc.
rights: © 2016
abstract: Despite decades of work in environmental science and ecology, estimating human influences on ecosystems remains challenging. This is partly due to complex chains of causation among ecosystem elements, exacerbated by the difficulty of collecting biological data at sufficient spatial, temporal, and taxonomic scales. Here, we demonstrate the utility of environmental DNA (eDNA) for quantifying associations between human land use and changes in an adjacent ecosystem. We analyze metazoan eDNA sequences from water sampled in nearshore marine eelgrass communities and assess the relationship between these ecological communities and the degree of urbanization in the surrounding watershed. Counter to conventional wisdom, we find strongly increasing richness and decreasing beta diversity with greater urbanization, and similar trends in the diversity of life histories with urbanization. We also find evidence that urbanization influences nearshore communities at local (hundreds of meters) rather than regional (tens of km) scales. Given that different survey methods sample different components of an ecosystem, we then discuss the advantages of eDNA—which we use here to detect hundreds of taxa simultaneously—as a complement to traditional ecological sampling, particularly in the context of broad ecological assessments where exhaustive manual sampling is impractical. Genetic data are a powerful means of uncovering human-ecosystem interactions that might otherwise remain hidden; nevertheless, no sampling method reveals the whole of a biological community.
bibliographic citation: Kelly et al. (2016) Genetic signatures of ecological diversity along an urbanization gradient. PeerJ 4:e2444 https://doi.org/10.7717/peerj.2444
date submitted: 2016-07-12
date accepted: 2016-08-13
issued: 2016-09-13
is part of: PeerJ
license: http://creativecommons.org/publicdomain/zero/1.0/
author list: Agent
  family name: Kelly
  given name: Ryan P.
author list: Agent
  family name: O’Donnell
  given name: James L.
author list: Agent
  family name: Lowell
  given name: Natalie C.
author list: Agent
  family name: Shelton
  given name: Andrew O.
author list: Agent
  family name: Samhouri
  given name: Jameal F.
author list: Agent
  family name: Hennessey
  given name: Shannon M.
author list: Agent
  family name: Feist
  given name: Blake E.
author list: Agent
  family name: Williams
  given name: Gregory D.
doi: 10.7717/peerj.2444
volume: 4
issn: 2167-8359
publication name: PeerJ
publication date: 2016-09-13

Comparative cephalopod shell strength and the role of septum morphology on stress distribution
type: item
type: AcademicArticle
description: The evolution of complexly folded septa in ammonoids has long been a controversial topic. Explanations of the function of these folded septa can be divided into physiological and mechanical hypotheses with the mechanical functions tending to find widespread support. The complexity of the cephalopod shell has made it difficult to directly test the mechanical properties of these structures without oversimplification of the septal morphology or extraction of a small sub-domain. However, the power of modern finite element analysis now permits direct testing of mechanical hypothesis on complete, empirical models of the shells taken from computed tomographic data. Here we compare, for the first time using empirical models, the capability of the shells of extant Nautilus pompilius, Spirula spirula, and the extinct ammonite Cadoceras sp. to withstand hydrostatic pressure and point loads. Results show hydrostatic pressure imparts highest stress on the final septum with the rest of the shell showing minimal compression. S. spirula shows the lowest stress under hydrostatic pressure while N. pompilius shows the highest stress. Cadoceras sp. shows the development of high stress along the attachment of the septal saddles with the shell wall. Stress due to point loads decreases when the point force is directed along the suture as opposed to the unsupported chamber wall. Cadoceras sp. shows the greatest decrease in stress between the point loads compared to all other models. Greater amplitude of septal flutes corresponds with greater stress due to hydrostatic pressure; however, greater amplitude decreases the stress magnitude of point loads directed along the suture. In our models, sutural complexity does not predict greater resistance to hydrostatic pressure but it does seem to increase resistance to point loads, such as would be from predators. This result permits discussion of palaeoecological reconstructions on the basis of septal morphology. We further suggest that the ratio u…
format: application/pdf
format: text/html
creator: Robert Lemanis
creator: Stefan Zachow
creator: René Hoffmann
subject: Computational Biology
subject: Marine Biology
subject: Paleontology
subject: Zoology
description: doi:10.7717/peerj.2434
publisher: PeerJ Inc.
rights: © 2016 Lemanis et al.
abstract: The evolution of complexly folded septa in ammonoids has long been a controversial topic. Explanations of the function of these folded septa can be divided into physiological and mechanical hypotheses with the mechanical functions tending to find widespread support. The complexity of the cephalopod shell has made it difficult to directly test the mechanical properties of these structures without oversimplification of the septal morphology or extraction of a small sub-domain. However, the power of modern finite element analysis now permits direct testing of mechanical hypothesis on complete, empirical models of the shells taken from computed tomographic data. Here we compare, for the first time using empirical models, the capability of the shells of extant Nautilus pompilius, Spirula spirula, and the extinct ammonite Cadoceras sp. to withstand hydrostatic pressure and point loads. Results show hydrostatic pressure imparts highest stress on the final septum with the rest of the shell showing minimal compression. S. spirula shows the lowest stress under hydrostatic pressure while N. pompilius shows the highest stress. Cadoceras sp. shows the development of high stress along the attachment of the septal saddles with the shell wall. Stress due to point loads decreases when the point force is directed along the suture as opposed to the unsupported chamber wall. Cadoceras sp. shows the greatest decrease in stress between the point loads compared to all other models. Greater amplitude of septal flutes corresponds with greater stress due to hydrostatic pressure; however, greater amplitude decreases the stress magnitude of point loads directed along the suture. In our models, sutural complexity does not predict greater resistance to hydrostatic pressure but it does seem to increase resistance to point loads, such as would be from predators. This result permits discussion of palaeoecological reconstructions on the basis of septal morphology. We further suggest that the ratio u…
bibliographic citation: Lemanis et al. (2016) Comparative cephalopod shell strength and the role of septum morphology on stress distribution. PeerJ 4:e2434 https://doi.org/10.7717/peerj.2434
date submitted: 2016-04-07
date accepted: 2016-08-12
issued: 2016-09-13
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Lemanis
  given name: Robert
author list: Agent
  family name: Zachow
  given name: Stefan
author list: Agent
  family name: Hoffmann
  given name: René
doi: 10.7717/peerj.2434
volume: 4
issn: 2167-8359
publication name: PeerJ
publication date: 2016-09-13
copyright: ©2016 Lemanis et al.
attribution name: Lemanis et al.

Characterization of novel bacteriophage phiC119 capable of lysing multidrug-resistant Shiga toxin-producing Escherichia coli O157:H7
type: item
type: AcademicArticle
description: Background Shiga toxin-producing Escherichia coli (STEC) is one of the most common and widely distributed foodborne pathogens that has been frequently implicated in gastrointestinal and urinary tract infections. Moreover, high rates of multiple antibiotic-resistant E. coli strains have been reported worldwide. Due to the emergence of antibiotic-resistant strains, bacteriophages are considered an attractive alternative to biocontrol pathogenic bacteria. Characterization is a preliminary step towards designing a phage for biocontrol. Methods In this study, we describe the characterization of a bacteriophage designated phiC119, which can infect and lyse several multidrug-resistant STEC strains and some Salmonella strains. The phage genome was screened to detect the stx-genes using PCR, morphological analysis, host range was determined, and genome sequencing were carried out, as well as an analysis of the cohesive ends and identification of the type of genetic material through enzymatic digestion of the genome. Results Analysis of the bacteriophage particles by transmission electron microscopy showed that it had an icosahedral head and a long tail, characteristic of the family Siphoviridae. The phage exhibits broad host range against multidrug-resistant and highly virulent E. coli isolates. One-step growth experiments revealed that the phiC119 phage presented a large burst size (210 PFU/cell) and a latent period of 20 min. Based on genomic analysis, the phage contains a linear double-stranded DNA genome with a size of 47,319 bp. The phage encodes 75 putative proteins, but lysogeny and virulence genes were not found in the phiC119 genome. Conclusion These results suggest that phage phiC119 may be a good biological control agent. However, further studies are required to ensure its control of STEC and to confirm the safety of phage use.
format: application/pdf
format: text/html
creator: Luis Amarillas
creator: Cristóbal Chaidez
creator: Arturo González-Robles
creator: Yadira Lugo-Melchor
creator: Josefina León-Félix
subject: Microbiology
subject: Molecular Biology
subject: Virology
description: doi:10.7717/peerj.2423
publisher: PeerJ Inc.
rights: © 2016 Amarillas et al.
abstract: Background Shiga toxin-producing Escherichia coli (STEC) is one of the most common and widely distributed foodborne pathogens that has been frequently implicated in gastrointestinal and urinary tract infections. Moreover, high rates of multiple antibiotic-resistant E. coli strains have been reported worldwide. Due to the emergence of antibiotic-resistant strains, bacteriophages are considered an attractive alternative to biocontrol pathogenic bacteria. Characterization is a preliminary step towards designing a phage for biocontrol. Methods In this study, we describe the characterization of a bacteriophage designated phiC119, which can infect and lyse several multidrug-resistant STEC strains and some Salmonella strains. The phage genome was screened to detect the stx-genes using PCR, morphological analysis, host range was determined, and genome sequencing were carried out, as well as an analysis of the cohesive ends and identification of the type of genetic material through enzymatic digestion of the genome. Results Analysis of the bacteriophage particles by transmission electron microscopy showed that it had an icosahedral head and a long tail, characteristic of the family Siphoviridae. The phage exhibits broad host range against multidrug-resistant and highly virulent E. coli isolates. One-step growth experiments revealed that the phiC119 phage presented a large burst size (210 PFU/cell) and a latent period of 20 min. Based on genomic analysis, the phage contains a linear double-stranded DNA genome with a size of 47,319 bp. The phage encodes 75 putative proteins, but lysogeny and virulence genes were not found in the phiC119 genome. Conclusion These results suggest that phage phiC119 may be a good biological control agent. However, further studies are required to ensure its control of STEC and to confirm the safety of phage use.
bibliographic citation: Amarillas et al. (2016) Characterization of novel bacteriophage phiC119 capable of lysing multidrug-resistant Shiga toxin-producing Escherichia coli O157:H7. PeerJ 4:e2423 https://doi.org/10.7717/peerj.2423
date submitted: 2016-04-15
date accepted: 2016-08-09
issued: 2016-09-13
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Amarillas
  given name: Luis
author list: Agent
  family name: Chaidez
  given name: Cristóbal
author list: Agent
  family name: González-Robles
  given name: Arturo
author list: Agent
  family name: Lugo-Melchor
  given name: Yadira
author list: Agent
  family name: León-Félix
  given name: Josefina
doi: 10.7717/peerj.2423
volume: 4
issn: 2167-8359
publication name: PeerJ
publication date: 2016-09-13
copyright: © 2016 Amarillas et al.
attribution name: Amarillas et al.

Effect of fragmentation on the Costa Rican dry forest avifauna
type: item
type: AcademicArticle
description: Deforestation and changes in land use have reduced the tropical dry forest to isolated forest patches in northwestern Costa Rica. We examined the effect of patch area and length of the dry season on nestedness of the entire avian community, forest fragment assemblages, and species occupancy across fragments for the entire native avifauna, and for a subset of forest dependent species. Species richness was independent of both fragment area and distance between fragments. Similarity in bird community composition between patches was related to habitat structure; fragments with similar forest structure have more similar avian assemblages. Size of forest patches influenced nestedness of the bird community and species occupancy, but not nestedness of assemblages across patches in northwestern Costa Rican avifauna. Forest dependent species (species that require large tracts of mature forest) and assemblages of these species were nested within patches ordered by a gradient of seasonality, and only occupancy of species was nested by area of patches. Thus, forest patches with a shorter dry season include more forest dependent species.
format: application/pdf
format: text/html
creator: Gilbert Barrantes
creator: Diego Ocampo
creator: José D. Ramírez-Fernández
creator: Eric J. Fuchs
subject: Biodiversity
subject: Biogeography
subject: Conservation Biology
subject: Ecology
subject: Zoology
description: doi:10.7717/peerj.2422
publisher: PeerJ Inc.
rights: © 2016 Barrantes et al.
abstract: Deforestation and changes in land use have reduced the tropical dry forest to isolated forest patches in northwestern Costa Rica. We examined the effect of patch area and length of the dry season on nestedness of the entire avian community, forest fragment assemblages, and species occupancy across fragments for the entire native avifauna, and for a subset of forest dependent species. Species richness was independent of both fragment area and distance between fragments. Similarity in bird community composition between patches was related to habitat structure; fragments with similar forest structure have more similar avian assemblages. Size of forest patches influenced nestedness of the bird community and species occupancy, but not nestedness of assemblages across patches in northwestern Costa Rican avifauna. Forest dependent species (species that require large tracts of mature forest) and assemblages of these species were nested within patches ordered by a gradient of seasonality, and only occupancy of species was nested by area of patches. Thus, forest patches with a shorter dry season include more forest dependent species.
bibliographic citation: Barrantes et al. (2016) Effect of fragmentation on the Costa Rican dry forest avifauna. PeerJ 4:e2422 https://doi.org/10.7717/peerj.2422
date submitted: 2016-04-19
date accepted: 2016-08-08
issued: 2016-09-13
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Barrantes
  given name: Gilbert
author list: Agent
  family name: Ocampo
  given name: Diego
author list: Agent
  family name: Ramírez-Fernández
  given name: José D.
author list: Agent
  family name: Fuchs
  given name: Eric J.
doi: 10.7717/peerj.2422
volume: 4
issn: 2167-8359
publication name: PeerJ
publication date: 2016-09-13
copyright: ©2016 Barrantes et al.
attribution name: Barrantes et al.

Distinctive personality profiles of fibromyalgia and chronic fatigue syndrome patients
type: item
type: AcademicArticle
description: Objective The current study is an innovative exploratory investigation, aiming at identifying differences in personality profiles within Fibromyalgia Syndrome (FMS) and Chronic Fatigue Syndrome (CFS) patients. Method In total, 344 participants (309 female, 35 male) reported suffering from FMS and/or CFS and consented to participate in the study. Participants were recruited at an Israeli FM/CFS patient meeting held in May 2013, and through an announcement posted on several social networks. Participants were asked to complete a research questionnaire, which included FMS criteria and severity scales, and measures of personality, emotional functioning, positivity, social support and subjective assessment of general health. In total, 204 participants completed the research questionnaire (40.7% attrition rate). Results A cluster analysis produced two distinct clusters, which differed significantly on psychological variables, but did not differ on demographic variables or illness severity. As compared to cluster number 2 (N = 107), participants classified into cluster number 1 (N = 97) showed a less adaptive pattern, with higher levels of Harm Avoidance and Alexithymia; higher prevalence of Type D personality; and lower levels of Persistence (PS), Reward dependence (RD), Cooperation, Self-directedness (SD), social support and positivity. Conclusion The significant pattern of results indicates at least two distinct personality profiles of FM and CFS patients. Findings from this research may help improve the evaluation and treatment of FM and CFS patients, based on each patient’s unique needs, psychological resources and weaknesses, as proposed by the current trend of personalized medicine.
format: application/pdf
format: text/html
creator: Jacob N. Ablin
creator: Ada H. Zohar
creator: Reut Zaraya-Blum
creator: Dan Buskila
subject: Anesthesiology and Pain Management
subject: Psychiatry and Psychology
subject: Rheumatology
description: doi:10.7717/peerj.2421
publisher: PeerJ Inc.
rights: © 2016 Ablin et al.
abstract: Objective The current study is an innovative exploratory investigation, aiming at identifying differences in personality profiles within Fibromyalgia Syndrome (FMS) and Chronic Fatigue Syndrome (CFS) patients. Method In total, 344 participants (309 female, 35 male) reported suffering from FMS and/or CFS and consented to participate in the study. Participants were recruited at an Israeli FM/CFS patient meeting held in May 2013, and through an announcement posted on several social networks. Participants were asked to complete a research questionnaire, which included FMS criteria and severity scales, and measures of personality, emotional functioning, positivity, social support and subjective assessment of general health. In total, 204 participants completed the research questionnaire (40.7% attrition rate). Results A cluster analysis produced two distinct clusters, which differed significantly on psychological variables, but did not differ on demographic variables or illness severity. As compared to cluster number 2 (N = 107), participants classified into cluster number 1 (N = 97) showed a less adaptive pattern, with higher levels of Harm Avoidance and Alexithymia; higher prevalence of Type D personality; and lower levels of Persistence (PS), Reward dependence (RD), Cooperation, Self-directedness (SD), social support and positivity. Conclusion The significant pattern of results indicates at least two distinct personality profiles of FM and CFS patients. Findings from this research may help improve the evaluation and treatment of FM and CFS patients, based on each patient’s unique needs, psychological resources and weaknesses, as proposed by the current trend of personalized medicine.
bibliographic citation: Ablin et al. (2016) Distinctive personality profiles of fibromyalgia and chronic fatigue syndrome patients. PeerJ 4:e2421 https://doi.org/10.7717/peerj.2421
date submitted: 2016-06-01
date accepted: 2016-08-08
issued: 2016-09-13
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Ablin
  given name: Jacob N.
author list: Agent
  family name: Zohar
  given name: Ada H.
author list: Agent
  family name: Zaraya-Blum
  given name: Reut
author list: Agent
  family name: Buskila
  given name: Dan
doi: 10.7717/peerj.2421
volume: 4
issn: 2167-8359
publication name: PeerJ
publication date: 2016-09-13
copyright: © 2016 Ablin et al.
attribution name: Ablin et al.

Mischievous responding in Internet Gaming Disorder research
type: item
type: AcademicArticle
description: The most recent update to the American Psychiatric Association’s (APA) Diagnostic and Statistical Manual of Mental Disorders (DSM-5) included Internet Gaming Disorder as a new potential psychiatric condition that merited further scientific study. The present research was conducted in response to the APA Substance-Related Disorders Working Group’s research call to estimate the extent to which mischievous responding—a known problematic pattern of participant self-report responding in questionnaires—is relevant to Internet Gaming Disorder research. In line with a registered sampling and analysis plan, findings from two studies (ntot = 11,908) provide clear evidence that mischievous responding is positively associated with the number of Internet Gaming Disorder indicators participants report. Results are discussed in the context of ongoing problem gaming research and the discussion provides recommendations for improving the quality of scientific practice in this area.
format: application/pdf
format: text/html
creator: Andrew K. Przybylski
subject: Psychiatry and Psychology
subject: Human-Computer Interaction
subject: Coupled Natural and Human Systems
description: doi:10.7717/peerj.2401
publisher: PeerJ Inc.
rights: © 2016 Przybylski
abstract: The most recent update to the American Psychiatric Association’s (APA) Diagnostic and Statistical Manual of Mental Disorders (DSM-5) included Internet Gaming Disorder as a new potential psychiatric condition that merited further scientific study. The present research was conducted in response to the APA Substance-Related Disorders Working Group’s research call to estimate the extent to which mischievous responding—a known problematic pattern of participant self-report responding in questionnaires—is relevant to Internet Gaming Disorder research. In line with a registered sampling and analysis plan, findings from two studies (ntot = 11,908) provide clear evidence that mischievous responding is positively associated with the number of Internet Gaming Disorder indicators participants report. Results are discussed in the context of ongoing problem gaming research and the discussion provides recommendations for improving the quality of scientific practice in this area.
bibliographic citation: Przybylski (2016) Mischievous responding in Internet Gaming Disorder research. PeerJ 4:e2401 https://doi.org/10.7717/peerj.2401
date submitted: 2016-07-18
date accepted: 2016-08-03
issued: 2016-09-13
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Przybylski
  given name: Andrew K.
doi: 10.7717/peerj.2401
volume: 4
issn: 2167-8359
publication name: PeerJ
publication date: 2016-09-13
copyright: ©2016 Przybylski
attribution name: Przybylski

Decoupling social status and status certainty effects on health in macaques: a network approach
type: item
type: AcademicArticle
description: Background Although a wealth of literature points to the importance of social factors on health, a detailed understanding of the complex interplay between social and biological systems is lacking. Social status is one aspect of social life that is made up of multiple structural (humans: income, education; animals: mating system, dominance rank) and relational components (perceived social status, dominance interactions). In a nonhuman primate model we use novel network techniques to decouple two components of social status, dominance rank (a commonly used measure of social status in animal models) and dominance certainty (the relative certainty vs. ambiguity of an individual’s status), allowing for a more complex examination of how social status impacts health. Methods Behavioral observations were conducted on three outdoor captive groups of rhesus macaques (N = 252 subjects). Subjects’ general physical health (diarrhea) was assessed twice weekly, and blood was drawn once to assess biomarkers of inflammation (interleukin-6 (IL-6), tumor necrosis factor-alpha (TNF-α), and C-reactive protein (CRP)). Results Dominance rank alone did not fully account for the complex way that social status exerted its effect on health. Instead, dominance certainty modified the impact of rank on biomarkers of inflammation. Specifically, high-ranked animals with more ambiguous status relationships had higher levels of inflammation than low-ranked animals, whereas little effect of rank was seen for animals with more certain status relationships. The impact of status on physical health was more straightforward: individuals with more ambiguous status relationships had more frequent diarrhea; there was marginal evidence that high-ranked animals had less frequent diarrhea. Discussion Social status has a complex and multi-faceted impact on individual health. Our work suggests an important role of uncertainty in one’s social status in status-health research. This work also suggests that in order …
format: application/pdf
format: text/html
creator: Jessica J. Vandeleest
creator: Brianne A. Beisner
creator: Darcy L. Hannibal
creator: Amy C. Nathman
creator: John P. Capitanio
creator: Fushing Hsieh
creator: Edward R. Atwill
creator: Brenda McCowan
subject: Animal Behavior
subject: Psychiatry and Psychology
subject: Statistics
description: doi:10.7717/peerj.2394
publisher: PeerJ Inc.
rights: © 2016 Vandeleest et al.
abstract: Background Although a wealth of literature points to the importance of social factors on health, a detailed understanding of the complex interplay between social and biological systems is lacking. Social status is one aspect of social life that is made up of multiple structural (humans: income, education; animals: mating system, dominance rank) and relational components (perceived social status, dominance interactions). In a nonhuman primate model we use novel network techniques to decouple two components of social status, dominance rank (a commonly used measure of social status in animal models) and dominance certainty (the relative certainty vs. ambiguity of an individual’s status), allowing for a more complex examination of how social status impacts health. Methods Behavioral observations were conducted on three outdoor captive groups of rhesus macaques (N = 252 subjects). Subjects’ general physical health (diarrhea) was assessed twice weekly, and blood was drawn once to assess biomarkers of inflammation (interleukin-6 (IL-6), tumor necrosis factor-alpha (TNF-α), and C-reactive protein (CRP)). Results Dominance rank alone did not fully account for the complex way that social status exerted its effect on health. Instead, dominance certainty modified the impact of rank on biomarkers of inflammation. Specifically, high-ranked animals with more ambiguous status relationships had higher levels of inflammation than low-ranked animals, whereas little effect of rank was seen for animals with more certain status relationships. The impact of status on physical health was more straightforward: individuals with more ambiguous status relationships had more frequent diarrhea; there was marginal evidence that high-ranked animals had less frequent diarrhea. Discussion Social status has a complex and multi-faceted impact on individual health. Our work suggests an important role of uncertainty in one’s social status in status-health research. This work also suggests that in order …
bibliographic citation: Vandeleest et al. (2016) Decoupling social status and status certainty effects on health in macaques: a network approach. PeerJ 4:e2394 https://doi.org/10.7717/peerj.2394
date submitted: 2016-03-09
date accepted: 2016-07-29
issued: 2016-09-13
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Vandeleest
  given name: Jessica J.
author list: Agent
  family name: Beisner
  given name: Brianne A.
author list: Agent
  family name: Hannibal
  given name: Darcy L.
author list: Agent
  family name: Nathman
  given name: Amy C.
author list: Agent
  family name: Capitanio
  given name: John P.
author list: Agent
  family name: Hsieh
  given name: Fushing
author list: Agent
  family name: Atwill
  given name: Edward R.
author list: Agent
  family name: McCowan
  given name: Brenda
doi: 10.7717/peerj.2394
volume: 4
issn: 2167-8359
publication name: PeerJ
publication date: 2016-09-13
copyright: © 2016 Vandeleest et al.
attribution name: Vandeleest et al.

Microbial diversity of extreme habitats in human homes
type: item
type: AcademicArticle
description: High-throughput sequencing techniques have opened up the world of microbial diversity to scientists, and a flurry of studies in the most remote and extreme habitats on earth have begun to elucidate the key roles of microbes in ecosystems with extreme conditions. These same environmental extremes can also be found closer to humans, even in our homes. Here, we used high-throughput sequencing techniques to assess bacterial and archaeal diversity in the extreme environments inside human homes (e.g., dishwashers, hot water heaters, washing machine bleach reservoirs, etc.). We focused on habitats in the home with extreme temperature, pH, and chemical environmental conditions. We found a lower diversity of microbes in these extreme home environments compared to less extreme habitats in the home. However, we were nonetheless able to detect sequences from a relatively diverse array of bacteria and archaea. Habitats with extreme temperatures alone appeared to be able to support a greater diversity of microbes than habitats with extreme pH or extreme chemical environments alone. Microbial diversity was lowest when habitats had both extreme temperature and one of these other extremes. In habitats with both extreme temperatures and extreme pH, taxa with known associations with extreme conditions dominated. Our findings highlight the importance of examining interactive effects of multiple environmental extremes on microbial communities. Inasmuch as taxa from extreme environments can be both beneficial and harmful to humans, our findings also suggest future work to understand both the threats and opportunities posed by the life in these habitats.
format: application/pdf
format: text/html
creator: Amy M. Savage
creator: Justin Hills
creator: Katherine Driscoll
creator: Daniel J. Fergus
creator: Amy M. Grunden
creator: Robert R. Dunn
subject: Biodiversity
subject: Ecology
subject: Microbiology
description: doi:10.7717/peerj.2376
publisher: PeerJ Inc.
rights: © 2016 Savage et al.
abstract: High-throughput sequencing techniques have opened up the world of microbial diversity to scientists, and a flurry of studies in the most remote and extreme habitats on earth have begun to elucidate the key roles of microbes in ecosystems with extreme conditions. These same environmental extremes can also be found closer to humans, even in our homes. Here, we used high-throughput sequencing techniques to assess bacterial and archaeal diversity in the extreme environments inside human homes (e.g., dishwashers, hot water heaters, washing machine bleach reservoirs, etc.). We focused on habitats in the home with extreme temperature, pH, and chemical environmental conditions. We found a lower diversity of microbes in these extreme home environments compared to less extreme habitats in the home. However, we were nonetheless able to detect sequences from a relatively diverse array of bacteria and archaea. Habitats with extreme temperatures alone appeared to be able to support a greater diversity of microbes than habitats with extreme pH or extreme chemical environments alone. Microbial diversity was lowest when habitats had both extreme temperature and one of these other extremes. In habitats with both extreme temperatures and extreme pH, taxa with known associations with extreme conditions dominated. Our findings highlight the importance of examining interactive effects of multiple environmental extremes on microbial communities. Inasmuch as taxa from extreme environments can be both beneficial and harmful to humans, our findings also suggest future work to understand both the threats and opportunities posed by the life in these habitats.
bibliographic citation: Savage et al. (2016) Microbial diversity of extreme habitats in human homes. PeerJ 4:e2376 https://doi.org/10.7717/peerj.2376
date submitted: 2016-03-16
date accepted: 2016-07-29
issued: 2016-09-13
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Savage
  given name: Amy M.
author list: Agent
  family name: Hills
  given name: Justin
author list: Agent
  family name: Driscoll
  given name: Katherine
author list: Agent
  family name: Fergus
  given name: Daniel J.
author list: Agent
  family name: Grunden
  given name: Amy M.
author list: Agent
  family name: Dunn
  given name: Robert R.
doi: 10.7717/peerj.2376
volume: 4
issn: 2167-8359
publication name: PeerJ
publication date: 2016-09-13
copyright: ©2016 Savage et al.
attribution name: Savage et al.

Talk the talk and walk the walk. Evaluation of autonomy in aging and Alzheimer disease by simulating instrumental activities of daily living: the S-IADL
type: item
type: AcademicArticle
description: Objective The autonomy of individuals is linked to the achievement of instrumental activities of daily living that require complex behavior. In the elderly, the assessment of autonomy is usually based on questionnaires that have strong subjective constraints. Considering this fact, we tested elderly healthy adults and Alzheimer disease patients using a new measure, the S-IADL (Simulation of Instrumental Activities for Daily Living), to assess the ability to perform effectively activities of daily living. Method The S-IADL shares many items with the well-known IADL questionnaire proposed by Lawton & Brody (1969). However, as opposed to the IADL, the assessment of autonomy is not based on the completion of a questionnaire but requires the realization or simulation of various activities of daily living. Eighty-three participants (69 healthy elderly, and 14 Alzheimer Disease patients) completed the IADL and performed the S-IADL assessment. Results Results revealed that, like the IADL, the S-IADL is able to identify AD patients who are likely to encounter difficulties in performing everyday activities, and no major differences were found between the IADL and the S-IADL. Conclusions We outlined some advantages for prefering, in certain situation, this new tool based on simulation of activities in functional evaluation. Finally, we discuss the main limits of the S-IADL that should be investigated prior to its utilization by clinicians.
format: application/pdf
format: text/html
creator: Véronique Quaglino
creator: Yannick Gounden
creator: Emilie Lacot
creator: Frédérique Couvillers
creator: Amandine Lions
creator: Mathieu Hainselin
subject: Neurology
subject: Psychiatry and Psychology
description: doi:10.7717/peerj.2351
publisher: PeerJ Inc.
rights: © 2016 Quaglino et al.
abstract: Objective The autonomy of individuals is linked to the achievement of instrumental activities of daily living that require complex behavior. In the elderly, the assessment of autonomy is usually based on questionnaires that have strong subjective constraints. Considering this fact, we tested elderly healthy adults and Alzheimer disease patients using a new measure, the S-IADL (Simulation of Instrumental Activities for Daily Living), to assess the ability to perform effectively activities of daily living. Method The S-IADL shares many items with the well-known IADL questionnaire proposed by Lawton & Brody (1969). However, as opposed to the IADL, the assessment of autonomy is not based on the completion of a questionnaire but requires the realization or simulation of various activities of daily living. Eighty-three participants (69 healthy elderly, and 14 Alzheimer Disease patients) completed the IADL and performed the S-IADL assessment. Results Results revealed that, like the IADL, the S-IADL is able to identify AD patients who are likely to encounter difficulties in performing everyday activities, and no major differences were found between the IADL and the S-IADL. Conclusions We outlined some advantages for prefering, in certain situation, this new tool based on simulation of activities in functional evaluation. Finally, we discuss the main limits of the S-IADL that should be investigated prior to its utilization by clinicians.
bibliographic citation: Quaglino et al. (2016) Talk the talk and walk the walk. Evaluation of autonomy in aging and Alzheimer disease by simulating instrumental activities of daily living: the S-IADL. PeerJ 4:e2351 https://doi.org/10.7717/peerj.2351
date submitted: 2016-03-01
date accepted: 2016-07-20
issued: 2016-09-13
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Quaglino
  given name: Véronique
author list: Agent
  family name: Gounden
  given name: Yannick
author list: Agent
  family name: Lacot
  given name: Emilie
author list: Agent
  family name: Couvillers
  given name: Frédérique
author list: Agent
  family name: Lions
  given name: Amandine
author list: Agent
  family name: Hainselin
  given name: Mathieu
doi: 10.7717/peerj.2351
volume: 4
issn: 2167-8359
publication name: PeerJ
publication date: 2016-09-13
copyright: ©2016 Quaglino et al.
attribution name: Quaglino et al.

Spatial heterogeneity of physicochemical properties explains differences in microbial composition in arid soils from Cuatro Cienegas, Mexico
type: item
type: AcademicArticle
description: Arid ecosystems are characterized by high spatial heterogeneity, and the variation among vegetation patches is a clear example. Soil biotic and abiotic factors associated with these patches have also been well documented as highly heterogeneous in space. Given the low vegetation cover and little precipitation in arid ecosystems, soil microorganisms are the main drivers of nutrient cycling. Nonetheless, little is known about the spatial distribution of microorganisms and the relationship that their diversity holds with nutrients and other physicochemical gradients in arid soils. In this study, we evaluated the spatial variability of soil microbial diversity and chemical parameters (nutrients and ion content) at local scale (meters) occurring in a gypsum-based desert soil, to gain knowledge on what soil abiotic factors control the distribution of microbes in arid ecosystems. We analyzed 32 soil samples within a 64 m2 plot and: (a) characterized microbial diversity using T-RFLPs of the bacterial 16S rRNA gene, (b) determined soil chemical parameters, and (c) identified relationships between microbial diversity and chemical properties. Overall, we found a strong correlation between microbial composition heterogeneity and spatial variation of cations (Ca2, K+) and anions (HCO ${}_{3}^{-}$ 3 − , Cl−, SO ${}_{4}^{2-}$ 4 2 − ) content in this small plot. Our results could be attributable to spatial differences of soil saline content, favoring the patchy emergence of salt and soil microbial communities.
format: application/pdf
format: text/html
creator: Silvia Pajares
creator: Ana E. Escalante
creator: Ana M. Noguez
creator: Felipe García-Oliva
creator: Celeste Martínez-Piedragil
creator: Silke S. Cram
creator: Luis Enrique Eguiarte
creator: Valeria Souza
subject: Biodiversity
subject: Ecology
subject: Microbiology
subject: Soil Science
description: doi:10.7717/peerj.2459
publisher: PeerJ Inc.
rights: © 2016 Pajares et al.
abstract: Arid ecosystems are characterized by high spatial heterogeneity, and the variation among vegetation patches is a clear example. Soil biotic and abiotic factors associated with these patches have also been well documented as highly heterogeneous in space. Given the low vegetation cover and little precipitation in arid ecosystems, soil microorganisms are the main drivers of nutrient cycling. Nonetheless, little is known about the spatial distribution of microorganisms and the relationship that their diversity holds with nutrients and other physicochemical gradients in arid soils. In this study, we evaluated the spatial variability of soil microbial diversity and chemical parameters (nutrients and ion content) at local scale (meters) occurring in a gypsum-based desert soil, to gain knowledge on what soil abiotic factors control the distribution of microbes in arid ecosystems. We analyzed 32 soil samples within a 64 m2 plot and: (a) characterized microbial diversity using T-RFLPs of the bacterial 16S rRNA gene, (b) determined soil chemical parameters, and (c) identified relationships between microbial diversity and chemical properties. Overall, we found a strong correlation between microbial composition heterogeneity and spatial variation of cations (Ca2, K+) and anions (HCO ${}_{3}^{-}$ 3 − , Cl−, SO ${}_{4}^{2-}$ 4 2 − ) content in this small plot. Our results could be attributable to spatial differences of soil saline content, favoring the patchy emergence of salt and soil microbial communities.
bibliographic citation: Pajares et al. (2016) Spatial heterogeneity of physicochemical properties explains differences in microbial composition in arid soils from Cuatro Cienegas, Mexico. PeerJ 4:e2459 https://doi.org/10.7717/peerj.2459
date submitted: 2016-04-07
date accepted: 2016-08-17
issued: 2016-09-08
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Pajares
  given name: Silvia
author list: Agent
  family name: Escalante
  given name: Ana E.
author list: Agent
  family name: Noguez
  given name: Ana M.
author list: Agent
  family name: García-Oliva
  given name: Felipe
author list: Agent
  family name: Martínez-Piedragil
  given name: Celeste
author list: Agent
  family name: Cram
  given name: Silke S.
author list: Agent
  family name: Eguiarte
  given name: Luis Enrique
author list: Agent
  family name: Souza
  given name: Valeria
doi: 10.7717/peerj.2459
volume: 4
issn: 2167-8359
publication name: PeerJ
publication date: 2016-09-08
copyright: ©2016 Pajares et al.
attribution name: Pajares et al.

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