PeerJ
type: channel
link: https://peerj.com/articles/
description: Articles published in PeerJ
publisher: PeerJ Inc.
publication name: PeerJ
issn: 2167-8359
items: Comparison of human papillomavirus (HPV) detection in urine and cervical swab samples using the HPV GenoArray Diagnostic assay
items: Histamine-2 receptor antagonist famotidine modulates cardiac stem cell characteristics in hypertensive heart disease
items: Influence of exercise duration on cardiorespiratory responses, energy cost and tissue oxygenation within a 6 hour treadmill run
items: Independent evolution of tetraloop in enterovirus oriL replicative element and its putative binding partners in virus protein 3C
items: Cryptic biodiversity and phylogeographic patterns of Seychellois Ligia isopods
items: Benchmark datasets for phylogenomic pipeline validation, applications for foodborne pathogen surveillance
items: Hearing assessment during deep brain stimulation of the central nucleus of the inferior colliculus and dentate cerebellar nucleus in rat
items: Genome methylation and regulatory functions for hypoxic adaptation in Tibetan chicken embryos
items: voomDDA: discovery of diagnostic biomarkers and classification of RNA-seq data
items: The isolation and identification of pathogenic fungi from Tessaratoma papillosa Drury (Hemiptera: Tessaratomidae)

Comparison of human papillomavirus (HPV) detection in urine and cervical swab samples using the HPV GenoArray Diagnostic assay
type: item
type: AcademicArticle
description: Human papillomavirus (HPV) is the leading cause of cervical cancer. Urine-based HPV testing offers a simple and non-invasive method because of its increasing acceptance. A total of 164 pairs of cervical swab and urine samples from Thai women who underwent cervical cancer screening were used for HPV testing with HPV GenoArray Diagnostic Kits. The overall concordance percentage for HPV detection in the cervical swab and urine samples was 65.2%. The HPV genotypes most commonly detected were HPV16 and HPV18. An analysis of the urine samples and a second analysis of the cervical swab samples showed that the differences in the overall HPV detection rate between women with normal and abnormal cytology were not significant (p > 0.05). Urine samples processed with the GenoArray assay is an alternative for women who decline to undergo Pap smear even though it is not ideal as the first-line screening option.
format: application/pdf
format: text/html
creator: Pornjarim Nilyanimit
creator: Jira Chansaenroj
creator: Anant Karalak
creator: Piyawat Laowahutanont
creator: Pairoj Junyangdikul
creator: Yong Poovorawan
subject: Infectious Diseases
subject: Oncology
subject: Virology
subject: Women's Health
description: doi:10.7717/peerj.3910
publisher: PeerJ Inc.
rights: © 2017 Nilyanimit et al.
abstract: Human papillomavirus (HPV) is the leading cause of cervical cancer. Urine-based HPV testing offers a simple and non-invasive method because of its increasing acceptance. A total of 164 pairs of cervical swab and urine samples from Thai women who underwent cervical cancer screening were used for HPV testing with HPV GenoArray Diagnostic Kits. The overall concordance percentage for HPV detection in the cervical swab and urine samples was 65.2%. The HPV genotypes most commonly detected were HPV16 and HPV18. An analysis of the urine samples and a second analysis of the cervical swab samples showed that the differences in the overall HPV detection rate between women with normal and abnormal cytology were not significant (p > 0.05). Urine samples processed with the GenoArray assay is an alternative for women who decline to undergo Pap smear even though it is not ideal as the first-line screening option.
bibliographic citation: Nilyanimit et al. (2017) Comparison of human papillomavirus (HPV) detection in urine and cervical swab samples using the HPV GenoArray Diagnostic assay. PeerJ 5:e3910 https://doi.org/10.7717/peerj.3910
date submitted: 2017-06-13
date accepted: 2017-09-19
issued: 2017-10-09
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Nilyanimit
  given name: Pornjarim
author list: Agent
  family name: Chansaenroj
  given name: Jira
author list: Agent
  family name: Karalak
  given name: Anant
author list: Agent
  family name: Laowahutanont
  given name: Piyawat
author list: Agent
  family name: Junyangdikul
  given name: Pairoj
author list: Agent
  family name: Poovorawan
  given name: Yong
doi: 10.7717/peerj.3910
volume: 5
issn: 2167-8359
publication name: PeerJ
publication date: 2017-10-09
copyright: ©2017 Nilyanimit et al.
attribution name: Nilyanimit et al.

Histamine-2 receptor antagonist famotidine modulates cardiac stem cell characteristics in hypertensive heart disease
type: item
type: AcademicArticle
description: Background Cardiac stem cells (CSCs) play a vital role in cardiac homeostasis. A decrease in the efficiency of cardiac stem cells is speculated in various cardiac abnormalities. The maintenance of a healthy stem cell population is essential for the prevention of adverse cardiac remodeling leading to cardiac failure. Famotidine, a histamine-2 receptor antagonist, is currently used to treat ulcers of the stomach and intestines. In repurposing the use of the drug, reduction of cardiac hypertrophy and improvement in cardiac function of spontaneously hypertensive rats (SHR) was reported by our group. Given that stem cells are affected in cardiac pathologies, the effect of histamine-2 receptor antagonism on CSC characteristics was investigated. Methods To examine whether famotidine has a positive effect on CSCs, spontaneously hypertensive rats (SHR) treated with the drug were sacrificed; and CSCs isolated from atrial appendages was evaluated. Six-month-old male SHRs were treated with famotidine (30 mg/kg/day) for two months. The effect of famotidine treatment on migration, proliferation and survival of CSCs was compared with untreated SHRs and normotensive Wistar rats. Results Functional efficiency of CSCs from SHR was compromised relative to that in Wistar rat. Famotidine increased the migration and proliferation potential, along with retention of stemness of CSCs in treated SHRs. Cellular senescence and oxidative stress were also reduced. The expression of H2R was unaffected by the treatment. Discussion As anticipated, CSCs from SHRs were functionally impaired. Stem cell attributes of famotidine-treated SHRs was comparable to that of Wistar rats. Therefore, in addition to being cardioprotective, the histamine 2 receptor antagonist modulated cardiac stem cells characteristics. Restoration of stem cell efficiency by famotidine is possibly mediated by reduction of oxidative stress as the expression of H2R was unaffected by the treatment. Maintenance of healthy stem cell po…
format: application/pdf
format: text/html
creator: Sherin Saheera
creator: Ajay G. Potnuri
creator: Renuka Nair
subject: Cell Biology
subject: Cardiology
description: doi:10.7717/peerj.3882
publisher: PeerJ Inc.
rights: © 2017 Saheera et al.
abstract: Background Cardiac stem cells (CSCs) play a vital role in cardiac homeostasis. A decrease in the efficiency of cardiac stem cells is speculated in various cardiac abnormalities. The maintenance of a healthy stem cell population is essential for the prevention of adverse cardiac remodeling leading to cardiac failure. Famotidine, a histamine-2 receptor antagonist, is currently used to treat ulcers of the stomach and intestines. In repurposing the use of the drug, reduction of cardiac hypertrophy and improvement in cardiac function of spontaneously hypertensive rats (SHR) was reported by our group. Given that stem cells are affected in cardiac pathologies, the effect of histamine-2 receptor antagonism on CSC characteristics was investigated. Methods To examine whether famotidine has a positive effect on CSCs, spontaneously hypertensive rats (SHR) treated with the drug were sacrificed; and CSCs isolated from atrial appendages was evaluated. Six-month-old male SHRs were treated with famotidine (30 mg/kg/day) for two months. The effect of famotidine treatment on migration, proliferation and survival of CSCs was compared with untreated SHRs and normotensive Wistar rats. Results Functional efficiency of CSCs from SHR was compromised relative to that in Wistar rat. Famotidine increased the migration and proliferation potential, along with retention of stemness of CSCs in treated SHRs. Cellular senescence and oxidative stress were also reduced. The expression of H2R was unaffected by the treatment. Discussion As anticipated, CSCs from SHRs were functionally impaired. Stem cell attributes of famotidine-treated SHRs was comparable to that of Wistar rats. Therefore, in addition to being cardioprotective, the histamine 2 receptor antagonist modulated cardiac stem cells characteristics. Restoration of stem cell efficiency by famotidine is possibly mediated by reduction of oxidative stress as the expression of H2R was unaffected by the treatment. Maintenance of healthy stem cell po…
bibliographic citation: Saheera et al. (2017) Histamine-2 receptor antagonist famotidine modulates cardiac stem cell characteristics in hypertensive heart disease. PeerJ 5:e3882 https://doi.org/10.7717/peerj.3882
date submitted: 2017-05-09
date accepted: 2017-09-12
issued: 2017-10-09
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Saheera
  given name: Sherin
author list: Agent
  family name: Potnuri
  given name: Ajay G.
author list: Agent
  family name: Nair
  given name: Renuka
doi: 10.7717/peerj.3882
volume: 5
issn: 2167-8359
publication name: PeerJ
publication date: 2017-10-09
copyright: ©2017 Saheera et al.
attribution name: Saheera et al.

Influence of exercise duration on cardiorespiratory responses, energy cost and tissue oxygenation within a 6 hour treadmill run
type: item
type: AcademicArticle
description: Purpose The physiological mechanisms for alterations in oxygen utilization ( $\dot {\mathrm{V }}{\mathrm{O}}_{2}$ V ̇ O 2 ) and the energy cost of running (Cr) during prolonged running are not completely understood, and could be linked with alterations in muscle and cerebral tissue oxygenation. Methods Eight trained ultramarathon runners (three women; mean ± SD; age 37 ± 7 yr; maximum $\dot {\mathrm{V }}{\mathrm{O}}_{2}$ V ̇ O 2 60 ± 15 mL min−1 kg−1) completed a 6 hr treadmill run (6TR), which consisted of four modules, including periods of moderate (3 min at 10 km h−1, 10-CR) and heavy exercise intensities (6 min at 70% of maximum $\dot {\mathrm{V }}{\mathrm{O}}_{2}$ V ̇ O 2 , HILL), separated by three, 100 min periods of self-paced running (SP). We measured $\dot {\mathrm{V }}{\mathrm{O}}_{2}$ V ̇ O 2 , minute ventilation ( ${\dot {\mathrm{V }}}_{\mathrm{E}}$ V ̇ E ), ventilatory efficiency ( ${\dot {\mathrm{V }}}_{\mathrm{E}}:\dot {\mathrm{V }}{\mathrm{O}}_{2}$ V ̇ E : V ̇ O 2 ), respiratory exchange ratio (RER), Cr, muscle and cerebral tissue saturation index (TSI) during the modules, and heart rate (HR) and perceived exertion (RPE) during the modules and SP. Results Participants ran 58.3 ± 10.5 km during 6TR. Speed decreased and HR and RPE increased during SP. Across the modules, HR and $\dot {\mathrm{V }}{\mathrm{O}}_{2}$ V ̇ O 2 increased (10-CR), and RER decreased (10-CR and HILL). There were no significant changes in ${\dot {\mathrm{V }}}_{\mathrm{E}}$ V ̇ E , ${\dot {\mathrm{V }}}_{\mathrm{E}}:\dot {\mathrm{V }}{\mathrm{O}}_{2}$ V ̇ E : V ̇ O 2 , Cr, TSI and RPE across the modules. Conclusions In the context of positive pacing (decreasing speed), increased cardiac drift and perceived exertion over the 6TR, we observed increased RER and increased HR at moderate and heavy exercise intensity, increased $\dot {\mathrm{V }}{\mathrm{O}}_{2}$ V ̇ O 2 at moderate intensity, and no effect of exercise duration on ventilatory efficiency, energy cost of running and t…
format: application/pdf
format: text/html
creator: Hugo A. Kerhervé
creator: Scott McLean
creator: Karen Birkenhead
creator: David Parr
creator: Colin Solomon
subject: Anatomy and Physiology
subject: Kinesiology
description: doi:10.7717/peerj.3694
publisher: PeerJ Inc.
rights: © 2017 Kerhervé et al.
abstract: Purpose The physiological mechanisms for alterations in oxygen utilization ( $\dot {\mathrm{V }}{\mathrm{O}}_{2}$ V ̇ O 2 ) and the energy cost of running (Cr) during prolonged running are not completely understood, and could be linked with alterations in muscle and cerebral tissue oxygenation. Methods Eight trained ultramarathon runners (three women; mean ± SD; age 37 ± 7 yr; maximum $\dot {\mathrm{V }}{\mathrm{O}}_{2}$ V ̇ O 2 60 ± 15 mL min−1 kg−1) completed a 6 hr treadmill run (6TR), which consisted of four modules, including periods of moderate (3 min at 10 km h−1, 10-CR) and heavy exercise intensities (6 min at 70% of maximum $\dot {\mathrm{V }}{\mathrm{O}}_{2}$ V ̇ O 2 , HILL), separated by three, 100 min periods of self-paced running (SP). We measured $\dot {\mathrm{V }}{\mathrm{O}}_{2}$ V ̇ O 2 , minute ventilation ( ${\dot {\mathrm{V }}}_{\mathrm{E}}$ V ̇ E ), ventilatory efficiency ( ${\dot {\mathrm{V }}}_{\mathrm{E}}:\dot {\mathrm{V }}{\mathrm{O}}_{2}$ V ̇ E : V ̇ O 2 ), respiratory exchange ratio (RER), Cr, muscle and cerebral tissue saturation index (TSI) during the modules, and heart rate (HR) and perceived exertion (RPE) during the modules and SP. Results Participants ran 58.3 ± 10.5 km during 6TR. Speed decreased and HR and RPE increased during SP. Across the modules, HR and $\dot {\mathrm{V }}{\mathrm{O}}_{2}$ V ̇ O 2 increased (10-CR), and RER decreased (10-CR and HILL). There were no significant changes in ${\dot {\mathrm{V }}}_{\mathrm{E}}$ V ̇ E , ${\dot {\mathrm{V }}}_{\mathrm{E}}:\dot {\mathrm{V }}{\mathrm{O}}_{2}$ V ̇ E : V ̇ O 2 , Cr, TSI and RPE across the modules. Conclusions In the context of positive pacing (decreasing speed), increased cardiac drift and perceived exertion over the 6TR, we observed increased RER and increased HR at moderate and heavy exercise intensity, increased $\dot {\mathrm{V }}{\mathrm{O}}_{2}$ V ̇ O 2 at moderate intensity, and no effect of exercise duration on ventilatory efficiency, energy cost of running and t…
bibliographic citation: Kerhervé et al. (2017) Influence of exercise duration on cardiorespiratory responses, energy cost and tissue oxygenation within a 6 hour treadmill run. PeerJ 5:e3694 https://doi.org/10.7717/peerj.3694
date submitted: 2017-04-08
date accepted: 2017-07-25
issued: 2017-10-09
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Kerhervé
  given name: Hugo A.
author list: Agent
  family name: McLean
  given name: Scott
author list: Agent
  family name: Birkenhead
  given name: Karen
author list: Agent
  family name: Parr
  given name: David
author list: Agent
  family name: Solomon
  given name: Colin
doi: 10.7717/peerj.3694
volume: 5
issn: 2167-8359
publication name: PeerJ
publication date: 2017-10-09
copyright: ©2017 Kerhervé et al.
attribution name: Kerhervé et al.

Independent evolution of tetraloop in enterovirus oriL replicative element and its putative binding partners in virus protein 3C
type: item
type: AcademicArticle
description: Background Enteroviruses are small non-enveloped viruses with a (+) ssRNA genome with one open reading frame. Enterovirus protein 3C (or 3CD for some species) binds the replicative element oriL to initiate replication. The replication of enteroviruses features a low-fidelity process, which allows the virus to adapt to the changing environment on the one hand, and requires additional mechanisms to maintain the genome stability on the other. Structural disturbances in the apical region of oriL domain d can be compensated by amino acid substitutions in positions 154 or 156 of 3C (amino acid numeration corresponds to poliovirus 3C), thus suggesting the co-evolution of these interacting sequences in nature. The aim of this work was to understand co-evolution patterns of two interacting replication machinery elements in enteroviruses, the apical region of oriL domain d and its putative binding partners in the 3C protein. Methods To evaluate the variability of the domain d loop sequence we retrieved all available full enterovirus sequences (>6, 400 nucleotides), which were present in the NCBI database on February 2017 and analysed the variety and abundance of sequences in domain d of the replicative element oriL and in the protein 3C. Results A total of 2,842 full genome sequences was analysed. The majority of domain d apical loops were tetraloops, which belonged to consensus YNHG (Y = U/C, N = any nucleotide, H = A/C/U). The putative RNA-binding tripeptide 154–156 (Enterovirus C 3C protein numeration) was less diverse than the apical domain d loop region and, in contrast to it, was species-specific. Discussion Despite the suggestion that the RNA-binding tripeptide interacts with the apical region of domain d, they evolve independently in nature. Together, our data indicate the plastic evolution of both interplayers of 3C-oriL recognition.
format: application/pdf
format: text/html
creator: Maria A. Prostova
creator: Andrei A. Deviatkin
creator: Irina O. Tcelykh
creator: Alexander N. Lukashev
creator: Anatoly P. Gmyl
subject: Evolutionary Studies
subject: Genomics
subject: Virology
description: doi:10.7717/peerj.3896
publisher: PeerJ Inc.
rights: © 2017 Prostova et al.
abstract: Background Enteroviruses are small non-enveloped viruses with a (+) ssRNA genome with one open reading frame. Enterovirus protein 3C (or 3CD for some species) binds the replicative element oriL to initiate replication. The replication of enteroviruses features a low-fidelity process, which allows the virus to adapt to the changing environment on the one hand, and requires additional mechanisms to maintain the genome stability on the other. Structural disturbances in the apical region of oriL domain d can be compensated by amino acid substitutions in positions 154 or 156 of 3C (amino acid numeration corresponds to poliovirus 3C), thus suggesting the co-evolution of these interacting sequences in nature. The aim of this work was to understand co-evolution patterns of two interacting replication machinery elements in enteroviruses, the apical region of oriL domain d and its putative binding partners in the 3C protein. Methods To evaluate the variability of the domain d loop sequence we retrieved all available full enterovirus sequences (>6, 400 nucleotides), which were present in the NCBI database on February 2017 and analysed the variety and abundance of sequences in domain d of the replicative element oriL and in the protein 3C. Results A total of 2,842 full genome sequences was analysed. The majority of domain d apical loops were tetraloops, which belonged to consensus YNHG (Y = U/C, N = any nucleotide, H = A/C/U). The putative RNA-binding tripeptide 154–156 (Enterovirus C 3C protein numeration) was less diverse than the apical domain d loop region and, in contrast to it, was species-specific. Discussion Despite the suggestion that the RNA-binding tripeptide interacts with the apical region of domain d, they evolve independently in nature. Together, our data indicate the plastic evolution of both interplayers of 3C-oriL recognition.
bibliographic citation: Prostova et al. (2017) Independent evolution of tetraloop in enterovirus oriL replicative element and its putative binding partners in virus protein 3C. PeerJ 5:e3896 https://doi.org/10.7717/peerj.3896
date submitted: 2017-08-08
date accepted: 2017-09-16
issued: 2017-10-06
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Prostova
  given name: Maria A.
author list: Agent
  family name: Deviatkin
  given name: Andrei A.
author list: Agent
  family name: Tcelykh
  given name: Irina O.
author list: Agent
  family name: Lukashev
  given name: Alexander N.
author list: Agent
  family name: Gmyl
  given name: Anatoly P.
doi: 10.7717/peerj.3896
volume: 5
issn: 2167-8359
publication name: PeerJ
publication date: 2017-10-06
copyright: ©2017 Prostova et al.
attribution name: Prostova et al.

Cryptic biodiversity and phylogeographic patterns of Seychellois Ligia isopods
type: item
type: AcademicArticle
description: Ligia isopods are conspicuous inhabitants of rocky intertidal habitats exhibiting several biological traits that severely limit their dispersal potential. Their presence in patchy habitats and low vagility may lead to long term isolation, allopatric isolation and possible cryptic speciation. Indeed, various species of Ligia have been suggested to represent instead cryptic species complexes. Past studies; however, have largely focused in Eastern Pacific and Atlantic species of Ligia, leaving in doubt whether cryptic diversity occurs in other highly biodiverse areas. The Seychelles consists of 115 islands of different ages and geological origins spread across the western Indian Ocean. They are well known for their rich biodiversity with recent reports of cryptic species in terrestrial Seychellois organisms. Despite these studies, it is unclear whether coastal invertebrates from the Seychelles harbor any cryptic diversity. In this study, we examined patterns of genetic diversity and isolation within Ligia isopods across the Seychelles archipelago by characterizing individuals from locations across both inner and outer islands of the Seychelles using mitochondrial and nuclear markers. We report the presence of highly divergent lineages of independent origin. At Aldabra Atoll, we uncovered a lineage closely related to the Ligia vitiensis cryptic species complex. Within the inner islands of Cousine, Silhouette, and Mahé we detected the presence of two moderately divergent and geographically disjunct lineages most closely related to Ligia dentipes. Our findings suggest that the Seychelles may harbor at least three novel species of Ligia in need of description and that these species may have originated independently.
format: application/pdf
format: text/html
creator: Carlos A. Santamaria
creator: Joanna K. Bluemel
creator: Nancy Bunbury
creator: Melinda Curran
subject: Biodiversity
subject: Biogeography
subject: Evolutionary Studies
subject: Marine Biology
subject: Zoology
description: doi:10.7717/peerj.3894
publisher: PeerJ Inc.
rights: © 2017 Santamaria et al.
abstract: Ligia isopods are conspicuous inhabitants of rocky intertidal habitats exhibiting several biological traits that severely limit their dispersal potential. Their presence in patchy habitats and low vagility may lead to long term isolation, allopatric isolation and possible cryptic speciation. Indeed, various species of Ligia have been suggested to represent instead cryptic species complexes. Past studies; however, have largely focused in Eastern Pacific and Atlantic species of Ligia, leaving in doubt whether cryptic diversity occurs in other highly biodiverse areas. The Seychelles consists of 115 islands of different ages and geological origins spread across the western Indian Ocean. They are well known for their rich biodiversity with recent reports of cryptic species in terrestrial Seychellois organisms. Despite these studies, it is unclear whether coastal invertebrates from the Seychelles harbor any cryptic diversity. In this study, we examined patterns of genetic diversity and isolation within Ligia isopods across the Seychelles archipelago by characterizing individuals from locations across both inner and outer islands of the Seychelles using mitochondrial and nuclear markers. We report the presence of highly divergent lineages of independent origin. At Aldabra Atoll, we uncovered a lineage closely related to the Ligia vitiensis cryptic species complex. Within the inner islands of Cousine, Silhouette, and Mahé we detected the presence of two moderately divergent and geographically disjunct lineages most closely related to Ligia dentipes. Our findings suggest that the Seychelles may harbor at least three novel species of Ligia in need of description and that these species may have originated independently.
bibliographic citation: Santamaria et al. (2017) Cryptic biodiversity and phylogeographic patterns of Seychellois Ligia isopods. PeerJ 5:e3894 https://doi.org/10.7717/peerj.3894
date submitted: 2017-08-15
date accepted: 2017-09-15
issued: 2017-10-06
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Santamaria
  given name: Carlos A.
author list: Agent
  family name: Bluemel
  given name: Joanna K.
author list: Agent
  family name: Bunbury
  given name: Nancy
author list: Agent
  family name: Curran
  given name: Melinda
doi: 10.7717/peerj.3894
volume: 5
issn: 2167-8359
publication name: PeerJ
publication date: 2017-10-06
copyright: ©2017 Santamaria et al.
attribution name: Santamaria et al.

Benchmark datasets for phylogenomic pipeline validation, applications for foodborne pathogen surveillance
type: item
type: AcademicArticle
description: Background As next generation sequence technology has advanced, there have been parallel advances in genome-scale analysis programs for determining evolutionary relationships as proxies for epidemiological relationship in public health. Most new programs skip traditional steps of ortholog determination and multi-gene alignment, instead identifying variants across a set of genomes, then summarizing results in a matrix of single-nucleotide polymorphisms or alleles for standard phylogenetic analysis. However, public health authorities need to document the performance of these methods with appropriate and comprehensive datasets so they can be validated for specific purposes, e.g., outbreak surveillance. Here we propose a set of benchmark datasets to be used for comparison and validation of phylogenomic pipelines. Methods We identified four well-documented foodborne pathogen events in which the epidemiology was concordant with routine phylogenomic analyses (reference-based SNP and wgMLST approaches). These are ideal benchmark datasets, as the trees, WGS data, and epidemiological data for each are all in agreement. We have placed these sequence data, sample metadata, and “known” phylogenetic trees in publicly-accessible databases and developed a standard descriptive spreadsheet format describing each dataset. To facilitate easy downloading of these benchmarks, we developed an automated script that uses the standard descriptive spreadsheet format. Results Our “outbreak” benchmark datasets represent the four major foodborne bacterial pathogens (Listeria monocytogenes, Salmonella enterica, Escherichia coli, and Campylobacter jejuni) and one simulated dataset where the “known tree” can be accurately called the “true tree”. The downloading script and associated table files are available on GitHub: https://github.com/WGS-standards-and-analysis/datasets. Discussion These five benchmark datasets will help standardize comparison of current and future phylogenomic pipelines, and fa…
format: application/pdf
format: text/html
creator: Ruth E. Timme
creator: Hugh Rand
creator: Martin Shumway
creator: Eija K. Trees
creator: Mustafa Simmons
creator: Richa Agarwala
creator: Steven Davis
creator: Glenn E. Tillman
creator: Stephanie Defibaugh-Chavez
creator: Heather A. Carleton
creator: William A. Klimke
creator: Lee S. Katz
subject: Bioinformatics
subject: Evolutionary Studies
subject: Food Science and Technology
subject: Genomics
subject: Epidemiology
description: doi:10.7717/peerj.3893
publisher: PeerJ Inc.
rights: © 2017
abstract: Background As next generation sequence technology has advanced, there have been parallel advances in genome-scale analysis programs for determining evolutionary relationships as proxies for epidemiological relationship in public health. Most new programs skip traditional steps of ortholog determination and multi-gene alignment, instead identifying variants across a set of genomes, then summarizing results in a matrix of single-nucleotide polymorphisms or alleles for standard phylogenetic analysis. However, public health authorities need to document the performance of these methods with appropriate and comprehensive datasets so they can be validated for specific purposes, e.g., outbreak surveillance. Here we propose a set of benchmark datasets to be used for comparison and validation of phylogenomic pipelines. Methods We identified four well-documented foodborne pathogen events in which the epidemiology was concordant with routine phylogenomic analyses (reference-based SNP and wgMLST approaches). These are ideal benchmark datasets, as the trees, WGS data, and epidemiological data for each are all in agreement. We have placed these sequence data, sample metadata, and “known” phylogenetic trees in publicly-accessible databases and developed a standard descriptive spreadsheet format describing each dataset. To facilitate easy downloading of these benchmarks, we developed an automated script that uses the standard descriptive spreadsheet format. Results Our “outbreak” benchmark datasets represent the four major foodborne bacterial pathogens (Listeria monocytogenes, Salmonella enterica, Escherichia coli, and Campylobacter jejuni) and one simulated dataset where the “known tree” can be accurately called the “true tree”. The downloading script and associated table files are available on GitHub: https://github.com/WGS-standards-and-analysis/datasets. Discussion These five benchmark datasets will help standardize comparison of current and future phylogenomic pipelines, and fa…
bibliographic citation: Timme et al. (2017) Benchmark datasets for phylogenomic pipeline validation, applications for foodborne pathogen surveillance. PeerJ 5:e3893 https://doi.org/10.7717/peerj.3893
date submitted: 2017-07-21
date accepted: 2017-09-15
issued: 2017-10-06
is part of: PeerJ
license: http://creativecommons.org/publicdomain/zero/1.0/
author list: Agent
  family name: Timme
  given name: Ruth E.
author list: Agent
  family name: Rand
  given name: Hugh
author list: Agent
  family name: Shumway
  given name: Martin
author list: Agent
  family name: Trees
  given name: Eija K.
author list: Agent
  family name: Simmons
  given name: Mustafa
author list: Agent
  family name: Agarwala
  given name: Richa
author list: Agent
  family name: Davis
  given name: Steven
author list: Agent
  family name: Tillman
  given name: Glenn E.
author list: Agent
  family name: Defibaugh-Chavez
  given name: Stephanie
author list: Agent
  family name: Carleton
  given name: Heather A.
author list: Agent
  family name: Klimke
  given name: William A.
author list: Agent
  family name: Katz
  given name: Lee S.
doi: 10.7717/peerj.3893
volume: 5
issn: 2167-8359
publication name: PeerJ
publication date: 2017-10-06

Hearing assessment during deep brain stimulation of the central nucleus of the inferior colliculus and dentate cerebellar nucleus in rat
type: item
type: AcademicArticle
description: Background Recently it has been shown in animal studies that deep brain stimulation (DBS) of auditory structures was able to reduce tinnitus-like behavior. However, the question arises whether hearing might be impaired when interfering in auditory-related network loops with DBS. Methods The auditory brainstem response (ABR) was measured in rats during high frequency stimulation (HFS) and low frequency stimulation (LFS) in the central nucleus of the inferior colliculus (CIC, n = 5) or dentate cerebellar nucleus (DCBN, n = 5). Besides hearing thresholds using ABR, relative measures of latency and amplitude can be extracted from the ABR. In this study ABR thresholds, interpeak latencies (I–III, III–V, I–V) and V/I amplitude ratio were measured during off-stimulation state and during LFS and HFS. Results In both the CIC and the CNBN groups, no significant differences were observed for all outcome measures. Discussion DBS in both the CIC and the CNBN did not have adverse effects on hearing measurements. These findings suggest that DBS does not hamper physiological processing in the auditory circuitry.
format: application/pdf
format: text/html
creator: Jasper V. Smit
creator: Ali Jahanshahi
creator: Marcus L.F. Janssen
creator: Robert J. Stokroos
creator: Yasin Temel
subject: Neurology
subject: Otorhinolaryngology
subject: Surgery and Surgical Specialties
description: doi:10.7717/peerj.3892
publisher: PeerJ Inc.
rights: © 2017 Smit et al.
abstract: Background Recently it has been shown in animal studies that deep brain stimulation (DBS) of auditory structures was able to reduce tinnitus-like behavior. However, the question arises whether hearing might be impaired when interfering in auditory-related network loops with DBS. Methods The auditory brainstem response (ABR) was measured in rats during high frequency stimulation (HFS) and low frequency stimulation (LFS) in the central nucleus of the inferior colliculus (CIC, n = 5) or dentate cerebellar nucleus (DCBN, n = 5). Besides hearing thresholds using ABR, relative measures of latency and amplitude can be extracted from the ABR. In this study ABR thresholds, interpeak latencies (I–III, III–V, I–V) and V/I amplitude ratio were measured during off-stimulation state and during LFS and HFS. Results In both the CIC and the CNBN groups, no significant differences were observed for all outcome measures. Discussion DBS in both the CIC and the CNBN did not have adverse effects on hearing measurements. These findings suggest that DBS does not hamper physiological processing in the auditory circuitry.
bibliographic citation: Smit et al. (2017) Hearing assessment during deep brain stimulation of the central nucleus of the inferior colliculus and dentate cerebellar nucleus in rat. PeerJ 5:e3892 https://doi.org/10.7717/peerj.3892
date submitted: 2017-05-10
date accepted: 2017-09-15
issued: 2017-10-06
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Smit
  given name: Jasper V.
author list: Agent
  family name: Jahanshahi
  given name: Ali
author list: Agent
  family name: Janssen
  given name: Marcus L.F.
author list: Agent
  family name: Stokroos
  given name: Robert J.
author list: Agent
  family name: Temel
  given name: Yasin
doi: 10.7717/peerj.3892
volume: 5
issn: 2167-8359
publication name: PeerJ
publication date: 2017-10-06
copyright: ©2017 Smit et al.
attribution name: Smit et al.

Genome methylation and regulatory functions for hypoxic adaptation in Tibetan chicken embryos
type: item
type: AcademicArticle
description: Tibetan chickens have unique adaptations to the extreme high-altitude environment that they inhabit. Epigenetic DNA methylation affects many biological processes, including hypoxic adaptation; however, the regulatory genes for DNA methylation in hypoxic adaptation remain unknown. In this study, methylated DNA immunoprecipitation with high-throughput sequencing (MeDIP-seq) was used to provide an atlas of the DNA methylomes of the heart tissue of hypoxic highland Tibetan and lowland Chahua chicken embryos. A total of 31.2 gigabases of sequence data were generated from six MeDIP-seq libraries. We identified 1,049 differentially methylated regions (DMRs) and 695 related differentially methylated genes (DMGs) between the two chicken breeds. The DMGs are involved in vascular smooth muscle contraction, VEGF signaling pathway, calcium signaling pathway, and other hypoxia-related pathways. Five candidate genes that had low methylation (EDNRA, EDNRB2, BMPR1B, BMPRII, and ITGA2) might play key regulatory roles in the adaptation to hypoxia in Tibetan chicken embryos. Our study provides significant explanations for the functions of genes and their epigenetic regulation for hypoxic adaptation in Tibetan chickens.
format: application/pdf
format: text/html
creator: Yawen Zhang
creator: Wenyu Gou
creator: Jun Ma
creator: Hongliang Zhang
creator: Ying Zhang
creator: Hao Zhang
subject: Agricultural Science
subject: Genomics
subject: Natural Resource Management
description: doi:10.7717/peerj.3891
publisher: PeerJ Inc.
rights: © 2017 Zhang et al.
abstract: Tibetan chickens have unique adaptations to the extreme high-altitude environment that they inhabit. Epigenetic DNA methylation affects many biological processes, including hypoxic adaptation; however, the regulatory genes for DNA methylation in hypoxic adaptation remain unknown. In this study, methylated DNA immunoprecipitation with high-throughput sequencing (MeDIP-seq) was used to provide an atlas of the DNA methylomes of the heart tissue of hypoxic highland Tibetan and lowland Chahua chicken embryos. A total of 31.2 gigabases of sequence data were generated from six MeDIP-seq libraries. We identified 1,049 differentially methylated regions (DMRs) and 695 related differentially methylated genes (DMGs) between the two chicken breeds. The DMGs are involved in vascular smooth muscle contraction, VEGF signaling pathway, calcium signaling pathway, and other hypoxia-related pathways. Five candidate genes that had low methylation (EDNRA, EDNRB2, BMPR1B, BMPRII, and ITGA2) might play key regulatory roles in the adaptation to hypoxia in Tibetan chicken embryos. Our study provides significant explanations for the functions of genes and their epigenetic regulation for hypoxic adaptation in Tibetan chickens.
bibliographic citation: Zhang et al. (2017) Genome methylation and regulatory functions for hypoxic adaptation in Tibetan chicken embryos. PeerJ 5:e3891 https://doi.org/10.7717/peerj.3891
date submitted: 2017-05-23
date accepted: 2017-09-14
issued: 2017-10-06
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Zhang
  given name: Yawen
author list: Agent
  family name: Gou
  given name: Wenyu
author list: Agent
  family name: Ma
  given name: Jun
author list: Agent
  family name: Zhang
  given name: Hongliang
author list: Agent
  family name: Zhang
  given name: Ying
author list: Agent
  family name: Zhang
  given name: Hao
doi: 10.7717/peerj.3891
volume: 5
issn: 2167-8359
publication name: PeerJ
publication date: 2017-10-06
copyright: ©2017 Zhang et al.
attribution name: Zhang et al.

voomDDA: discovery of diagnostic biomarkers and classification of RNA-seq data
type: item
type: AcademicArticle
description: RNA-Seq is a recent and efficient technique that uses the capabilities of next-generation sequencing technology for characterizing and quantifying transcriptomes. One important task using gene-expression data is to identify a small subset of genes that can be used to build diagnostic classifiers particularly for cancer diseases. Microarray based classifiers are not directly applicable to RNA-Seq data due to its discrete nature. Overdispersion is another problem that requires careful modeling of mean and variance relationship of the RNA-Seq data. In this study, we present voomDDA classifiers: variance modeling at the observational level (voom) extensions of the nearest shrunken centroids (NSC) and the diagonal discriminant classifiers. VoomNSC is one of these classifiers and brings voom and NSC approaches together for the purpose of gene-expression based classification. For this purpose, we propose weighted statistics and put these weighted statistics into the NSC algorithm. The VoomNSC is a sparse classifier that models the mean-variance relationship using the voom method and incorporates voom’s precision weights into the NSC classifier via weighted statistics. A comprehensive simulation study was designed and four real datasets are used for performance assessment. The overall results indicate that voomNSC performs as the sparsest classifier. It also provides the most accurate results together with power-transformed Poisson linear discriminant analysis, rlog transformed support vector machines and random forests algorithms. In addition to prediction purposes, the voomNSC classifier can be used to identify the potential diagnostic biomarkers for a condition of interest. Through this work, statistical learning methods proposed for microarrays can be reused for RNA-Seq data. An interactive web application is freely available at http://www.biosoft.hacettepe.edu.tr/voomDDA/.
format: application/pdf
format: text/html
creator: Gokmen Zararsiz
creator: Dincer Goksuluk
creator: Bernd Klaus
creator: Selcuk Korkmaz
creator: Vahap Eldem
creator: Erdem Karabulut
creator: Ahmet Ozturk
subject: Bioinformatics
subject: Computational Biology
subject: Statistics
subject: Medical Genetics
subject: Computational Science
description: doi:10.7717/peerj.3890
publisher: PeerJ Inc.
rights: © 2017 Zararsiz et al.
abstract: RNA-Seq is a recent and efficient technique that uses the capabilities of next-generation sequencing technology for characterizing and quantifying transcriptomes. One important task using gene-expression data is to identify a small subset of genes that can be used to build diagnostic classifiers particularly for cancer diseases. Microarray based classifiers are not directly applicable to RNA-Seq data due to its discrete nature. Overdispersion is another problem that requires careful modeling of mean and variance relationship of the RNA-Seq data. In this study, we present voomDDA classifiers: variance modeling at the observational level (voom) extensions of the nearest shrunken centroids (NSC) and the diagonal discriminant classifiers. VoomNSC is one of these classifiers and brings voom and NSC approaches together for the purpose of gene-expression based classification. For this purpose, we propose weighted statistics and put these weighted statistics into the NSC algorithm. The VoomNSC is a sparse classifier that models the mean-variance relationship using the voom method and incorporates voom’s precision weights into the NSC classifier via weighted statistics. A comprehensive simulation study was designed and four real datasets are used for performance assessment. The overall results indicate that voomNSC performs as the sparsest classifier. It also provides the most accurate results together with power-transformed Poisson linear discriminant analysis, rlog transformed support vector machines and random forests algorithms. In addition to prediction purposes, the voomNSC classifier can be used to identify the potential diagnostic biomarkers for a condition of interest. Through this work, statistical learning methods proposed for microarrays can be reused for RNA-Seq data. An interactive web application is freely available at http://www.biosoft.hacettepe.edu.tr/voomDDA/.
bibliographic citation: Zararsiz et al. (2017) voomDDA: discovery of diagnostic biomarkers and classification of RNA-seq data. PeerJ 5:e3890 https://doi.org/10.7717/peerj.3890
date submitted: 2017-06-29
date accepted: 2017-09-14
issued: 2017-10-06
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Zararsiz
  given name: Gokmen
author list: Agent
  family name: Goksuluk
  given name: Dincer
author list: Agent
  family name: Klaus
  given name: Bernd
author list: Agent
  family name: Korkmaz
  given name: Selcuk
author list: Agent
  family name: Eldem
  given name: Vahap
author list: Agent
  family name: Karabulut
  given name: Erdem
author list: Agent
  family name: Ozturk
  given name: Ahmet
doi: 10.7717/peerj.3890
volume: 5
issn: 2167-8359
publication name: PeerJ
publication date: 2017-10-06
copyright: ©2017 Zararsiz et al.
attribution name: Zararsiz et al.

The isolation and identification of pathogenic fungi from Tessaratoma papillosa Drury (Hemiptera: Tessaratomidae)
type: item
type: AcademicArticle
description: Background Litchi stink-bug, Tessaratoma papillosa Drury (Hemiptera: Tessaratomidae), is one of the most widespread and destructive pest species on Litchi chinensis Sonn and Dimocarpus longan Lour in Southern China. Inappropriate use of chemical pesticides has resulted in serious environmental problems and food pollution. Generating an improved Integrated Pest Management (IPM) strategy for litchi stink-bug in orchard farming requires development of an effective biological control agent. Entomopathogenic fungi are regarded as a vital ecological factor in the suppression of pest populations under field conditions. With few effective fungi and pathogenic strains available to control litchi stink-bug, exploration of natural resources for promising entomopathogenic fungi is warranted. Methods & Results In this study, two pathogenic fungi were isolated from cadavers of adult T. papillosa. They were identified as Paecilomyces lilacinus and Beauveria bassiana by morphological identification and rDNA-ITS homogeneous analysis. Infection of T. papillosa with B. bassiana and P. lilacinus occurred initially from the antennae, metameres, and inter-segmental membranes. Biological tests showed that the two entomopathogenic fungi induced high mortality in 2nd and 5th instar nymphs of T. papillosa. B. bassiana was highly virulent on 2nd instar nymphs of T. papillosa, with values for cadaver rate, LC50 and LT50 of 88.89%, 1.92 × 107 conidia/mL and 4.34 days respectively. Discussion This study provides two valuable entomopathogenic fungi from T. papillosa. This finding suggests that the highly virulent P. lilacinus and B. bassiana play an important role in the biocontrol of T. papillosa in China. These pathogenic fungi had no pollution or residue risk, and could provide an alternative option for IPM of litchi stink-bug.
format: application/pdf
format: text/html
creator: Xiang Meng
creator: Junjie Hu
creator: Gecheng Ouyang
subject: Agricultural Science
subject: Entomology
subject: Microbiology
subject: Mycology
subject: Toxicology
description: doi:10.7717/peerj.3888
publisher: PeerJ Inc.
rights: © 2017 Meng et al.
abstract: Background Litchi stink-bug, Tessaratoma papillosa Drury (Hemiptera: Tessaratomidae), is one of the most widespread and destructive pest species on Litchi chinensis Sonn and Dimocarpus longan Lour in Southern China. Inappropriate use of chemical pesticides has resulted in serious environmental problems and food pollution. Generating an improved Integrated Pest Management (IPM) strategy for litchi stink-bug in orchard farming requires development of an effective biological control agent. Entomopathogenic fungi are regarded as a vital ecological factor in the suppression of pest populations under field conditions. With few effective fungi and pathogenic strains available to control litchi stink-bug, exploration of natural resources for promising entomopathogenic fungi is warranted. Methods & Results In this study, two pathogenic fungi were isolated from cadavers of adult T. papillosa. They were identified as Paecilomyces lilacinus and Beauveria bassiana by morphological identification and rDNA-ITS homogeneous analysis. Infection of T. papillosa with B. bassiana and P. lilacinus occurred initially from the antennae, metameres, and inter-segmental membranes. Biological tests showed that the two entomopathogenic fungi induced high mortality in 2nd and 5th instar nymphs of T. papillosa. B. bassiana was highly virulent on 2nd instar nymphs of T. papillosa, with values for cadaver rate, LC50 and LT50 of 88.89%, 1.92 × 107 conidia/mL and 4.34 days respectively. Discussion This study provides two valuable entomopathogenic fungi from T. papillosa. This finding suggests that the highly virulent P. lilacinus and B. bassiana play an important role in the biocontrol of T. papillosa in China. These pathogenic fungi had no pollution or residue risk, and could provide an alternative option for IPM of litchi stink-bug.
bibliographic citation: Meng et al. (2017) The isolation and identification of pathogenic fungi from Tessaratoma papillosa Drury (Hemiptera: Tessaratomidae). PeerJ 5:e3888 https://doi.org/10.7717/peerj.3888
date submitted: 2017-03-01
date accepted: 2017-09-13
issued: 2017-10-06
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Meng
  given name: Xiang
author list: Agent
  family name: Hu
  given name: Junjie
author list: Agent
  family name: Ouyang
  given name: Gecheng
doi: 10.7717/peerj.3888
volume: 5
issn: 2167-8359
publication name: PeerJ
publication date: 2017-10-06
copyright: ©2017 Meng et al.
attribution name: Meng et al.

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