PeerJ
type: channel
link: https://peerj.com/articles/
description: Articles published in PeerJ
publisher: PeerJ Inc.
publication name: PeerJ
issn: 2167-8359
items: The Spanish version of the Fatigue Assessment Scale: reliability and validity assessment in postpartum women
items: Estimating the age of Heliconius butterflies from calibrated photographs
items: Increased utilization of fructose has a positive effect on the development of breast cancer
items: Identification of reference genes in blood before and after entering the plateau for SYBR green RT-qPCR studies
items: Estimated effects of implementing an open access policy for grantees at a private foundation
items: Historical dynamics and current environmental effects explain the spatial distribution of species richness patterns of New World monkeys
items: The Legionella pneumophila effector Lpg1137 is a homologue of mitochondrial SLC25 carrier proteins, not of known serine proteases
items: Ananke: temporal clustering reveals ecological dynamics of microbial communities
items: Gene expression of benthic amphipods (genus: Diporeia) in relation to a circular ssDNA virus across two Laurentian Great Lakes
items: Bacterial community associated with worker honeybees (Apis mellifera) affected by European foulbrood

The Spanish version of the Fatigue Assessment Scale: reliability and validity assessment in postpartum women
type: item
type: AcademicArticle
description: Background Fatigue is the most widely reported symptom by women during pregnancy, labour, the postpartum period, and early parenting. The objective was to translate the Fatigue Assessment Scale (FAS) into Spanish and assess its psychometric properties. Methods Instrumental Design. The FAS was translated into Spanish (FAS-e) using forward and back translation. A convenience sample was constituted with 870 postpartum women recruited at discharge from 17 public hospitals in Eastern Spain. Data was obtained from clinical records and self-administered questionnaires at discharge. Internal consistency, factor structure, comparisons between known groups and correlations with other variables were assessed. Results Cronbach’s alpha coefficient was .80. Findings on the dimensionality of the FAS-e scale indicated that it was sufficiently unidimensional. FAS-e scores were higher among women who had undergone caesarean births (p < .05), had a higher level of postpartum pain (p < .01), experienced difficulties during breastfeeding (p < .01) and had lower levels of self-efficacy for breastfeeding (p < .01). Conclusions An equivalent Spanish version of the FAS was obtained with good reliability and validity properties. FAS-e is an appropriate tool to measure postpartum fatigue.
format: application/pdf
format: text/html
creator: Antoni Cano-Climent
creator: Antonio Oliver-Roig
creator: Julio Cabrero-García
creator: Jolanda de Vries
creator: Miguel Richart-Martínez
subject: Nursing
subject: Psychiatry and Psychology
subject: Women's Health
description: doi:10.7717/peerj.3832
publisher: PeerJ Inc.
rights: © 2017 Cano-Climent et al.
abstract: Background Fatigue is the most widely reported symptom by women during pregnancy, labour, the postpartum period, and early parenting. The objective was to translate the Fatigue Assessment Scale (FAS) into Spanish and assess its psychometric properties. Methods Instrumental Design. The FAS was translated into Spanish (FAS-e) using forward and back translation. A convenience sample was constituted with 870 postpartum women recruited at discharge from 17 public hospitals in Eastern Spain. Data was obtained from clinical records and self-administered questionnaires at discharge. Internal consistency, factor structure, comparisons between known groups and correlations with other variables were assessed. Results Cronbach’s alpha coefficient was .80. Findings on the dimensionality of the FAS-e scale indicated that it was sufficiently unidimensional. FAS-e scores were higher among women who had undergone caesarean births (p < .05), had a higher level of postpartum pain (p < .01), experienced difficulties during breastfeeding (p < .01) and had lower levels of self-efficacy for breastfeeding (p < .01). Conclusions An equivalent Spanish version of the FAS was obtained with good reliability and validity properties. FAS-e is an appropriate tool to measure postpartum fatigue.
bibliographic citation: Cano-Climent et al. (2017) The Spanish version of the Fatigue Assessment Scale: reliability and validity assessment in postpartum women. PeerJ 5:e3832 https://doi.org/10.7717/peerj.3832
date submitted: 2017-04-28
date accepted: 2017-08-30
issued: 2017-09-27
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Cano-Climent
  given name: Antoni
author list: Agent
  family name: Oliver-Roig
  given name: Antonio
author list: Agent
  family name: Cabrero-García
  given name: Julio
author list: Agent
  family name: de Vries
  given name: Jolanda
author list: Agent
  family name: Richart-Martínez
  given name: Miguel
doi: 10.7717/peerj.3832
volume: 5
issn: 2167-8359
publication name: PeerJ
publication date: 2017-09-27
copyright: ©2017 Cano-Climent et al.
attribution name: Cano-Climent et al.

Estimating the age of Heliconius butterflies from calibrated photographs
type: item
type: AcademicArticle
description: Mating behaviour and predation avoidance in Heliconius involve visual colour signals; however, there is considerable inter-individual phenotypic variation in the appearance of colours. In particular, the red pigment varies from bright crimson to faded red. It has been thought that this variation is primarily due to pigment fading with age, although this has not been explicitly tested. Previous studies have shown the importance of red patterns in mate choice and that birds and butterflies might perceive these small colour differences. Using digital photography and calibrated colour images, we investigated whether the hue variation in the forewing dorsal red band of Heliconius melpomene rosina corresponds with age. We found that the red hue and age were highly associated, suggesting that red colour can indeed be used as a proxy for age in the study of wild-caught butterflies.
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creator: Denise Dalbosco Dell’Aglio
creator: Derya Akkaynak
creator: W. Owen McMillan
creator: Chris D. Jiggins
subject: Animal Behavior
subject: Bioinformatics
subject: Ecology
subject: Entomology
subject: Zoology
description: doi:10.7717/peerj.3821
publisher: PeerJ Inc.
rights: © 2017 Dalbosco Dell’Aglio et al.
abstract: Mating behaviour and predation avoidance in Heliconius involve visual colour signals; however, there is considerable inter-individual phenotypic variation in the appearance of colours. In particular, the red pigment varies from bright crimson to faded red. It has been thought that this variation is primarily due to pigment fading with age, although this has not been explicitly tested. Previous studies have shown the importance of red patterns in mate choice and that birds and butterflies might perceive these small colour differences. Using digital photography and calibrated colour images, we investigated whether the hue variation in the forewing dorsal red band of Heliconius melpomene rosina corresponds with age. We found that the red hue and age were highly associated, suggesting that red colour can indeed be used as a proxy for age in the study of wild-caught butterflies.
bibliographic citation: Dalbosco Dell’Aglio et al. (2017) Estimating the age of Heliconius butterflies from calibrated photographs. PeerJ 5:e3821 https://doi.org/10.7717/peerj.3821
date submitted: 2017-06-01
date accepted: 2017-08-28
issued: 2017-09-27
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Dalbosco Dell’Aglio
  given name: Denise
author list: Agent
  family name: Akkaynak
  given name: Derya
author list: Agent
  family name: McMillan
  given name: W. Owen
author list: Agent
  family name: Jiggins
  given name: Chris D.
doi: 10.7717/peerj.3821
volume: 5
issn: 2167-8359
publication name: PeerJ
publication date: 2017-09-27
copyright: ©2017 Dalbosco Dell’Aglio et al.
attribution name: Dalbosco Dell’Aglio et al.

Increased utilization of fructose has a positive effect on the development of breast cancer
type: item
type: AcademicArticle
description: Rapid proliferation and Warburg effect make cancer cells consume plenty of glucose, which induces a low glucose micro-environment within the tumor. Up to date, how cancer cells keep proliferating in the condition of glucose insufficiency still remains to be explored. Recent studies have revealed a close correlation between excessive fructose consumption and breast cancer genesis and progression, but there is no convincing evidence showing that fructose could directly promote breast cancer development. Herein, we found that fructose, not amino acids, could functionally replace glucose to support proliferation of breast cancer cells. Fructose endowed breast cancer cells with the colony formation ability and migratory capacity as effective as glucose. Interestingly, although fructose was readily used by breast cancer cells, it failed to restore proliferation of non-tumor cells in the absence of glucose. These results suggest that fructose could be relatively selectively employed by breast cancer cells. Indeed, we observed that a main transporter of fructose, GLUT5, was highly expressed in breast cancer cells and tumor tissues but not in their normal counterparts. Furthermore, we demonstrated that the fructose diet promoted metastasis of 4T1 cells in the mouse models. Taken together, our data show that fructose can be used by breast cancer cells specifically in glucose-deficiency, and suggest that the high-fructose diet could accelerate the progress of breast cancer in vivo.
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creator: Xiajing Fan
creator: Hongru Liu
creator: Miao Liu
creator: Yuanyuan Wang
creator: Li Qiu
creator: Yanfen Cui
subject: Biochemistry
subject: Cell Biology
subject: Oncology
description: doi:10.7717/peerj.3804
publisher: PeerJ Inc.
rights: © 2017 Fan et al.
abstract: Rapid proliferation and Warburg effect make cancer cells consume plenty of glucose, which induces a low glucose micro-environment within the tumor. Up to date, how cancer cells keep proliferating in the condition of glucose insufficiency still remains to be explored. Recent studies have revealed a close correlation between excessive fructose consumption and breast cancer genesis and progression, but there is no convincing evidence showing that fructose could directly promote breast cancer development. Herein, we found that fructose, not amino acids, could functionally replace glucose to support proliferation of breast cancer cells. Fructose endowed breast cancer cells with the colony formation ability and migratory capacity as effective as glucose. Interestingly, although fructose was readily used by breast cancer cells, it failed to restore proliferation of non-tumor cells in the absence of glucose. These results suggest that fructose could be relatively selectively employed by breast cancer cells. Indeed, we observed that a main transporter of fructose, GLUT5, was highly expressed in breast cancer cells and tumor tissues but not in their normal counterparts. Furthermore, we demonstrated that the fructose diet promoted metastasis of 4T1 cells in the mouse models. Taken together, our data show that fructose can be used by breast cancer cells specifically in glucose-deficiency, and suggest that the high-fructose diet could accelerate the progress of breast cancer in vivo.
bibliographic citation: Fan et al. (2017) Increased utilization of fructose has a positive effect on the development of breast cancer. PeerJ 5:e3804 https://doi.org/10.7717/peerj.3804
date submitted: 2017-04-18
date accepted: 2017-08-23
issued: 2017-09-27
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Fan
  given name: Xiajing
author list: Agent
  family name: Liu
  given name: Hongru
author list: Agent
  family name: Liu
  given name: Miao
author list: Agent
  family name: Wang
  given name: Yuanyuan
author list: Agent
  family name: Qiu
  given name: Li
author list: Agent
  family name: Cui
  given name: Yanfen
doi: 10.7717/peerj.3804
volume: 5
issn: 2167-8359
publication name: PeerJ
publication date: 2017-09-27
copyright: ©2017 Fan et al.
attribution name: Fan et al.

Identification of reference genes in blood before and after entering the plateau for SYBR green RT-qPCR studies
type: item
type: AcademicArticle
description: Background Tibetans have lived at high altitudes for thousands of years, and they have unique physiological traits that enable them to tolerate this hypoxic environment. However, the genetic basis of these traits is still unknown. As a sensitive and highly efficient technique, RT-qPCR is widely used in gene expression analyses to provide insight into the molecular mechanisms underlying environmental changes. However, the quantitative analysis of gene expression in blood is limited by a shortage of stable reference genes for the normalization of mRNA levels. Thus, systematic approaches were used to identify potential reference genes. Results The expression levels of eight candidate human reference genes (GAPDH, ACTB, 18S RNA, β2-MG, PPIA, RPL13A, TBP and SDHA) were assessed in blood from hypoxic environments. The expression stability of these selected reference genes was evaluated using the geNorm, NormFinder and BestKeeper programs. Interestingly, RPL13A was identified as the ideal reference gene for normalizing target gene expression in human blood before and after exposure to high-altitude conditions. Conclusion These results indicate that different reference genes should be selected for the normalization of gene expression in blood from different environmental settings.
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creator: Jun Xiao
creator: Xiaowei Li
creator: Juan Liu
creator: Xiu Fan
creator: Huifen Lei
creator: Cuiying Li
subject: Molecular Biology
subject: Hematology
description: doi:10.7717/peerj.3726
publisher: PeerJ Inc.
rights: © 2017 Xiao et al.
abstract: Background Tibetans have lived at high altitudes for thousands of years, and they have unique physiological traits that enable them to tolerate this hypoxic environment. However, the genetic basis of these traits is still unknown. As a sensitive and highly efficient technique, RT-qPCR is widely used in gene expression analyses to provide insight into the molecular mechanisms underlying environmental changes. However, the quantitative analysis of gene expression in blood is limited by a shortage of stable reference genes for the normalization of mRNA levels. Thus, systematic approaches were used to identify potential reference genes. Results The expression levels of eight candidate human reference genes (GAPDH, ACTB, 18S RNA, β2-MG, PPIA, RPL13A, TBP and SDHA) were assessed in blood from hypoxic environments. The expression stability of these selected reference genes was evaluated using the geNorm, NormFinder and BestKeeper programs. Interestingly, RPL13A was identified as the ideal reference gene for normalizing target gene expression in human blood before and after exposure to high-altitude conditions. Conclusion These results indicate that different reference genes should be selected for the normalization of gene expression in blood from different environmental settings.
bibliographic citation: Xiao et al. (2017) Identification of reference genes in blood before and after entering the plateau for SYBR green RT-qPCR studies. PeerJ 5:e3726 https://doi.org/10.7717/peerj.3726
date submitted: 2017-04-13
date accepted: 2017-08-01
issued: 2017-09-27
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Xiao
  given name: Jun
author list: Agent
  family name: Li
  given name: Xiaowei
author list: Agent
  family name: Liu
  given name: Juan
author list: Agent
  family name: Fan
  given name: Xiu
author list: Agent
  family name: Lei
  given name: Huifen
author list: Agent
  family name: Li
  given name: Cuiying
doi: 10.7717/peerj.3726
volume: 5
issn: 2167-8359
publication name: PeerJ
publication date: 2017-09-27
copyright: ©2017 Xiao et al.
attribution name: Xiao et al.

Estimated effects of implementing an open access policy for grantees at a private foundation
type: item
type: AcademicArticle
description: Background The Gordon and Betty Moore Foundation (GBMF) was interested in understanding the potential effects of requiring that grantees publish their peer-reviewed research in open access journals. Methods We collected data on more than 2,000 publications in over 500 journals that were generated by GBMF grantees since 2001. We then examined the journal policies to establish how two possible open access policies might have affected grantee publishing habits. Results We found that 99.3% of the articles published by grantees would have complied with a policy that requires open access within 12 months of publication. We also estimated the maximum annual costs to GBMF for covering fees associated with “gold open access” to be between $400,000 and $2,600,000 annually. Discussion Based in part on this study, GBMF has implemented a new open access policy that requires grantees make peer-reviewed publications fully available within 12 months.
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creator: Carly Strasser
creator: Eesha Khare
subject: Ethical Issues
subject: Science and Medical Education
subject: Science Policy
description: doi:10.7717/peerj.3853
publisher: PeerJ Inc.
rights: © 2017 Strasser and Khare
abstract: Background The Gordon and Betty Moore Foundation (GBMF) was interested in understanding the potential effects of requiring that grantees publish their peer-reviewed research in open access journals. Methods We collected data on more than 2,000 publications in over 500 journals that were generated by GBMF grantees since 2001. We then examined the journal policies to establish how two possible open access policies might have affected grantee publishing habits. Results We found that 99.3% of the articles published by grantees would have complied with a policy that requires open access within 12 months of publication. We also estimated the maximum annual costs to GBMF for covering fees associated with “gold open access” to be between $400,000 and $2,600,000 annually. Discussion Based in part on this study, GBMF has implemented a new open access policy that requires grantees make peer-reviewed publications fully available within 12 months.
bibliographic citation: Strasser et al. (2017) Estimated effects of implementing an open access policy for grantees at a private foundation. PeerJ 5:e3853 https://doi.org/10.7717/peerj.3853
date submitted: 2017-05-10
date accepted: 2017-09-05
issued: 2017-09-26
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Strasser
  given name: Carly
author list: Agent
  family name: Khare
  given name: Eesha
doi: 10.7717/peerj.3853
volume: 5
issn: 2167-8359
publication name: PeerJ
publication date: 2017-09-26
copyright: ©2017 Strasser and Khare
attribution name: Strasser and Khare

Historical dynamics and current environmental effects explain the spatial distribution of species richness patterns of New World monkeys
type: item
type: AcademicArticle
description: Background Why biodiversity is not uniformly distributed on the Earth is a major research question of biogeography. One of the most striking patterns of disparity in species distribution are the biodiversity hotspots, which generally do not fit with the distribution of relevant components of the Neotropical biota. In this study, we assess the proximal causes of the species-richness pattern of one of the most conspicuous groups of Neotropical mammals, the New World monkeys the Platyrrhini. We test two complementary hypotheses: (1) there is a historical source-sink dynamic (addressed using macroevolutionary and macroecological approaches); (2) the large number of species in the Amazon basin is due to the constraints imposed by environmental variables occurring outside this area. Methods We first characterize spatial patterns of species richness and biodiversity hotspots using a new, objective protocol based on probabilities. Then we evaluate the source-sink hypothesis using BioGeoBEARS analysis and nestedness analysis of species richness patterns. Complementarily, to measure how often different species pairs appear in the same sites, we used null models to estimate the checkerboard score index (C-score). Finally, we evaluate the relationship between several climatic variables and species richness through ordinary least squares (OLS) and spatial autoregressive (SAR) models, and the potential environmental constraints on the pattern. Results We found one significant cluster of high values for species richness in the Amazon basin. Most dispersal events occurred from the Amazonian subregion to other Neotropical areas. Temperature (T), discrepancy (BR), and NODF indexes show a significant nesting in the matrix ordered by species richness and available energy. The C-score observed was significantly smaller than the null expectation for all sites in the Neotropics where there are records of platyrrhine species. Ten climatic variables comprised the best-fitting model that exp…
format: application/pdf
format: text/html
creator: Paulo Vallejos-Garrido
creator: Reinaldo Rivera
creator: Oscar Inostroza-Michael
creator: Enrique Rodríguez-Serrano
creator: Cristián E. Hernández
subject: Biodiversity
subject: Biogeography
description: doi:10.7717/peerj.3850
publisher: PeerJ Inc.
rights: © 2017 Vallejos-Garrido et al.
abstract: Background Why biodiversity is not uniformly distributed on the Earth is a major research question of biogeography. One of the most striking patterns of disparity in species distribution are the biodiversity hotspots, which generally do not fit with the distribution of relevant components of the Neotropical biota. In this study, we assess the proximal causes of the species-richness pattern of one of the most conspicuous groups of Neotropical mammals, the New World monkeys the Platyrrhini. We test two complementary hypotheses: (1) there is a historical source-sink dynamic (addressed using macroevolutionary and macroecological approaches); (2) the large number of species in the Amazon basin is due to the constraints imposed by environmental variables occurring outside this area. Methods We first characterize spatial patterns of species richness and biodiversity hotspots using a new, objective protocol based on probabilities. Then we evaluate the source-sink hypothesis using BioGeoBEARS analysis and nestedness analysis of species richness patterns. Complementarily, to measure how often different species pairs appear in the same sites, we used null models to estimate the checkerboard score index (C-score). Finally, we evaluate the relationship between several climatic variables and species richness through ordinary least squares (OLS) and spatial autoregressive (SAR) models, and the potential environmental constraints on the pattern. Results We found one significant cluster of high values for species richness in the Amazon basin. Most dispersal events occurred from the Amazonian subregion to other Neotropical areas. Temperature (T), discrepancy (BR), and NODF indexes show a significant nesting in the matrix ordered by species richness and available energy. The C-score observed was significantly smaller than the null expectation for all sites in the Neotropics where there are records of platyrrhine species. Ten climatic variables comprised the best-fitting model that exp…
bibliographic citation: Vallejos-Garrido et al. (2017) Historical dynamics and current environmental effects explain the spatial distribution of species richness patterns of New World monkeys. PeerJ 5:e3850 https://doi.org/10.7717/peerj.3850
date submitted: 2017-01-11
date accepted: 2017-09-05
issued: 2017-09-26
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Vallejos-Garrido
  given name: Paulo
author list: Agent
  family name: Rivera
  given name: Reinaldo
author list: Agent
  family name: Inostroza-Michael
  given name: Oscar
author list: Agent
  family name: Rodríguez-Serrano
  given name: Enrique
author list: Agent
  family name: Hernández
  given name: Cristián E.
doi: 10.7717/peerj.3850
volume: 5
issn: 2167-8359
publication name: PeerJ
publication date: 2017-09-26
copyright: ©2017 Vallejos-Garrido et al.
attribution name: Vallejos-Garrido et al.

The Legionella pneumophila effector Lpg1137 is a homologue of mitochondrial SLC25 carrier proteins, not of known serine proteases
type: item
type: AcademicArticle
description: Many bacterial effector proteins that are delivered to host cells during infection are enzymes targeting host cell signalling. Recently, Legionella pneumophila effector Lpg1137 was experimentally characterised as a serine protease that cleaves human syntaxin 17. We present strong bioinformatic evidence that Lpg1137 is a homologue of mitochondrial carrier proteins and is not related to known serine proteases. We also discuss how this finding can be reconciled with the apparently contradictory experimental results.
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creator: Marcin Gradowski
creator: Krzysztof Pawłowski
subject: Bioinformatics
subject: Molecular Biology
description: doi:10.7717/peerj.3849
publisher: PeerJ Inc.
rights: © 2017 Gradowski and Pawłowski
abstract: Many bacterial effector proteins that are delivered to host cells during infection are enzymes targeting host cell signalling. Recently, Legionella pneumophila effector Lpg1137 was experimentally characterised as a serine protease that cleaves human syntaxin 17. We present strong bioinformatic evidence that Lpg1137 is a homologue of mitochondrial carrier proteins and is not related to known serine proteases. We also discuss how this finding can be reconciled with the apparently contradictory experimental results.
bibliographic citation: Gradowski et al. (2017) The Legionella pneumophila effector Lpg1137 is a homologue of mitochondrial SLC25 carrier proteins, not of known serine proteases. PeerJ 5:e3849 https://doi.org/10.7717/peerj.3849
date submitted: 2017-06-16
date accepted: 2017-09-01
issued: 2017-09-26
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Gradowski
  given name: Marcin
author list: Agent
  family name: Pawłowski
  given name: Krzysztof
doi: 10.7717/peerj.3849
volume: 5
issn: 2167-8359
publication name: PeerJ
publication date: 2017-09-26
copyright: ©2017 Gradowski and Pawłowski
attribution name: Gradowski and Pawłowski

Ananke: temporal clustering reveals ecological dynamics of microbial communities
type: item
type: AcademicArticle
description: Taxonomic markers such as the 16S ribosomal RNA gene are widely used in microbial community analysis. A common first step in marker-gene analysis is grouping genes into clusters to reduce data sets to a more manageable size and potentially mitigate the effects of sequencing error. Instead of clustering based on sequence identity, marker-gene data sets collected over time can be clustered based on temporal correlation to reveal ecologically meaningful associations. We present Ananke, a free and open-source algorithm and software package that complements existing sequence-identity-based clustering approaches by clustering marker-gene data based on time-series profiles and provides interactive visualization of clusters, including highlighting of internal OTU inconsistencies. Ananke is able to cluster distinct temporal patterns from simulations of multiple ecological patterns, such as periodic seasonal dynamics and organism appearances/disappearances. We apply our algorithm to two longitudinal marker gene data sets: faecal communities from the human gut of an individual sampled over one year, and communities from a freshwater lake sampled over eleven years. Within the gut, the segregation of the bacterial community around a food-poisoning event was immediately clear. In the freshwater lake, we found that high sequence identity between marker genes does not guarantee similar temporal dynamics, and Ananke time-series clusters revealed patterns obscured by clustering based on sequence identity or taxonomy. Ananke is free and open-source software available at https://github.com/beiko-lab/ananke.
format: application/pdf
format: text/html
creator: Michael W. Hall
creator: Robin R. Rohwer
creator: Jonathan Perrie
creator: Katherine D. McMahon
creator: Robert G. Beiko
subject: Bioinformatics
subject: Ecology
subject: Microbiology
subject: Computational Science
description: doi:10.7717/peerj.3812
publisher: PeerJ Inc.
rights: © 2017 Hall et al.
abstract: Taxonomic markers such as the 16S ribosomal RNA gene are widely used in microbial community analysis. A common first step in marker-gene analysis is grouping genes into clusters to reduce data sets to a more manageable size and potentially mitigate the effects of sequencing error. Instead of clustering based on sequence identity, marker-gene data sets collected over time can be clustered based on temporal correlation to reveal ecologically meaningful associations. We present Ananke, a free and open-source algorithm and software package that complements existing sequence-identity-based clustering approaches by clustering marker-gene data based on time-series profiles and provides interactive visualization of clusters, including highlighting of internal OTU inconsistencies. Ananke is able to cluster distinct temporal patterns from simulations of multiple ecological patterns, such as periodic seasonal dynamics and organism appearances/disappearances. We apply our algorithm to two longitudinal marker gene data sets: faecal communities from the human gut of an individual sampled over one year, and communities from a freshwater lake sampled over eleven years. Within the gut, the segregation of the bacterial community around a food-poisoning event was immediately clear. In the freshwater lake, we found that high sequence identity between marker genes does not guarantee similar temporal dynamics, and Ananke time-series clusters revealed patterns obscured by clustering based on sequence identity or taxonomy. Ananke is free and open-source software available at https://github.com/beiko-lab/ananke.
bibliographic citation: Hall et al. (2017) Ananke: temporal clustering reveals ecological dynamics of microbial communities. PeerJ 5:e3812 https://doi.org/10.7717/peerj.3812
date submitted: 2017-03-13
date accepted: 2017-08-25
issued: 2017-09-26
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Hall
  given name: Michael W.
author list: Agent
  family name: Rohwer
  given name: Robin R.
author list: Agent
  family name: Perrie
  given name: Jonathan
author list: Agent
  family name: McMahon
  given name: Katherine D.
author list: Agent
  family name: Beiko
  given name: Robert G.
doi: 10.7717/peerj.3812
volume: 5
issn: 2167-8359
publication name: PeerJ
publication date: 2017-09-26
copyright: ©2017 Hall et al.
attribution name: Hall et al.

Gene expression of benthic amphipods (genus: Diporeia) in relation to a circular ssDNA virus across two Laurentian Great Lakes
type: item
type: AcademicArticle
description: Circular rep-encoding ssDNA (CRESS-DNA) viruses are common constituents of invertebrate viral consortia. Despite their ubiquity and sequence diversity, the effects of CRESS-DNA viruses on invertebrate biology and ecology remain largely unknown. This study assessed the relationship between the transcriptional profile of benthic amphipods of genus Diporeia and the presence of the CRESS-DNA virus, LM29173, in the Laurentian Great Lakes to provide potential insight into the influence of these viruses on invertebrate gene expression. Twelve transcriptomes derived from Diporeia were compared, representing organisms from two amphipod haplotype clades (Great Lakes Michigan and Superior, defined by COI barcode sequencing) with varying viral loads (up to 3 × 106 genome copies organism−1). Read recruitment to de novo assembled transcripts revealed 2,208 significantly over or underexpressed contigs in transcriptomes with above average LM29173 load. Of these contigs, 31.5% were assigned a putative function. The greatest proportion of annotated, differentially expressed transcripts were associated with functions including: (1) replication, recombination, and repair, (2) cell structure/biogenesis, and (3) post-translational modification, protein turnover, and chaperones. Contigs putatively associated with innate immunity displayed no consistent pattern of expression, though several transcripts were significantly overexpressed in amphipods with high viral load. Quantitation (RT-qPCR) of target transcripts, non-muscular myosin heavy chain, β-actin, and ubiquitin-conjugating enzyme E2, corroborated transcriptome analysis and indicated that Lake Michigan and Lake Superior amphipods with high LM29173 load exhibit lake-specific trends in gene expression. While this investigation provides the first comparative survey of the transcriptional profile of invertebrates of variable CRESS-DNA viral load, additional inquiry is required to define the scope of host-specific responses to potential …
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creator: Kalia S.I. Bistolas
creator: Lars G. Rudstam
creator: Ian Hewson
subject: Ecology
subject: Genomics
subject: Microbiology
subject: Virology
subject: Freshwater Biology
description: doi:10.7717/peerj.3810
publisher: PeerJ Inc.
rights: © 2017 Bistolas et al.
abstract: Circular rep-encoding ssDNA (CRESS-DNA) viruses are common constituents of invertebrate viral consortia. Despite their ubiquity and sequence diversity, the effects of CRESS-DNA viruses on invertebrate biology and ecology remain largely unknown. This study assessed the relationship between the transcriptional profile of benthic amphipods of genus Diporeia and the presence of the CRESS-DNA virus, LM29173, in the Laurentian Great Lakes to provide potential insight into the influence of these viruses on invertebrate gene expression. Twelve transcriptomes derived from Diporeia were compared, representing organisms from two amphipod haplotype clades (Great Lakes Michigan and Superior, defined by COI barcode sequencing) with varying viral loads (up to 3 × 106 genome copies organism−1). Read recruitment to de novo assembled transcripts revealed 2,208 significantly over or underexpressed contigs in transcriptomes with above average LM29173 load. Of these contigs, 31.5% were assigned a putative function. The greatest proportion of annotated, differentially expressed transcripts were associated with functions including: (1) replication, recombination, and repair, (2) cell structure/biogenesis, and (3) post-translational modification, protein turnover, and chaperones. Contigs putatively associated with innate immunity displayed no consistent pattern of expression, though several transcripts were significantly overexpressed in amphipods with high viral load. Quantitation (RT-qPCR) of target transcripts, non-muscular myosin heavy chain, β-actin, and ubiquitin-conjugating enzyme E2, corroborated transcriptome analysis and indicated that Lake Michigan and Lake Superior amphipods with high LM29173 load exhibit lake-specific trends in gene expression. While this investigation provides the first comparative survey of the transcriptional profile of invertebrates of variable CRESS-DNA viral load, additional inquiry is required to define the scope of host-specific responses to potential …
bibliographic citation: Bistolas et al. (2017) Gene expression of benthic amphipods (genus: Diporeia) in relation to a circular ssDNA virus across two Laurentian Great Lakes. PeerJ 5:e3810 https://doi.org/10.7717/peerj.3810
date submitted: 2017-06-29
date accepted: 2017-08-23
issued: 2017-09-26
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Bistolas
  given name: Kalia S.I.
author list: Agent
  family name: Rudstam
  given name: Lars G.
author list: Agent
  family name: Hewson
  given name: Ian
doi: 10.7717/peerj.3810
volume: 5
issn: 2167-8359
publication name: PeerJ
publication date: 2017-09-26
copyright: © 2017 Bistolas et al.
attribution name: Bistolas et al.

Bacterial community associated with worker honeybees (Apis mellifera) affected by European foulbrood
type: item
type: AcademicArticle
description: Background Melissococcus plutonius is an entomopathogenic bacterium that causes European foulbrood (EFB), a honeybee (Apis mellifera L.) disease that necessitates quarantine in some countries. In Czechia, positive evidence of EFB was absent for almost 40 years, until an outbreak in the Krkonose Mountains National Park in 2015. This occurrence of EFB gave us the opportunity to study the epizootiology of EFB by focusing on the microbiome of honeybee workers, which act as vectors of honeybee diseases within and between colonies. Methods The study included worker bees collected from brood combs of colonies (i) with no signs of EFB (EFB0), (ii) without clinical symptoms but located at an apiary showing clinical signs of EFB (EFB1), and (iii) with clinical symptoms of EFB (EFB2). In total, 49 samples from 27 honeybee colonies were included in the dataset evaluated in this study. Each biological sample consisted of 10 surface-sterilized worker bees processed for DNA extraction. All subjects were analyzed using conventional PCR and by metabarcoding analysis based on the 16S rRNA gene V1–V3 region, as performed through Illumina MiSeq amplicon sequencing. Results The bees from EFB2 colonies with clinical symptoms exhibited a 75-fold-higher incidence of M. plutonius than those from EFB1 asymptomatic colonies. Melissococcus plutonius was identified in all EFB1 colonies as well as in some of the control colonies. The proportions of Fructobacillus fructosus, Lactobacillus kunkeei, Gilliamella apicola, Frischella perrara, and Bifidobacterium coryneforme were higher in EFB2 than in EFB1, whereas Lactobacillus mellis was significantly higher in EFB2 than in EFB0. Snodgrassella alvi and L. melliventris, L. helsingborgensis and, L. kullabergensis exhibited higher proportion in EFB1 than in EFB2 and EFB0. The occurrence of Bartonella apis and Commensalibacter intestini were higher in EFB0 than in EFB2 and EFB1. Enterococcus faecalis incidence was highest in EFB2. Conclusions High-throu…
format: application/pdf
format: text/html
creator: Tomas Erban
creator: Ondrej Ledvinka
creator: Martin Kamler
creator: Bronislava Hortova
creator: Marta Nesvorna
creator: Jan Tyl
creator: Dalibor Titera
creator: Martin Markovic
creator: Jan Hubert
subject: Ecology
subject: Entomology
subject: Microbiology
subject: Veterinary Medicine
subject: Zoology
description: doi:10.7717/peerj.3816
publisher: PeerJ Inc.
rights: © 2017 Erban et al.
abstract: Background Melissococcus plutonius is an entomopathogenic bacterium that causes European foulbrood (EFB), a honeybee (Apis mellifera L.) disease that necessitates quarantine in some countries. In Czechia, positive evidence of EFB was absent for almost 40 years, until an outbreak in the Krkonose Mountains National Park in 2015. This occurrence of EFB gave us the opportunity to study the epizootiology of EFB by focusing on the microbiome of honeybee workers, which act as vectors of honeybee diseases within and between colonies. Methods The study included worker bees collected from brood combs of colonies (i) with no signs of EFB (EFB0), (ii) without clinical symptoms but located at an apiary showing clinical signs of EFB (EFB1), and (iii) with clinical symptoms of EFB (EFB2). In total, 49 samples from 27 honeybee colonies were included in the dataset evaluated in this study. Each biological sample consisted of 10 surface-sterilized worker bees processed for DNA extraction. All subjects were analyzed using conventional PCR and by metabarcoding analysis based on the 16S rRNA gene V1–V3 region, as performed through Illumina MiSeq amplicon sequencing. Results The bees from EFB2 colonies with clinical symptoms exhibited a 75-fold-higher incidence of M. plutonius than those from EFB1 asymptomatic colonies. Melissococcus plutonius was identified in all EFB1 colonies as well as in some of the control colonies. The proportions of Fructobacillus fructosus, Lactobacillus kunkeei, Gilliamella apicola, Frischella perrara, and Bifidobacterium coryneforme were higher in EFB2 than in EFB1, whereas Lactobacillus mellis was significantly higher in EFB2 than in EFB0. Snodgrassella alvi and L. melliventris, L. helsingborgensis and, L. kullabergensis exhibited higher proportion in EFB1 than in EFB2 and EFB0. The occurrence of Bartonella apis and Commensalibacter intestini were higher in EFB0 than in EFB2 and EFB1. Enterococcus faecalis incidence was highest in EFB2. Conclusions High-throu…
bibliographic citation: Erban et al. (2017) Bacterial community associated with worker honeybees (Apis mellifera) affected by European foulbrood. PeerJ 5:e3816 https://doi.org/10.7717/peerj.3816
date submitted: 2016-11-30
date accepted: 2017-08-26
issued: 2017-09-25
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Erban
  given name: Tomas
author list: Agent
  family name: Ledvinka
  given name: Ondrej
author list: Agent
  family name: Kamler
  given name: Martin
author list: Agent
  family name: Hortova
  given name: Bronislava
author list: Agent
  family name: Nesvorna
  given name: Marta
author list: Agent
  family name: Tyl
  given name: Jan
author list: Agent
  family name: Titera
  given name: Dalibor
author list: Agent
  family name: Markovic
  given name: Martin
author list: Agent
  family name: Hubert
  given name: Jan
doi: 10.7717/peerj.3816
volume: 5
issn: 2167-8359
publication name: PeerJ
publication date: 2017-09-25
copyright: ©2017 Erban et al.
attribution name: Erban et al.

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