PeerJ
type: channel
link: https://peerj.com/articles/
description: Articles published in PeerJ
publisher: PeerJ Inc.
publication name: PeerJ
issn: 2167-8359
items: Modafinil decreases anxiety-like behaviour in zebrafish
items: An open source device for operant licking in rats
items: ­Genomic data mining of the marine actinobacteria Streptomyces sp. H-KF8 unveils insights into multi-stress related genes and metabolic pathways involved in antimicrobial synthesis
items: Comparison of hand grip strength and upper limb pressure pain threshold between older adults with or without non-specific shoulder pain
items: Pattern analysis of total item score and item response of the Kessler Screening Scale for Psychological Distress (K6) in a nationally representative sample of US adults
items: Comparison of 3D laser-based photonic scans and manual anthropometric measurements of body size and shape in a validation study of 123 young Swiss men
items: Phylogenetic factorization of compositional data yields lineage-level associations in microbiome datasets
items: Acoustic monitoring indicates a correlation between calling and spawning in captive spotted seatrout (Cynoscion nebulosus)
items: Molecular characterization and genetic diversity of Jatropha curcas L. in Costa Rica
items: Candidate genes that have facilitated freshwater adaptation by palaemonid prawns in the genus Macrobrachium: identification and expression validation in a model species (M. koombooloomba)

Modafinil decreases anxiety-like behaviour in zebrafish
type: item
type: AcademicArticle
description: Modafinil (2-((diphenylmethyl)sulfinyl)acetamide), a selective dopamine and norepinephrine transporter inhibitor, is most commonly prescribed for narcolepsy but has gained recent interest for treating a variety of disorders. Zebrafish (Danio rerio) are becoming a model of choice for pharmacological and behavioural research. To investigate the behavioural effects of modafinil on anxiety, we administered doses of 0, 2, 20, and 200 mg/L for 30 minutes then tested zebrafish in the novel approach test. In this test, the fish was placed into a circular arena with a novel object in the center and motion-tracking software was used to quantify the time the fish spent in the outer area of the arena (thigmotaxis zone), middle third of the arena (transition zone) and center of the arena, as well as total distance traveled, immobility and meandering. Modafinil caused a decrease in time spent in the thigmotaxis zone and increased time spent in the transition zone across all doses. Modafinil did not significantly alter the time spent in the center zone (near the novel object), the distance moved, meandering, or the duration of time spent immobile. We also validated this test as a measure of anxiety with the administration of ethanol (1%) which decreased time spent in the thigmotaxis zone and increased time spent in the transition zone. These results suggest that modafinil decreases anxiety-like behaviour in zebrafish.
format: application/pdf
format: text/html
creator: Adrian Johnson
creator: Trevor James Hamilton
subject: Animal Behavior
subject: Aquaculture, Fisheries and Fish Science
subject: Neuroscience
subject: Pharmacology
description: doi:10.7717/peerj.2994
publisher: PeerJ Inc.
rights: © 2017 Johnson and Hamilton
abstract: Modafinil (2-((diphenylmethyl)sulfinyl)acetamide), a selective dopamine and norepinephrine transporter inhibitor, is most commonly prescribed for narcolepsy but has gained recent interest for treating a variety of disorders. Zebrafish (Danio rerio) are becoming a model of choice for pharmacological and behavioural research. To investigate the behavioural effects of modafinil on anxiety, we administered doses of 0, 2, 20, and 200 mg/L for 30 minutes then tested zebrafish in the novel approach test. In this test, the fish was placed into a circular arena with a novel object in the center and motion-tracking software was used to quantify the time the fish spent in the outer area of the arena (thigmotaxis zone), middle third of the arena (transition zone) and center of the arena, as well as total distance traveled, immobility and meandering. Modafinil caused a decrease in time spent in the thigmotaxis zone and increased time spent in the transition zone across all doses. Modafinil did not significantly alter the time spent in the center zone (near the novel object), the distance moved, meandering, or the duration of time spent immobile. We also validated this test as a measure of anxiety with the administration of ethanol (1%) which decreased time spent in the thigmotaxis zone and increased time spent in the transition zone. These results suggest that modafinil decreases anxiety-like behaviour in zebrafish.
bibliographic citation: Johnson et al. (2017) Modafinil decreases anxiety-like behaviour in zebrafish. PeerJ 5:e2994 https://doi.org/10.7717/peerj.2994
date submitted: 2016-11-01
date accepted: 2017-01-16
issued: 2017-02-14
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Johnson
  given name: Adrian
author list: Agent
  family name: Hamilton
  given name: Trevor James
doi: 10.7717/peerj.2994
volume: 5
issn: 2167-8359
publication name: PeerJ
publication date: 2017-02-14
copyright: ©2017 Johnson and and Hamilton
attribution name: Johnson and Hamilton

An open source device for operant licking in rats
type: item
type: AcademicArticle
description: We created an easy-to-use device for operant licking experiments and another device that records environmental variables. Both devices use the Raspberry Pi computer to obtain data from multiple input devices (e.g., radio frequency identification tag readers, touch and motion sensors, environmental sensors) and activate output devices (e.g., LED lights, syringe pumps) as needed. Data gathered from these devices are stored locally on the computer but can be automatically transferred to a remote server via a wireless network. We tested the operant device by training rats to obtain either sucrose or water under the control of a fixed ratio, a variable ratio, or a progressive ratio reinforcement schedule. The lick data demonstrated that the device has sufficient precision and time resolution to record the fast licking behavior of rats. Data from the environment monitoring device also showed reliable measurements. By providing the source code and 3D design under an open source license, we believe these examples will stimulate innovation in behavioral studies. The source code can be found at http://github.com/chen42/openbehavior.
format: application/pdf
format: text/html
creator: Matthew Longley
creator: Ethan L. Willis
creator: Cindy X. Tay
creator: Hao Chen
subject: Animal Behavior
subject: Bioengineering
subject: Neuroscience
description: doi:10.7717/peerj.2981
publisher: PeerJ Inc.
rights: © 2017 Longley et al.
abstract: We created an easy-to-use device for operant licking experiments and another device that records environmental variables. Both devices use the Raspberry Pi computer to obtain data from multiple input devices (e.g., radio frequency identification tag readers, touch and motion sensors, environmental sensors) and activate output devices (e.g., LED lights, syringe pumps) as needed. Data gathered from these devices are stored locally on the computer but can be automatically transferred to a remote server via a wireless network. We tested the operant device by training rats to obtain either sucrose or water under the control of a fixed ratio, a variable ratio, or a progressive ratio reinforcement schedule. The lick data demonstrated that the device has sufficient precision and time resolution to record the fast licking behavior of rats. Data from the environment monitoring device also showed reliable measurements. By providing the source code and 3D design under an open source license, we believe these examples will stimulate innovation in behavioral studies. The source code can be found at http://github.com/chen42/openbehavior.
bibliographic citation: Longley et al. (2017) An open source device for operant licking in rats. PeerJ 5:e2981 https://doi.org/10.7717/peerj.2981
date submitted: 2016-09-10
date accepted: 2017-01-11
issued: 2017-02-14
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Longley
  given name: Matthew
author list: Agent
  family name: Willis
  given name: Ethan L.
author list: Agent
  family name: Tay
  given name: Cindy X.
author list: Agent
  family name: Chen
  given name: Hao
doi: 10.7717/peerj.2981
volume: 5
issn: 2167-8359
publication name: PeerJ
publication date: 2017-02-14
copyright: ©2017 Longley et al.
attribution name: Longley et al.

­Genomic data mining of the marine actinobacteria Streptomyces sp. H-KF8 unveils insights into multi-stress related genes and metabolic pathways involved in antimicrobial synthesis
type: item
type: AcademicArticle
description: Streptomyces sp. H-KF8 is an actinobacterial strain isolated from marine sediments of a Chilean Patagonian fjord. Morphological characterization together with antibacterial activity was assessed in various culture media, revealing a carbon-source dependent activity mainly against Gram-positive bacteria (S. aureus and L. monocytogenes). Genome mining of this antibacterial-producing bacterium revealed the presence of 26 biosynthetic gene clusters (BGCs) for secondary metabolites, where among them, 81% have low similarities with known BGCs. In addition, a genomic search in Streptomyces sp. H-KF8 unveiled the presence of a wide variety of genetic determinants related to heavy metal resistance (49 genes), oxidative stress (69 genes) and antibiotic resistance (97 genes). This study revealed that the marine-derived Streptomyces sp. H-KF8 bacterium has the capability to tolerate a diverse set of heavy metals such as copper, cobalt, mercury, chromate and nickel; as well as the highly toxic tellurite, a feature first time described for Streptomyces. In addition, Streptomyces sp. H-KF8 possesses a major resistance towards oxidative stress, in comparison to the soil reference strain Streptomyces violaceoruber A3(2). Moreover, Streptomyces sp. H-KF8 showed resistance to 88% of the antibiotics tested, indicating overall, a strong response to several abiotic stressors. The combination of these biological traits confirms the metabolic versatility of Streptomyces sp. H-KF8, a genetically well-prepared microorganism with the ability to confront the dynamics of the fjord-unique marine environment.
format: application/pdf
format: text/html
creator: Agustina Undabarrena
creator: Juan A. Ugalde
creator: Michael Seeger
creator: Beatriz Cámara
subject: Genomics
subject: Microbiology
description: doi:10.7717/peerj.2912
publisher: PeerJ Inc.
rights: © 2017 Undabarrena et al.
abstract: Streptomyces sp. H-KF8 is an actinobacterial strain isolated from marine sediments of a Chilean Patagonian fjord. Morphological characterization together with antibacterial activity was assessed in various culture media, revealing a carbon-source dependent activity mainly against Gram-positive bacteria (S. aureus and L. monocytogenes). Genome mining of this antibacterial-producing bacterium revealed the presence of 26 biosynthetic gene clusters (BGCs) for secondary metabolites, where among them, 81% have low similarities with known BGCs. In addition, a genomic search in Streptomyces sp. H-KF8 unveiled the presence of a wide variety of genetic determinants related to heavy metal resistance (49 genes), oxidative stress (69 genes) and antibiotic resistance (97 genes). This study revealed that the marine-derived Streptomyces sp. H-KF8 bacterium has the capability to tolerate a diverse set of heavy metals such as copper, cobalt, mercury, chromate and nickel; as well as the highly toxic tellurite, a feature first time described for Streptomyces. In addition, Streptomyces sp. H-KF8 possesses a major resistance towards oxidative stress, in comparison to the soil reference strain Streptomyces violaceoruber A3(2). Moreover, Streptomyces sp. H-KF8 showed resistance to 88% of the antibiotics tested, indicating overall, a strong response to several abiotic stressors. The combination of these biological traits confirms the metabolic versatility of Streptomyces sp. H-KF8, a genetically well-prepared microorganism with the ability to confront the dynamics of the fjord-unique marine environment.
bibliographic citation: Undabarrena et al. (2017) ­Genomic data mining of the marine actinobacteria Streptomyces sp. H-KF8 unveils insights into multi-stress related genes and metabolic pathways involved in antimicrobial synthesis. PeerJ 5:e2912 https://doi.org/10.7717/peerj.2912
date submitted: 2016-09-13
date accepted: 2016-12-14
issued: 2017-02-14
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Undabarrena
  given name: Agustina
author list: Agent
  family name: Ugalde
  given name: Juan A.
author list: Agent
  family name: Seeger
  given name: Michael
author list: Agent
  family name: Cámara
  given name: Beatriz
doi: 10.7717/peerj.2912
volume: 5
issn: 2167-8359
publication name: PeerJ
publication date: 2017-02-14
copyright: ©2017 Undabarrena et al.
attribution name: Undabarrena et al.

Comparison of hand grip strength and upper limb pressure pain threshold between older adults with or without non-specific shoulder pain
type: item
type: AcademicArticle
description: Background There is a high prevalence of non-specific shoulder pain associated with upper limb functional limitations in older adults. The purpose of this study was to determine the minimal clinically important differences (MCID) of grip strength and pressure pain threshold (PPT) in the upper limb between older adults with or without non-specific shoulder pain. Methods A case-control study was carried out following the Strengthening the Reporting of Observational Studies in Epidemiology (STROBE) criteria. A sample of 132 shoulders (mean ± SD years) with (n = 66; 76.04 ± 7.58) and without (n = 66; 75.05 ± 6.26) non-specific pain were recruited. The grip strength and PPT of the anterior deltoid and extensor carpi radialis brevis (ECRB) muscles were assessed. Results There were statistically significant differences (mean ± SD; P-value) for anterior deltoid PPT (2.51 ± 0.69 vs 3.68 ± 0.65, kg/cm2; P < .001), ECRB PPT (2.20 ± 0.60 vs 3.35 ± 0.38 kg/cm2; P < .001) and grip strength (20.78 ± 10.94 vs 24.63 ± 9.38 kg; P = .032) between shoulders with and without non-specific pain, respectively. Discussion The MCID of 1.17 kg/cm2, 1.15 kg/cm2 and 3.84 kg were proposed for anterior deltoid PPT, ECRB PPT and grip strength, respectively, to assess the upper limb of older adults with non-specific shoulder pain after treatment. In addition, univariate and multivariate (linear regression and regression trees) analyses may be used to consider age distribution, sex, pain intensity, grip strength and PPT in older adults including clinical and epidemiological studies with non-specific shoulder pain.
format: application/pdf
format: text/html
creator: Cesar Calvo Lobo
creator: Carlos Romero Morales
creator: David Rodríguez Sanz
creator: Irene Sanz Corbalán
creator: Eleuterio A. Sánchez Romero
creator: Josué Fernández Carnero
creator: Daniel López López
subject: Geriatrics
subject: Orthopedics
subject: Rheumatology
description: doi:10.7717/peerj.2995
publisher: PeerJ Inc.
rights: © 2017 Calvo Lobo et al.
abstract: Background There is a high prevalence of non-specific shoulder pain associated with upper limb functional limitations in older adults. The purpose of this study was to determine the minimal clinically important differences (MCID) of grip strength and pressure pain threshold (PPT) in the upper limb between older adults with or without non-specific shoulder pain. Methods A case-control study was carried out following the Strengthening the Reporting of Observational Studies in Epidemiology (STROBE) criteria. A sample of 132 shoulders (mean ± SD years) with (n = 66; 76.04 ± 7.58) and without (n = 66; 75.05 ± 6.26) non-specific pain were recruited. The grip strength and PPT of the anterior deltoid and extensor carpi radialis brevis (ECRB) muscles were assessed. Results There were statistically significant differences (mean ± SD; P-value) for anterior deltoid PPT (2.51 ± 0.69 vs 3.68 ± 0.65, kg/cm2; P < .001), ECRB PPT (2.20 ± 0.60 vs 3.35 ± 0.38 kg/cm2; P < .001) and grip strength (20.78 ± 10.94 vs 24.63 ± 9.38 kg; P = .032) between shoulders with and without non-specific pain, respectively. Discussion The MCID of 1.17 kg/cm2, 1.15 kg/cm2 and 3.84 kg were proposed for anterior deltoid PPT, ECRB PPT and grip strength, respectively, to assess the upper limb of older adults with non-specific shoulder pain after treatment. In addition, univariate and multivariate (linear regression and regression trees) analyses may be used to consider age distribution, sex, pain intensity, grip strength and PPT in older adults including clinical and epidemiological studies with non-specific shoulder pain.
bibliographic citation: Calvo Lobo et al. (2017) Comparison of hand grip strength and upper limb pressure pain threshold between older adults with or without non-specific shoulder pain. PeerJ 5:e2995 https://doi.org/10.7717/peerj.2995
date submitted: 2016-11-22
date accepted: 2017-01-16
issued: 2017-02-09
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Calvo Lobo
  given name: Cesar
author list: Agent
  family name: Romero Morales
  given name: Carlos
author list: Agent
  family name: Rodríguez Sanz
  given name: David
author list: Agent
  family name: Sanz Corbalán
  given name: Irene
author list: Agent
  family name: Sánchez Romero
  given name: Eleuterio A.
author list: Agent
  family name: Fernández Carnero
  given name: Josué
author list: Agent
  family name: López López
  given name: Daniel
doi: 10.7717/peerj.2995
volume: 5
issn: 2167-8359
publication name: PeerJ
publication date: 2017-02-09
copyright: ©2017 Calvo Lobo et al.
attribution name: Calvo Lobo et al.

Pattern analysis of total item score and item response of the Kessler Screening Scale for Psychological Distress (K6) in a nationally representative sample of US adults
type: item
type: AcademicArticle
description: Background Several recent studies have shown that total scores on depressive symptom measures in a general population approximate an exponential pattern except for the lower end of the distribution. Furthermore, we confirmed that the exponential pattern is present for the individual item responses on the Center for Epidemiologic Studies Depression Scale (CES-D). To confirm the reproducibility of such findings, we investigated the total score distribution and item responses of the Kessler Screening Scale for Psychological Distress (K6) in a nationally representative study. Methods Data were drawn from the National Survey of Midlife Development in the United States (MIDUS), which comprises four subsamples: (1) a national random digit dialing (RDD) sample, (2) oversamples from five metropolitan areas, (3) siblings of individuals from the RDD sample, and (4) a national RDD sample of twin pairs. K6 items are scored using a 5-point scale: “none of the time,” “a little of the time,” “some of the time,” “most of the time,” and “all of the time.” The pattern of total score distribution and item responses were analyzed using graphical analysis and exponential regression model. Results The total score distributions of the four subsamples exhibited an exponential pattern with similar rate parameters. The item responses of the K6 approximated a linear pattern from “a little of the time” to “all of the time” on log-normal scales, while “none of the time” response was not related to this exponential pattern. Discussion The total score distribution and item responses of the K6 showed exponential patterns, consistent with other depressive symptom scales.
format: application/pdf
format: text/html
creator: Shinichiro Tomitaka
creator: Yohei Kawasaki
creator: Kazuki Ide
creator: Maiko Akutagawa
creator: Hiroshi Yamada
creator: Ono Yutaka
creator: Toshiaki A. Furukawa
subject: Epidemiology
subject: Psychiatry and Psychology
subject: Statistics
description: doi:10.7717/peerj.2987
publisher: PeerJ Inc.
rights: © 2017 Tomitaka et al.
abstract: Background Several recent studies have shown that total scores on depressive symptom measures in a general population approximate an exponential pattern except for the lower end of the distribution. Furthermore, we confirmed that the exponential pattern is present for the individual item responses on the Center for Epidemiologic Studies Depression Scale (CES-D). To confirm the reproducibility of such findings, we investigated the total score distribution and item responses of the Kessler Screening Scale for Psychological Distress (K6) in a nationally representative study. Methods Data were drawn from the National Survey of Midlife Development in the United States (MIDUS), which comprises four subsamples: (1) a national random digit dialing (RDD) sample, (2) oversamples from five metropolitan areas, (3) siblings of individuals from the RDD sample, and (4) a national RDD sample of twin pairs. K6 items are scored using a 5-point scale: “none of the time,” “a little of the time,” “some of the time,” “most of the time,” and “all of the time.” The pattern of total score distribution and item responses were analyzed using graphical analysis and exponential regression model. Results The total score distributions of the four subsamples exhibited an exponential pattern with similar rate parameters. The item responses of the K6 approximated a linear pattern from “a little of the time” to “all of the time” on log-normal scales, while “none of the time” response was not related to this exponential pattern. Discussion The total score distribution and item responses of the K6 showed exponential patterns, consistent with other depressive symptom scales.
bibliographic citation: Tomitaka et al. (2017) Pattern analysis of total item score and item response of the Kessler Screening Scale for Psychological Distress (K6) in a nationally representative sample of US adults. PeerJ 5:e2987 https://doi.org/10.7717/peerj.2987
date submitted: 2016-10-21
date accepted: 2017-01-12
issued: 2017-02-09
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Tomitaka
  given name: Shinichiro
author list: Agent
  family name: Kawasaki
  given name: Yohei
author list: Agent
  family name: Ide
  given name: Kazuki
author list: Agent
  family name: Akutagawa
  given name: Maiko
author list: Agent
  family name: Yamada
  given name: Hiroshi
author list: Agent
  family name: Yutaka
  given name: Ono
author list: Agent
  family name: Furukawa
  given name: Toshiaki A.
doi: 10.7717/peerj.2987
volume: 5
issn: 2167-8359
publication name: PeerJ
publication date: 2017-02-09
copyright: ©2017 Tomitaka et al.
attribution name: Tomitaka et al.

Comparison of 3D laser-based photonic scans and manual anthropometric measurements of body size and shape in a validation study of 123 young Swiss men
type: item
type: AcademicArticle
description: Background Manual anthropometric measurements are time-consuming and challenging to perform within acceptable intra- and inter-individual error margins in large studies. Three-dimensional (3D) laser body scanners provide a fast and precise alternative: within a few seconds the system produces a 3D image of the body topography and calculates some 150 standardised body size measurements. Objective The aim was to enhance the small number of existing validation studies and compare scan and manual techniques based on five selected measurements. We assessed the agreement between two repeated measurements within the two methods, analysed the direct agreement between the two methods, and explored the differences between the techniques when used in regressions assessing the effect of health related determinants on body shape indices. Methods We performed two repeated body scans on 123 volunteering young men using a Vitus Smart XXL body scanner. We manually measured height, waist, hip, buttock, and chest circumferences twice for each participant according to the WHO guidelines. The participants also filled in a basic questionnaire. Results Mean differences between the two scan measurements were smaller than between the two manual measurements, and precision as well as intra-class correlation coefficients were higher. Both techniques were strongly correlated. When comparing means between both techniques we found significant differences: Height was systematically shorter by 2.1 cm, whereas waist, hip and bust circumference measurements were larger in the scans by 1.17–4.37 cm. In consequence, body shape indices also became larger and the prevalence of overweight was greater when calculated from the scans. Between 4.1% and 7.3% of the probands changed risk category from normal to overweight when classified based on the scans. However, when employing regression analyses the two measurement techniques resulted in very similar coefficients, confidence intervals, and p-values. Concl…
format: application/pdf
format: text/html
creator: Nikola Koepke
creator: Marcel Zwahlen
creator: Jonathan C. Wells
creator: Nicole Bender
creator: Maciej Henneberg
creator: Frank J. Rühli
creator: Kaspar Staub
subject: Anthropology
subject: Anatomy and Physiology
subject: Epidemiology
subject: Public Health
subject: Radiology and Medical Imaging
description: doi:10.7717/peerj.2980
publisher: PeerJ Inc.
rights: © 2017 Koepke et al.
abstract: Background Manual anthropometric measurements are time-consuming and challenging to perform within acceptable intra- and inter-individual error margins in large studies. Three-dimensional (3D) laser body scanners provide a fast and precise alternative: within a few seconds the system produces a 3D image of the body topography and calculates some 150 standardised body size measurements. Objective The aim was to enhance the small number of existing validation studies and compare scan and manual techniques based on five selected measurements. We assessed the agreement between two repeated measurements within the two methods, analysed the direct agreement between the two methods, and explored the differences between the techniques when used in regressions assessing the effect of health related determinants on body shape indices. Methods We performed two repeated body scans on 123 volunteering young men using a Vitus Smart XXL body scanner. We manually measured height, waist, hip, buttock, and chest circumferences twice for each participant according to the WHO guidelines. The participants also filled in a basic questionnaire. Results Mean differences between the two scan measurements were smaller than between the two manual measurements, and precision as well as intra-class correlation coefficients were higher. Both techniques were strongly correlated. When comparing means between both techniques we found significant differences: Height was systematically shorter by 2.1 cm, whereas waist, hip and bust circumference measurements were larger in the scans by 1.17–4.37 cm. In consequence, body shape indices also became larger and the prevalence of overweight was greater when calculated from the scans. Between 4.1% and 7.3% of the probands changed risk category from normal to overweight when classified based on the scans. However, when employing regression analyses the two measurement techniques resulted in very similar coefficients, confidence intervals, and p-values. Concl…
bibliographic citation: Koepke et al. (2017) Comparison of 3D laser-based photonic scans and manual anthropometric measurements of body size and shape in a validation study of 123 young Swiss men. PeerJ 5:e2980 https://doi.org/10.7717/peerj.2980
date submitted: 2016-08-26
date accepted: 2017-01-10
issued: 2017-02-09
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Koepke
  given name: Nikola
author list: Agent
  family name: Zwahlen
  given name: Marcel
author list: Agent
  family name: Wells
  given name: Jonathan C.
author list: Agent
  family name: Bender
  given name: Nicole
author list: Agent
  family name: Henneberg
  given name: Maciej
author list: Agent
  family name: Rühli
  given name: Frank J.
author list: Agent
  family name: Staub
  given name: Kaspar
doi: 10.7717/peerj.2980
volume: 5
issn: 2167-8359
publication name: PeerJ
publication date: 2017-02-09
copyright: ©2017 Koepke et al.
attribution name: Koepke et al.

Phylogenetic factorization of compositional data yields lineage-level associations in microbiome datasets
type: item
type: AcademicArticle
description: Marker gene sequencing of microbial communities has generated big datasets of microbial relative abundances varying across environmental conditions, sample sites and treatments. These data often come with putative phylogenies, providing unique opportunities to investigate how shared evolutionary history affects microbial abundance patterns. Here, we present a method to identify the phylogenetic factors driving patterns in microbial community composition. We use the method, “phylofactorization,” to re-analyze datasets from the human body and soil microbial communities, demonstrating how phylofactorization is a dimensionality-reducing tool, an ordination-visualization tool, and an inferential tool for identifying edges in the phylogeny along which putative functional ecological traits may have arisen.
format: application/pdf
format: text/html
creator: Alex D. Washburne
creator: Justin D. Silverman
creator: Jonathan W. Leff
creator: Dominic J. Bennett
creator: John L. Darcy
creator: Sayan Mukherjee
creator: Noah Fierer
creator: Lawrence A. David
subject: Computational Biology
subject: Ecology
subject: Mathematical Biology
subject: Microbiology
subject: Statistics
description: doi:10.7717/peerj.2969
publisher: PeerJ Inc.
rights: © 2017 Washburne et al.
abstract: Marker gene sequencing of microbial communities has generated big datasets of microbial relative abundances varying across environmental conditions, sample sites and treatments. These data often come with putative phylogenies, providing unique opportunities to investigate how shared evolutionary history affects microbial abundance patterns. Here, we present a method to identify the phylogenetic factors driving patterns in microbial community composition. We use the method, “phylofactorization,” to re-analyze datasets from the human body and soil microbial communities, demonstrating how phylofactorization is a dimensionality-reducing tool, an ordination-visualization tool, and an inferential tool for identifying edges in the phylogeny along which putative functional ecological traits may have arisen.
bibliographic citation: Washburne et al. (2017) Phylogenetic factorization of compositional data yields lineage-level associations in microbiome datasets. PeerJ 5:e2969 https://doi.org/10.7717/peerj.2969
date submitted: 2016-10-18
date accepted: 2017-01-09
issued: 2017-02-09
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Washburne
  given name: Alex D.
author list: Agent
  family name: Silverman
  given name: Justin D.
author list: Agent
  family name: Leff
  given name: Jonathan W.
author list: Agent
  family name: Bennett
  given name: Dominic J.
author list: Agent
  family name: Darcy
  given name: John L.
author list: Agent
  family name: Mukherjee
  given name: Sayan
author list: Agent
  family name: Fierer
  given name: Noah
author list: Agent
  family name: David
  given name: Lawrence A.
doi: 10.7717/peerj.2969
volume: 5
issn: 2167-8359
publication name: PeerJ
publication date: 2017-02-09
copyright: ©2017 Washburne et al.
attribution name: Washburne et al.

Acoustic monitoring indicates a correlation between calling and spawning in captive spotted seatrout (Cynoscion nebulosus)
type: item
type: AcademicArticle
description: Background Fish sound production is widespread throughout many families. Territorial displays and courtship are the most common reasons for fish sound production. Yet, there is still some questions on how acoustic signaling and reproduction are correlated in many sound-producing species. In the present study, our aim was to determine if a quantitative relationship exists between calling and egg deposition in captive spotted seatrout (Cynoscion nebulosus). This type of data is essential if passive acoustics is to be used to identify spawning aggregations over large spatial scales and monitor reproductive activity over annual and decadal timeframes. Methods Acoustic recorders (i.e., DSG-Oceans) were placed in three laboratory tanks to record underwater sound over an entire, simulated reproductive season. We enumerated the number of calls, calculated the received sound pressure level, and counted the number of eggs every morning in each tank. Results Spotted seatrout produced three distinct call types characterized as “drums,” “grunts,” and “staccatos.” Spotted seatrout calling increased as the light cycle shifted from 13.5 to 14.5 h of light, and the temperature increased to 27.7 °C. Calling decreased once the temperature fell below 27.7 °C, and the light cycle shifted to 12 h of light. These temperature and light patterns followed the natural reproductive season observed in wild spotted seatrout in the Southeast United States. Spotted seatrout exhibited daily rhythms in calling. Acoustic signaling began once the lights turned off, and calling reached maximum activity approximately 3 h later. Eggs were released only on evenings in which spotted seatrout were calling. In all tanks, spotted seatrout were more likely to spawn when male fish called more frequently. A positive relationship between SPL and the number of eggs collected was found in Tanks 1 and 3. Discussion Our findings indicate that acoustic metrics can predict spawning potential. These findings are importa…
format: application/pdf
format: text/html
creator: Eric W. Montie
creator: Matt Hoover
creator: Christopher Kehrer
creator: Justin Yost
creator: Karl Brenkert
creator: Tim O’Donnell
creator: Michael R. Denson
subject: Animal Behavior
subject: Marine Biology
description: doi:10.7717/peerj.2944
publisher: PeerJ Inc.
rights: © 2017 Montie et al.
abstract: Background Fish sound production is widespread throughout many families. Territorial displays and courtship are the most common reasons for fish sound production. Yet, there is still some questions on how acoustic signaling and reproduction are correlated in many sound-producing species. In the present study, our aim was to determine if a quantitative relationship exists between calling and egg deposition in captive spotted seatrout (Cynoscion nebulosus). This type of data is essential if passive acoustics is to be used to identify spawning aggregations over large spatial scales and monitor reproductive activity over annual and decadal timeframes. Methods Acoustic recorders (i.e., DSG-Oceans) were placed in three laboratory tanks to record underwater sound over an entire, simulated reproductive season. We enumerated the number of calls, calculated the received sound pressure level, and counted the number of eggs every morning in each tank. Results Spotted seatrout produced three distinct call types characterized as “drums,” “grunts,” and “staccatos.” Spotted seatrout calling increased as the light cycle shifted from 13.5 to 14.5 h of light, and the temperature increased to 27.7 °C. Calling decreased once the temperature fell below 27.7 °C, and the light cycle shifted to 12 h of light. These temperature and light patterns followed the natural reproductive season observed in wild spotted seatrout in the Southeast United States. Spotted seatrout exhibited daily rhythms in calling. Acoustic signaling began once the lights turned off, and calling reached maximum activity approximately 3 h later. Eggs were released only on evenings in which spotted seatrout were calling. In all tanks, spotted seatrout were more likely to spawn when male fish called more frequently. A positive relationship between SPL and the number of eggs collected was found in Tanks 1 and 3. Discussion Our findings indicate that acoustic metrics can predict spawning potential. These findings are importa…
bibliographic citation: Montie et al. (2017) Acoustic monitoring indicates a correlation between calling and spawning in captive spotted seatrout (Cynoscion nebulosus). PeerJ 5:e2944 https://doi.org/10.7717/peerj.2944
date submitted: 2016-10-11
date accepted: 2016-12-27
issued: 2017-02-09
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Montie
  given name: Eric W.
author list: Agent
  family name: Hoover
  given name: Matt
author list: Agent
  family name: Kehrer
  given name: Christopher
author list: Agent
  family name: Yost
  given name: Justin
author list: Agent
  family name: Brenkert
  given name: Karl
author list: Agent
  family name: O’Donnell
  given name: Tim
author list: Agent
  family name: Denson
  given name: Michael R.
doi: 10.7717/peerj.2944
volume: 5
issn: 2167-8359
publication name: PeerJ
publication date: 2017-02-09
copyright: ©2017 Montie et al.
attribution name: Montie et al.

Molecular characterization and genetic diversity of Jatropha curcas L. in Costa Rica
type: item
type: AcademicArticle
description: We estimated the genetic diversity of 50 Jatropha curcas samples from the Costa Rican germplasm bank using 18 EST-SSR, one G-SSR and nrDNA-ITS markers. We also evaluated the phylogenetic relationships among samples using nuclear ribosomal ITS markers. Non-toxicity was evaluated using G-SSRs and SCARs markers. A Neighbor-Joining (NJ) tree and a Maximum Likelihood (ML) tree were constructed using SSR markers and ITS sequences, respectively. Heterozygosity was moderate (He = 0.346), but considerable compared to worldwide values for J. curcas. The PIC (PIC = 0.274) and inbreeding coefficient (f = − 0.102) were both low. Clustering was not related to the geographical origin of accessions. International accessions clustered independently of collection sites, suggesting a lack of genetic structure, probably due to the wide distribution of this crop and ample gene flow. Molecular markers identified only one non-toxic accession (JCCR-24) from Mexico. This work is part of a countrywide effort to characterize the genetic diversity of the Jatropha curcas germplasm bank in Costa Rica.
format: application/pdf
format: text/html
creator: Marcela Vásquez-Mayorga
creator: Eric J. Fuchs
creator: Eduardo J. Hernández
creator: Franklin Herrera
creator: Jesús Hernández
creator: Ileana Moreira
creator: Elizabeth Arnáez
creator: Natalia M. Barboza
subject: Biodiversity
subject: Molecular Biology
subject: Plant Science
description: doi:10.7717/peerj.2931
publisher: PeerJ Inc.
rights: © 2017 Vásquez-Mayorga et al.
abstract: We estimated the genetic diversity of 50 Jatropha curcas samples from the Costa Rican germplasm bank using 18 EST-SSR, one G-SSR and nrDNA-ITS markers. We also evaluated the phylogenetic relationships among samples using nuclear ribosomal ITS markers. Non-toxicity was evaluated using G-SSRs and SCARs markers. A Neighbor-Joining (NJ) tree and a Maximum Likelihood (ML) tree were constructed using SSR markers and ITS sequences, respectively. Heterozygosity was moderate (He = 0.346), but considerable compared to worldwide values for J. curcas. The PIC (PIC = 0.274) and inbreeding coefficient (f = − 0.102) were both low. Clustering was not related to the geographical origin of accessions. International accessions clustered independently of collection sites, suggesting a lack of genetic structure, probably due to the wide distribution of this crop and ample gene flow. Molecular markers identified only one non-toxic accession (JCCR-24) from Mexico. This work is part of a countrywide effort to characterize the genetic diversity of the Jatropha curcas germplasm bank in Costa Rica.
bibliographic citation: Vásquez-Mayorga et al. (2017) Molecular characterization and genetic diversity of Jatropha curcas L. in Costa Rica. PeerJ 5:e2931 https://doi.org/10.7717/peerj.2931
date submitted: 2016-09-20
date accepted: 2016-12-21
issued: 2017-02-09
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Vásquez-Mayorga
  given name: Marcela
author list: Agent
  family name: Fuchs
  given name: Eric J.
author list: Agent
  family name: Hernández
  given name: Eduardo J.
author list: Agent
  family name: Herrera
  given name: Franklin
author list: Agent
  family name: Hernández
  given name: Jesús
author list: Agent
  family name: Moreira
  given name: Ileana
author list: Agent
  family name: Arnáez
  given name: Elizabeth
author list: Agent
  family name: Barboza
  given name: Natalia M.
doi: 10.7717/peerj.2931
volume: 5
issn: 2167-8359
publication name: PeerJ
publication date: 2017-02-09
copyright: ©2017 Vásquez-Mayorga et al.
attribution name: Vásquez-Mayorga et al.

Candidate genes that have facilitated freshwater adaptation by palaemonid prawns in the genus Macrobrachium: identification and expression validation in a model species (M. koombooloomba)
type: item
type: AcademicArticle
description: Background The endemic Australian freshwater prawn, Macrobrachium koombooloomba, provides a model for exploring genes involved with freshwater adaptation because it is one of the relatively few Macrobrachium species that can complete its entire life cycle in freshwater. Methods The present study was conducted to identify potential candidate genes that are likely to contribute to effective freshwater adaptation by M. koombooloomba using a transcriptomics approach. De novo assembly of 75 bp paired end 227,564,643 high quality Illumina raw reads from 6 different cDNA libraries revealed 125,917 contigs of variable lengths (200–18,050 bp) with an N50 value of 1597. Results In total, 31,272 (24.83%) of the assembled contigs received significant blast hits, of which 27,686 and 22,560 contigs were mapped and functionally annotated, respectively. CEGMA (Core Eukaryotic Genes Mapping Approach) based transcriptome quality assessment revealed 96.37% completeness. We identified 43 different potential genes that are likely to be involved with freshwater adaptation in M. koombooloomba. Identified candidate genes included: 25 genes for osmoregulation, five for cell volume regulation, seven for stress tolerance, three for body fluid (haemolymph) maintenance, eight for epithelial permeability and water channel regulation, nine for egg size control and three for larval development. RSEM (RNA-Seq Expectation Maximization) based abundance estimation revealed that 6,253, 5,753 and 3,795 transcripts were expressed (at TPM value ≥10) in post larvae, juveniles and adults, respectively. Differential gene expression (DGE) analysis showed that 15 genes were expressed differentially in different individuals but these genes apparently were not involved with freshwater adaptation but rather were involved in growth, development and reproductive maturation. Discussion The genomic resources developed here will be useful for better understanding the molecular basis of freshwater adaptation in Macrobr…
format: application/pdf
format: text/html
creator: Md Lifat Rahi
creator: Shorash Amin
creator: Peter B. Mather
creator: David A. Hurwood
subject: Aquaculture, Fisheries and Fish Science
subject: Evolutionary Studies
subject: Freshwater Biology
subject: Genomics
subject: Marine Biology
description: doi:10.7717/peerj.2977
publisher: PeerJ Inc.
rights: © 2017 Rahi et al.
abstract: Background The endemic Australian freshwater prawn, Macrobrachium koombooloomba, provides a model for exploring genes involved with freshwater adaptation because it is one of the relatively few Macrobrachium species that can complete its entire life cycle in freshwater. Methods The present study was conducted to identify potential candidate genes that are likely to contribute to effective freshwater adaptation by M. koombooloomba using a transcriptomics approach. De novo assembly of 75 bp paired end 227,564,643 high quality Illumina raw reads from 6 different cDNA libraries revealed 125,917 contigs of variable lengths (200–18,050 bp) with an N50 value of 1597. Results In total, 31,272 (24.83%) of the assembled contigs received significant blast hits, of which 27,686 and 22,560 contigs were mapped and functionally annotated, respectively. CEGMA (Core Eukaryotic Genes Mapping Approach) based transcriptome quality assessment revealed 96.37% completeness. We identified 43 different potential genes that are likely to be involved with freshwater adaptation in M. koombooloomba. Identified candidate genes included: 25 genes for osmoregulation, five for cell volume regulation, seven for stress tolerance, three for body fluid (haemolymph) maintenance, eight for epithelial permeability and water channel regulation, nine for egg size control and three for larval development. RSEM (RNA-Seq Expectation Maximization) based abundance estimation revealed that 6,253, 5,753 and 3,795 transcripts were expressed (at TPM value ≥10) in post larvae, juveniles and adults, respectively. Differential gene expression (DGE) analysis showed that 15 genes were expressed differentially in different individuals but these genes apparently were not involved with freshwater adaptation but rather were involved in growth, development and reproductive maturation. Discussion The genomic resources developed here will be useful for better understanding the molecular basis of freshwater adaptation in Macrobr…
bibliographic citation: Rahi et al. (2017) Candidate genes that have facilitated freshwater adaptation by palaemonid prawns in the genus Macrobrachium: identification and expression validation in a model species (M. koombooloomba). PeerJ 5:e2977 https://doi.org/10.7717/peerj.2977
date submitted: 2016-09-28
date accepted: 2017-01-10
issued: 2017-02-08
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Rahi
  given name: Md Lifat
author list: Agent
  family name: Amin
  given name: Shorash
author list: Agent
  family name: Mather
  given name: Peter B.
author list: Agent
  family name: Hurwood
  given name: David A.
doi: 10.7717/peerj.2977
volume: 5
issn: 2167-8359
publication name: PeerJ
publication date: 2017-02-08
copyright: ©2017 Rahi et al.
attribution name: Rahi et al.

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