PeerJ
type: channel
link: https://peerj.com/articles/
description: Articles published in PeerJ
publisher: PeerJ Inc.
publication name: PeerJ
issn: 2167-8359
items: Differential roles of prostaglandin E-type receptors in activation of hypoxia-inducible factor 1 by prostaglandin E1 in vascular-derived cells under non-hypoxic conditions
items: Diversity and distribution of extra-floral nectaries in the cerrado savanna vegetation of Brazil
items: Fine motor deficits in reading disability and language impairment: same or different?
items: A feasibility open trial of internet-delivered cognitive-behavioural therapy (iCBT) among consumers of a non-governmental mental health organisation with anxiety
items: Altering an extended phenotype reduces intraspecific male aggression and can maintain diversity in cichlid fish
items: An empirical evaluation of four variants of a universal species–area relationship
items: Predominant intragenic methylation is associated with gene expression characteristics in a bivalve mollusc
items: Cannabidivarin (CBDV) suppresses pentylenetetrazole (PTZ)-induced increases in epilepsy-related gene expression
items: Effects of ocean acidification on the dissolution rates of reef-coral skeletons
items: The relationship between resilience and personality traits in doctors: implications for enhancing well being
items: Examination of spotted sand bass (Paralabrax maculatofasciatus) pollutant bioaccumulation in San Diego Bay, San Diego, California
items: ezRAD: a simplified method for genomic genotyping in non-model organisms
items: Amino-acid site variability among natural and designed proteins
items: An integrated pipeline for next generation sequencing and annotation of the complete mitochondrial genome of the giant intestinal fluke, Fasciolopsis buski (Lankester, 1857) Looss, 1899
items: How migratory thrushes conquered northern North America: a comparative phylogeography approach
items: Bird migratory flyways influence the phylogeography of the invasive brine shrimp Artemia franciscana in its native American range
items: A longitudinal analysis of associations between traffic-related air pollution with asthma, allergies and sensitization in the GINIplus and LISAplus birth cohorts
items: Size and shape in the evolution of ant worker morphology
items: Beware the black box: investigating the sensitivity of FEA simulations to modelling factors in comparative biomechanics
items: Comparative selenoproteome analysis reveals a reduced utilization of selenium in parasitic platyhelminthes
items: Iranian and Swedish adolescents: differences in personality traits and well-being
items: Characterization of RNA in exosomes secreted by human breast cancer cell lines using next-generation sequencing

Differential roles of prostaglandin E-type receptors in activation of hypoxia-inducible factor 1 by prostaglandin E1 in vascular-derived cells under non-hypoxic conditions
type: item
type: AcademicArticle
description: Prostaglandin E1 (PGE1), known pharmaceutically as alprostadil, has vasodilatory properties and is used widely in various clinical settings. In addition to acute vasodilatory properties, PGE1 may exert beneficial effects by altering protein expression of vascular cells. PGE1 is reported to be a potent stimulator of angiogenesis via upregulation of VEGF expression, which is under the control of the transcription factor hypoxia-inducible factor 1 (HIF-1). However, the molecular mechanisms behind the phenomenon are largely unknown. In the present study, we investigated the mechanism by which PGE1 induces HIF-1 activation and VEGF gene expression in human aortic smooth muscle cells (HASMCs) and human umbilical vein endothelial cells (HUVECs), both vascular-derived cells. HUVECs and HASMCs were treated with PGE1 at clinically relevant concentrations under 20% O2 conditions and HIF-1 protein expression was investigated. Expression of HIF- 1α protein and the HIF-1-downstream genes were low under 20% O2 conditions and increased in response to PGE1 treatment in both HUVECs and HASMCs in a dose- and time-dependent manner under 20% O2 conditions as comparable to exposure to 1% O2 conditions. Studies using EP-receptor-specific agonists and antagonists revealed that EP1 and EP3 are critical to PGE1-induced HIF-1 activation. In vitro vascular permeability assays using HUVECs indicated that PGE1 increased vascular permeability in HUVECs. Thus, we demonstrate that PGE1 induces HIF- 1α protein expression and HIF-1 activation under non-hypoxic conditions and also provide evidence that the activity of multiple signal transduction pathways downstream of EP1 and EP3 receptors is required for HIF-1 activation.
format: application/pdf
format: text/html
creator: Kengo Suzuki
creator: Kenichiro Nishi
creator: Satoshi Takabuchi
creator: Shinichi Kai
creator: Tomonori Matsuyama
creator: Shin Kurosawa
creator: Takehiko Adachi
creator: Takayuki Maruyama
creator: Kazuhiko Fukuda
creator: Kiichi Hirota
subject: Anesthesiology and Pain Management
subject: Cell Biology
subject: Molecular Biology
subject: Pharmacology
description: doi:10.7717/peerj.220
publisher: PeerJ Inc.
rights: © 2013 Suzuki et al.
abstract: Prostaglandin E1 (PGE1), known pharmaceutically as alprostadil, has vasodilatory properties and is used widely in various clinical settings. In addition to acute vasodilatory properties, PGE1 may exert beneficial effects by altering protein expression of vascular cells. PGE1 is reported to be a potent stimulator of angiogenesis via upregulation of VEGF expression, which is under the control of the transcription factor hypoxia-inducible factor 1 (HIF-1). However, the molecular mechanisms behind the phenomenon are largely unknown. In the present study, we investigated the mechanism by which PGE1 induces HIF-1 activation and VEGF gene expression in human aortic smooth muscle cells (HASMCs) and human umbilical vein endothelial cells (HUVECs), both vascular-derived cells. HUVECs and HASMCs were treated with PGE1 at clinically relevant concentrations under 20% O2 conditions and HIF-1 protein expression was investigated. Expression of HIF- 1α protein and the HIF-1-downstream genes were low under 20% O2 conditions and increased in response to PGE1 treatment in both HUVECs and HASMCs in a dose- and time-dependent manner under 20% O2 conditions as comparable to exposure to 1% O2 conditions. Studies using EP-receptor-specific agonists and antagonists revealed that EP1 and EP3 are critical to PGE1-induced HIF-1 activation. In vitro vascular permeability assays using HUVECs indicated that PGE1 increased vascular permeability in HUVECs. Thus, we demonstrate that PGE1 induces HIF- 1α protein expression and HIF-1 activation under non-hypoxic conditions and also provide evidence that the activity of multiple signal transduction pathways downstream of EP1 and EP3 receptors is required for HIF-1 activation.
bibliographic citation: Suzuki et al. (2013) Differential roles of prostaglandin E-type receptors in activation of hypoxia-inducible factor 1 by prostaglandin E1 in vascular-derived cells under non-hypoxic conditions. PeerJ 1:e220 https://doi.org/10.7717/peerj.220
date submitted: 2013-07-23
date accepted: 2013-11-11
issued: 2013-11-28
is part of: PeerJ
license: http://creativecommons.org/licenses/by/3.0/
author list: Agent
  family name: Suzuki
  given name: Kengo
author list: Agent
  family name: Nishi
  given name: Kenichiro
author list: Agent
  family name: Takabuchi
  given name: Satoshi
author list: Agent
  family name: Kai
  given name: Shinichi
author list: Agent
  family name: Matsuyama
  given name: Tomonori
author list: Agent
  family name: Kurosawa
  given name: Shin
author list: Agent
  family name: Adachi
  given name: Takehiko
author list: Agent
  family name: Maruyama
  given name: Takayuki
author list: Agent
  family name: Fukuda
  given name: Kazuhiko
author list: Agent
  family name: Hirota
  given name: Kiichi
doi: 10.7717/peerj.220
volume: 1
issn: 2167-8359
publication name: PeerJ
publication date: 2013-11-28
copyright: © 2013 Suzuki et al.
attribution name: Suzuki et al.

Diversity and distribution of extra-floral nectaries in the cerrado savanna vegetation of Brazil
type: item
type: AcademicArticle
description: Aim. Throughout evolutionary history, plants and animals have evolved alongside one another. This is especially apparent when considering mutualistic relationships such as between plants with extra-floral nectaries (EFNs, glands on leaves or stems that secrete nectar) and the ants that visit them. Ants are attracted by the nectar and then protect the plant against destructive herbivores. The distribution of these plants is of particular interest, because it can provide insights into the evolutionary history of this unique trait and the plants that possess it. In this study, we investigated factors driving the distribution of woody plants with EFNs in the cerrado vegetation of Brazil. Location. Brazil Methods. We used a database detailing the incidence of 849 plant species at 367 cerrado sites throughout Brazil. We determined which species possessed EFNs and mapped their distributions. We tested for correlations between the proportion of EFN species at each site and (i) three environmental variables (mean annual temperature, mean annual precipitation, and the precipitation in the driest quarter of the year), (ii) a broad soil classification, and (iii) the total species diversity of each site. Results. We found a wide range in the proportion of EFN species at any one site (0–57%). However, whilst low diversity sites had wide variation in the number of EFN species, high diversity sites all had few EFN species. The proportion of EFN species was positively correlated with absolute latitude and negatively correlated with longitude. When accounting for total species diversity, the proportion of EFN species per site was negatively correlated with precipitation in the driest quarter of the year and positively correlated with temperature range. Main Conclusions. These results suggest either that herbivore pressure may be lower in drier sites, or that ants are not as dominant in these locations, or that plant lineages at these sites were unable to evolve EFNs.
format: application/pdf
format: text/html
creator: John Boudouris
creator: Simon A. Queenborough
subject: Biodiversity
subject: Biogeography
subject: Ecology
description: doi:10.7717/peerj.219
publisher: PeerJ Inc.
rights: © 2013 Boudouris and Queenborough
abstract: Aim. Throughout evolutionary history, plants and animals have evolved alongside one another. This is especially apparent when considering mutualistic relationships such as between plants with extra-floral nectaries (EFNs, glands on leaves or stems that secrete nectar) and the ants that visit them. Ants are attracted by the nectar and then protect the plant against destructive herbivores. The distribution of these plants is of particular interest, because it can provide insights into the evolutionary history of this unique trait and the plants that possess it. In this study, we investigated factors driving the distribution of woody plants with EFNs in the cerrado vegetation of Brazil. Location. Brazil Methods. We used a database detailing the incidence of 849 plant species at 367 cerrado sites throughout Brazil. We determined which species possessed EFNs and mapped their distributions. We tested for correlations between the proportion of EFN species at each site and (i) three environmental variables (mean annual temperature, mean annual precipitation, and the precipitation in the driest quarter of the year), (ii) a broad soil classification, and (iii) the total species diversity of each site. Results. We found a wide range in the proportion of EFN species at any one site (0–57%). However, whilst low diversity sites had wide variation in the number of EFN species, high diversity sites all had few EFN species. The proportion of EFN species was positively correlated with absolute latitude and negatively correlated with longitude. When accounting for total species diversity, the proportion of EFN species per site was negatively correlated with precipitation in the driest quarter of the year and positively correlated with temperature range. Main Conclusions. These results suggest either that herbivore pressure may be lower in drier sites, or that ants are not as dominant in these locations, or that plant lineages at these sites were unable to evolve EFNs.
bibliographic citation: Boudouris et al. (2013) Diversity and distribution of extra-floral nectaries in the cerrado savanna vegetation of Brazil. PeerJ 1:e219 https://doi.org/10.7717/peerj.219
date submitted: 2013-07-31
date accepted: 2013-11-11
issued: 2013-11-28
is part of: PeerJ
license: http://creativecommons.org/licenses/by/3.0/
author list: Agent
  family name: Boudouris
  given name: John
author list: Agent
  family name: Queenborough
  given name: Simon A.
doi: 10.7717/peerj.219
volume: 1
issn: 2167-8359
publication name: PeerJ
publication date: 2013-11-28
copyright: © 2013 Boudouris and Queenborough
attribution name: Boudouris and Queenborough

Fine motor deficits in reading disability and language impairment: same or different?
type: item
type: AcademicArticle
description: Several studies have found evidence of motor deficits in poor readers. There is no obvious reason for motor and literacy skills to go together, and it has been suggested that both deficits could be indicative of an underlying problem with cerebellar function and/or procedural learning. However, the picture is complicated by the fact that reading problems often co-occur with oral language impairments, which have also been linked with motor deficits. This raises the question of whether motor deficits characterise poor readers when language impairment has been accounted for – and vice versa. We considered these questions by assessing motor deficits associated with reading disability (RD) and language impairment (LI). A large community sample provided a subset of 9- to 10-year-olds, selected to oversample children with reading and/or language difficulties, to give 37 children with comorbid LI + RD, 67 children with RD only, 32 children with LI only, and 117 typically-developing (TD) children with neither type of difficulty. These children were given four motor tasks that taxed speed, sequence, and imitation abilities to differing extents. Different patterns of results were found for the four motor tasks. There was no effect of RD or LI on two speeded fingertip tapping tasks, one of which involved sequencing of movements. LI, but not RD, was associated with problems in imitating hand positions and slowed performance on a speeded peg-moving task that required a precision grip. Fine motor deficits in poor readers may be more a function of language impairment than literacy problems.
format: application/pdf
format: text/html
creator: Annie Brookman
creator: Sarah McDonald
creator: David McDonald
creator: Dorothy V.M. Bishop
subject: Cognitive Disorders
subject: Psychiatry and Psychology
description: doi:10.7717/peerj.217
publisher: PeerJ Inc.
rights: © 2013 Brookman et al.
abstract: Several studies have found evidence of motor deficits in poor readers. There is no obvious reason for motor and literacy skills to go together, and it has been suggested that both deficits could be indicative of an underlying problem with cerebellar function and/or procedural learning. However, the picture is complicated by the fact that reading problems often co-occur with oral language impairments, which have also been linked with motor deficits. This raises the question of whether motor deficits characterise poor readers when language impairment has been accounted for – and vice versa. We considered these questions by assessing motor deficits associated with reading disability (RD) and language impairment (LI). A large community sample provided a subset of 9- to 10-year-olds, selected to oversample children with reading and/or language difficulties, to give 37 children with comorbid LI + RD, 67 children with RD only, 32 children with LI only, and 117 typically-developing (TD) children with neither type of difficulty. These children were given four motor tasks that taxed speed, sequence, and imitation abilities to differing extents. Different patterns of results were found for the four motor tasks. There was no effect of RD or LI on two speeded fingertip tapping tasks, one of which involved sequencing of movements. LI, but not RD, was associated with problems in imitating hand positions and slowed performance on a speeded peg-moving task that required a precision grip. Fine motor deficits in poor readers may be more a function of language impairment than literacy problems.
bibliographic citation: Brookman et al. (2013) Fine motor deficits in reading disability and language impairment: same or different?. PeerJ 1:e217 https://doi.org/10.7717/peerj.217
date submitted: 2013-07-25
date accepted: 2013-11-06
issued: 2013-11-28
is part of: PeerJ
license: http://creativecommons.org/licenses/by/3.0/
author list: Agent
  family name: Brookman
  given name: Annie
author list: Agent
  family name: McDonald
  given name: Sarah
author list: Agent
  family name: McDonald
  given name: David
author list: Agent
  family name: Bishop
  given name: Dorothy V.M.
doi: 10.7717/peerj.217
volume: 1
issn: 2167-8359
publication name: PeerJ
publication date: 2013-11-28
copyright: © 2013 Brookman et al.
attribution name: Brookman et al.

A feasibility open trial of internet-delivered cognitive-behavioural therapy (iCBT) among consumers of a non-governmental mental health organisation with anxiety
type: item
type: AcademicArticle
description: Background. To date the efficacy and acceptability of internet-delivered cognitive behavioural treatments (iCBT) has been examined in clinical trials and specialist facilities. The present study reports the acceptability, feasibility and preliminary efficacy of an established iCBT treatment course (the Wellbeing Course) administered by a not-for-profit non-governmental organisation, the Mental Health Association (MHA) of New South Wales, to consumers with symptoms of anxiety. Methods. Ten individuals who contacted the MHA’s telephone support line or visited the MHA’s website and reported at least mild symptoms of anxiety (GAD-7 total scores ≥5) were admitted to the study. Participants were provided access to the Wellbeing Course, which comprises five online lessons and homework assignments, and brief weekly support from an MHA staff member via telephone and email. The MHA staff member was an experienced mental health professional and received minimal training in administering the intervention. Results. All 10 participants completed the course within the 8 weeks. Post-treatment and two month follow-up questionnaires were completed by all participants. Mean within-group effect sizes (Cohen’s d) for the Generalized Anxiety Disorder 7 Item (GAD-7) and Patient Health Questionnaire 9 Item (PHQ-9) were large (i.e., > .80) and consistent with previous controlled research. The Course was also rated as highly acceptable with all 10 participants reporting it was worth their time and they would recommend it to a friend. Conclusions. These results provide support for the potential clinical utility of iCBT interventions and the acceptability and feasibility of employing non-governmental mental health organisations to deliver these treatments. However, further research is needed to examine the clinical efficacy and cost-effectiveness of delivering iCBT via such organisations.
format: application/pdf
format: text/html
creator: Terry Kirkpatrick
creator: Linda Manoukian
creator: Blake F. Dear
creator: Luke Johnston
creator: Nickolai Titov
subject: Clinical Trials
subject: Psychiatry and Psychology
subject: Public Health
description: doi:10.7717/peerj.210
publisher: PeerJ Inc.
rights: © 2013 Kirkpatrick et al.
abstract: Background. To date the efficacy and acceptability of internet-delivered cognitive behavioural treatments (iCBT) has been examined in clinical trials and specialist facilities. The present study reports the acceptability, feasibility and preliminary efficacy of an established iCBT treatment course (the Wellbeing Course) administered by a not-for-profit non-governmental organisation, the Mental Health Association (MHA) of New South Wales, to consumers with symptoms of anxiety. Methods. Ten individuals who contacted the MHA’s telephone support line or visited the MHA’s website and reported at least mild symptoms of anxiety (GAD-7 total scores ≥5) were admitted to the study. Participants were provided access to the Wellbeing Course, which comprises five online lessons and homework assignments, and brief weekly support from an MHA staff member via telephone and email. The MHA staff member was an experienced mental health professional and received minimal training in administering the intervention. Results. All 10 participants completed the course within the 8 weeks. Post-treatment and two month follow-up questionnaires were completed by all participants. Mean within-group effect sizes (Cohen’s d) for the Generalized Anxiety Disorder 7 Item (GAD-7) and Patient Health Questionnaire 9 Item (PHQ-9) were large (i.e., > .80) and consistent with previous controlled research. The Course was also rated as highly acceptable with all 10 participants reporting it was worth their time and they would recommend it to a friend. Conclusions. These results provide support for the potential clinical utility of iCBT interventions and the acceptability and feasibility of employing non-governmental mental health organisations to deliver these treatments. However, further research is needed to examine the clinical efficacy and cost-effectiveness of delivering iCBT via such organisations.
bibliographic citation: Kirkpatrick et al. (2013) A feasibility open trial of internet-delivered cognitive-behavioural therapy (iCBT) among consumers of a non-governmental mental health organisation with anxiety. PeerJ 1:e210 https://doi.org/10.7717/peerj.210
date submitted: 2013-07-12
date accepted: 2013-10-23
issued: 2013-11-28
is part of: PeerJ
license: http://creativecommons.org/licenses/by/3.0/
author list: Agent
  family name: Kirkpatrick
  given name: Terry
author list: Agent
  family name: Manoukian
  given name: Linda
author list: Agent
  family name: Dear
  given name: Blake F.
author list: Agent
  family name: Johnston
  given name: Luke
author list: Agent
  family name: Titov
  given name: Nickolai
doi: 10.7717/peerj.210
volume: 1
issn: 2167-8359
publication name: PeerJ
publication date: 2013-11-28
copyright: © 2013 Kirkpatrick et al.
attribution name: Kirkpatrick et al.

Altering an extended phenotype reduces intraspecific male aggression and can maintain diversity in cichlid fish
type: item
type: AcademicArticle
description: Reduced male aggression towards different phenotypes generating negative frequency-dependent intrasexual selection has been suggested as a mechanism to facilitate the invasion and maintenance of novel phenotypes in a population. To date, the best empirical evidence for the phenomenon has been provided by laboratory studies on cichlid fish with different colour polymorphisms. Here we experimentally tested the hypothesis in a natural population of Lake Malawi cichlid fish, in which males build sand-castles (bowers) to attract females during seasonal leks. We predicted that if bower shape plays an important role in male aggressive interactions, aggression among conspecific males should decrease when their bower shape is altered. Accordingly, we allocated randomly chosen bowers in a Nyassachromis cf. microcephalus lek into three treatments: control, manipulated to a different shape, and simulated manipulation. We then measured male behaviours and bower shape before and after these treatments. We found that once bower shape was altered, males were involved in significantly fewer aggressive interactions with conspecific males than before manipulation. Mating success was not affected. Our results support the idea that an extended phenotype, such as bower shape, can be important in maintaining polymorphic populations. Specifically, reduced male conspecific aggression towards males with different extended phenotypes (here, bower shapes) may cause negative frequency-dependent selection, allowing the invasion and establishment of a new phenotype (bower builder). This could help our understanding of mechanisms of diversification within populations, and in particular, the overall diversification of bower shapes within Lake Malawi cichlids.
format: application/pdf
format: text/html
creator: Isabel Santos Magalhaes
creator: Guy E. Croft
creator: Domino A. Joyce
subject: Animal Behavior
subject: Evolutionary Studies
subject: Zoology
description: doi:10.7717/peerj.209
publisher: PeerJ Inc.
rights: © 2013 magalhaes et al.
abstract: Reduced male aggression towards different phenotypes generating negative frequency-dependent intrasexual selection has been suggested as a mechanism to facilitate the invasion and maintenance of novel phenotypes in a population. To date, the best empirical evidence for the phenomenon has been provided by laboratory studies on cichlid fish with different colour polymorphisms. Here we experimentally tested the hypothesis in a natural population of Lake Malawi cichlid fish, in which males build sand-castles (bowers) to attract females during seasonal leks. We predicted that if bower shape plays an important role in male aggressive interactions, aggression among conspecific males should decrease when their bower shape is altered. Accordingly, we allocated randomly chosen bowers in a Nyassachromis cf. microcephalus lek into three treatments: control, manipulated to a different shape, and simulated manipulation. We then measured male behaviours and bower shape before and after these treatments. We found that once bower shape was altered, males were involved in significantly fewer aggressive interactions with conspecific males than before manipulation. Mating success was not affected. Our results support the idea that an extended phenotype, such as bower shape, can be important in maintaining polymorphic populations. Specifically, reduced male conspecific aggression towards males with different extended phenotypes (here, bower shapes) may cause negative frequency-dependent selection, allowing the invasion and establishment of a new phenotype (bower builder). This could help our understanding of mechanisms of diversification within populations, and in particular, the overall diversification of bower shapes within Lake Malawi cichlids.
bibliographic citation: Magalhaes et al. (2013) Altering an extended phenotype reduces intraspecific male aggression and can maintain diversity in cichlid fish. PeerJ 1:e209 https://doi.org/10.7717/peerj.209
date submitted: 2013-07-15
date accepted: 2013-10-23
issued: 2013-11-26
is part of: PeerJ
license: http://creativecommons.org/licenses/by/3.0/
author list: Agent
  family name: Magalhaes
  given name: Isabel Santos
author list: Agent
  family name: Croft
  given name: Guy E.
author list: Agent
  family name: Joyce
  given name: Domino A.
doi: 10.7717/peerj.209
volume: 1
issn: 2167-8359
publication name: PeerJ
publication date: 2013-11-26
copyright: © 2013 magalhaes et al.
attribution name: magalhaes et al.

An empirical evaluation of four variants of a universal species–area relationship
type: item
type: AcademicArticle
description: The Maximum Entropy Theory of Ecology (METE) predicts a universal species–area relationship (SAR) that can be fully characterized using only the total abundance (N) and species richness (S) at a single spatial scale. This theory has shown promise for characterizing scale dependence in the SAR. However, there are currently four different approaches to applying METE to predict the SAR and it is unclear which approach should be used due to a lack of empirical comparison. Specifically, METE can be applied recursively or non-recursively and can use either a theoretical or observed species-abundance distribution (SAD). We compared the four different combinations of approaches using empirical data from 16 datasets containing over 1000 species and 300,000 individual trees and herbs. In general, METE accurately downscaled the SAR (R2 > 0.94), but the recursive approach consistently under-predicted richness. METE’s accuracy did not depend strongly on using the observed or predicted SAD. This suggests that the best approach to scaling diversity using METE is to use a combination of non-recursive scaling and the theoretical abundance distribution, which allows predictions to be made across a broad range of spatial scales with only knowledge of the species richness and total abundance at a single scale.
format: application/pdf
format: text/html
creator: Daniel J. McGlinn
creator: Xiao Xiao
creator: Ethan P. White
subject: Biodiversity
subject: Ecology
description: doi:10.7717/peerj.212
publisher: PeerJ Inc.
rights: © 2013 McGlinn et al.
abstract: The Maximum Entropy Theory of Ecology (METE) predicts a universal species–area relationship (SAR) that can be fully characterized using only the total abundance (N) and species richness (S) at a single spatial scale. This theory has shown promise for characterizing scale dependence in the SAR. However, there are currently four different approaches to applying METE to predict the SAR and it is unclear which approach should be used due to a lack of empirical comparison. Specifically, METE can be applied recursively or non-recursively and can use either a theoretical or observed species-abundance distribution (SAD). We compared the four different combinations of approaches using empirical data from 16 datasets containing over 1000 species and 300,000 individual trees and herbs. In general, METE accurately downscaled the SAR (R2 > 0.94), but the recursive approach consistently under-predicted richness. METE’s accuracy did not depend strongly on using the observed or predicted SAD. This suggests that the best approach to scaling diversity using METE is to use a combination of non-recursive scaling and the theoretical abundance distribution, which allows predictions to be made across a broad range of spatial scales with only knowledge of the species richness and total abundance at a single scale.
bibliographic citation: McGlinn et al. (2013) An empirical evaluation of four variants of a universal species–area relationship. PeerJ 1:e212 https://doi.org/10.7717/peerj.212
date submitted: 2013-08-27
date accepted: 2013-10-30
issued: 2013-11-21
is part of: PeerJ
license: http://creativecommons.org/licenses/by/3.0/
author list: Agent
  family name: McGlinn
  given name: Daniel J.
author list: Agent
  family name: Xiao
  given name: Xiao
author list: Agent
  family name: White
  given name: Ethan P.
doi: 10.7717/peerj.212
volume: 1
issn: 2167-8359
publication name: PeerJ
publication date: 2013-11-21
copyright: © 2013 McGlinn et al.
attribution name: McGlinn et al.

Predominant intragenic methylation is associated with gene expression characteristics in a bivalve mollusc
type: item
type: AcademicArticle
description: Characterization of DNA methylation patterns in the Pacific oyster, Crassostrea gigas, indicates that this epigenetic mechanism plays an important functional role in gene regulation and may be involved in the regulation of developmental processes and environmental responses. However, previous studies have been limited to in silico analyses or characterization of DNA methylation at the single gene level. Here, we have employed a genome-wide approach to gain insight into how DNA methylation supports the regulation of the genome in C. gigas. Using a combination of methylation enrichment and high-throughput bisulfite sequencing, we have been able to map methylation at over 2.5 million individual CpG loci. This is the first high-resolution methylome generated for a molluscan species. Results indicate that methylation varies spatially across the genome with a majority of the methylated sites mapping to intra genic regions. The bisulfite sequencing data was combined with RNA-seq data to examine genome-wide relationships between gene body methylation and gene expression, where it was shown that methylated genes are associated with high transcript abundance and low variation in expression between tissue types. The combined data suggest DNA methylation plays a complex role in regulating genome activity in bivalves.
format: application/pdf
format: text/html
creator: Mackenzie R. Gavery
creator: Steven B. Roberts
subject: Aquaculture, Fisheries and Fish Science
subject: Genomics
subject: Molecular Biology
description: doi:10.7717/peerj.215
publisher: PeerJ Inc.
rights: © 2013 Gavery and Roberts
abstract: Characterization of DNA methylation patterns in the Pacific oyster, Crassostrea gigas, indicates that this epigenetic mechanism plays an important functional role in gene regulation and may be involved in the regulation of developmental processes and environmental responses. However, previous studies have been limited to in silico analyses or characterization of DNA methylation at the single gene level. Here, we have employed a genome-wide approach to gain insight into how DNA methylation supports the regulation of the genome in C. gigas. Using a combination of methylation enrichment and high-throughput bisulfite sequencing, we have been able to map methylation at over 2.5 million individual CpG loci. This is the first high-resolution methylome generated for a molluscan species. Results indicate that methylation varies spatially across the genome with a majority of the methylated sites mapping to intra genic regions. The bisulfite sequencing data was combined with RNA-seq data to examine genome-wide relationships between gene body methylation and gene expression, where it was shown that methylated genes are associated with high transcript abundance and low variation in expression between tissue types. The combined data suggest DNA methylation plays a complex role in regulating genome activity in bivalves.
bibliographic citation: Gavery et al. (2013) Predominant intragenic methylation is associated with gene expression characteristics in a bivalve mollusc. PeerJ 1:e215 https://doi.org/10.7717/peerj.215
date submitted: 2013-09-26
date accepted: 2013-11-01
issued: 2013-11-21
is part of: PeerJ
license: http://creativecommons.org/licenses/by/3.0/
author list: Agent
  family name: Gavery
  given name: Mackenzie R.
author list: Agent
  family name: Roberts
  given name: Steven B.
doi: 10.7717/peerj.215
volume: 1
issn: 2167-8359
publication name: PeerJ
publication date: 2013-11-21
copyright: © 2013 Gavery and Roberts
attribution name: Gavery and Roberts

Cannabidivarin (CBDV) suppresses pentylenetetrazole (PTZ)-induced increases in epilepsy-related gene expression
type: item
type: AcademicArticle
description: To date, anticonvulsant effects of the plant cannabinoid, cannabidivarin (CBDV), have been reported in several animal models of seizure. However, these behaviourally observed anticonvulsant effects have not been confirmed at the molecular level. To examine changes to epilepsy-related gene expression following chemical convulsant treatment and their subsequent control by phytocannabinoid administration, we behaviourally evaluated effects of CBDV (400 mg/kg, p.o.) on acute, pentylenetetrazole (PTZ: 95 mg/kg, i.p.)-induced seizures, quantified expression levels of several epilepsy-related genes (Fos, Casp 3, Ccl3, Ccl4, Npy, Arc, Penk, Camk2a, Bdnf and Egr1) by qPCR using hippocampal, neocortical and prefrontal cortical tissue samples before examining correlations between expression changes and seizure severity. PTZ treatment alone produced generalised seizures (median: 5.00) and significantly increased expression of Fos, Egr1, Arc, Ccl4 and Bdnf. Consistent with previous findings, CBDV significantly decreased PTZ-induced seizure severity (median: 3.25) and increased latency to the first sign of seizure. Furthermore, there were correlations between reductions of seizure severity and mRNA expression of Fos, Egr1, Arc, Ccl4 and Bdnf in the majority of brain regions in the CBDV+PTZ treated group. When CBDV treated animals were grouped into CBDV responders (criterion: seizure severity ≤3.25) and non-responders (criterion: seizure severity >3.25), PTZ-induced increases of Fos, Egr1, Arc, Ccl4 and Bdnf expression were suppressed in CBDV responders. These results provide the first molecular confirmation of behaviourally observed effects of the non-psychoactive, anticonvulsant cannabinoid, CBDV, upon chemically-induced seizures and serve to underscore its suitability for clinical development.
format: application/pdf
format: text/html
creator: Naoki Amada
creator: Yuki Yamasaki
creator: Claire M. Williams
creator: Benjamin J. Whalley
subject: Molecular Biology
subject: Neuroscience
subject: Neurology
subject: Pharmacology
description: doi:10.7717/peerj.214
publisher: PeerJ Inc.
rights: © 2013 Amada et al.
abstract: To date, anticonvulsant effects of the plant cannabinoid, cannabidivarin (CBDV), have been reported in several animal models of seizure. However, these behaviourally observed anticonvulsant effects have not been confirmed at the molecular level. To examine changes to epilepsy-related gene expression following chemical convulsant treatment and their subsequent control by phytocannabinoid administration, we behaviourally evaluated effects of CBDV (400 mg/kg, p.o.) on acute, pentylenetetrazole (PTZ: 95 mg/kg, i.p.)-induced seizures, quantified expression levels of several epilepsy-related genes (Fos, Casp 3, Ccl3, Ccl4, Npy, Arc, Penk, Camk2a, Bdnf and Egr1) by qPCR using hippocampal, neocortical and prefrontal cortical tissue samples before examining correlations between expression changes and seizure severity. PTZ treatment alone produced generalised seizures (median: 5.00) and significantly increased expression of Fos, Egr1, Arc, Ccl4 and Bdnf. Consistent with previous findings, CBDV significantly decreased PTZ-induced seizure severity (median: 3.25) and increased latency to the first sign of seizure. Furthermore, there were correlations between reductions of seizure severity and mRNA expression of Fos, Egr1, Arc, Ccl4 and Bdnf in the majority of brain regions in the CBDV+PTZ treated group. When CBDV treated animals were grouped into CBDV responders (criterion: seizure severity ≤3.25) and non-responders (criterion: seizure severity >3.25), PTZ-induced increases of Fos, Egr1, Arc, Ccl4 and Bdnf expression were suppressed in CBDV responders. These results provide the first molecular confirmation of behaviourally observed effects of the non-psychoactive, anticonvulsant cannabinoid, CBDV, upon chemically-induced seizures and serve to underscore its suitability for clinical development.
bibliographic citation: Amada et al. (2013) Cannabidivarin (CBDV) suppresses pentylenetetrazole (PTZ)-induced increases in epilepsy-related gene expression. PeerJ 1:e214 https://doi.org/10.7717/peerj.214
date submitted: 2013-06-18
date accepted: 2013-10-30
issued: 2013-11-21
is part of: PeerJ
license: http://creativecommons.org/licenses/by/3.0/
author list: Agent
  family name: Amada
  given name: Naoki
author list: Agent
  family name: Yamasaki
  given name: Yuki
author list: Agent
  family name: Williams
  given name: Claire M.
author list: Agent
  family name: Whalley
  given name: Benjamin J.
doi: 10.7717/peerj.214
volume: 1
issn: 2167-8359
publication name: PeerJ
publication date: 2013-11-21
copyright: © 2013 Amada et al.
attribution name: Amada et al.

Effects of ocean acidification on the dissolution rates of reef-coral skeletons
type: item
type: AcademicArticle
description: Ocean acidification threatens the foundation of tropical coral reefs. This study investigated three aspects of ocean acidification: (i) the rates at which perforate and imperforate coral-colony skeletons passively dissolve when pH is 7.8, which is predicted to occur globally by 2100, (ii) the rates of passive dissolution of corals with respect to coral-colony surface areas, and (iii) the comparative rates of a vertical reef-growth model, incorporating passive dissolution rates, and predicted sea-level rise. By 2100, when the ocean pH is expected to be 7.8, perforate Montipora coral skeletons will lose on average 15 kg CaCO3 m−2 y−1, which is approximately −10.5 mm of vertical reduction of reef framework per year. This rate of passive dissolution is higher than the average rate of reef growth over the last several millennia and suggests that reefs composed of perforate Montipora coral skeletons will have trouble keeping up with sea-level rise under ocean acidification. Reefs composed of primarily imperforate coral skeletons will not likely dissolve as rapidly, but our model shows they will also have trouble keeping up with sea-level rise by 2050.
format: application/pdf
format: text/html
creator: Robert van Woesik
creator: Kelly van Woesik
creator: Liana van Woesik
creator: Sandra van Woesik
subject: Biological Oceanography
subject: Climate Change Biology
subject: Environmental Sciences
subject: Marine Biology
description: doi:10.7717/peerj.208
publisher: PeerJ Inc.
rights: © 2013 van Woesik et al.
abstract: Ocean acidification threatens the foundation of tropical coral reefs. This study investigated three aspects of ocean acidification: (i) the rates at which perforate and imperforate coral-colony skeletons passively dissolve when pH is 7.8, which is predicted to occur globally by 2100, (ii) the rates of passive dissolution of corals with respect to coral-colony surface areas, and (iii) the comparative rates of a vertical reef-growth model, incorporating passive dissolution rates, and predicted sea-level rise. By 2100, when the ocean pH is expected to be 7.8, perforate Montipora coral skeletons will lose on average 15 kg CaCO3 m−2 y−1, which is approximately −10.5 mm of vertical reduction of reef framework per year. This rate of passive dissolution is higher than the average rate of reef growth over the last several millennia and suggests that reefs composed of perforate Montipora coral skeletons will have trouble keeping up with sea-level rise under ocean acidification. Reefs composed of primarily imperforate coral skeletons will not likely dissolve as rapidly, but our model shows they will also have trouble keeping up with sea-level rise by 2050.
bibliographic citation: van Woesik et al. (2013) Effects of ocean acidification on the dissolution rates of reef-coral skeletons. PeerJ 1:e208 https://doi.org/10.7717/peerj.208
date submitted: 2013-08-26
date accepted: 2013-10-22
issued: 2013-11-21
is part of: PeerJ
license: http://creativecommons.org/licenses/by/3.0/
author list: Agent
  family name: van Woesik
  given name: Robert
author list: Agent
  family name: van Woesik
  given name: Kelly
author list: Agent
  family name: van Woesik
  given name: Liana
author list: Agent
  family name: van Woesik
  given name: Sandra
doi: 10.7717/peerj.208
volume: 1
issn: 2167-8359
publication name: PeerJ
publication date: 2013-11-21
copyright: © 2013 van Woesik et al.
attribution name: van Woesik et al.

The relationship between resilience and personality traits in doctors: implications for enhancing well being
type: item
type: AcademicArticle
description: Objective. The health and well being of medical doctors is vital to their longevity and safe practice. The concept of resilience is recognised as a key component of well being and is an important factor in medical training to help doctors learn to cope with challenge, stress, and adversity. This study examined the relationship of resilience to personality traits and resilience in doctors in order to identify the key traits that promote or impair resilience. Methods. A cross sectional cohort of 479 family practitioners in practice across Australia was studied. The Temperament and Character Inventory measured levels of the seven basic dimensions of personality and the Resilience Scale provided an overall measure of resilience. The associations between resilience and personality were examined by Pearson product-moment correlation coefficients, controlling for age and gender (α = 0.05 with an accompanying 95% confidence level) and multiple regression analyses. Results. Strong to medium positive correlations were found between Resilience and Self-directedness (r = .614, p < .01), Persistence (r = .498, p < .01), and Cooperativeness (r = .363, p < .01) and negative with Harm Avoidance (r = .−555, p < .01). Individual differences in personality explained 39% of the variance in resilience [F(7, 460) = 38.40, p < .001]. The three traits which contributed significantly to this variance were Self-directedness (β = .33, p < .001), Persistence (β = .22, p < .001) and Harm Avoidance (β = .19, p < .001). Conclusion. Resilience was associated with a personality trait pattern that is mature, responsible, optimistic, persevering, and cooperative. Findings support the inclusion of resilience as a component of optimal functioning and well being in doctors. Strategies for enhancing resilience should consider the key traits that drive or impair it.
format: application/pdf
format: text/html
creator: Diann S. Eley
creator: C. Robert Cloninger
creator: Lucie Walters
creator: Caroline Laurence
creator: Robyn Synnott
creator: David Wilkinson
subject: Psychiatry and Psychology
subject: Science and Medical Education
description: doi:10.7717/peerj.216
publisher: PeerJ Inc.
rights: © 2013 Eley et al.
abstract: Objective. The health and well being of medical doctors is vital to their longevity and safe practice. The concept of resilience is recognised as a key component of well being and is an important factor in medical training to help doctors learn to cope with challenge, stress, and adversity. This study examined the relationship of resilience to personality traits and resilience in doctors in order to identify the key traits that promote or impair resilience. Methods. A cross sectional cohort of 479 family practitioners in practice across Australia was studied. The Temperament and Character Inventory measured levels of the seven basic dimensions of personality and the Resilience Scale provided an overall measure of resilience. The associations between resilience and personality were examined by Pearson product-moment correlation coefficients, controlling for age and gender (α = 0.05 with an accompanying 95% confidence level) and multiple regression analyses. Results. Strong to medium positive correlations were found between Resilience and Self-directedness (r = .614, p < .01), Persistence (r = .498, p < .01), and Cooperativeness (r = .363, p < .01) and negative with Harm Avoidance (r = .−555, p < .01). Individual differences in personality explained 39% of the variance in resilience [F(7, 460) = 38.40, p < .001]. The three traits which contributed significantly to this variance were Self-directedness (β = .33, p < .001), Persistence (β = .22, p < .001) and Harm Avoidance (β = .19, p < .001). Conclusion. Resilience was associated with a personality trait pattern that is mature, responsible, optimistic, persevering, and cooperative. Findings support the inclusion of resilience as a component of optimal functioning and well being in doctors. Strategies for enhancing resilience should consider the key traits that drive or impair it.
bibliographic citation: Eley et al. (2013) The relationship between resilience and personality traits in doctors: implications for enhancing well being. PeerJ 1:e216 https://doi.org/10.7717/peerj.216
date submitted: 2013-09-09
date accepted: 2013-11-02
issued: 2013-11-19
is part of: PeerJ
license: http://creativecommons.org/licenses/by/3.0/
author list: Agent
  family name: Eley
  given name: Diann S.
author list: Agent
  family name: Cloninger
  given name: C. Robert
author list: Agent
  family name: Walters
  given name: Lucie
author list: Agent
  family name: Laurence
  given name: Caroline
author list: Agent
  family name: Synnott
  given name: Robyn
author list: Agent
  family name: Wilkinson
  given name: David
doi: 10.7717/peerj.216
volume: 1
issn: 2167-8359
publication name: PeerJ
publication date: 2013-11-19
copyright: © 2013 Eley et al.
attribution name: Eley et al.

Examination of spotted sand bass (Paralabrax maculatofasciatus) pollutant bioaccumulation in San Diego Bay, San Diego, California
type: item
type: AcademicArticle
description: The spotted sand bass (Paralabrax maculatofasciatus) is an important recreational sport and subsistence food fish within San Diego Bay, a large industrialized harbor in San Diego, California. Despite this importance, few studies examining the species life history relative to pollutant tissue concentrations and the consumptive fishery exist. This study utilized data from three independent spotted sand bass studies from 1989 to 2002 to investigate PCB, DDT, and mercury tissue concentrations relative to spotted sand bass age and growth in San Diego Bay, with subsequent comparisons to published pollutant advisory levels and fishery regulations for recreational and subsistence consumption of the species. Subsequent analysis focused on examining temporal and spatial differences for different regions of San Diego Bay. Study results for growth confirmed previous work, finding the species to exhibit highly asymptotic growth, making tissue pollutant concentrations at initial take size difficult if not impossible to predict. This was corroborated by independent tissue concentration results for mercury, which found no relationship between fish size and pollutant bioaccumulation observed. However, a positive though highly variable relationship was observed between fish size and PCB tissue concentration. Despite these findings, a significant proportion of fish exhibited pollutant levels above recommended state recreational angler consumption advisory levels for PCBs and mercury, especially for fish above the minimum take size, making the necessity of at-size predictions less critical. Lastly, no difference in tissue concentration was found temporally or spatially within San Diego Bay.
format: application/pdf
format: text/html
creator: Chad L. Loflen
subject: Aquaculture, Fisheries and Fish Science
subject: Ecology
subject: Marine Biology
description: doi:10.7717/peerj.213
publisher: PeerJ Inc.
rights: © 2013 Loflen
abstract: The spotted sand bass (Paralabrax maculatofasciatus) is an important recreational sport and subsistence food fish within San Diego Bay, a large industrialized harbor in San Diego, California. Despite this importance, few studies examining the species life history relative to pollutant tissue concentrations and the consumptive fishery exist. This study utilized data from three independent spotted sand bass studies from 1989 to 2002 to investigate PCB, DDT, and mercury tissue concentrations relative to spotted sand bass age and growth in San Diego Bay, with subsequent comparisons to published pollutant advisory levels and fishery regulations for recreational and subsistence consumption of the species. Subsequent analysis focused on examining temporal and spatial differences for different regions of San Diego Bay. Study results for growth confirmed previous work, finding the species to exhibit highly asymptotic growth, making tissue pollutant concentrations at initial take size difficult if not impossible to predict. This was corroborated by independent tissue concentration results for mercury, which found no relationship between fish size and pollutant bioaccumulation observed. However, a positive though highly variable relationship was observed between fish size and PCB tissue concentration. Despite these findings, a significant proportion of fish exhibited pollutant levels above recommended state recreational angler consumption advisory levels for PCBs and mercury, especially for fish above the minimum take size, making the necessity of at-size predictions less critical. Lastly, no difference in tissue concentration was found temporally or spatially within San Diego Bay.
bibliographic citation: Loflen (2013) Examination of spotted sand bass (Paralabrax maculatofasciatus) pollutant bioaccumulation in San Diego Bay, San Diego, California. PeerJ 1:e213 https://doi.org/10.7717/peerj.213
date submitted: 2013-09-26
date accepted: 2013-10-30
issued: 2013-11-19
is part of: PeerJ
license: http://creativecommons.org/licenses/by/3.0/
author list: Agent
  family name: Loflen
  given name: Chad L.
doi: 10.7717/peerj.213
volume: 1
issn: 2167-8359
publication name: PeerJ
publication date: 2013-11-19
copyright: © 2013 Loflen
attribution name: Loflen

ezRAD: a simplified method for genomic genotyping in non-model organisms
type: item
type: AcademicArticle
description: Here, we introduce ezRAD, a novel strategy for restriction site–associated DNA (RAD) that requires little technical expertise or investment in laboratory equipment, and demonstrate its utility for ten non-model organisms across a wide taxonomic range. ezRAD differs from other RAD methods primarily through its use of standard Illumina TruSeq library preparation kits, which makes it possible for any laboratory to send out to a commercial genomic core facility for library preparation and next-generation sequencing with virtually no additional investment beyond the cost of the service itself. This simplification opens RADseq to any lab with the ability to extract DNA and perform a restriction digest. ezRAD also differs from others in its flexibility to use any restriction enzyme (or combination of enzymes) that cuts frequently enough to generate fragments of the desired size range, without requiring the purchase of separate adapters for each enzyme or a sonication step, which can further decrease the cost involved in choosing optimal enzymes for particular species and research questions. We apply this method across a wide taxonomic diversity of non-model organisms to demonstrate the utility and flexibility of our approach. The simplicity of ezRAD makes it particularly useful for the discovery of single nucleotide polymorphisms and targeted amplicon sequencing in natural populations of non-model organisms that have been historically understudied because of lack of genomic information.
format: application/pdf
format: text/html
creator: Robert J. Toonen
creator: Jonathan B. Puritz
creator: Zac H. Forsman
creator: Jonathan L. Whitney
creator: Iria Fernandez-Silva
creator: Kimberly R. Andrews
creator: Christopher E. Bird
subject: Genetics
subject: Genomics
subject: Marine Biology
subject: Molecular Biology
description: doi:10.7717/peerj.203
publisher: PeerJ Inc.
rights: © 2013 Toonen et al.
abstract: Here, we introduce ezRAD, a novel strategy for restriction site–associated DNA (RAD) that requires little technical expertise or investment in laboratory equipment, and demonstrate its utility for ten non-model organisms across a wide taxonomic range. ezRAD differs from other RAD methods primarily through its use of standard Illumina TruSeq library preparation kits, which makes it possible for any laboratory to send out to a commercial genomic core facility for library preparation and next-generation sequencing with virtually no additional investment beyond the cost of the service itself. This simplification opens RADseq to any lab with the ability to extract DNA and perform a restriction digest. ezRAD also differs from others in its flexibility to use any restriction enzyme (or combination of enzymes) that cuts frequently enough to generate fragments of the desired size range, without requiring the purchase of separate adapters for each enzyme or a sonication step, which can further decrease the cost involved in choosing optimal enzymes for particular species and research questions. We apply this method across a wide taxonomic diversity of non-model organisms to demonstrate the utility and flexibility of our approach. The simplicity of ezRAD makes it particularly useful for the discovery of single nucleotide polymorphisms and targeted amplicon sequencing in natural populations of non-model organisms that have been historically understudied because of lack of genomic information.
bibliographic citation: Toonen et al. (2013) ezRAD: a simplified method for genomic genotyping in non-model organisms. PeerJ 1:e203 https://doi.org/10.7717/peerj.203
date submitted: 2013-07-16
date accepted: 2013-10-13
issued: 2013-11-19
is part of: PeerJ
license: http://creativecommons.org/licenses/by/3.0/
author list: Agent
  family name: Toonen
  given name: Robert J.
author list: Agent
  family name: Puritz
  given name: Jonathan B.
author list: Agent
  family name: Forsman
  given name: Zac H.
author list: Agent
  family name: Whitney
  given name: Jonathan L.
author list: Agent
  family name: Fernandez-Silva
  given name: Iria
author list: Agent
  family name: Andrews
  given name: Kimberly R.
author list: Agent
  family name: Bird
  given name: Christopher E.
doi: 10.7717/peerj.203
volume: 1
issn: 2167-8359
publication name: PeerJ
publication date: 2013-11-19
copyright: © 2013 Toonen et al.
attribution name: Toonen et al.

Amino-acid site variability among natural and designed proteins
type: item
type: AcademicArticle
description: Computational protein design attempts to create protein sequences that fold stably into pre-specified structures. Here we compare alignments of designed proteins to alignments of natural proteins and assess how closely designed sequences recapitulate patterns of sequence variation found in natural protein sequences. We design proteins using RosettaDesign, and we evaluate both fixed-backbone designs and variable-backbone designs with different amounts of backbone flexibility. We find that proteins designed with a fixed backbone tend to underestimate the amount of site variability observed in natural proteins while proteins designed with an intermediate amount of backbone flexibility result in more realistic site variability. Further, the correlation between solvent exposure and site variability in designed proteins is lower than that in natural proteins. This finding suggests that site variability is too uniform across different solvent exposure states (i.e., buried residues are too variable or exposed residues too conserved). When comparing the amino acid frequencies in the designed proteins with those in natural proteins we find that in the designed proteins hydrophobic residues are underrepresented in the core. From these results we conclude that intermediate backbone flexibility during design results in more accurate protein design and that either scoring functions or backbone sampling methods require further improvement to accurately replicate structural constraints on site variability.
format: application/pdf
format: text/html
creator: Eleisha L. Jackson
creator: Noah Ollikainen
creator: Arthur W. Covert
creator: Tanja Kortemme
creator: Claus O. Wilke
subject: Biochemistry
subject: Computational Biology
subject: Computational Science
description: doi:10.7717/peerj.211
publisher: PeerJ Inc.
rights: © 2013 Jackson et al.
abstract: Computational protein design attempts to create protein sequences that fold stably into pre-specified structures. Here we compare alignments of designed proteins to alignments of natural proteins and assess how closely designed sequences recapitulate patterns of sequence variation found in natural protein sequences. We design proteins using RosettaDesign, and we evaluate both fixed-backbone designs and variable-backbone designs with different amounts of backbone flexibility. We find that proteins designed with a fixed backbone tend to underestimate the amount of site variability observed in natural proteins while proteins designed with an intermediate amount of backbone flexibility result in more realistic site variability. Further, the correlation between solvent exposure and site variability in designed proteins is lower than that in natural proteins. This finding suggests that site variability is too uniform across different solvent exposure states (i.e., buried residues are too variable or exposed residues too conserved). When comparing the amino acid frequencies in the designed proteins with those in natural proteins we find that in the designed proteins hydrophobic residues are underrepresented in the core. From these results we conclude that intermediate backbone flexibility during design results in more accurate protein design and that either scoring functions or backbone sampling methods require further improvement to accurately replicate structural constraints on site variability.
bibliographic citation: Jackson et al. (2013) Amino-acid site variability among natural and designed proteins. PeerJ 1:e211 https://doi.org/10.7717/peerj.211
date submitted: 2013-10-03
date accepted: 2013-10-24
issued: 2013-11-12
is part of: PeerJ
license: http://creativecommons.org/licenses/by/3.0/
author list: Agent
  family name: Jackson
  given name: Eleisha L.
author list: Agent
  family name: Ollikainen
  given name: Noah
author list: Agent
  family name: Covert
  given name: Arthur W.
author list: Agent
  family name: Kortemme
  given name: Tanja
author list: Agent
  family name: Wilke
  given name: Claus O.
doi: 10.7717/peerj.211
volume: 1
issn: 2167-8359
publication name: PeerJ
publication date: 2013-11-12
copyright: © 2013 Jackson et al.
attribution name: Jackson et al.

An integrated pipeline for next generation sequencing and annotation of the complete mitochondrial genome of the giant intestinal fluke, Fasciolopsis buski (Lankester, 1857) Looss, 1899
type: item
type: AcademicArticle
description: Helminths include both parasitic nematodes (roundworms) and platyhelminths (trematode and cestode flatworms) that are abundant, and are of clinical importance. The genetic characterization of parasitic flatworms using advanced molecular tools is central to the diagnosis and control of infections. Although the nuclear genome houses suitable genetic markers (e.g., in ribosomal (r) DNA) for species identification and molecular characterization, the mitochondrial (mt) genome consistently provides a rich source of novel markers for informative systematics and epidemiological studies. In the last decade, there have been some important advances in mtDNA genomics of helminths, especially lung flukes, liver flukes and intestinal flukes. Fasciolopsis buski, often called the giant intestinal fluke, is one of the largest digenean trematodes infecting humans and found primarily in Asia, in particular the Indian subcontinent. Next-generation sequencing (NGS) technologies now provide opportunities for high throughput sequencing, assembly and annotation within a short span of time. Herein, we describe a high-throughput sequencing and bioinformatics pipeline for mt genomics for F. buski that emphasizes the utility of short read NGS platforms such as Ion Torrent and Illumina in successfully sequencing and assembling the mt genome using innovative approaches for PCR primer design as well as assembly. We took advantage of our NGS whole genome sequence data (unpublished so far) for F. buski and its comparison with available data for the Fasciola hepatica mtDNA as the reference genome for design of precise and specific primers for amplification of mt genome sequences from F. buski. A long-range PCR was carried out to create an NGS library enriched in mt DNA sequences. Two different NGS platforms were employed for complete sequencing, assembly and annotation of the F. buski mt genome. The complete mt genome sequences of the intestinal fluke comprise 14,118 bp and is thus the shortest trem…
format: application/pdf
format: text/html
creator: Devendra Kumar Biswal
creator: Sudeep Ghatani
creator: Jollin A. Shylla
creator: Ranjana Sahu
creator: Nandita Mullapudi
creator: Alok Bhattacharya
creator: Veena Tandon
subject: Bioinformatics
subject: Evolutionary Studies
subject: Genomics
subject: Parasitology
subject: Zoology
description: doi:10.7717/peerj.207
publisher: PeerJ Inc.
rights: © 2013 Biswal et al.
abstract: Helminths include both parasitic nematodes (roundworms) and platyhelminths (trematode and cestode flatworms) that are abundant, and are of clinical importance. The genetic characterization of parasitic flatworms using advanced molecular tools is central to the diagnosis and control of infections. Although the nuclear genome houses suitable genetic markers (e.g., in ribosomal (r) DNA) for species identification and molecular characterization, the mitochondrial (mt) genome consistently provides a rich source of novel markers for informative systematics and epidemiological studies. In the last decade, there have been some important advances in mtDNA genomics of helminths, especially lung flukes, liver flukes and intestinal flukes. Fasciolopsis buski, often called the giant intestinal fluke, is one of the largest digenean trematodes infecting humans and found primarily in Asia, in particular the Indian subcontinent. Next-generation sequencing (NGS) technologies now provide opportunities for high throughput sequencing, assembly and annotation within a short span of time. Herein, we describe a high-throughput sequencing and bioinformatics pipeline for mt genomics for F. buski that emphasizes the utility of short read NGS platforms such as Ion Torrent and Illumina in successfully sequencing and assembling the mt genome using innovative approaches for PCR primer design as well as assembly. We took advantage of our NGS whole genome sequence data (unpublished so far) for F. buski and its comparison with available data for the Fasciola hepatica mtDNA as the reference genome for design of precise and specific primers for amplification of mt genome sequences from F. buski. A long-range PCR was carried out to create an NGS library enriched in mt DNA sequences. Two different NGS platforms were employed for complete sequencing, assembly and annotation of the F. buski mt genome. The complete mt genome sequences of the intestinal fluke comprise 14,118 bp and is thus the shortest trem…
bibliographic citation: Biswal et al. (2013) An integrated pipeline for next generation sequencing and annotation of the complete mitochondrial genome of the giant intestinal fluke, Fasciolopsis buski (Lankester, 1857) Looss, 1899. PeerJ 1:e207 https://doi.org/10.7717/peerj.207
date submitted: 2013-09-05
date accepted: 2013-10-21
issued: 2013-11-12
is part of: PeerJ
license: http://creativecommons.org/licenses/by/3.0/
author list: Agent
  family name: Biswal
  given name: Devendra Kumar
author list: Agent
  family name: Ghatani
  given name: Sudeep
author list: Agent
  family name: Shylla
  given name: Jollin A.
author list: Agent
  family name: Sahu
  given name: Ranjana
author list: Agent
  family name: Mullapudi
  given name: Nandita
author list: Agent
  family name: Bhattacharya
  given name: Alok
author list: Agent
  family name: Tandon
  given name: Veena
doi: 10.7717/peerj.207
volume: 1
issn: 2167-8359
publication name: PeerJ
publication date: 2013-11-12
copyright: © 2013 Biswal et al.
attribution name: Biswal et al.

How migratory thrushes conquered northern North America: a comparative phylogeography approach
type: item
type: AcademicArticle
description: Five species of migratory thrushes (Turdidae) occupy a transcontinental distribution across northern North America. They have largely overlapping breeding ranges, relatively similar ecological niches, and mutualistic relationships with northern woodland communities as insectivores and seed-dispersing frugivores. As an assemblage of ecologically similar species, and given other vertebrate studies, we predicted a shared pattern of genetic divergence among these species between their eastern and western populations, and also that the timing of the coalescent events might be similar and coincident with historical glacial events. To determine how these five lineages effectively established transcontinental distributions, we used mitochondrial cytochrome b sequences to assess genetic structure and lineage coalescence from populations on each side of the continent. Two general patterns occur. Hermit and Swainson’s thrushes (Catharus guttatus and C. ustulatus) have relatively deep divergences between eastern and western phylogroups, probably reflecting shared historic vicariance. The Veery (C. fuscescens), Gray-cheeked Thrush (C. minimus), and American Robin (Turdus migratorius) have relatively shallow divergences between eastern and western populations. However, coalescent and approximate Bayesian computational analyses indicated that among all species as many as five transcontinental divergence events occurred. Divergence within both Hermit and Swainson’s thrushes resembled the divergence between Gray-cheeked Thrushes and Veeries and probably occurred during a similar time period. Despite these species’ ecological similarities, the assemblage exhibits heterogeneity at the species level in how they came to occupy transcontinental northern North America but two general continental patterns at an among-species organizational level, likely related to lineage age.
format: application/pdf
format: text/html
creator: Carrie M. Topp
creator: Christin L. Pruett
creator: Kevin G. McCracken
creator: Kevin Winker
subject: Biogeography
subject: Ecology
subject: Evolutionary Studies
subject: Genetics
subject: Zoology
description: doi:10.7717/peerj.206
publisher: PeerJ Inc.
rights: © 2013 Topp et al.
abstract: Five species of migratory thrushes (Turdidae) occupy a transcontinental distribution across northern North America. They have largely overlapping breeding ranges, relatively similar ecological niches, and mutualistic relationships with northern woodland communities as insectivores and seed-dispersing frugivores. As an assemblage of ecologically similar species, and given other vertebrate studies, we predicted a shared pattern of genetic divergence among these species between their eastern and western populations, and also that the timing of the coalescent events might be similar and coincident with historical glacial events. To determine how these five lineages effectively established transcontinental distributions, we used mitochondrial cytochrome b sequences to assess genetic structure and lineage coalescence from populations on each side of the continent. Two general patterns occur. Hermit and Swainson’s thrushes (Catharus guttatus and C. ustulatus) have relatively deep divergences between eastern and western phylogroups, probably reflecting shared historic vicariance. The Veery (C. fuscescens), Gray-cheeked Thrush (C. minimus), and American Robin (Turdus migratorius) have relatively shallow divergences between eastern and western populations. However, coalescent and approximate Bayesian computational analyses indicated that among all species as many as five transcontinental divergence events occurred. Divergence within both Hermit and Swainson’s thrushes resembled the divergence between Gray-cheeked Thrushes and Veeries and probably occurred during a similar time period. Despite these species’ ecological similarities, the assemblage exhibits heterogeneity at the species level in how they came to occupy transcontinental northern North America but two general continental patterns at an among-species organizational level, likely related to lineage age.
bibliographic citation: Topp et al. (2013) How migratory thrushes conquered northern North America: a comparative phylogeography approach. PeerJ 1:e206 https://doi.org/10.7717/peerj.206
date submitted: 2013-07-30
date accepted: 2013-10-21
issued: 2013-11-12
is part of: PeerJ
license: http://creativecommons.org/licenses/by/3.0/
author list: Agent
  family name: Topp
  given name: Carrie M.
author list: Agent
  family name: Pruett
  given name: Christin L.
author list: Agent
  family name: McCracken
  given name: Kevin G.
author list: Agent
  family name: Winker
  given name: Kevin
doi: 10.7717/peerj.206
volume: 1
issn: 2167-8359
publication name: PeerJ
publication date: 2013-11-12
copyright: © 2013 Topp et al.
attribution name: Topp et al.

Bird migratory flyways influence the phylogeography of the invasive brine shrimp Artemia franciscana in its native American range
type: item
type: AcademicArticle
description: Since Darwin’s time, waterbirds have been considered an important vector for the dispersal of continental aquatic invertebrates. Bird movements have facilitated the worldwide invasion of the American brine shrimp Artemia franciscana, transporting cysts (diapausing eggs), and favouring rapid range expansions from introduction sites. Here we address the impact of bird migratory flyways on the population genetic structure and phylogeography of A. franciscana in its native range in the Americas. We examined sequence variation for two mitochondrial gene fragments (COI and 16S for a subset of the data) in a large set of population samples representing the entire native range of A. franciscana. Furthermore, we performed Mantel tests and redundancy analyses (RDA) to test the role of flyways, geography and human introductions on the phylogeography and population genetic structure at a continental scale. A. franciscana mitochondrial DNA was very diverse, with two main clades, largely corresponding to Pacific and Atlantic populations, mirroring American bird flyways. There was a high degree of regional endemism, with populations subdivided into at least 12 divergent, geographically restricted and largely allopatric mitochondrial lineages, and high levels of population structure (ΦST of 0.92), indicating low ongoing gene flow. We found evidence of human-mediated introductions in nine out of 39 populations analysed. Once these populations were removed, Mantel tests revealed a strong association between genetic variation and geographic distance (i.e., isolation-by-distance pattern). RDA showed that shared bird flyways explained around 20% of the variance in genetic distance between populations and this was highly significant, once geographic distance was controlled for. The variance explained increased to 30% when the factor human introduction was included in the model. Our findings suggest that bird-mediated transport of brine shrimp propagules does not result in substantial ong…
format: application/pdf
format: text/html
creator: Joaquín Muñoz
creator: Francisco Amat
creator: Andy J. Green
creator: Jordi Figuerola
creator: Africa Gómez
subject: Biogeography
subject: Ecology
subject: Evolutionary Studies
description: doi:10.7717/peerj.200
publisher: PeerJ Inc.
rights: © 2013 Muoz et al.
abstract: Since Darwin’s time, waterbirds have been considered an important vector for the dispersal of continental aquatic invertebrates. Bird movements have facilitated the worldwide invasion of the American brine shrimp Artemia franciscana, transporting cysts (diapausing eggs), and favouring rapid range expansions from introduction sites. Here we address the impact of bird migratory flyways on the population genetic structure and phylogeography of A. franciscana in its native range in the Americas. We examined sequence variation for two mitochondrial gene fragments (COI and 16S for a subset of the data) in a large set of population samples representing the entire native range of A. franciscana. Furthermore, we performed Mantel tests and redundancy analyses (RDA) to test the role of flyways, geography and human introductions on the phylogeography and population genetic structure at a continental scale. A. franciscana mitochondrial DNA was very diverse, with two main clades, largely corresponding to Pacific and Atlantic populations, mirroring American bird flyways. There was a high degree of regional endemism, with populations subdivided into at least 12 divergent, geographically restricted and largely allopatric mitochondrial lineages, and high levels of population structure (ΦST of 0.92), indicating low ongoing gene flow. We found evidence of human-mediated introductions in nine out of 39 populations analysed. Once these populations were removed, Mantel tests revealed a strong association between genetic variation and geographic distance (i.e., isolation-by-distance pattern). RDA showed that shared bird flyways explained around 20% of the variance in genetic distance between populations and this was highly significant, once geographic distance was controlled for. The variance explained increased to 30% when the factor human introduction was included in the model. Our findings suggest that bird-mediated transport of brine shrimp propagules does not result in substantial ong…
bibliographic citation: Muñoz et al. (2013) Bird migratory flyways influence the phylogeography of the invasive brine shrimp Artemia franciscana in its native American range. PeerJ 1:e200 https://doi.org/10.7717/peerj.200
date submitted: 2013-07-25
date accepted: 2013-10-12
issued: 2013-11-07
is part of: PeerJ
license: http://creativecommons.org/licenses/by/3.0/
author list: Agent
  family name: Muñoz
  given name: Joaquín
author list: Agent
  family name: Amat
  given name: Francisco
author list: Agent
  family name: Green
  given name: Andy J.
author list: Agent
  family name: Figuerola
  given name: Jordi
author list: Agent
  family name: Gómez
  given name: Africa
doi: 10.7717/peerj.200
volume: 1
issn: 2167-8359
publication name: PeerJ
publication date: 2013-11-07
copyright: © 2013 Muoz et al.
attribution name: Muoz et al.

A longitudinal analysis of associations between traffic-related air pollution with asthma, allergies and sensitization in the GINIplus and LISAplus birth cohorts
type: item
type: AcademicArticle
description: Background. There is a need to study whether the adverse effects of traffic-related air pollution (TRAP) on childhood asthma and allergic diseases documented during early-life persist into later childhood. This longitudinal study examined whether TRAP is associated with the prevalence of asthma, allergic rhinitis and aeroallergen sensitization in two German cohorts followed from birth to 10 years. Materials. Questionnaire-derived annual reports of doctor diagnosed asthma and allergic rhinitis, as well as eye and nose symptoms, were collected from 6,604 children. Aeroallergen sensitization was assessed for 3,655 children who provided blood samples. Associations between these health outcomes and nitrogen dioxide (NO2), particles with aerodynamic diameters less than 2.5 µg/m3 (PM2.5) mass, PM2.5 absorbance and ozone, individually estimated for each child at the birth, six and 10 year home addresses, were assessed using generalized estimation equations including adjustments for relevant covariates. Odds ratios [95% confidence intervals] per increase in interquartile range of pollutant are presented for the total population and per geographical area (GINI/LISA South, GINI/LISA North and LISA East, Germany). Results. The risk estimates for the total population were generally null across outcomes and pollutants. The area-specific results were heterogeneous. In GINI/LISA North, all associations were null. In LISA East, associations with ozone were elevated for all outcomes, and those for allergic rhinitis and eyes and nose symptom prevalence reached statistical significance (1.30 [1.02, 1.64] and 1.35 [1.16, 1.59], respectively). For GINI/LISA South, two associations with aeroallergen sensitization were significant (0.84 [0.73, 0.97] for NO2 and 0.87 [0.78, 0.97] for PM2.5 absorbance), as well as the association between allergic rhinitis and PM2.5 absorbance (0.83 [0.72, 0.96]). Conclusions. This study did not find consistent evidence that TRAP increases the prevalence of c…
format: application/pdf
format: text/html
creator: Elaine Fuertes
creator: Marie Standl
creator: Josef Cyrys
creator: Dietrich Berdel
creator: Andrea von Berg
creator: Carl-Peter Bauer
creator: Ursula Krämer
creator: Dorothea Sugiri
creator: Irina Lehmann
creator: Sibylle Koletzko
creator: Chris Carlsten
creator: Michael Brauer
creator: Joachim Heinrich
subject: Allergy and Clinical Immunology
subject: Epidemiology
subject: Public Health
description: doi:10.7717/peerj.193
publisher: PeerJ Inc.
rights: © 2013 Fuertes et al.
abstract: Background. There is a need to study whether the adverse effects of traffic-related air pollution (TRAP) on childhood asthma and allergic diseases documented during early-life persist into later childhood. This longitudinal study examined whether TRAP is associated with the prevalence of asthma, allergic rhinitis and aeroallergen sensitization in two German cohorts followed from birth to 10 years. Materials. Questionnaire-derived annual reports of doctor diagnosed asthma and allergic rhinitis, as well as eye and nose symptoms, were collected from 6,604 children. Aeroallergen sensitization was assessed for 3,655 children who provided blood samples. Associations between these health outcomes and nitrogen dioxide (NO2), particles with aerodynamic diameters less than 2.5 µg/m3 (PM2.5) mass, PM2.5 absorbance and ozone, individually estimated for each child at the birth, six and 10 year home addresses, were assessed using generalized estimation equations including adjustments for relevant covariates. Odds ratios [95% confidence intervals] per increase in interquartile range of pollutant are presented for the total population and per geographical area (GINI/LISA South, GINI/LISA North and LISA East, Germany). Results. The risk estimates for the total population were generally null across outcomes and pollutants. The area-specific results were heterogeneous. In GINI/LISA North, all associations were null. In LISA East, associations with ozone were elevated for all outcomes, and those for allergic rhinitis and eyes and nose symptom prevalence reached statistical significance (1.30 [1.02, 1.64] and 1.35 [1.16, 1.59], respectively). For GINI/LISA South, two associations with aeroallergen sensitization were significant (0.84 [0.73, 0.97] for NO2 and 0.87 [0.78, 0.97] for PM2.5 absorbance), as well as the association between allergic rhinitis and PM2.5 absorbance (0.83 [0.72, 0.96]). Conclusions. This study did not find consistent evidence that TRAP increases the prevalence of c…
bibliographic citation: Fuertes et al. (2013) A longitudinal analysis of associations between traffic-related air pollution with asthma, allergies and sensitization in the GINIplus and LISAplus birth cohorts. PeerJ 1:e193 https://doi.org/10.7717/peerj.193
date submitted: 2013-07-24
date accepted: 2013-10-08
issued: 2013-11-07
is part of: PeerJ
license: http://creativecommons.org/licenses/by/3.0/
author list: Agent
  family name: Fuertes
  given name: Elaine
author list: Agent
  family name: Standl
  given name: Marie
author list: Agent
  family name: Cyrys
  given name: Josef
author list: Agent
  family name: Berdel
  given name: Dietrich
author list: Agent
  family name: von Berg
  given name: Andrea
author list: Agent
  family name: Bauer
  given name: Carl-Peter
author list: Agent
  family name: Krämer
  given name: Ursula
author list: Agent
  family name: Sugiri
  given name: Dorothea
author list: Agent
  family name: Lehmann
  given name: Irina
author list: Agent
  family name: Koletzko
  given name: Sibylle
author list: Agent
  family name: Carlsten
  given name: Chris
author list: Agent
  family name: Brauer
  given name: Michael
author list: Agent
  family name: Heinrich
  given name: Joachim
doi: 10.7717/peerj.193
volume: 1
issn: 2167-8359
publication name: PeerJ
publication date: 2013-11-07
copyright: © 2013 Fuertes et al.
attribution name: Fuertes et al.

Size and shape in the evolution of ant worker morphology
type: item
type: AcademicArticle
description: Morphological evolution in ants has been traditionally thought as being strongly influenced by selection for colony ergonomic efficiency. Although many studies have focused on the evolution of social characteristics in ants, little is known about the evolution of worker morphology at a macroevolutionary scale. In this study, we investigate the tempo and mode of the evolution of worker morphology, focusing on changes in size and shape. Our datasets included a large sample of species from different ant genera, as well as variation within the hyperdiverse genus Pheidole, for a total of 1650 measurements. The rate of size evolution was at least five times faster than the rate of shape evolution. The fit of alternative models of morphological evolution indicated statistically significant phylogenetic signal in both size and shape and in all datasets. Finally, tests of rate heterogeneity in phenotypic evolution among lineages identified several shifts in rates of evolution in both datasets, although the timing of shifts in size and shape was usually not concordant.
format: application/pdf
format: text/html
creator: Marcio R. Pie
creator: Marcel K. Tschá
subject: Entomology
subject: Evolutionary Studies
subject: Zoology
description: doi:10.7717/peerj.205
publisher: PeerJ Inc.
rights: © 2013 Pie and Tschá
abstract: Morphological evolution in ants has been traditionally thought as being strongly influenced by selection for colony ergonomic efficiency. Although many studies have focused on the evolution of social characteristics in ants, little is known about the evolution of worker morphology at a macroevolutionary scale. In this study, we investigate the tempo and mode of the evolution of worker morphology, focusing on changes in size and shape. Our datasets included a large sample of species from different ant genera, as well as variation within the hyperdiverse genus Pheidole, for a total of 1650 measurements. The rate of size evolution was at least five times faster than the rate of shape evolution. The fit of alternative models of morphological evolution indicated statistically significant phylogenetic signal in both size and shape and in all datasets. Finally, tests of rate heterogeneity in phenotypic evolution among lineages identified several shifts in rates of evolution in both datasets, although the timing of shifts in size and shape was usually not concordant.
bibliographic citation: Pie et al. (2013) Size and shape in the evolution of ant worker morphology. PeerJ 1:e205 https://doi.org/10.7717/peerj.205
date submitted: 2013-06-22
date accepted: 2013-10-16
issued: 2013-11-05
is part of: PeerJ
license: http://creativecommons.org/licenses/by/3.0/
author list: Agent
  family name: Pie
  given name: Marcio R.
author list: Agent
  family name: Tschá
  given name: Marcel K.
doi: 10.7717/peerj.205
volume: 1
issn: 2167-8359
publication name: PeerJ
publication date: 2013-11-05
copyright: © 2013 Pie and Tschá
attribution name: Pie and Tschá

Beware the black box: investigating the sensitivity of FEA simulations to modelling factors in comparative biomechanics
type: item
type: AcademicArticle
description: Finite element analysis (FEA) is a computational technique of growing popularity in the field of comparative biomechanics, and is an easily accessible platform for form-function analyses of biological structures. However, its rapid evolution in recent years from a novel approach to common practice demands some scrutiny in regards to the validity of results and the appropriateness of assumptions inherent in setting up simulations. Both validation and sensitivity analyses remain unexplored in many comparative analyses, and assumptions considered to be ‘reasonable’ are often assumed to have little influence on the results and their interpretation. Here we report an extensive sensitivity analysis where high resolution finite element (FE) models of mandibles from seven species of crocodile were analysed under loads typical for comparative analysis: biting, shaking, and twisting. Simulations explored the effect on both the absolute response and the interspecies pattern of results to variations in commonly used input parameters. Our sensitivity analysis focuses on assumptions relating to the selection of material properties (heterogeneous or homogeneous), scaling (standardising volume, surface area, or length), tooth position (front, mid, or back tooth engagement), and linear load case (type of loading for each feeding type). Our findings show that in a comparative context, FE models are far less sensitive to the selection of material property values and scaling to either volume or surface area than they are to those assumptions relating to the functional aspects of the simulation, such as tooth position and linear load case. Results show a complex interaction between simulation assumptions, depending on the combination of assumptions and the overall shape of each specimen. Keeping assumptions consistent between models in an analysis does not ensure that results can be generalised beyond the specific set of assumptions used. Logically, different comparative datasets would …
format: application/pdf
format: text/html
creator: Christopher W. Walmsley
creator: Matthew R. McCurry
creator: Phillip D. Clausen
creator: Colin R. McHenry
subject: Bioengineering
subject: Computational Biology
subject: Paleontology
subject: Zoology
subject: Anatomy and Physiology
description: doi:10.7717/peerj.204
publisher: PeerJ Inc.
rights: © 2013 Walmsleyet al.
abstract: Finite element analysis (FEA) is a computational technique of growing popularity in the field of comparative biomechanics, and is an easily accessible platform for form-function analyses of biological structures. However, its rapid evolution in recent years from a novel approach to common practice demands some scrutiny in regards to the validity of results and the appropriateness of assumptions inherent in setting up simulations. Both validation and sensitivity analyses remain unexplored in many comparative analyses, and assumptions considered to be ‘reasonable’ are often assumed to have little influence on the results and their interpretation. Here we report an extensive sensitivity analysis where high resolution finite element (FE) models of mandibles from seven species of crocodile were analysed under loads typical for comparative analysis: biting, shaking, and twisting. Simulations explored the effect on both the absolute response and the interspecies pattern of results to variations in commonly used input parameters. Our sensitivity analysis focuses on assumptions relating to the selection of material properties (heterogeneous or homogeneous), scaling (standardising volume, surface area, or length), tooth position (front, mid, or back tooth engagement), and linear load case (type of loading for each feeding type). Our findings show that in a comparative context, FE models are far less sensitive to the selection of material property values and scaling to either volume or surface area than they are to those assumptions relating to the functional aspects of the simulation, such as tooth position and linear load case. Results show a complex interaction between simulation assumptions, depending on the combination of assumptions and the overall shape of each specimen. Keeping assumptions consistent between models in an analysis does not ensure that results can be generalised beyond the specific set of assumptions used. Logically, different comparative datasets would …
bibliographic citation: Walmsley et al. (2013) Beware the black box: investigating the sensitivity of FEA simulations to modelling factors in comparative biomechanics. PeerJ 1:e204 https://doi.org/10.7717/peerj.204
date submitted: 2013-07-16
date accepted: 2013-10-14
issued: 2013-11-05
is part of: PeerJ
license: http://creativecommons.org/licenses/by/3.0/
author list: Agent
  family name: Walmsley
  given name: Christopher W.
author list: Agent
  family name: McCurry
  given name: Matthew R.
author list: Agent
  family name: Clausen
  given name: Phillip D.
author list: Agent
  family name: McHenry
  given name: Colin R.
doi: 10.7717/peerj.204
volume: 1
issn: 2167-8359
publication name: PeerJ
publication date: 2013-11-05
copyright: © 2013 Walmsleyet al.
attribution name: Walmsleyet al.

Comparative selenoproteome analysis reveals a reduced utilization of selenium in parasitic platyhelminthes
type: item
type: AcademicArticle
description: Background. The selenocysteine(Sec)-containing proteins, selenoproteins, are an important group of proteins present in all three kingdoms of life. Although the selenoproteomes of many organisms have been analyzed, systematic studies on selenoproteins in platyhelminthes are still lacking. Moreover, comparison of selenoproteomes between free-living and parasitic animals is rarely studied. Results. In this study, three representative organisms (Schmidtea mediterranea, Schistosoma japonicum and Taenia solium) were selected for comparative analysis of selenoproteomes in Platyhelminthes. Using a SelGenAmic-based selenoprotein prediction algorithm, a total of 37 selenoprotein genes were identified in these organisms. The size of selenoproteomes and selenoprotein families were found to be associated with different lifestyles: free-living organisms have larger selenoproteome whereas parasitic lifestyle corresponds to reduced selenoproteomes. Five selenoproteins, SelT, Sel15, GPx, SPS2 and TR, were found to be present in all examined platyhelminthes as well as almost all sequenced animals, suggesting their essential role in metazoans. Finally, a new splicing form of SelW that lacked the first exon was found to be present in S. japonicum. Conclusions. Our data provide a first glance into the selenoproteomes of organisms in the phylum Platyhelminthes and may help understand function and evolutionary dynamics of selenium utilization in diversified metazoans.
format: application/pdf
format: text/html
creator: Liang Jiang
creator: Hua-Zhang Zhu
creator: Yin-Zhen Xu
creator: Jia-Zuan Ni
creator: Yan Zhang
creator: Qiong Liu
subject: Bioinformatics
description: doi:10.7717/peerj.202
publisher: PeerJ Inc.
rights: © 2013 Jiang et al.
abstract: Background. The selenocysteine(Sec)-containing proteins, selenoproteins, are an important group of proteins present in all three kingdoms of life. Although the selenoproteomes of many organisms have been analyzed, systematic studies on selenoproteins in platyhelminthes are still lacking. Moreover, comparison of selenoproteomes between free-living and parasitic animals is rarely studied. Results. In this study, three representative organisms (Schmidtea mediterranea, Schistosoma japonicum and Taenia solium) were selected for comparative analysis of selenoproteomes in Platyhelminthes. Using a SelGenAmic-based selenoprotein prediction algorithm, a total of 37 selenoprotein genes were identified in these organisms. The size of selenoproteomes and selenoprotein families were found to be associated with different lifestyles: free-living organisms have larger selenoproteome whereas parasitic lifestyle corresponds to reduced selenoproteomes. Five selenoproteins, SelT, Sel15, GPx, SPS2 and TR, were found to be present in all examined platyhelminthes as well as almost all sequenced animals, suggesting their essential role in metazoans. Finally, a new splicing form of SelW that lacked the first exon was found to be present in S. japonicum. Conclusions. Our data provide a first glance into the selenoproteomes of organisms in the phylum Platyhelminthes and may help understand function and evolutionary dynamics of selenium utilization in diversified metazoans.
bibliographic citation: Jiang et al. (2013) Comparative selenoproteome analysis reveals a reduced utilization of selenium in parasitic platyhelminthes. PeerJ 1:e202 https://doi.org/10.7717/peerj.202
date submitted: 2013-09-23
date accepted: 2013-10-13
issued: 2013-11-05
is part of: PeerJ
license: http://creativecommons.org/licenses/by/3.0/
author list: Agent
  family name: Jiang
  given name: Liang
author list: Agent
  family name: Zhu
  given name: Hua-Zhang
author list: Agent
  family name: Xu
  given name: Yin-Zhen
author list: Agent
  family name: Ni
  given name: Jia-Zuan
author list: Agent
  family name: Zhang
  given name: Yan
author list: Agent
  family name: Liu
  given name: Qiong
doi: 10.7717/peerj.202
volume: 1
issn: 2167-8359
publication name: PeerJ
publication date: 2013-11-05
copyright: © 2013 Jiang et al.
attribution name: Jiang et al.

Iranian and Swedish adolescents: differences in personality traits and well-being
type: item
type: AcademicArticle
description: Introduction. This study addresses the need to further contextualize research on well-being (e.g., Kjell, 2011) in terms of cross-cultural aspects of personality traits among adolescents and by examining two different conceptualizations of well-being: subjective well-being (i.e., life satisfaction, positive and negative affect) and psychological well-being (i.e., positive relations with others, environmental mastery, self-acceptance, autonomy, personal growth, and life purpose). Methods. Iranian (N = 122, mean age 15.23 years) and Swedish (N = 109, mean age 16.69 years) adolescents were asked to fill out a Big Five personality test, as well as questionnaires assessing subjective well-being and psychological well-being. Results. Swedes reported higher subjective and psychological well-being, while Iranians reported higher degree of Agreeableness, Openness and Conscientiousness. Neuroticism and Extraversion did not differ between cultures. Neuroticism was related to well-being within both cultures. Openness was related to well-being only among Iranians, and Extraversion only among Swedes. A mediation analysis within the Swedish sample, the only sample meeting statistical criteria for mediation analysis to be conducted, demonstrated that psychological well-being mediated the relationship between Neuroticism and subjective well-being as well as between Extraversion and subjective well-being. Conclusions. Certain personality traits, such as Extraversion, Openness, and Conscientiousness, relate differently to well-being measures across cultures. Meanwhile, Neuroticism seems to relate similarly across cultures at least with regard to subjective well-being. Furthermore, the results give an indication on how psychological well-being might mediate the relationship between certain personality traits and subjective well-being. Overall, the complexity of the results illustrates the need for more research whilst supporting the importance of contextualizing well-being research.
format: application/pdf
format: text/html
creator: Oscar N.E. Kjell
creator: Ali A. Nima
creator: Sverker Sikström
creator: Trevor Archer
creator: Danilo Garcia
subject: Psychiatry and Psychology
subject: Public Health
description: doi:10.7717/peerj.197
publisher: PeerJ Inc.
rights: © 2013 Kjell et al.
abstract: Introduction. This study addresses the need to further contextualize research on well-being (e.g., Kjell, 2011) in terms of cross-cultural aspects of personality traits among adolescents and by examining two different conceptualizations of well-being: subjective well-being (i.e., life satisfaction, positive and negative affect) and psychological well-being (i.e., positive relations with others, environmental mastery, self-acceptance, autonomy, personal growth, and life purpose). Methods. Iranian (N = 122, mean age 15.23 years) and Swedish (N = 109, mean age 16.69 years) adolescents were asked to fill out a Big Five personality test, as well as questionnaires assessing subjective well-being and psychological well-being. Results. Swedes reported higher subjective and psychological well-being, while Iranians reported higher degree of Agreeableness, Openness and Conscientiousness. Neuroticism and Extraversion did not differ between cultures. Neuroticism was related to well-being within both cultures. Openness was related to well-being only among Iranians, and Extraversion only among Swedes. A mediation analysis within the Swedish sample, the only sample meeting statistical criteria for mediation analysis to be conducted, demonstrated that psychological well-being mediated the relationship between Neuroticism and subjective well-being as well as between Extraversion and subjective well-being. Conclusions. Certain personality traits, such as Extraversion, Openness, and Conscientiousness, relate differently to well-being measures across cultures. Meanwhile, Neuroticism seems to relate similarly across cultures at least with regard to subjective well-being. Furthermore, the results give an indication on how psychological well-being might mediate the relationship between certain personality traits and subjective well-being. Overall, the complexity of the results illustrates the need for more research whilst supporting the importance of contextualizing well-being research.
bibliographic citation: Kjell et al. (2013) Iranian and Swedish adolescents: differences in personality traits and well-being. PeerJ 1:e197 https://doi.org/10.7717/peerj.197
date submitted: 2013-09-05
date accepted: 2013-10-10
issued: 2013-11-05
is part of: PeerJ
license: http://creativecommons.org/licenses/by/3.0/
author list: Agent
  family name: Kjell
  given name: Oscar N.E.
author list: Agent
  family name: Nima
  given name: Ali A.
author list: Agent
  family name: Sikström
  given name: Sverker
author list: Agent
  family name: Archer
  given name: Trevor
author list: Agent
  family name: Garcia
  given name: Danilo
doi: 10.7717/peerj.197
volume: 1
issn: 2167-8359
publication name: PeerJ
publication date: 2013-11-05
copyright: © 2013 Kjell et al.
attribution name: Kjell et al.

Characterization of RNA in exosomes secreted by human breast cancer cell lines using next-generation sequencing
type: item
type: AcademicArticle
description: Exosomes are nanosized (30–100 nm) membrane vesicles secreted by most cell types. Exosomes have been found to contain various RNA species including miRNA, mRNA and long non-protein coding RNAs. A number of cancer cells produce elevated levels of exosomes. Because exosomes have been isolated from most body fluids they may provide a source for non-invasive cancer diagnostics. Transcriptome profiling that uses deep-sequencing technologies (RNA-Seq) offers enormous amount of data that can be used for biomarkers discovery, however, in case of exosomes this approach was applied only for the analysis of small RNAs. In this study, we utilized RNA-Seq technology to analyze RNAs present in microvesicles secreted by human breast cancer cell lines. Exosomes were isolated from the media conditioned by two human breast cancer cell lines, MDA-MB-231 and MDA-MB-436. Exosomal RNA was profiled using the Ion Torrent semiconductor chip-based technology. Exosomes were found to contain various classes of RNA with the major class represented by fragmented ribosomal RNA (rRNA), in particular 28S and 18S rRNA subunits. Analysis of exosomal RNA content revealed that it reflects RNA content of the donor cells. Although exosomes produced by the two cancer cell lines shared most of the RNA species, there was a number of non-coding transcripts unique to MDA-MB-231 and MDA-MB-436 cells. This suggests that RNA analysis might distinguish exosomes produced by low metastatic breast cancer cell line (MDA-MB-436) from that produced by highly metastatic breast cancer cell line (MDA-MB-231). The analysis of gene ontologies (GOs) associated with the most abundant transcripts present in exosomes revealed significant enrichment in genes encoding proteins involved in translation and rRNA and ncRNA processing. These GO terms indicate most expressed genes for both, cellular and exosomal RNA. For the first time, using RNA-seq, we examined the transcriptomes of exosomes secreted by human breast cancer cells. We …
format: application/pdf
format: text/html
creator: Piroon Jenjaroenpun
creator: Yuliya Kremenska
creator: Vrundha M. Nair
creator: Maksym Kremenskoy
creator: Baby Joseph
creator: Igor V. Kurochkin
subject: Bioinformatics
subject: Cell Biology
subject: Computational Biology
subject: Genetics
subject: Oncology
description: doi:10.7717/peerj.201
publisher: PeerJ Inc.
rights: © 2013 Jenjaroenpun et al.
abstract: Exosomes are nanosized (30–100 nm) membrane vesicles secreted by most cell types. Exosomes have been found to contain various RNA species including miRNA, mRNA and long non-protein coding RNAs. A number of cancer cells produce elevated levels of exosomes. Because exosomes have been isolated from most body fluids they may provide a source for non-invasive cancer diagnostics. Transcriptome profiling that uses deep-sequencing technologies (RNA-Seq) offers enormous amount of data that can be used for biomarkers discovery, however, in case of exosomes this approach was applied only for the analysis of small RNAs. In this study, we utilized RNA-Seq technology to analyze RNAs present in microvesicles secreted by human breast cancer cell lines. Exosomes were isolated from the media conditioned by two human breast cancer cell lines, MDA-MB-231 and MDA-MB-436. Exosomal RNA was profiled using the Ion Torrent semiconductor chip-based technology. Exosomes were found to contain various classes of RNA with the major class represented by fragmented ribosomal RNA (rRNA), in particular 28S and 18S rRNA subunits. Analysis of exosomal RNA content revealed that it reflects RNA content of the donor cells. Although exosomes produced by the two cancer cell lines shared most of the RNA species, there was a number of non-coding transcripts unique to MDA-MB-231 and MDA-MB-436 cells. This suggests that RNA analysis might distinguish exosomes produced by low metastatic breast cancer cell line (MDA-MB-436) from that produced by highly metastatic breast cancer cell line (MDA-MB-231). The analysis of gene ontologies (GOs) associated with the most abundant transcripts present in exosomes revealed significant enrichment in genes encoding proteins involved in translation and rRNA and ncRNA processing. These GO terms indicate most expressed genes for both, cellular and exosomal RNA. For the first time, using RNA-seq, we examined the transcriptomes of exosomes secreted by human breast cancer cells. We …
bibliographic citation: Jenjaroenpun et al. (2013) Characterization of RNA in exosomes secreted by human breast cancer cell lines using next-generation sequencing. PeerJ 1:e201 https://doi.org/10.7717/peerj.201
date submitted: 2013-09-06
date accepted: 2013-10-13
issued: 2013-11-05
is part of: PeerJ
license: http://creativecommons.org/licenses/by/3.0/
author list: Agent
  family name: Jenjaroenpun
  given name: Piroon
author list: Agent
  family name: Kremenska
  given name: Yuliya
author list: Agent
  family name: Nair
  given name: Vrundha M.
author list: Agent
  family name: Kremenskoy
  given name: Maksym
author list: Agent
  family name: Joseph
  given name: Baby
author list: Agent
  family name: Kurochkin
  given name: Igor V.
doi: 10.7717/peerj.201
volume: 1
issn: 2167-8359
publication name: PeerJ
publication date: 2013-11-05
copyright: © 2013 Jenjaroenpun et al.
attribution name: Jenjaroenpun et al.

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