PeerJ
type: channel
link: https://peerj.com/articles/
description: Articles published in PeerJ
publisher: PeerJ Inc.
publication name: PeerJ
issn: 2167-8359
items: VirSorter: mining viral signal from microbial genomic data
items: ACE and UCP2 gene polymorphisms and their association with baseline and exercise-related changes in the functional performance of older adults
items: Vorinostat enhances chemosensitivity to arsenic trioxide in K562 cell line
items: Morphometric comparisons of Diaphorina citri (Hemiptera: Liviidae) populations from Iran, USA and Pakistan
items: Using 3D printed eggs to examine the egg-rejection behaviour of wild birds
items: Have the “mega-journals” reached the limits to growth?
items: Earthworm assemblages in different intensity of agricultural uses and their relation to edaphic variables
items: Evolution of heritable behavioural differences in a model of social division of labour
items: Caveolar disruption causes contraction of rat femoral arteries via reduced basal NO release and subsequent closure of BKCa channels
items: Trans-species polymorphism at antimicrobial innate immunity cathelicidin genes of Atlantic cod and related species

VirSorter: mining viral signal from microbial genomic data
type: item
type: AcademicArticle
description: Viruses of microbes impact all ecosystems where microbes drive key energy and substrate transformations including the oceans, humans and industrial fermenters. However, despite this recognized importance, our understanding of viral diversity and impacts remains limited by too few model systems and reference genomes. One way to fill these gaps in our knowledge of viral diversity is through the detection of viral signal in microbial genomic data. While multiple approaches have been developed and applied for the detection of prophages (viral genomes integrated in a microbial genome), new types of microbial genomic data are emerging that are more fragmented and larger scale, such as Single-cell Amplified Genomes (SAGs) of uncultivated organisms or genomic fragments assembled from metagenomic sequencing. Here, we present VirSorter, a tool designed to detect viral signal in these different types of microbial sequence data in both a reference-dependent and reference-independent manner, leveraging probabilistic models and extensive virome data to maximize detection of novel viruses. Performance testing shows that VirSorter’s prophage prediction capability compares to that of available prophage predictors for complete genomes, but is superior in predicting viral sequences outside of a host genome (i.e., from extrachromosomal prophages, lytic infections, or partially assembled prophages). Furthermore, VirSorter outperforms existing tools for fragmented genomic and metagenomic datasets, and can identify viral signal in assembled sequence (contigs) as short as 3kb, while providing near-perfect identification (>95% Recall and 100% Precision) on contigs of at least 10kb. Because VirSorter scales to large datasets, it can also be used in “reverse” to more confidently identify viral sequence in viral metagenomes by sorting away cellular DNA whether derived from gene transfer agents, generalized transduction or contamination. Finally, VirSorter is made available through the iPlant C…
format: application/pdf
format: text/html
creator: Simon Roux
creator: Francois Enault
creator: Bonnie L. Hurwitz
creator: Matthew B. Sullivan
subject: Bioinformatics
subject: Genomics
subject: Microbiology
subject: Virology
description: doi:10.7717/peerj.985
publisher: PeerJ Inc.
rights: © 2015 Roux et al.
abstract: Viruses of microbes impact all ecosystems where microbes drive key energy and substrate transformations including the oceans, humans and industrial fermenters. However, despite this recognized importance, our understanding of viral diversity and impacts remains limited by too few model systems and reference genomes. One way to fill these gaps in our knowledge of viral diversity is through the detection of viral signal in microbial genomic data. While multiple approaches have been developed and applied for the detection of prophages (viral genomes integrated in a microbial genome), new types of microbial genomic data are emerging that are more fragmented and larger scale, such as Single-cell Amplified Genomes (SAGs) of uncultivated organisms or genomic fragments assembled from metagenomic sequencing. Here, we present VirSorter, a tool designed to detect viral signal in these different types of microbial sequence data in both a reference-dependent and reference-independent manner, leveraging probabilistic models and extensive virome data to maximize detection of novel viruses. Performance testing shows that VirSorter’s prophage prediction capability compares to that of available prophage predictors for complete genomes, but is superior in predicting viral sequences outside of a host genome (i.e., from extrachromosomal prophages, lytic infections, or partially assembled prophages). Furthermore, VirSorter outperforms existing tools for fragmented genomic and metagenomic datasets, and can identify viral signal in assembled sequence (contigs) as short as 3kb, while providing near-perfect identification (>95% Recall and 100% Precision) on contigs of at least 10kb. Because VirSorter scales to large datasets, it can also be used in “reverse” to more confidently identify viral sequence in viral metagenomes by sorting away cellular DNA whether derived from gene transfer agents, generalized transduction or contamination. Finally, VirSorter is made available through the iPlant C…
bibliographic citation: Roux et al. (2015) VirSorter: mining viral signal from microbial genomic data. PeerJ 3:e985 https://doi.org/10.7717/peerj.985
date submitted: 2015-04-09
date accepted: 2015-05-08
issued: 2015-05-28
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Roux
  given name: Simon
author list: Agent
  family name: Enault
  given name: Francois
author list: Agent
  family name: Hurwitz
  given name: Bonnie L.
author list: Agent
  family name: Sullivan
  given name: Matthew B.
doi: 10.7717/peerj.985
volume: 3
issn: 2167-8359
publication name: PeerJ
publication date: 2015-05-28
copyright: © 2015 Roux et al.
attribution name: Roux et al.

ACE and UCP2 gene polymorphisms and their association with baseline and exercise-related changes in the functional performance of older adults
type: item
type: AcademicArticle
description: Maintaining high levels of physical function is an important aspect of successful ageing. While muscle mass and strength contribute to functional performance in older adults, little is known about the possible genetic basis for the heterogeneity of physical function in older adults and in how older adults respond to exercise. Two genes that have possible roles in determining levels of muscle mass, strength and function in young and older adults are angiotensin-converting enzyme (ACE) and mitochondrial uncoupling protein 2 (UCP2). This study examined whether polymorphisms in these two individual genes were associated with baseline functional performance levels and/or the training-related changes following exercise in previously untrained older adults. Five-eight Caucasian older adults (mean age 69.8 years) with no recent history of resistance training enrolled in a 12 week program of resistance, balance and cardiovascular exercises aimed at improving functional performance. Performance in 6 functional tasks was recorded at baseline and after 12 weeks. Genomic DNA was assayed for the ACE intron 16 insertion/deletion (I/D) and the UCP2 G-866A polymorphism. Baseline differences among genotype groups were tested using analysis of variance. Genotype differences in absolute and relative changes in physical function among the exercisers were tested using a general linear model, adjusting for age and gender. The genotype frequencies for each of the studied polymorphisms conformed to the Hardy-Weinberg equilibrium. The ACE I/D genotype was significantly associated with mean baseline measures of handgrip strength (II 30.9 ± 3.01 v. ID 31.7 ± 1.48 v. DD 29.3 ± 2.18 kg, p < 0.001), 8ft Up and Go time (II 6.45 ± 0.48 v. ID/DD 4.41 ± 0.19 s, p < 0.001) and 6 min walk distance (II 458 ± 28.7 v. ID/DD 546 ± 12.1m, p = 0.008). The UCP2 G-866A genotype was also associated with baseline 8ft Up and Go time (GG 5.45 ± 0.35 v. GA 4.47 ± 0.26 v. AA 3.89 ± 0.71 s, p = 0.045). After 12 weeks…
format: application/pdf
format: text/html
creator: Justin W.L. Keogh
creator: Barry R. Palmer
creator: Denise Taylor
creator: Andrew E. Kilding
subject: Genetics
subject: Genomics
subject: Geriatrics
subject: Kinesiology
description: doi:10.7717/peerj.980
publisher: PeerJ Inc.
rights: © 2015 Keogh et al.
abstract: Maintaining high levels of physical function is an important aspect of successful ageing. While muscle mass and strength contribute to functional performance in older adults, little is known about the possible genetic basis for the heterogeneity of physical function in older adults and in how older adults respond to exercise. Two genes that have possible roles in determining levels of muscle mass, strength and function in young and older adults are angiotensin-converting enzyme (ACE) and mitochondrial uncoupling protein 2 (UCP2). This study examined whether polymorphisms in these two individual genes were associated with baseline functional performance levels and/or the training-related changes following exercise in previously untrained older adults. Five-eight Caucasian older adults (mean age 69.8 years) with no recent history of resistance training enrolled in a 12 week program of resistance, balance and cardiovascular exercises aimed at improving functional performance. Performance in 6 functional tasks was recorded at baseline and after 12 weeks. Genomic DNA was assayed for the ACE intron 16 insertion/deletion (I/D) and the UCP2 G-866A polymorphism. Baseline differences among genotype groups were tested using analysis of variance. Genotype differences in absolute and relative changes in physical function among the exercisers were tested using a general linear model, adjusting for age and gender. The genotype frequencies for each of the studied polymorphisms conformed to the Hardy-Weinberg equilibrium. The ACE I/D genotype was significantly associated with mean baseline measures of handgrip strength (II 30.9 ± 3.01 v. ID 31.7 ± 1.48 v. DD 29.3 ± 2.18 kg, p < 0.001), 8ft Up and Go time (II 6.45 ± 0.48 v. ID/DD 4.41 ± 0.19 s, p < 0.001) and 6 min walk distance (II 458 ± 28.7 v. ID/DD 546 ± 12.1m, p = 0.008). The UCP2 G-866A genotype was also associated with baseline 8ft Up and Go time (GG 5.45 ± 0.35 v. GA 4.47 ± 0.26 v. AA 3.89 ± 0.71 s, p = 0.045). After 12 weeks…
bibliographic citation: Keogh et al. (2015) ACE and UCP2 gene polymorphisms and their association with baseline and exercise-related changes in the functional performance of older adults. PeerJ 3:e980 https://doi.org/10.7717/peerj.980
date submitted: 2014-12-06
date accepted: 2015-05-07
issued: 2015-05-28
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Keogh
  given name: Justin W.L.
author list: Agent
  family name: Palmer
  given name: Barry R.
author list: Agent
  family name: Taylor
  given name: Denise
author list: Agent
  family name: Kilding
  given name: Andrew E.
doi: 10.7717/peerj.980
volume: 3
issn: 2167-8359
publication name: PeerJ
publication date: 2015-05-28
copyright: © 2015 Keogh et al.
attribution name: Keogh et al.

Vorinostat enhances chemosensitivity to arsenic trioxide in K562 cell line
type: item
type: AcademicArticle
description: Objective. This study aimed to investigate the chemosensitive augmentation effect and mechanism of HDAC inhibitor Vorinostat (SAHA) in combination with arsenic trioxide (ATO) on proliferation and apoptosis of K562 cells. Methods. The CCK-8 assay was used to compare proliferation of the cells. Annexin-V and PI staining by flow cytometry and acridine orange/ethidium bromide stains were used to detect and quantify apoptosis. Western blot was used to detect expression of p21, Akt, pAkt, p210, Acetyl-Histone H3, and Acetyl-Histone H4 proteins. Results. SAHA and ATO inhibited proliferation of K562 cells in an additive and time- and dose-dependent manner. SAHA in combination with ATO showed significant apoptosis of K562 cells in comparison to the single drugs alone (p < 0.01). Both SAHA and ATO alone and in combination showed lower levels of p210 expression. SAHA and SAHA and ATO combined treatment showed increased levels of Acetyl-Histone H3 and Acetyl-Histone H4 protein expression. SAHA alone showed increased expression of p21, while ATO alone and in combination with SAHA showed no significant change. SAHA and ATO combined therapy showed lower levels of Akt and pAkt protein expression than SAHA or ATO alone. Conclusion. SAHA and ATO combined treatment inhibited proliferation, induced apoptosis, and showed a chemosensitive augmentation effect on K562 cells. The mechanism might be associated with increasing histone acetylation levels as well as regulating the Akt signaling pathway.
format: application/pdf
format: text/html
creator: Nainong Li
creator: Xiaoyan Guan
creator: Fang Li
creator: Xiaofan Li
creator: Yuanzhong Chen
subject: Cell Biology
subject: Hematology
subject: Oncology
description: doi:10.7717/peerj.962
publisher: PeerJ Inc.
rights: © 2015 Li et al.
abstract: Objective. This study aimed to investigate the chemosensitive augmentation effect and mechanism of HDAC inhibitor Vorinostat (SAHA) in combination with arsenic trioxide (ATO) on proliferation and apoptosis of K562 cells. Methods. The CCK-8 assay was used to compare proliferation of the cells. Annexin-V and PI staining by flow cytometry and acridine orange/ethidium bromide stains were used to detect and quantify apoptosis. Western blot was used to detect expression of p21, Akt, pAkt, p210, Acetyl-Histone H3, and Acetyl-Histone H4 proteins. Results. SAHA and ATO inhibited proliferation of K562 cells in an additive and time- and dose-dependent manner. SAHA in combination with ATO showed significant apoptosis of K562 cells in comparison to the single drugs alone (p < 0.01). Both SAHA and ATO alone and in combination showed lower levels of p210 expression. SAHA and SAHA and ATO combined treatment showed increased levels of Acetyl-Histone H3 and Acetyl-Histone H4 protein expression. SAHA alone showed increased expression of p21, while ATO alone and in combination with SAHA showed no significant change. SAHA and ATO combined therapy showed lower levels of Akt and pAkt protein expression than SAHA or ATO alone. Conclusion. SAHA and ATO combined treatment inhibited proliferation, induced apoptosis, and showed a chemosensitive augmentation effect on K562 cells. The mechanism might be associated with increasing histone acetylation levels as well as regulating the Akt signaling pathway.
bibliographic citation: Li et al. (2015) Vorinostat enhances chemosensitivity to arsenic trioxide in K562 cell line. PeerJ 3:e962 https://doi.org/10.7717/peerj.962
date submitted: 2015-01-16
date accepted: 2015-04-26
issued: 2015-05-28
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Li
  given name: Nainong
author list: Agent
  family name: Guan
  given name: Xiaoyan
author list: Agent
  family name: Li
  given name: Fang
author list: Agent
  family name: Li
  given name: Xiaofan
author list: Agent
  family name: Chen
  given name: Yuanzhong
doi: 10.7717/peerj.962
volume: 3
issn: 2167-8359
publication name: PeerJ
publication date: 2015-05-28
copyright: © 2015 Li et al.
attribution name: Li et al.

Morphometric comparisons of Diaphorina citri (Hemiptera: Liviidae) populations from Iran, USA and Pakistan
type: item
type: AcademicArticle
description: The Asian citrus psyllid (ACP), Diaphorina citri Kuwayama (Hemiptera: Liviidae), vector of citrus greening disease pathogen, Huanglongbing (HLB), is considered the most serious pest of citrus in the world. Prior molecular based studies have hypothesized a link between the D. citri in Iran and the USA (Florida). The purpose of this study was to collect morphometric data from D. citri populations from Iran (mtCOI haplotype-1), Florida (mtCOI haplotype-1), and Pakistan (mtCOI haplotype-6), to determine whether different mtCOI haplotypes have a relationship to a specific morphometric variation. 240 samples from 6 ACP populations (Iran—Jiroft, Chabahar; Florida—Ft. Pierce, Palm Beach Gardens, Port St. Lucie; and Pakistan—Punjab) were collected for comparison. Measurements of 20 morphological characters were selected, measured and analysed using ANOVA and MANOVA. The results indicate differences among the 6 ACP populations (Wilks’ lambda = 0.0376, F = 7.29, P < 0.0001). The body length (BL), circumanal ring length (CL), antenna length (AL), forewing length (WL) and Rs vein length of forewing (RL) were the most important characters separating the populations. The cluster analysis showed that the Iran and Florida populations are distinct from each other but separate from the Pakistan population. Thus, three subgroups can be morphologically discriminated within D. citri species in this study, (1) Iran, (2) USA (Florida) and (3) Pakistan population. Morphometric comparisons provided further resolution to the mtCOI haplotypes and distinguished the Florida and Iranian populations.
format: application/pdf
format: text/html
creator: Mohammadreza Lashkari
creator: Matthew G. Hentz
creator: Laura M. Boykin
subject: Entomology
subject: Taxonomy
description: doi:10.7717/peerj.946
publisher: PeerJ Inc.
rights: © 2015 Lashkari et al.
abstract: The Asian citrus psyllid (ACP), Diaphorina citri Kuwayama (Hemiptera: Liviidae), vector of citrus greening disease pathogen, Huanglongbing (HLB), is considered the most serious pest of citrus in the world. Prior molecular based studies have hypothesized a link between the D. citri in Iran and the USA (Florida). The purpose of this study was to collect morphometric data from D. citri populations from Iran (mtCOI haplotype-1), Florida (mtCOI haplotype-1), and Pakistan (mtCOI haplotype-6), to determine whether different mtCOI haplotypes have a relationship to a specific morphometric variation. 240 samples from 6 ACP populations (Iran—Jiroft, Chabahar; Florida—Ft. Pierce, Palm Beach Gardens, Port St. Lucie; and Pakistan—Punjab) were collected for comparison. Measurements of 20 morphological characters were selected, measured and analysed using ANOVA and MANOVA. The results indicate differences among the 6 ACP populations (Wilks’ lambda = 0.0376, F = 7.29, P < 0.0001). The body length (BL), circumanal ring length (CL), antenna length (AL), forewing length (WL) and Rs vein length of forewing (RL) were the most important characters separating the populations. The cluster analysis showed that the Iran and Florida populations are distinct from each other but separate from the Pakistan population. Thus, three subgroups can be morphologically discriminated within D. citri species in this study, (1) Iran, (2) USA (Florida) and (3) Pakistan population. Morphometric comparisons provided further resolution to the mtCOI haplotypes and distinguished the Florida and Iranian populations.
bibliographic citation: Lashkari et al. (2015) Morphometric comparisons of Diaphorina citri (Hemiptera: Liviidae) populations from Iran, USA and Pakistan. PeerJ 3:e946 https://doi.org/10.7717/peerj.946
date submitted: 2015-01-21
date accepted: 2015-04-18
issued: 2015-05-28
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Lashkari
  given name: Mohammadreza
author list: Agent
  family name: Hentz
  given name: Matthew G.
author list: Agent
  family name: Boykin
  given name: Laura M.
doi: 10.7717/peerj.946
volume: 3
issn: 2167-8359
publication name: PeerJ
publication date: 2015-05-28
copyright: © 2015 Lashkari et al.
attribution name: Lashkari et al.

Using 3D printed eggs to examine the egg-rejection behaviour of wild birds
type: item
type: AcademicArticle
description: The coevolutionary relationships between brood parasites and their hosts are often studied by examining the egg rejection behaviour of host species using artificial eggs. However, the traditional methods for producing artificial eggs out of plasticine, plastic, wood, or plaster-of-Paris are laborious, imprecise, and prone to human error. As an alternative, 3D printing may reduce human error, enable more precise manipulation of egg size and shape, and provide a more accurate and replicable protocol for generating artificial stimuli than traditional methods. However, the usefulness of 3D printing technology for egg rejection research remains to be tested. Here, we applied 3D printing technology to the extensively studied egg rejection behaviour of American robins, Turdus migratorius. Eggs of the robin’s brood parasites, brown-headed cowbirds, Molothrus ater, vary greatly in size and shape, but it is unknown whether host egg rejection decisions differ across this gradient of natural variation. We printed artificial eggs that encompass the natural range of shapes and sizes of cowbird eggs, painted them to resemble either robin or cowbird egg colour, and used them to artificially parasitize nests of breeding wild robins. In line with previous studies, we show that robins accept mimetically coloured and reject non-mimetically coloured artificial eggs. Although we found no evidence that subtle differences in parasitic egg size or shape affect robins’ rejection decisions, 3D printing will provide an opportunity for more extensive experimentation on the potential biological or evolutionary significance of size and shape variation of foreign eggs in rejection decisions. We provide a detailed protocol for generating 3D printed eggs using either personal 3D printers or commercial printing services, and highlight additional potential future applications for this technology in the study of egg rejection.
format: application/pdf
format: text/html
creator: Branislav Igic
creator: Valerie Nunez
creator: Henning U. Voss
creator: Rebecca Croston
creator: Zachary Aidala
creator: Analía V. López
creator: Aimee Van Tatenhove
creator: Mandë E. Holford
creator: Matthew D. Shawkey
creator: Mark E. Hauber
subject: Animal Behavior
subject: Ecology
subject: Zoology
description: doi:10.7717/peerj.965
publisher: PeerJ Inc.
rights: © 2015 Igic et al.
abstract: The coevolutionary relationships between brood parasites and their hosts are often studied by examining the egg rejection behaviour of host species using artificial eggs. However, the traditional methods for producing artificial eggs out of plasticine, plastic, wood, or plaster-of-Paris are laborious, imprecise, and prone to human error. As an alternative, 3D printing may reduce human error, enable more precise manipulation of egg size and shape, and provide a more accurate and replicable protocol for generating artificial stimuli than traditional methods. However, the usefulness of 3D printing technology for egg rejection research remains to be tested. Here, we applied 3D printing technology to the extensively studied egg rejection behaviour of American robins, Turdus migratorius. Eggs of the robin’s brood parasites, brown-headed cowbirds, Molothrus ater, vary greatly in size and shape, but it is unknown whether host egg rejection decisions differ across this gradient of natural variation. We printed artificial eggs that encompass the natural range of shapes and sizes of cowbird eggs, painted them to resemble either robin or cowbird egg colour, and used them to artificially parasitize nests of breeding wild robins. In line with previous studies, we show that robins accept mimetically coloured and reject non-mimetically coloured artificial eggs. Although we found no evidence that subtle differences in parasitic egg size or shape affect robins’ rejection decisions, 3D printing will provide an opportunity for more extensive experimentation on the potential biological or evolutionary significance of size and shape variation of foreign eggs in rejection decisions. We provide a detailed protocol for generating 3D printed eggs using either personal 3D printers or commercial printing services, and highlight additional potential future applications for this technology in the study of egg rejection.
bibliographic citation: Igic et al. (2015) Using 3D printed eggs to examine the egg-rejection behaviour of wild birds. PeerJ 3:e965 https://doi.org/10.7717/peerj.965
date submitted: 2015-03-28
date accepted: 2015-04-29
issued: 2015-05-26
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Igic
  given name: Branislav
author list: Agent
  family name: Nunez
  given name: Valerie
author list: Agent
  family name: Voss
  given name: Henning U.
author list: Agent
  family name: Croston
  given name: Rebecca
author list: Agent
  family name: Aidala
  given name: Zachary
author list: Agent
  family name: López
  given name: Analía V.
author list: Agent
  family name: Van Tatenhove
  given name: Aimee
author list: Agent
  family name: Holford
  given name: Mandë E.
author list: Agent
  family name: Shawkey
  given name: Matthew D.
author list: Agent
  family name: Hauber
  given name: Mark E.
doi: 10.7717/peerj.965
volume: 3
issn: 2167-8359
publication name: PeerJ
publication date: 2015-05-26
copyright: © 2015 Igic et al.
attribution name: Igic et al.

Have the “mega-journals” reached the limits to growth?
type: item
type: AcademicArticle
description: A “mega-journal” is a new type of scientific journal that publishes freely accessible articles, which have been peer reviewed for scientific trustworthiness, but leaves it to the readers to decide which articles are of interest and importance to them. In the wake of the phenomenal success of PLOS ONE, several other publishers have recently started mega-journals. This article presents the evolution of mega-journals since 2010 in terms of article publication rates. The fastest growth seems to have ebbed out at around 35,000 annual articles for the 14 journals combined. Acceptance rates are in the range of 50–70%, and speed of publication is around 3–5 months. Common features in mega-journals are alternative impact metrics, easy reusability of figures and data, post-publication discussions and portable reviews from other journals.
format: application/pdf
format: text/html
creator: Bo-Christer Björk
subject: Science and Medical Education
subject: Science Policy
description: doi:10.7717/peerj.981
publisher: PeerJ Inc.
rights: © 2015 Björk
abstract: A “mega-journal” is a new type of scientific journal that publishes freely accessible articles, which have been peer reviewed for scientific trustworthiness, but leaves it to the readers to decide which articles are of interest and importance to them. In the wake of the phenomenal success of PLOS ONE, several other publishers have recently started mega-journals. This article presents the evolution of mega-journals since 2010 in terms of article publication rates. The fastest growth seems to have ebbed out at around 35,000 annual articles for the 14 journals combined. Acceptance rates are in the range of 50–70%, and speed of publication is around 3–5 months. Common features in mega-journals are alternative impact metrics, easy reusability of figures and data, post-publication discussions and portable reviews from other journals.
bibliographic citation: Björk (2015) Have the “mega-journals” reached the limits to growth?. PeerJ 3:e981 https://doi.org/10.7717/peerj.981
date submitted: 2015-04-07
date accepted: 2015-05-07
issued: 2015-05-26
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Björk
  given name: Bo-Christer
doi: 10.7717/peerj.981
volume: 3
issn: 2167-8359
publication name: PeerJ
publication date: 2015-05-26
copyright: © 2015 Björk
attribution name: Björk

Earthworm assemblages in different intensity of agricultural uses and their relation to edaphic variables
type: item
type: AcademicArticle
description: The objective of this study was to relate earthworm assemblage structure with three different soil use intensities, and to indentify the physical, chemical, and microbiological soil variables that are associated to the observed differences. Three soil uses were evaluated: 1-Fifty year old naturalized grasslands, low use intensity; 2-Recent agricultural fields, intermediate use intensity, and 3-Fifty year old intensive agricultural fields, high use intensity. Three different sites for each soil use were evaluated from winter 2008 through summer 2011. Nine earthworm species were identified across all sampling sites. The sites shared five species: the native Microscolex dubius, and the introduced Aporrectodea caliginosa, A. rosea, Octalasion cyaneum, and O. lacteum, but they differed in relative abundance by soil use. The results show that the earthworm community structure is linked to and modulated by soil properties. Both species abundance and diversity showed significant differences depending on soil use intensity. A principal component analysis showed that species composition is closely related to the environmental variability. The ratio of native to exotic species was significantly lower in the intensive agricultural system when compared to the other two, lower disturbance systems. Microscolex dubius abundance was related to naturalized grasslands along with soil Ca, pH, mechanical resistance, and microbial respiration. Aporrectodea caliginosa abundance was related to high K levels, low enzymatic activity, slightly low pH, low Ca, and appeared related to the highly disturbed environment. Eukerria stagnalis and Aporrectodea rosea, commonly found in the recent agricultural system, were related to high soil moisture condition, low pH, low Ca and low enzymatic activity. These results show that earthworm assemblages can be good indicators of soil use intensities. In particular, Microscolex dubius, Aporrectodea caliginosa, and Aporrectodea rosea, showed different tempor…
format: application/pdf
format: text/html
creator: LB Falco
creator: R Sandler
creator: F Momo
creator: C Di Ciocco
creator: L Saravia
creator: C Coviella
subject: Agricultural Science
subject: Biosphere Interactions
subject: Ecology
subject: Ecosystem Science
subject: Environmental Sciences
description: doi:10.7717/peerj.979
publisher: PeerJ Inc.
rights: © 2015 Falco et al.
abstract: The objective of this study was to relate earthworm assemblage structure with three different soil use intensities, and to indentify the physical, chemical, and microbiological soil variables that are associated to the observed differences. Three soil uses were evaluated: 1-Fifty year old naturalized grasslands, low use intensity; 2-Recent agricultural fields, intermediate use intensity, and 3-Fifty year old intensive agricultural fields, high use intensity. Three different sites for each soil use were evaluated from winter 2008 through summer 2011. Nine earthworm species were identified across all sampling sites. The sites shared five species: the native Microscolex dubius, and the introduced Aporrectodea caliginosa, A. rosea, Octalasion cyaneum, and O. lacteum, but they differed in relative abundance by soil use. The results show that the earthworm community structure is linked to and modulated by soil properties. Both species abundance and diversity showed significant differences depending on soil use intensity. A principal component analysis showed that species composition is closely related to the environmental variability. The ratio of native to exotic species was significantly lower in the intensive agricultural system when compared to the other two, lower disturbance systems. Microscolex dubius abundance was related to naturalized grasslands along with soil Ca, pH, mechanical resistance, and microbial respiration. Aporrectodea caliginosa abundance was related to high K levels, low enzymatic activity, slightly low pH, low Ca, and appeared related to the highly disturbed environment. Eukerria stagnalis and Aporrectodea rosea, commonly found in the recent agricultural system, were related to high soil moisture condition, low pH, low Ca and low enzymatic activity. These results show that earthworm assemblages can be good indicators of soil use intensities. In particular, Microscolex dubius, Aporrectodea caliginosa, and Aporrectodea rosea, showed different tempor…
bibliographic citation: Falco et al. (2015) Earthworm assemblages in different intensity of agricultural uses and their relation to edaphic variables. PeerJ 3:e979 https://doi.org/10.7717/peerj.979
date submitted: 2014-12-19
date accepted: 2015-05-06
issued: 2015-05-26
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Falco
  given name: LB
author list: Agent
  family name: Sandler
  given name: R
author list: Agent
  family name: Momo
  given name: F
author list: Agent
  family name: Di Ciocco
  given name: C
author list: Agent
  family name: Saravia
  given name: L
author list: Agent
  family name: Coviella
  given name: C
doi: 10.7717/peerj.979
volume: 3
issn: 2167-8359
publication name: PeerJ
publication date: 2015-05-26
copyright: © 2015 Falco et al.
attribution name: Falco et al.

Evolution of heritable behavioural differences in a model of social division of labour
type: item
type: AcademicArticle
description: The spectacular diversity of personality and behaviour of animals and humans has evoked many hypotheses intended to explain its developmental and evolutionary background. Although the list of the possible contributing mechanisms seems long, we propose that an underemphasised explanation is the division of labour creating negative frequency dependent selection. We use analytical and numerical models of social division of labour to show how selection can create consistent and heritable behavioural differences in a population, where randomly sampled individuals solve a collective task together. We assume that the collective task needs collaboration of individuals performing one of the two possible subtasks. The total benefit of the group is highest when the ratio of different subtasks is closest to 1. The probability of choosing one of the two costly subtasks and the costs assigned to them are under selection. By using adaptive dynamics we show that if a trade-off between the costs of the subtasks is strong enough, then evolution leads to coexistence of specialized individuals performing one of the subtasks with high probability and low cost. Our analytical results were verified and extended by numerical simulations.
format: application/pdf
format: text/html
creator: Zsóka Vásárhelyi
creator: Géza Meszéna
creator: István Scheuring
subject: Computational Biology
subject: Evolutionary Studies
subject: Mathematical Biology
description: doi:10.7717/peerj.977
publisher: PeerJ Inc.
rights: © 2015 Vásárhelyi et al.
abstract: The spectacular diversity of personality and behaviour of animals and humans has evoked many hypotheses intended to explain its developmental and evolutionary background. Although the list of the possible contributing mechanisms seems long, we propose that an underemphasised explanation is the division of labour creating negative frequency dependent selection. We use analytical and numerical models of social division of labour to show how selection can create consistent and heritable behavioural differences in a population, where randomly sampled individuals solve a collective task together. We assume that the collective task needs collaboration of individuals performing one of the two possible subtasks. The total benefit of the group is highest when the ratio of different subtasks is closest to 1. The probability of choosing one of the two costly subtasks and the costs assigned to them are under selection. By using adaptive dynamics we show that if a trade-off between the costs of the subtasks is strong enough, then evolution leads to coexistence of specialized individuals performing one of the subtasks with high probability and low cost. Our analytical results were verified and extended by numerical simulations.
bibliographic citation: Vásárhelyi et al. (2015) Evolution of heritable behavioural differences in a model of social division of labour. PeerJ 3:e977 https://doi.org/10.7717/peerj.977
date submitted: 2015-03-23
date accepted: 2015-05-06
issued: 2015-05-26
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Vásárhelyi
  given name: Zsóka
author list: Agent
  family name: Meszéna
  given name: Géza
author list: Agent
  family name: Scheuring
  given name: István
doi: 10.7717/peerj.977
volume: 3
issn: 2167-8359
publication name: PeerJ
publication date: 2015-05-26
copyright: © 2015 Vásárhelyi et al.
attribution name: Vásárhelyi et al.

Caveolar disruption causes contraction of rat femoral arteries via reduced basal NO release and subsequent closure of BKCa channels
type: item
type: AcademicArticle
description: Background and Purpose. Caveolae act as signalling hubs in endothelial and smooth muscle cells. Caveolar disruption by the membrane cholesterol depleting agent methyl-β-cyclodextrin (M-β-CD) has various functional effects on arteries including (i) impairment of endothelium-dependent relaxation, and (ii) alteration of smooth muscle cell (SMC) contraction independently of the endothelium. The aim of this study was to explore the effects of M-β-CD on rat femoral arteries. Methods. Isometric force was measured in rat femoral arteries stimulated to contract with a solution containing 20 mM K+ and 200 nM Bay K 8644 (20 K/Bay K) or with one containing 80 mM K+(80 K). Results. Incubation of arteries with M-β-CD (5 mM, 60 min) increased force in response to 20 K/Bay K but not that induced by 80 K. Application of cholesterol saturated M-β-CD (Ch-MCD, 5 mM, 50 min) reversed the effects of M-β-CD. After mechanical removal of endothelial cells M-β-CD caused only a small enhancement of contractions to 20 K/Bay K. This result suggests M-β-CD acts via altering release of an endothelial-derived vasodilator or vasoconstrictor. When nitric oxide synthase was blocked by pre-incubation of arteries with L-NAME (250 µM) the contraction of arteries to 20 K/Bay K was enhanced, and this effect was abolished by pre-treatment with M-β-CD. This suggests M-β-CD is inhibiting endothelial NO release. Inhibition of large conductance voltage- and Ca2+-activated (BKCa) channels with 2 mM TEA+ or 100 nM Iberiotoxin (IbTX) enhanced 20 K/Bay K contractions. L-NAME attenuated the contractile effect of IbTX, as did endothelial removal. Conclusions. Our results suggest caveolar disruption results in decreased release of endothelial-derived nitric oxide in rat femoral artery, resulting in a reduced contribution of BKCa channels to the smooth muscle cell membrane potential, causing depolarisation and contraction.
format: application/pdf
format: text/html
creator: AY Al-Brakati
creator: T Kamishima
creator: C Dart
creator: JM Quayle
subject: Anatomy and Physiology
subject: Cardiology
description: doi:10.7717/peerj.966
publisher: PeerJ Inc.
rights: © 2015 Al-Brakati et al.
abstract: Background and Purpose. Caveolae act as signalling hubs in endothelial and smooth muscle cells. Caveolar disruption by the membrane cholesterol depleting agent methyl-β-cyclodextrin (M-β-CD) has various functional effects on arteries including (i) impairment of endothelium-dependent relaxation, and (ii) alteration of smooth muscle cell (SMC) contraction independently of the endothelium. The aim of this study was to explore the effects of M-β-CD on rat femoral arteries. Methods. Isometric force was measured in rat femoral arteries stimulated to contract with a solution containing 20 mM K+ and 200 nM Bay K 8644 (20 K/Bay K) or with one containing 80 mM K+(80 K). Results. Incubation of arteries with M-β-CD (5 mM, 60 min) increased force in response to 20 K/Bay K but not that induced by 80 K. Application of cholesterol saturated M-β-CD (Ch-MCD, 5 mM, 50 min) reversed the effects of M-β-CD. After mechanical removal of endothelial cells M-β-CD caused only a small enhancement of contractions to 20 K/Bay K. This result suggests M-β-CD acts via altering release of an endothelial-derived vasodilator or vasoconstrictor. When nitric oxide synthase was blocked by pre-incubation of arteries with L-NAME (250 µM) the contraction of arteries to 20 K/Bay K was enhanced, and this effect was abolished by pre-treatment with M-β-CD. This suggests M-β-CD is inhibiting endothelial NO release. Inhibition of large conductance voltage- and Ca2+-activated (BKCa) channels with 2 mM TEA+ or 100 nM Iberiotoxin (IbTX) enhanced 20 K/Bay K contractions. L-NAME attenuated the contractile effect of IbTX, as did endothelial removal. Conclusions. Our results suggest caveolar disruption results in decreased release of endothelial-derived nitric oxide in rat femoral artery, resulting in a reduced contribution of BKCa channels to the smooth muscle cell membrane potential, causing depolarisation and contraction.
bibliographic citation: Al-Brakati et al. (2015) Caveolar disruption causes contraction of rat femoral arteries via reduced basal NO release and subsequent closure of BKCa channels. PeerJ 3:e966 https://doi.org/10.7717/peerj.966
date submitted: 2015-02-10
date accepted: 2015-04-29
issued: 2015-05-26
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Al-Brakati
  given name: AY
author list: Agent
  family name: Kamishima
  given name: T
author list: Agent
  family name: Dart
  given name: C
author list: Agent
  family name: Quayle
  given name: JM
doi: 10.7717/peerj.966
volume: 3
issn: 2167-8359
publication name: PeerJ
publication date: 2015-05-26
copyright: © 2015 Al-Brakati et al.
attribution name: Al-Brakati et al.

Trans-species polymorphism at antimicrobial innate immunity cathelicidin genes of Atlantic cod and related species
type: item
type: AcademicArticle
description: Natural selection, the most important force in evolution, comes in three forms. Negative purifying selection removes deleterious variation and maintains adaptations. Positive directional selection fixes beneficial variants, producing new adaptations. Balancing selection maintains variation in a population. Important mechanisms of balancing selection include heterozygote advantage, frequency-dependent advantage of rarity, and local and fluctuating episodic selection. A rare pathogen gains an advantage because host defenses are predominantly effective against prevalent types. Similarly, a rare immune variant gives its host an advantage because the prevalent pathogens cannot escape the host’s apostatic defense. Due to the stochastic nature of evolution, neutral variation may accumulate on genealogical branches, but trans-species polymorphisms are rare under neutrality and are strong evidence for balancing selection. Balanced polymorphism maintains diversity at the major histocompatibility complex (MHC) in vertebrates. The Atlantic cod is missing genes for both MHC-II and CD4, vital parts of the adaptive immune system. Nevertheless, cod are healthy in their ecological niche, maintaining large populations that support major commercial fisheries. Innate immunity is of interest from an evolutionary perspective, particularly in taxa lacking adaptive immunity. Here, we analyze extensive amino acid and nucleotide polymorphisms of the cathelicidin gene family in Atlantic cod and closely related taxa. There are three major clusters, Cath1, Cath2, and Cath3, that we consider to be paralogous genes. There is extensive nucleotide and amino acid allelic variation between and within clusters. The major feature of the results is that the variation clusters by alleles and not by species in phylogenetic trees and discriminant analysis of principal components. Variation within the three groups shows trans-species polymorphism that is older than speciation and that is suggestive of balan…
format: application/pdf
format: text/html
creator: Katrín Halldórsdóttir
creator: Einar Árnason
subject: Aquaculture, Fisheries and Fish Science
subject: Evolutionary Studies
subject: Genetics
subject: Marine Biology
subject: Immunology
description: doi:10.7717/peerj.976
publisher: PeerJ Inc.
rights: © 2015 Halldórsdóttir and Árnason
abstract: Natural selection, the most important force in evolution, comes in three forms. Negative purifying selection removes deleterious variation and maintains adaptations. Positive directional selection fixes beneficial variants, producing new adaptations. Balancing selection maintains variation in a population. Important mechanisms of balancing selection include heterozygote advantage, frequency-dependent advantage of rarity, and local and fluctuating episodic selection. A rare pathogen gains an advantage because host defenses are predominantly effective against prevalent types. Similarly, a rare immune variant gives its host an advantage because the prevalent pathogens cannot escape the host’s apostatic defense. Due to the stochastic nature of evolution, neutral variation may accumulate on genealogical branches, but trans-species polymorphisms are rare under neutrality and are strong evidence for balancing selection. Balanced polymorphism maintains diversity at the major histocompatibility complex (MHC) in vertebrates. The Atlantic cod is missing genes for both MHC-II and CD4, vital parts of the adaptive immune system. Nevertheless, cod are healthy in their ecological niche, maintaining large populations that support major commercial fisheries. Innate immunity is of interest from an evolutionary perspective, particularly in taxa lacking adaptive immunity. Here, we analyze extensive amino acid and nucleotide polymorphisms of the cathelicidin gene family in Atlantic cod and closely related taxa. There are three major clusters, Cath1, Cath2, and Cath3, that we consider to be paralogous genes. There is extensive nucleotide and amino acid allelic variation between and within clusters. The major feature of the results is that the variation clusters by alleles and not by species in phylogenetic trees and discriminant analysis of principal components. Variation within the three groups shows trans-species polymorphism that is older than speciation and that is suggestive of balan…
bibliographic citation: Halldórsdóttir et al. (2015) Trans-species polymorphism at antimicrobial innate immunity cathelicidin genes of Atlantic cod and related species. PeerJ 3:e976 https://doi.org/10.7717/peerj.976
date submitted: 2015-03-24
date accepted: 2015-05-05
issued: 2015-05-21
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Halldórsdóttir
  given name: Katrín
author list: Agent
  family name: Árnason
  given name: Einar
doi: 10.7717/peerj.976
volume: 3
issn: 2167-8359
publication name: PeerJ
publication date: 2015-05-21
copyright: © 2015 Halldórsdóttir and Árnason
attribution name: Halldórsdóttir and Árnason

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