PeerJ
type: channel
link: https://peerj.com/articles/
description: Articles published in PeerJ
publisher: PeerJ Inc.
publication name: PeerJ
issn: 2167-8359
items: The metabolic cost of walking on an incline in the Peacock (Pavo cristatus)
items: A four-year cardiovascular risk score for type 2 diabetic inpatients
items: Elevational gradient of Hemiptera (Heteroptera, Auchenorrhyncha) on a tropical mountain in Papua New Guinea
items: Prior CT imaging history for patients who undergo PAN CT for acute traumatic injury
items: The role of multiple negative social relationships in inflammatory cytokine responses to a laboratory stressor
items: Genetic approaches to the conservation of migratory bats: a study of the eastern red bat (Lasiurus borealis)
items: VirSorter: mining viral signal from microbial genomic data
items: ACE and UCP2 gene polymorphisms and their association with baseline and exercise-related changes in the functional performance of older adults
items: Vorinostat enhances chemosensitivity to arsenic trioxide in K562 cell line
items: Morphometric comparisons of Diaphorina citri (Hemiptera: Liviidae) populations from Iran, USA and Pakistan

The metabolic cost of walking on an incline in the Peacock (Pavo cristatus)
type: item
type: AcademicArticle
description: Altering speed and moving on a gradient can affect an animal’s posture and gait, which in turn can change the energetic requirements of terrestrial locomotion. Here, the energetic and kinematic effects of locomoting on an incline were investigated in the Indian peacock, Pavo cristatus. The mass-specific metabolic rate of the Indian peacock was elevated on an incline, but this change was not dependent on the angle ascended and the cost of lifting remained similar between the two inclines (+5 and +7°). Interestingly, the Indian peacock had the highest efficiency when compared to any other previously studied avian biped, despite the presence of a large train. Duty factors were higher for birds moving on an incline, but there was no difference between +5 and +7°. Our results highlight the importance of investigating kinematic responses during energetic studies, as these may enable explanation of what is driving the underlying metabolic differences when moving on inclines. Further investigations are required to elucidate the underlying mechanical processes occurring during incline movement.
format: application/pdf
format: text/html
creator: Holly Wilkinson
creator: Nathan Thavarajah
creator: Jonathan Codd
subject: Animal Behavior
subject: Zoology
subject: Anatomy and Physiology
subject: Metabolic Sciences
description: doi:10.7717/peerj.987
publisher: PeerJ Inc.
rights: © 2015 Wilkinson et al.
abstract: Altering speed and moving on a gradient can affect an animal’s posture and gait, which in turn can change the energetic requirements of terrestrial locomotion. Here, the energetic and kinematic effects of locomoting on an incline were investigated in the Indian peacock, Pavo cristatus. The mass-specific metabolic rate of the Indian peacock was elevated on an incline, but this change was not dependent on the angle ascended and the cost of lifting remained similar between the two inclines (+5 and +7°). Interestingly, the Indian peacock had the highest efficiency when compared to any other previously studied avian biped, despite the presence of a large train. Duty factors were higher for birds moving on an incline, but there was no difference between +5 and +7°. Our results highlight the importance of investigating kinematic responses during energetic studies, as these may enable explanation of what is driving the underlying metabolic differences when moving on inclines. Further investigations are required to elucidate the underlying mechanical processes occurring during incline movement.
bibliographic citation: Wilkinson et al. (2015) The metabolic cost of walking on an incline in the Peacock (Pavo cristatus). PeerJ 3:e987 https://doi.org/10.7717/peerj.987
date submitted: 2015-03-10
date accepted: 2015-05-09
issued: 2015-06-02
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Wilkinson
  given name: Holly
author list: Agent
  family name: Thavarajah
  given name: Nathan
author list: Agent
  family name: Codd
  given name: Jonathan
doi: 10.7717/peerj.987
volume: 3
issn: 2167-8359
publication name: PeerJ
publication date: 2015-06-02
copyright: © 2015 Wilkinson et al.
attribution name: Wilkinson et al.

A four-year cardiovascular risk score for type 2 diabetic inpatients
type: item
type: AcademicArticle
description: As cardiovascular risk tables currently in use were constructed using data from the general population, the cardiovascular risk of patients admitted via the hospital emergency department may be underestimated. Accordingly, we constructed a predictive model for the appearance of cardiovascular diseases in patients with type 2 diabetes admitted via the emergency department. We undertook a four-year follow-up of a cohort of 112 adult patients with type 2 diabetes admitted via the emergency department for any cause except patients admitted with acute myocardial infarction, stroke, cancer, or a palliative status. The sample was selected randomly between 2010 and 2012. The primary outcome was time to cardiovascular disease. Other variables (at baseline) were gender, age, heart failure, renal failure, depression, asthma/chronic obstructive pulmonary disease, hypertension, dyslipidaemia, insulin, smoking, admission for cardiovascular causes, pills per day, walking habit, fasting blood glucose and creatinine. A cardiovascular risk table was constructed based on the score to estimate the likelihood of cardiovascular disease. Risk groups were established and the c-statistic was calculated. Over a mean follow-up of 2.31 years, 39 patients had cardiovascular disease (34.8%, 95% CI [26.0–43.6%]). Predictive factors were gender, age, hypertension, renal failure, insulin, admission due to cardiovascular reasons and walking habit. The c-statistic was 0.734 (standard error: 0.049). After validation, this study will provide a tool for the primary health care services to enable the short-term prediction of cardiovascular disease after hospital discharge in patients with type 2 diabetes admitted via the emergency department.
format: application/pdf
format: text/html
creator: Dolores Ramírez-Prado
creator: Antonio Palazón-Bru
creator: David Manuel Folgado-de la Rosa
creator: María Ángeles Carbonell-Torregrosa
creator: Ana María Martínez-Díaz
creator: Damian Robert James Martínez-St. John
creator: Vicente Francisco Gil-Guillén
subject: Diabetes and Endocrinology
subject: Epidemiology
subject: Public Health
description: doi:10.7717/peerj.984
publisher: PeerJ Inc.
rights: © 2015 Ramírez-Prado et al.
abstract: As cardiovascular risk tables currently in use were constructed using data from the general population, the cardiovascular risk of patients admitted via the hospital emergency department may be underestimated. Accordingly, we constructed a predictive model for the appearance of cardiovascular diseases in patients with type 2 diabetes admitted via the emergency department. We undertook a four-year follow-up of a cohort of 112 adult patients with type 2 diabetes admitted via the emergency department for any cause except patients admitted with acute myocardial infarction, stroke, cancer, or a palliative status. The sample was selected randomly between 2010 and 2012. The primary outcome was time to cardiovascular disease. Other variables (at baseline) were gender, age, heart failure, renal failure, depression, asthma/chronic obstructive pulmonary disease, hypertension, dyslipidaemia, insulin, smoking, admission for cardiovascular causes, pills per day, walking habit, fasting blood glucose and creatinine. A cardiovascular risk table was constructed based on the score to estimate the likelihood of cardiovascular disease. Risk groups were established and the c-statistic was calculated. Over a mean follow-up of 2.31 years, 39 patients had cardiovascular disease (34.8%, 95% CI [26.0–43.6%]). Predictive factors were gender, age, hypertension, renal failure, insulin, admission due to cardiovascular reasons and walking habit. The c-statistic was 0.734 (standard error: 0.049). After validation, this study will provide a tool for the primary health care services to enable the short-term prediction of cardiovascular disease after hospital discharge in patients with type 2 diabetes admitted via the emergency department.
bibliographic citation: Ramírez-Prado et al. (2015) A four-year cardiovascular risk score for type 2 diabetic inpatients. PeerJ 3:e984 https://doi.org/10.7717/peerj.984
date submitted: 2015-02-08
date accepted: 2015-05-08
issued: 2015-06-02
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Ramírez-Prado
  given name: Dolores
author list: Agent
  family name: Palazón-Bru
  given name: Antonio
author list: Agent
  family name: Folgado-de la Rosa
  given name: David Manuel
author list: Agent
  family name: Carbonell-Torregrosa
  given name: María Ángeles
author list: Agent
  family name: Martínez-Díaz
  given name: Ana María
author list: Agent
  family name: Martínez-St. John
  given name: Damian Robert James
author list: Agent
  family name: Gil-Guillén
  given name: Vicente Francisco
doi: 10.7717/peerj.984
volume: 3
issn: 2167-8359
publication name: PeerJ
publication date: 2015-06-02
copyright: © 2015 Ramírez-Prado et al.
attribution name: Ramírez-Prado et al.

Elevational gradient of Hemiptera (Heteroptera, Auchenorrhyncha) on a tropical mountain in Papua New Guinea
type: item
type: AcademicArticle
description: Malaise trap sampling of Hemiptera (Heteroptera; Auchenorrhyncha) was conducted at 500 m intervals along an elevational gradient from 200 m to 3,700 m on the east slope of Mount Wilhelm, Madang Province, Papua New Guinea. Hemiptera had a decrease in morphospecies richness and overall abundance with increasing elevation, however, the Heteroptera did not exhibit either pattern. A few species were relatively abundant at each elevation, whereas the majority of species were represented by ≤5 specimens. Morphospecies richness of Auchenorrhyncha, Cicadomorpha, Fulgoromorpha, Cicadellidae, Cixiidae, and Derbidae also decreased with increasing elevation but abundance decline was not significant due to the large number of specimens captured at 200 m relative to those captured at higher elevations. The percentage of Cicadomorpha specimens decreased with increasing elevation relative to that of the Fulgoromorpha which increased with increasing elevation. Environmental factors that may influence patterns of species richness along the elevational gradient are discussed.
format: application/pdf
format: text/html
creator: Maxime Le Cesne
creator: Stephen W. Wilson
creator: Adeline Soulier-Perkins
subject: Biodiversity
subject: Ecology
subject: Entomology
description: doi:10.7717/peerj.978
publisher: PeerJ Inc.
rights: © 2015 Le Cesne et al.
abstract: Malaise trap sampling of Hemiptera (Heteroptera; Auchenorrhyncha) was conducted at 500 m intervals along an elevational gradient from 200 m to 3,700 m on the east slope of Mount Wilhelm, Madang Province, Papua New Guinea. Hemiptera had a decrease in morphospecies richness and overall abundance with increasing elevation, however, the Heteroptera did not exhibit either pattern. A few species were relatively abundant at each elevation, whereas the majority of species were represented by ≤5 specimens. Morphospecies richness of Auchenorrhyncha, Cicadomorpha, Fulgoromorpha, Cicadellidae, Cixiidae, and Derbidae also decreased with increasing elevation but abundance decline was not significant due to the large number of specimens captured at 200 m relative to those captured at higher elevations. The percentage of Cicadomorpha specimens decreased with increasing elevation relative to that of the Fulgoromorpha which increased with increasing elevation. Environmental factors that may influence patterns of species richness along the elevational gradient are discussed.
bibliographic citation: Le Cesne et al. (2015) Elevational gradient of Hemiptera (Heteroptera, Auchenorrhyncha) on a tropical mountain in Papua New Guinea. PeerJ 3:e978 https://doi.org/10.7717/peerj.978
date submitted: 2014-10-16
date accepted: 2015-05-06
issued: 2015-06-02
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Le Cesne
  given name: Maxime
author list: Agent
  family name: Wilson
  given name: Stephen W.
author list: Agent
  family name: Soulier-Perkins
  given name: Adeline
doi: 10.7717/peerj.978
volume: 3
issn: 2167-8359
publication name: PeerJ
publication date: 2015-06-02
copyright: © 2015 Le Cesne et al.
attribution name: Le Cesne et al.

Prior CT imaging history for patients who undergo PAN CT for acute traumatic injury
type: item
type: AcademicArticle
description: Objective. A single PAN scan may provide more radiation to a patient than is felt to be safe within a one-year period. Our objective was to determine how many patients admitted to the trauma service following a PAN scan had prior CT imaging within our six-hospital system. Methods. We performed a secondary analysis of a prospectively collected trauma registry. The study was based at a level-two trauma center and five affiliated hospitals, which comprise 70.6% of all Emergency Department visits within a twelve county region of southern Texas. Electronic medical records were reviewed dating from the point of trauma evaluation back to December 5, 2005 to determine evidence of prior CT imaging. Results. There were 867 patients were admitted to the trauma service between January 1, 2012 and December 31, 2012. 460 (53%) received a PAN scan and were included in the study group. The mean age of the study group was 37.7 ± 1.54 years old, 24.8% were female, and the mean ISS score was 13.4 ± 1.07. The most common mechanism of injury was motor vehicle collision (47%). 65 (14%; 95% CI [11–18]%) of the patients had at least one prior CT. The most common prior studies performed were: CT head (29%; 19–42%), CT Face (29%; 19–42%) and CT Abdomen and Pelvis (18%; 11–30%). Conclusion. Within our trauma registry, 14% of patients had prior CT imaging within our hospital system before their traumatic event and PAN scan.
format: application/pdf
format: text/html
creator: Jeremy Kenter
creator: Osbert Blow
creator: Scott P. Krall
creator: Albert Gest
creator: Cynthia Smith
creator: Peter B. Richman
subject: Emergency and Critical Care
subject: Public Health
subject: Radiology and Medical Imaging
subject: Surgery and Surgical Specialties
subject: Statistics
description: doi:10.7717/peerj.963
publisher: PeerJ Inc.
rights: © 2015 Kenter et al.
abstract: Objective. A single PAN scan may provide more radiation to a patient than is felt to be safe within a one-year period. Our objective was to determine how many patients admitted to the trauma service following a PAN scan had prior CT imaging within our six-hospital system. Methods. We performed a secondary analysis of a prospectively collected trauma registry. The study was based at a level-two trauma center and five affiliated hospitals, which comprise 70.6% of all Emergency Department visits within a twelve county region of southern Texas. Electronic medical records were reviewed dating from the point of trauma evaluation back to December 5, 2005 to determine evidence of prior CT imaging. Results. There were 867 patients were admitted to the trauma service between January 1, 2012 and December 31, 2012. 460 (53%) received a PAN scan and were included in the study group. The mean age of the study group was 37.7 ± 1.54 years old, 24.8% were female, and the mean ISS score was 13.4 ± 1.07. The most common mechanism of injury was motor vehicle collision (47%). 65 (14%; 95% CI [11–18]%) of the patients had at least one prior CT. The most common prior studies performed were: CT head (29%; 19–42%), CT Face (29%; 19–42%) and CT Abdomen and Pelvis (18%; 11–30%). Conclusion. Within our trauma registry, 14% of patients had prior CT imaging within our hospital system before their traumatic event and PAN scan.
bibliographic citation: Kenter et al. (2015) Prior CT imaging history for patients who undergo PAN CT for acute traumatic injury. PeerJ 3:e963 https://doi.org/10.7717/peerj.963
date submitted: 2015-03-03
date accepted: 2015-04-26
issued: 2015-06-02
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Kenter
  given name: Jeremy
author list: Agent
  family name: Blow
  given name: Osbert
author list: Agent
  family name: Krall
  given name: Scott P.
author list: Agent
  family name: Gest
  given name: Albert
author list: Agent
  family name: Smith
  given name: Cynthia
author list: Agent
  family name: Richman
  given name: Peter B.
doi: 10.7717/peerj.963
volume: 3
issn: 2167-8359
publication name: PeerJ
publication date: 2015-06-02
copyright: © 2015 Kenter et al.
attribution name: Kenter et al.

The role of multiple negative social relationships in inflammatory cytokine responses to a laboratory stressor
type: item
type: AcademicArticle
description: The present study examined the unique impact of perceived negativity in multiple social relationships on endocrine and inflammatory responses to a laboratory stressor. Via hierarchical cluster analysis, those who reported negative social exchanges across relationships with a romantic partner, family, and their closest friend had higher mean IL-6 across time and a greater increase in TNF-α from 15 min to 75 min post stress. Those who reported negative social exchanges across relationships with roommates, family, and their closest friend showed greater IL-6 responses to stress. Differences in mean IL-6 were accounted for by either depressed mood or hostility, whereas differences in the cytokine stress responses remained significant after controlling for those factors. Overall, this research provides preliminary evidence to suggest that having multiple negative relationships may exacerbate acute inflammatory responses to a laboratory stressor independent of hostility and depressed mood.
format: application/pdf
format: text/html
creator: Sunmi Song
creator: Jennifer E. Graham-Engeland
creator: Elizabeth J. Corwin
creator: Rachel M. Ceballos
creator: Shelley E. Taylor
creator: Teresa Seeman
creator: Laura Cousino Klein
subject: Immunology
subject: Psychiatry and Psychology
description: doi:10.7717/peerj.959
publisher: PeerJ Inc.
rights: © 2015 Song et al.
abstract: The present study examined the unique impact of perceived negativity in multiple social relationships on endocrine and inflammatory responses to a laboratory stressor. Via hierarchical cluster analysis, those who reported negative social exchanges across relationships with a romantic partner, family, and their closest friend had higher mean IL-6 across time and a greater increase in TNF-α from 15 min to 75 min post stress. Those who reported negative social exchanges across relationships with roommates, family, and their closest friend showed greater IL-6 responses to stress. Differences in mean IL-6 were accounted for by either depressed mood or hostility, whereas differences in the cytokine stress responses remained significant after controlling for those factors. Overall, this research provides preliminary evidence to suggest that having multiple negative relationships may exacerbate acute inflammatory responses to a laboratory stressor independent of hostility and depressed mood.
bibliographic citation: Song et al. (2015) The role of multiple negative social relationships in inflammatory cytokine responses to a laboratory stressor. PeerJ 3:e959 https://doi.org/10.7717/peerj.959
date submitted: 2015-01-20
date accepted: 2015-04-24
issued: 2015-06-02
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Song
  given name: Sunmi
author list: Agent
  family name: Graham-Engeland
  given name: Jennifer E.
author list: Agent
  family name: Corwin
  given name: Elizabeth J.
author list: Agent
  family name: Ceballos
  given name: Rachel M.
author list: Agent
  family name: Taylor
  given name: Shelley E.
author list: Agent
  family name: Seeman
  given name: Teresa
author list: Agent
  family name: Klein
  given name: Laura Cousino
doi: 10.7717/peerj.959
volume: 3
issn: 2167-8359
publication name: PeerJ
publication date: 2015-06-02
copyright: © 2015 Song et al.
attribution name: Song et al.

Genetic approaches to the conservation of migratory bats: a study of the eastern red bat (Lasiurus borealis)
type: item
type: AcademicArticle
description: Documented fatalities of bats at wind turbines have raised serious concerns about the future impacts of increased wind power development on populations of migratory bat species. However, for most bat species we have no knowledge of the size of populations and their demographic trends, the degree of structuring into discrete subpopulations, and whether different subpopulations use spatially segregated migratory routes. Here, we utilize genetic data from eastern red bats (Lasiurus borealis), one of the species most highly affected by wind power development in North America, to (1) evaluate patterns of population structure across the landscape, (2) estimate effective population size (Ne), and (3) assess signals of growth or decline in population size. Using data on both nuclear and mitochondrial DNA variation, we demonstrate that this species forms a single, panmictic population across their range with no evidence for the historical use of divergent migratory pathways by any portion of the population. Further, using coalescent estimates we estimate that the effective size of this population is in the hundreds of thousands to millions of individuals. The high levels of gene flow and connectivity across the population of eastern red bats indicate that monitoring and management of eastern red bats must integrate information across the range of this species.
format: application/pdf
format: text/html
creator: Maarten J. Vonhof
creator: Amy L. Russell
subject: Biodiversity
subject: Conservation Biology
subject: Evolutionary Studies
subject: Genetics
subject: Zoology
description: doi:10.7717/peerj.983
publisher: PeerJ Inc.
rights: © 2015 Vonhof and Russell
abstract: Documented fatalities of bats at wind turbines have raised serious concerns about the future impacts of increased wind power development on populations of migratory bat species. However, for most bat species we have no knowledge of the size of populations and their demographic trends, the degree of structuring into discrete subpopulations, and whether different subpopulations use spatially segregated migratory routes. Here, we utilize genetic data from eastern red bats (Lasiurus borealis), one of the species most highly affected by wind power development in North America, to (1) evaluate patterns of population structure across the landscape, (2) estimate effective population size (Ne), and (3) assess signals of growth or decline in population size. Using data on both nuclear and mitochondrial DNA variation, we demonstrate that this species forms a single, panmictic population across their range with no evidence for the historical use of divergent migratory pathways by any portion of the population. Further, using coalescent estimates we estimate that the effective size of this population is in the hundreds of thousands to millions of individuals. The high levels of gene flow and connectivity across the population of eastern red bats indicate that monitoring and management of eastern red bats must integrate information across the range of this species.
bibliographic citation: Vonhof et al. (2015) Genetic approaches to the conservation of migratory bats: a study of the eastern red bat (Lasiurus borealis). PeerJ 3:e983 https://doi.org/10.7717/peerj.983
date submitted: 2015-01-09
date accepted: 2015-05-08
issued: 2015-05-28
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Vonhof
  given name: Maarten J.
author list: Agent
  family name: Russell
  given name: Amy L.
doi: 10.7717/peerj.983
volume: 3
issn: 2167-8359
publication name: PeerJ
publication date: 2015-05-28
copyright: © 2015 Vonhof and Russell
attribution name: Vonhof and Russell

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

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

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

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

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