PeerJ
type: channel
link: https://peerj.com/articles/
description: Articles published in PeerJ
publisher: PeerJ Inc.
publication name: PeerJ
issn: 2167-8359
items: Age, but not short-term intensive swimming, affects chondrocyte turnover in zebrafish vertebral cartilage
items: Can secondary contact following range expansion be distinguished from barriers to gene flow?
items: Influence of sports expertise level on attention in multiple object tracking
items: Sunset Yellow and Allura Red modulate Bcl2 and COX2 expression levels and confer oxidative stress-mediated renal and hepatic toxicity in male rats
items: Modeled larval connectivity of a multi-species reef fish and invertebrate assemblage off the coast of Moloka‘i, Hawai‘i
items: Functions of Candida albicans cell wall glycosidases Dfg5p and Dcw1p in biofilm formation and HOG MAPK pathway
items: Meta-analysis of northeast Atlantic marine taxa shows contrasting phylogeographic patterns following post-LGM expansions
items: Cellular production of a counterfeit viral protein confers immunity to infection by a related virus
items: Distinguishing between enduring and dynamic concussion symptoms: applying Generalisability Theory to the Rivermead Post Concussion Symptoms Questionnaire (RPQ)
items: Size dimorphism and sexual segregation in pheasants: tests of three competing hypotheses

Age, but not short-term intensive swimming, affects chondrocyte turnover in zebrafish vertebral cartilage
type: item
type: AcademicArticle
description: Both age and intensive exercise are generally considered critical risk factors for osteoarthritis. In this work, we intend to establish zebrafish models to assess the role of these two factors on cartilage homeostasis. We designed a swimming device for zebrafish intensive exercise. The body measurements, bone mineral density (BMD) and the histology of spinal cartilages of 4- and 12-month-old zebrafish, as well the 12-month-old zebrafish before and after a 2-week exercise were compared. Our results indicate that both age and exercise affect the body length and body weight, and the micro-computed tomography reveals that both age and exercise affect the spinal BMD. However, quantitative analysis of immunohistochemistry and histochemistry indicate that short-term intensive exercise does not affect the extracellular matrix (ECM) of spinal cartilage. On the other hand, the cartilage ECM significantly grew from 4 to 12 months of age with an increase in total chondrocytes. dUTP nick end labeling staining shows that the percentages of apoptotic cells significantly increase as the zebrafish grows, whereas the BrdU labeling shows that proliferative cells dramatically decrease from 4 to 12 months of age. A 30-day chase of BrdU labeling shows some retention of labeling in cells in 4-month-old spinal cartilage but not in cartilage from 12-month-old zebrafish. Taken together, our results suggest that zebrafish chondrocytes are actively turned over, and indicate that aging is a critical factor that alters cartilage homeostasis. Zebrafish vertebral cartilage may serve as a good model to study the maturation and homeostasis of articular cartilage.
format: application/pdf
format: text/html
creator: Quan-Liang Jian
creator: Wei-Chun HuangFu
creator: Yen-Hua Lee
creator: I-Hsuan Liu
subject: Cell Biology
subject: Veterinary Medicine
subject: Zoology
subject: Rheumatology
description: doi:10.7717/peerj.5739
publisher: PeerJ Inc.
rights: © 2018 Jian et al.
abstract: Both age and intensive exercise are generally considered critical risk factors for osteoarthritis. In this work, we intend to establish zebrafish models to assess the role of these two factors on cartilage homeostasis. We designed a swimming device for zebrafish intensive exercise. The body measurements, bone mineral density (BMD) and the histology of spinal cartilages of 4- and 12-month-old zebrafish, as well the 12-month-old zebrafish before and after a 2-week exercise were compared. Our results indicate that both age and exercise affect the body length and body weight, and the micro-computed tomography reveals that both age and exercise affect the spinal BMD. However, quantitative analysis of immunohistochemistry and histochemistry indicate that short-term intensive exercise does not affect the extracellular matrix (ECM) of spinal cartilage. On the other hand, the cartilage ECM significantly grew from 4 to 12 months of age with an increase in total chondrocytes. dUTP nick end labeling staining shows that the percentages of apoptotic cells significantly increase as the zebrafish grows, whereas the BrdU labeling shows that proliferative cells dramatically decrease from 4 to 12 months of age. A 30-day chase of BrdU labeling shows some retention of labeling in cells in 4-month-old spinal cartilage but not in cartilage from 12-month-old zebrafish. Taken together, our results suggest that zebrafish chondrocytes are actively turned over, and indicate that aging is a critical factor that alters cartilage homeostasis. Zebrafish vertebral cartilage may serve as a good model to study the maturation and homeostasis of articular cartilage.
bibliographic citation: Jian et al. (2018) Age, but not short-term intensive swimming, affects chondrocyte turnover in zebrafish vertebral cartilage. PeerJ 6:e5739 https://doi.org/10.7717/peerj.5739
date submitted: 2018-01-22
date accepted: 2018-08-30
issued: 2018-10-01
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Jian
  given name: Quan-Liang
author list: Agent
  family name: HuangFu
  given name: Wei-Chun
author list: Agent
  family name: Lee
  given name: Yen-Hua
author list: Agent
  family name: Liu
  given name: I-Hsuan
doi: 10.7717/peerj.5739
volume: 6
issn: 2167-8359
publication name: PeerJ
publication date: 2018-10-01
copyright: © 2018 Jian et al.
attribution name: Jian et al.

Can secondary contact following range expansion be distinguished from barriers to gene flow?
type: item
type: AcademicArticle
description: Secondary contact is the reestablishment of gene flow between sister populations that have diverged. For instance, at the end of the Quaternary glaciations in Europe, secondary contact occurred during the northward expansion of the populations which had found refugia in the southern peninsulas. With the advent of multi-locus markers, secondary contact can be investigated using various molecular signatures including gradients of allele frequency, admixture clines, and local increase of genetic differentiation. We use coalescent simulations to investigate if molecular data provide enough information to distinguish between secondary contact following range expansion and an alternative evolutionary scenario consisting of a barrier to gene flow in an isolation-by-distance model. We find that an excess of linkage disequilibrium and of genetic diversity at the suture zone is a unique signature of secondary contact. We also find that the directionality index ψ, which was proposed to study range expansion, is informative to distinguish between the two hypotheses. However, although evidence for secondary contact is usually conveyed by statistics related to admixture coefficients, we find that they can be confounded by isolation-by-distance. We recommend to account for the spatial repartition of individuals when investigating secondary contact in order to better reflect the complex spatio-temporal evolution of populations and species.
format: application/pdf
format: text/html
creator: Johanna Bertl
creator: Harald Ringbauer
creator: Michael G.B. Blum
subject: Computational Biology
subject: Ecology
subject: Evolutionary Studies
subject: Population Biology
description: doi:10.7717/peerj.5325
publisher: PeerJ Inc.
rights: © 2018 Bertl et al.
abstract: Secondary contact is the reestablishment of gene flow between sister populations that have diverged. For instance, at the end of the Quaternary glaciations in Europe, secondary contact occurred during the northward expansion of the populations which had found refugia in the southern peninsulas. With the advent of multi-locus markers, secondary contact can be investigated using various molecular signatures including gradients of allele frequency, admixture clines, and local increase of genetic differentiation. We use coalescent simulations to investigate if molecular data provide enough information to distinguish between secondary contact following range expansion and an alternative evolutionary scenario consisting of a barrier to gene flow in an isolation-by-distance model. We find that an excess of linkage disequilibrium and of genetic diversity at the suture zone is a unique signature of secondary contact. We also find that the directionality index ψ, which was proposed to study range expansion, is informative to distinguish between the two hypotheses. However, although evidence for secondary contact is usually conveyed by statistics related to admixture coefficients, we find that they can be confounded by isolation-by-distance. We recommend to account for the spatial repartition of individuals when investigating secondary contact in order to better reflect the complex spatio-temporal evolution of populations and species.
bibliographic citation: Bertl et al. (2018) Can secondary contact following range expansion be distinguished from barriers to gene flow?. PeerJ 6:e5325 https://doi.org/10.7717/peerj.5325
date submitted: 2016-11-29
date accepted: 2018-07-01
issued: 2018-10-01
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Bertl
  given name: Johanna
author list: Agent
  family name: Ringbauer
  given name: Harald
author list: Agent
  family name: Blum
  given name: Michael G.B.
doi: 10.7717/peerj.5325
volume: 6
issn: 2167-8359
publication name: PeerJ
publication date: 2018-10-01
copyright: © 2018 Bertl et al.
attribution name: Bertl et al.

Influence of sports expertise level on attention in multiple object tracking
type: item
type: AcademicArticle
description: Background This study aimed to investigate whether performance in a multiple object tracking (MOT) task could be improved incrementally with sports expertise, and whether differences between experienced and less experienced athletes, or non-athletes, were modulated by load. Methods We asked 22 elite and 20 intermediate basketball players, and 23 non-athletes, to perform an MOT task under three attentional load conditions (two, three, and four targets). Accuracies were analyzed to examine whether different levels of sports expertise influence MOT task performance. Results The elite athletes displayed better tracking performance compared with the intermediate or non-athletes when tracking three or four targets. However, no significant difference was found between the intermediate athletes and the non-athletes. Further, no differences were observed among the three groups when tracking two targets. Discussion The results suggest that the effects of expertise in team ball sports could transfer to a non-sports-specific attention task. These transfer effects to general cognitive functions occur only in elite athletes with extensive training under higher attentional load.
format: application/pdf
format: text/html
creator: Fanghui Qiu
creator: Yanling Pi
creator: Ke Liu
creator: Xuepei Li
creator: Jian Zhang
creator: Yin Wu
subject: Kinesiology
description: doi:10.7717/peerj.5732
publisher: PeerJ Inc.
rights: © 2018 Qiu et al.
abstract: Background This study aimed to investigate whether performance in a multiple object tracking (MOT) task could be improved incrementally with sports expertise, and whether differences between experienced and less experienced athletes, or non-athletes, were modulated by load. Methods We asked 22 elite and 20 intermediate basketball players, and 23 non-athletes, to perform an MOT task under three attentional load conditions (two, three, and four targets). Accuracies were analyzed to examine whether different levels of sports expertise influence MOT task performance. Results The elite athletes displayed better tracking performance compared with the intermediate or non-athletes when tracking three or four targets. However, no significant difference was found between the intermediate athletes and the non-athletes. Further, no differences were observed among the three groups when tracking two targets. Discussion The results suggest that the effects of expertise in team ball sports could transfer to a non-sports-specific attention task. These transfer effects to general cognitive functions occur only in elite athletes with extensive training under higher attentional load.
bibliographic citation: Qiu et al. (2018) Influence of sports expertise level on attention in multiple object tracking. PeerJ 6:e5732 https://doi.org/10.7717/peerj.5732
date submitted: 2018-06-06
date accepted: 2018-09-12
issued: 2018-09-28
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Qiu
  given name: Fanghui
author list: Agent
  family name: Pi
  given name: Yanling
author list: Agent
  family name: Liu
  given name: Ke
author list: Agent
  family name: Li
  given name: Xuepei
author list: Agent
  family name: Zhang
  given name: Jian
author list: Agent
  family name: Wu
  given name: Yin
doi: 10.7717/peerj.5732
volume: 6
issn: 2167-8359
publication name: PeerJ
publication date: 2018-09-28
copyright: © 2018 Qiu et al.
attribution name: Qiu et al.

Sunset Yellow and Allura Red modulate Bcl2 and COX2 expression levels and confer oxidative stress-mediated renal and hepatic toxicity in male rats
type: item
type: AcademicArticle
description: Studies on the adverse health effects caused by azo dyes are insufficient and quite contradictory. This work aims to investigate the possible toxic effect of two types of widely used food additives, Sunset Yellow and Allura Red, by assessing the physiological, histopathological and ultrastructural changes in the liver and kidney. Also, we investigated the genotoxic effect of both dyes on white blood cells. Thirty adult male albino rats were divided into three groups of 10 animals each: control (received water), Sunset Yellow-treated (2.5 mg/kg body weight) and Allura Red-treated (seven mg/kg body weight). The doses were orally applied for 4 weeks. Our results indicated an increase in the biochemical markers of hepatic and renal function (Aspartate aminotransferase, alanine aminotransferase, urea, uric acid and creatinine) in animals administered with the azo dyes. We also observed a noticeable increase in MDA and a marked decrease in total antioxidant levels in azo dye-treated animals compared to controls. Conversely, both dyes adversely affected the liver and kidney of albino rats and altered their histological and fine structure, with downregulation of Bcl2 and upregulation of COX2 expression. Our comet assay results showed a significant elevation in the fold change of tail moment in response to application of Sunset Yellow but not Allura Red. Collectively, we show that Sunset Yellow and Allura Red cause histopathological and physiological aberrations in the liver and kidney of male Wistar albino rats. Moreover, Sunset Yellow but not Allura Red induces a potential genotoxic effect.
format: application/pdf
format: text/html
creator: Latifa I. Khayyat
creator: Amina E. Essawy
creator: Jehan M. Sorour
creator: Ahmed Soffar
subject: Cell Biology
subject: Molecular Biology
subject: Toxicology
subject: Public Health
subject: Histology
description: doi:10.7717/peerj.5689
publisher: PeerJ Inc.
rights: © 2018 Khayyat et al.
abstract: Studies on the adverse health effects caused by azo dyes are insufficient and quite contradictory. This work aims to investigate the possible toxic effect of two types of widely used food additives, Sunset Yellow and Allura Red, by assessing the physiological, histopathological and ultrastructural changes in the liver and kidney. Also, we investigated the genotoxic effect of both dyes on white blood cells. Thirty adult male albino rats were divided into three groups of 10 animals each: control (received water), Sunset Yellow-treated (2.5 mg/kg body weight) and Allura Red-treated (seven mg/kg body weight). The doses were orally applied for 4 weeks. Our results indicated an increase in the biochemical markers of hepatic and renal function (Aspartate aminotransferase, alanine aminotransferase, urea, uric acid and creatinine) in animals administered with the azo dyes. We also observed a noticeable increase in MDA and a marked decrease in total antioxidant levels in azo dye-treated animals compared to controls. Conversely, both dyes adversely affected the liver and kidney of albino rats and altered their histological and fine structure, with downregulation of Bcl2 and upregulation of COX2 expression. Our comet assay results showed a significant elevation in the fold change of tail moment in response to application of Sunset Yellow but not Allura Red. Collectively, we show that Sunset Yellow and Allura Red cause histopathological and physiological aberrations in the liver and kidney of male Wistar albino rats. Moreover, Sunset Yellow but not Allura Red induces a potential genotoxic effect.
bibliographic citation: Khayyat et al. (2018) Sunset Yellow and Allura Red modulate Bcl2 and COX2 expression levels and confer oxidative stress-mediated renal and hepatic toxicity in male rats. PeerJ 6:e5689 https://doi.org/10.7717/peerj.5689
date submitted: 2018-03-19
date accepted: 2018-09-03
issued: 2018-09-28
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Khayyat
  given name: Latifa I.
author list: Agent
  family name: Essawy
  given name: Amina E.
author list: Agent
  family name: Sorour
  given name: Jehan M.
author list: Agent
  family name: Soffar
  given name: Ahmed
doi: 10.7717/peerj.5689
volume: 6
issn: 2167-8359
publication name: PeerJ
publication date: 2018-09-28
copyright: ©2018 Khayyat et al.
attribution name: Khayyat et al.

Modeled larval connectivity of a multi-species reef fish and invertebrate assemblage off the coast of Moloka‘i, Hawai‘i
type: item
type: AcademicArticle
description: We use a novel individual-based model (IBM) to simulate larval dispersal around the island of Moloka‘i in the Hawaiian Archipelago. Our model uses ocean current output from the Massachusetts Institute of Technology general circulation model (MITgcm) as well as biological data on four invertebrate and seven fish species of management relevance to produce connectivity maps among sites around the island of Moloka‘i. These 11 species span the range of life history characteristics of Hawaiian coral reef species and show different spatial and temporal patterns of connectivity as a result. As expected, the longer the pelagic larval duration (PLD), the greater the proportion of larvae that disperse longer distances, but regardless of PLD (3–270 d) most successful dispersal occurs either over short distances within an island (<30 km) or to adjacent islands (50–125 km). Again, regardless of PLD, around the island of Moloka‘i, connectivity tends to be greatest among sites along the same coastline and exchange between northward, southward, eastward and westward-facing shores is limited. Using a graph-theoretic approach to visualize the data, we highlight that the eastern side of the island tends to show the greatest out-degree and betweenness centrality, which indicate important larval sources and connectivity pathways for the rest of the island. The marine protected area surrounding Kalaupapa National Historical Park emerges as a potential source for between-island larval connections, and the west coast of the Park is one of the few regions on Moloka‘i that acts as a net larval source across all species. Using this IBM and visualization approach reveals patterns of exchange between habitat regions and highlights critical larval sources and multi-generational pathways to indicate priority areas for marine resource managers.
format: application/pdf
format: text/html
creator: Emily E. Conklin
creator: Anna B. Neuheimer
creator: Robert J. Toonen
subject: Aquaculture, Fisheries and Fish Science
subject: Conservation Biology
subject: Ecology
subject: Marine Biology
subject: Biological Oceanography
description: doi:10.7717/peerj.5688
publisher: PeerJ Inc.
rights: © 2018 Conklin et al.
abstract: We use a novel individual-based model (IBM) to simulate larval dispersal around the island of Moloka‘i in the Hawaiian Archipelago. Our model uses ocean current output from the Massachusetts Institute of Technology general circulation model (MITgcm) as well as biological data on four invertebrate and seven fish species of management relevance to produce connectivity maps among sites around the island of Moloka‘i. These 11 species span the range of life history characteristics of Hawaiian coral reef species and show different spatial and temporal patterns of connectivity as a result. As expected, the longer the pelagic larval duration (PLD), the greater the proportion of larvae that disperse longer distances, but regardless of PLD (3–270 d) most successful dispersal occurs either over short distances within an island (<30 km) or to adjacent islands (50–125 km). Again, regardless of PLD, around the island of Moloka‘i, connectivity tends to be greatest among sites along the same coastline and exchange between northward, southward, eastward and westward-facing shores is limited. Using a graph-theoretic approach to visualize the data, we highlight that the eastern side of the island tends to show the greatest out-degree and betweenness centrality, which indicate important larval sources and connectivity pathways for the rest of the island. The marine protected area surrounding Kalaupapa National Historical Park emerges as a potential source for between-island larval connections, and the west coast of the Park is one of the few regions on Moloka‘i that acts as a net larval source across all species. Using this IBM and visualization approach reveals patterns of exchange between habitat regions and highlights critical larval sources and multi-generational pathways to indicate priority areas for marine resource managers.
bibliographic citation: Conklin et al. (2018) Modeled larval connectivity of a multi-species reef fish and invertebrate assemblage off the coast of Moloka‘i, Hawai‘i. PeerJ 6:e5688 https://doi.org/10.7717/peerj.5688
date submitted: 2018-03-21
date accepted: 2018-09-04
issued: 2018-09-28
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Conklin
  given name: Emily E.
author list: Agent
  family name: Neuheimer
  given name: Anna B.
author list: Agent
  family name: Toonen
  given name: Robert J.
doi: 10.7717/peerj.5688
volume: 6
issn: 2167-8359
publication name: PeerJ
publication date: 2018-09-28
copyright: ©2018 Conklin et al.
attribution name: Conklin et al.

Functions of Candida albicans cell wall glycosidases Dfg5p and Dcw1p in biofilm formation and HOG MAPK pathway
type: item
type: AcademicArticle
description: Background Candida albicans is a commensal fungus that inhabits the oral mucosal surface and causes oral and systemic candidiasis. Oral candidiasis most commonly occurs in patients with AIDS, denture wearers and newborn children. Systemic candidiasis occurs mainly in immunocompromised patients and patients admitted to hospitals for prolonged periods. C. albicans homologous genes, DFG5 and DCW1, encode for two closely related cell wall proteins with putative glycosyltransferase enzyme activity and C-terminal GPI-anchors. Past studies have shown that individual DFG5 and DCW1 mutations are viable but simultaneous deletion of DFG5 and DCW1 in C. albicans results in lethality. However, the exact functions of these cell wall based enzymes, which represent potential drug targets, are not understood. Methods C. albicans DFG5/DCW1 heterologous and conditional double mutant strains were assessed for growth and biofilm formation in comparison to wild type and parental strains. Cell wall and heat stress susceptibility of the mutant and control strains were assessed using agar spotting assays. Growth was assessed under normal and osmotic stress conditions along with light microscopy imaging. Biofilm dry weight and microscopic imaging analysis of biofilms was performed. Hypha formation in response to serum was analyzed using light microscopy imaging. Western blot analysis of mutant strains and control strains was performed to assess Hog1 basal levels and phosphorylation status. Results Analysis of the heterologous mutants indicated that Dfg5p is more important for growth while Dcw1p appeared to play a role in cell wall integrity response. The conditional double mutant was observed to be less resistant to cell wall stress. However, growth of the mutants was similar under control and osmotic stress conditions. The mutants were also able to grow similar to wild type under heat stress. Biofilm formation was reduced in the mutants where DFG5 was deleted or suppressed. Hyphal morphogen…
format: application/pdf
format: text/html
creator: Ryan Mancuso
creator: Jennifer Chinnici
creator: Charlene Tsou
creator: Sujay Busarajan
creator: Raveena Munnangi
creator: Abhiram Maddi
subject: Microbiology
subject: Dentistry
subject: Infectious Diseases
subject: Women’s Health
description: doi:10.7717/peerj.5685
publisher: PeerJ Inc.
rights: © 2018 Mancuso et al.
abstract: Background Candida albicans is a commensal fungus that inhabits the oral mucosal surface and causes oral and systemic candidiasis. Oral candidiasis most commonly occurs in patients with AIDS, denture wearers and newborn children. Systemic candidiasis occurs mainly in immunocompromised patients and patients admitted to hospitals for prolonged periods. C. albicans homologous genes, DFG5 and DCW1, encode for two closely related cell wall proteins with putative glycosyltransferase enzyme activity and C-terminal GPI-anchors. Past studies have shown that individual DFG5 and DCW1 mutations are viable but simultaneous deletion of DFG5 and DCW1 in C. albicans results in lethality. However, the exact functions of these cell wall based enzymes, which represent potential drug targets, are not understood. Methods C. albicans DFG5/DCW1 heterologous and conditional double mutant strains were assessed for growth and biofilm formation in comparison to wild type and parental strains. Cell wall and heat stress susceptibility of the mutant and control strains were assessed using agar spotting assays. Growth was assessed under normal and osmotic stress conditions along with light microscopy imaging. Biofilm dry weight and microscopic imaging analysis of biofilms was performed. Hypha formation in response to serum was analyzed using light microscopy imaging. Western blot analysis of mutant strains and control strains was performed to assess Hog1 basal levels and phosphorylation status. Results Analysis of the heterologous mutants indicated that Dfg5p is more important for growth while Dcw1p appeared to play a role in cell wall integrity response. The conditional double mutant was observed to be less resistant to cell wall stress. However, growth of the mutants was similar under control and osmotic stress conditions. The mutants were also able to grow similar to wild type under heat stress. Biofilm formation was reduced in the mutants where DFG5 was deleted or suppressed. Hyphal morphogen…
bibliographic citation: Mancuso et al. (2018) Functions of Candida albicans cell wall glycosidases Dfg5p and Dcw1p in biofilm formation and HOG MAPK pathway. PeerJ 6:e5685 https://doi.org/10.7717/peerj.5685
date submitted: 2018-02-13
date accepted: 2018-08-30
issued: 2018-09-28
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Mancuso
  given name: Ryan
author list: Agent
  family name: Chinnici
  given name: Jennifer
author list: Agent
  family name: Tsou
  given name: Charlene
author list: Agent
  family name: Busarajan
  given name: Sujay
author list: Agent
  family name: Munnangi
  given name: Raveena
author list: Agent
  family name: Maddi
  given name: Abhiram
doi: 10.7717/peerj.5685
volume: 6
issn: 2167-8359
publication name: PeerJ
publication date: 2018-09-28
copyright: ©2018 Mancuso et al.
attribution name: Mancuso et al.

Meta-analysis of northeast Atlantic marine taxa shows contrasting phylogeographic patterns following post-LGM expansions
type: item
type: AcademicArticle
description: Background Comparative phylogeography enables the study of historical and evolutionary processes that have contributed to shaping patterns of contemporary genetic diversity across co-distributed species. In this study, we explored genetic structure and historical demography in a range of coastal marine species across the northeast Atlantic to assess whether there are commonalities in phylogeographic patterns across taxa and to evaluate whether the timings of population expansions were linked to the Last Glacial Maximum (LGM). Methods A literature search was conducted using Web of Science. Search terms were chosen to maximise the inclusion of articles reporting on population structure and phylogeography from the northeast Atlantic; titles and abstracts were screened to identify suitable articles within the scope of this study. Given the proven utility of mtDNA in comparative phylogeography and the availability of these data in the public domain, a meta-analysis was conducted using published mtDNA gene sequences. A standardised methodology was implemented to ensure that the genealogy and demographic history of all mtDNA datasets were reanalysed in a consistent and directly comparable manner. Results Mitochondrial DNA datasets were built for 21 species. The meta-analysis revealed significant population differentiation in 16 species and four main types of haplotype network were found, with haplotypes in some species unique to specific geographical locations. A signal of rapid expansion was detected in 16 species, whereas five species showed evidence of a stable population size. Corrected mutation rates indicated that the majority of expansions were estimated to have occurred after the earliest estimate for the LGM (∼26.5 Kyr), while few expansions were estimated to have pre-dated the LGM. Conclusion This study suggests that post-LGM expansion appeared to be common in a range of marine taxa, supporting the concept of rapid expansions after the LGM as the ice sheets start…
format: application/pdf
format: text/html
creator: Tom L. Jenkins
creator: Rita Castilho
creator: Jamie R. Stevens
subject: Biogeography
subject: Genetics
subject: Marine Biology
description: doi:10.7717/peerj.5684
publisher: PeerJ Inc.
rights: © 2018 Jenkins et al.
abstract: Background Comparative phylogeography enables the study of historical and evolutionary processes that have contributed to shaping patterns of contemporary genetic diversity across co-distributed species. In this study, we explored genetic structure and historical demography in a range of coastal marine species across the northeast Atlantic to assess whether there are commonalities in phylogeographic patterns across taxa and to evaluate whether the timings of population expansions were linked to the Last Glacial Maximum (LGM). Methods A literature search was conducted using Web of Science. Search terms were chosen to maximise the inclusion of articles reporting on population structure and phylogeography from the northeast Atlantic; titles and abstracts were screened to identify suitable articles within the scope of this study. Given the proven utility of mtDNA in comparative phylogeography and the availability of these data in the public domain, a meta-analysis was conducted using published mtDNA gene sequences. A standardised methodology was implemented to ensure that the genealogy and demographic history of all mtDNA datasets were reanalysed in a consistent and directly comparable manner. Results Mitochondrial DNA datasets were built for 21 species. The meta-analysis revealed significant population differentiation in 16 species and four main types of haplotype network were found, with haplotypes in some species unique to specific geographical locations. A signal of rapid expansion was detected in 16 species, whereas five species showed evidence of a stable population size. Corrected mutation rates indicated that the majority of expansions were estimated to have occurred after the earliest estimate for the LGM (∼26.5 Kyr), while few expansions were estimated to have pre-dated the LGM. Conclusion This study suggests that post-LGM expansion appeared to be common in a range of marine taxa, supporting the concept of rapid expansions after the LGM as the ice sheets start…
bibliographic citation: Jenkins et al. (2018) Meta-analysis of northeast Atlantic marine taxa shows contrasting phylogeographic patterns following post-LGM expansions. PeerJ 6:e5684 https://doi.org/10.7717/peerj.5684
date submitted: 2018-05-30
date accepted: 2018-08-30
issued: 2018-09-28
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Jenkins
  given name: Tom L.
author list: Agent
  family name: Castilho
  given name: Rita
author list: Agent
  family name: Stevens
  given name: Jamie R.
doi: 10.7717/peerj.5684
volume: 6
issn: 2167-8359
publication name: PeerJ
publication date: 2018-09-28
copyright: ©2018 Jenkins et al.
attribution name: Jenkins et al.

Cellular production of a counterfeit viral protein confers immunity to infection by a related virus
type: item
type: AcademicArticle
description: DNA copies of many non-retroviral RNA virus genes or portions thereof (NIRVs) are present in the nuclear genomes of many eukaryotes. These have often been preserved for millions of years of evolution, suggesting that they play an important cellular function. One possible function is resistance to infection by related viruses. In some cases, this appears to occur through the piRNA system, but in others by way of counterfeit viral proteins encoded by NIRVs. In the fungi, NIRVs may be as long as 1,400 uninterrupted codons. In one such case in the yeast Debaryomyces hansenii, one of these genes provides immunity to a related virus by virtue of expression of a counterfeit viral capsid protein, which interferes with assembly of viral capsids by negative complementation. The widespread occurrence of non-retroviral RNA virus genes in eukaryotes may reflect an underappreciated method of host resistance to infection. This work demonstrates for the first time that an endogenous host protein encoded by a gene that has been naturally acquired from a virus and fixed in a eukaryote can interfere with the replication of a related virus and do so by negative complementation.
format: application/pdf
format: text/html
creator: Benjamin E. Warner
creator: Matthew J. Ballinger
creator: Pradeep Yerramsetty
creator: Jennifer Reed
creator: Derek J. Taylor
creator: Thomas J. Smith
creator: Jeremy A. Bruenn
subject: Evolutionary Studies
subject: Microbiology
subject: Molecular Biology
subject: Mycology
subject: Virology
description: doi:10.7717/peerj.5679
publisher: PeerJ Inc.
rights: © 2018 Warner et al.
abstract: DNA copies of many non-retroviral RNA virus genes or portions thereof (NIRVs) are present in the nuclear genomes of many eukaryotes. These have often been preserved for millions of years of evolution, suggesting that they play an important cellular function. One possible function is resistance to infection by related viruses. In some cases, this appears to occur through the piRNA system, but in others by way of counterfeit viral proteins encoded by NIRVs. In the fungi, NIRVs may be as long as 1,400 uninterrupted codons. In one such case in the yeast Debaryomyces hansenii, one of these genes provides immunity to a related virus by virtue of expression of a counterfeit viral capsid protein, which interferes with assembly of viral capsids by negative complementation. The widespread occurrence of non-retroviral RNA virus genes in eukaryotes may reflect an underappreciated method of host resistance to infection. This work demonstrates for the first time that an endogenous host protein encoded by a gene that has been naturally acquired from a virus and fixed in a eukaryote can interfere with the replication of a related virus and do so by negative complementation.
bibliographic citation: Warner et al. (2018) Cellular production of a counterfeit viral protein confers immunity to infection by a related virus. PeerJ 6:e5679 https://doi.org/10.7717/peerj.5679
date submitted: 2018-06-01
date accepted: 2018-08-29
issued: 2018-09-28
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Warner
  given name: Benjamin E.
author list: Agent
  family name: Ballinger
  given name: Matthew J.
author list: Agent
  family name: Yerramsetty
  given name: Pradeep
author list: Agent
  family name: Reed
  given name: Jennifer
author list: Agent
  family name: Taylor
  given name: Derek J.
author list: Agent
  family name: Smith
  given name: Thomas J.
author list: Agent
  family name: Bruenn
  given name: Jeremy A.
doi: 10.7717/peerj.5679
volume: 6
issn: 2167-8359
publication name: PeerJ
publication date: 2018-09-28
copyright: ©2018 Warner et al.
attribution name: Warner et al.

Distinguishing between enduring and dynamic concussion symptoms: applying Generalisability Theory to the Rivermead Post Concussion Symptoms Questionnaire (RPQ)
type: item
type: AcademicArticle
description: Background The Rivermead Post Concussion Symptoms Questionnaire (RPQ) is a widely-used, 16-item measure of concussion symptoms yet its ability to assess change in the symptom experience over time has come under criticism. We applied Generalisability theory to differentiate between dynamic and enduring aspects of post-concussion symptoms and to examine sources of measurement error in the RPQ. Materials and Methods Generalisability theory was applied using the longitudinal design with persons as the object of measurement. Patients with a traumatic brain injury (n = 145; aged ≥16 years) were assessed at three time occasions (1, 6 and 12 months post-injury) using the RPQ. Results The RPQ showed overall strong generalisability of scores (G = .98) across persons and occasions with a minor proportion of variance attributed to the dynamic aspect of symptoms reflected by interaction between person and occasion. Items measuring concentration, fatigue, restlessness and irritability reflected more dynamic patterns compared to more enduring patterns of sensitivity to noise, impatience, nausea and sleep disturbance. Conclusion The RPQ demonstrated strong reliability in assessing enduring post-concussion symptoms but its ability to assess dynamic symptoms is limited. Clinicians should exercise caution in use of the RPQ to track dynamic symptom change over time. Further investigation is necessary to enhance the RPQ’s ability to assess dynamic symptoms and to address measurement error associated with individual items.
format: application/pdf
format: text/html
creator: Oleg N. Medvedev
creator: Alice Theadom
creator: Suzanne Barker-Collo
creator: Valery Feigin
subject: Neurology
subject: Psychiatry and Psychology
subject: Public Health
description: doi:10.7717/peerj.5676
publisher: PeerJ Inc.
rights: © 2018 Medvedev et al.
abstract: Background The Rivermead Post Concussion Symptoms Questionnaire (RPQ) is a widely-used, 16-item measure of concussion symptoms yet its ability to assess change in the symptom experience over time has come under criticism. We applied Generalisability theory to differentiate between dynamic and enduring aspects of post-concussion symptoms and to examine sources of measurement error in the RPQ. Materials and Methods Generalisability theory was applied using the longitudinal design with persons as the object of measurement. Patients with a traumatic brain injury (n = 145; aged ≥16 years) were assessed at three time occasions (1, 6 and 12 months post-injury) using the RPQ. Results The RPQ showed overall strong generalisability of scores (G = .98) across persons and occasions with a minor proportion of variance attributed to the dynamic aspect of symptoms reflected by interaction between person and occasion. Items measuring concentration, fatigue, restlessness and irritability reflected more dynamic patterns compared to more enduring patterns of sensitivity to noise, impatience, nausea and sleep disturbance. Conclusion The RPQ demonstrated strong reliability in assessing enduring post-concussion symptoms but its ability to assess dynamic symptoms is limited. Clinicians should exercise caution in use of the RPQ to track dynamic symptom change over time. Further investigation is necessary to enhance the RPQ’s ability to assess dynamic symptoms and to address measurement error associated with individual items.
bibliographic citation: Medvedev et al. (2018) Distinguishing between enduring and dynamic concussion symptoms: applying Generalisability Theory to the Rivermead Post Concussion Symptoms Questionnaire (RPQ). PeerJ 6:e5676 https://doi.org/10.7717/peerj.5676
date submitted: 2018-03-02
date accepted: 2018-08-30
issued: 2018-09-28
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Medvedev
  given name: Oleg N.
author list: Agent
  family name: Theadom
  given name: Alice
author list: Agent
  family name: Barker-Collo
  given name: Suzanne
author list: Agent
  family name: Feigin
  given name: Valery
doi: 10.7717/peerj.5676
volume: 6
issn: 2167-8359
publication name: PeerJ
publication date: 2018-09-28
copyright: ©2018 Medvedev et al.
attribution name: Medvedev et al.

Size dimorphism and sexual segregation in pheasants: tests of three competing hypotheses
type: item
type: AcademicArticle
description: Fine scale sexual segregation outside of the mating season is common in sexually dimorphic and polygamous species, particularly in ungulates. A number of hypotheses predict sexual segregation but these are often contradictory with no agreement as to a common cause, perhaps because they are species specific. We explicitly tested three of these hypotheses which are commonly linked by a dependence on sexual dimorphism for animals which exhibit fine-scale sexual segregation; the Predation Risk Hypothesis, the Forage Selection Hypothesis, and the Activity Budget Hypothesis, in a single system the pheasant, Phasianus colchicus; a large, sedentary bird that is predominantly terrestrial and therefore analogous to ungulates rather than many avian species which sexually segregate. Over four years we reared 2,400 individually tagged pheasants from one day old and after a period of 8–10 weeks we released them into the wild. We then followed the birds for 7 months, during the period that they sexually segregate, determined their fate and collected behavioural and morphological measures pertinent to the hypotheses. Pheasants are sexually dimorphic during the entire period that they sexually segregate in the wild; males are larger than females in both body size and gut measurements. However, this did not influence predation risk and predation rates (as predicted by the Predation Risk Hypothesis), diet choice (as predicted by the Forage Selection Hypothesis), or the amount of time spent foraging, resting or walking (as predicted by the Activity Budget Hypothesis). We conclude that adult sexual size dimorphism is not responsible for sexual segregation in the pheasant in the wild. Instead, we consider that segregation may be mediated by other, perhaps social, factors. We highlight the importance of studies on a wide range of taxa to help further the knowledge of sexual segregation.
format: application/pdf
format: text/html
creator: Mark A. Whiteside
creator: Jayden O. van Horik
creator: Ellis J.G. Langley
creator: Christine E. Beardsworth
creator: Joah R. Madden
subject: Animal Behavior
subject: Zoology
subject: Population Biology
description: doi:10.7717/peerj.5674
publisher: PeerJ Inc.
rights: © 2018 Whiteside et al.
abstract: Fine scale sexual segregation outside of the mating season is common in sexually dimorphic and polygamous species, particularly in ungulates. A number of hypotheses predict sexual segregation but these are often contradictory with no agreement as to a common cause, perhaps because they are species specific. We explicitly tested three of these hypotheses which are commonly linked by a dependence on sexual dimorphism for animals which exhibit fine-scale sexual segregation; the Predation Risk Hypothesis, the Forage Selection Hypothesis, and the Activity Budget Hypothesis, in a single system the pheasant, Phasianus colchicus; a large, sedentary bird that is predominantly terrestrial and therefore analogous to ungulates rather than many avian species which sexually segregate. Over four years we reared 2,400 individually tagged pheasants from one day old and after a period of 8–10 weeks we released them into the wild. We then followed the birds for 7 months, during the period that they sexually segregate, determined their fate and collected behavioural and morphological measures pertinent to the hypotheses. Pheasants are sexually dimorphic during the entire period that they sexually segregate in the wild; males are larger than females in both body size and gut measurements. However, this did not influence predation risk and predation rates (as predicted by the Predation Risk Hypothesis), diet choice (as predicted by the Forage Selection Hypothesis), or the amount of time spent foraging, resting or walking (as predicted by the Activity Budget Hypothesis). We conclude that adult sexual size dimorphism is not responsible for sexual segregation in the pheasant in the wild. Instead, we consider that segregation may be mediated by other, perhaps social, factors. We highlight the importance of studies on a wide range of taxa to help further the knowledge of sexual segregation.
bibliographic citation: Whiteside et al. (2018) Size dimorphism and sexual segregation in pheasants: tests of three competing hypotheses. PeerJ 6:e5674 https://doi.org/10.7717/peerj.5674
date submitted: 2018-03-07
date accepted: 2018-08-30
issued: 2018-09-28
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Whiteside
  given name: Mark A.
author list: Agent
  family name: van Horik
  given name: Jayden O.
author list: Agent
  family name: Langley
  given name: Ellis J.G.
author list: Agent
  family name: Beardsworth
  given name: Christine E.
author list: Agent
  family name: Madden
  given name: Joah R.
doi: 10.7717/peerj.5674
volume: 6
issn: 2167-8359
publication name: PeerJ
publication date: 2018-09-28
copyright: ©2018 Whiteside et al.
attribution name: Whiteside et al.

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