PeerJ
type: channel
link: https://peerj.com/articles/
description: Articles published in PeerJ
publisher: PeerJ Inc.
publication name: PeerJ
issn: 2167-8359
items: Phylogeographic investigation and ecological niche modelling of the endemic frog species Nanorana pleskei revealed multiple refugia in the eastern Tibetan Plateau
items: Genomic and functional analysis of Romboutsia ilealis CRIBT reveals adaptation to the small intestine
items: Development and evaluation of rapid novel isothermal amplification assays for important veterinary pathogens: Chlamydia psittaci and Chlamydia pecorum
items: Variance component testing for identifying differentially expressed genes in RNA-seq data
items: Age, growth, mortality and reproductive seasonality of jolthead porgy, Calamus bajonado, from Florida waters
items: Current practice in the management of new-onset atrial fibrillation in critically ill patients: a UK-wide survey
items: Early-branching euteleost relationships: areas of congruence between concatenation and coalescent model inferences
items: A comparison of the morphological and biochemical characteristics of Chlorella sorokiniana and Chlorella zofingiensis cultured under photoautotrophic and mixotrophic conditions
items: MetaCRAST: reference-guided extraction of CRISPR spacers from unassembled metagenomes
items: Lectins: an effective tool for screening of potential cancer biomarkers

Phylogeographic investigation and ecological niche modelling of the endemic frog species Nanorana pleskei revealed multiple refugia in the eastern Tibetan Plateau
type: item
type: AcademicArticle
description: The largest plateau Tibetan Plateau supplied an excellent opportunity to investigate the influence of the Pleistocene events on the high-elevation species. To test for the alternative hypotheses of Pleistocene glacial refugia, we used partial sequences of two mitochondrial genes and one nuclear gene to examine the phylogeographic patterns of the endemic frog species Nanorana pleskei across its known range in the eastern Tibetan Plateau, and conducted species distribution modelling (SDM) to explore changes of its distribution range through current and paleo periods. In all data sets, the species was divided into lineage north occupying open plateau platform and lineage south colonizing the mountainous plateau. The divergence of two major clades was estimated at the early Pleistocene. In mtDNA, lineage north contained northeastern and northwestern sublineages, and lineage south had two overlapping-distributed sublineages. Different lineages possessed distinct demographic characteristics, i.e., subdivision in the northeastern sublineage, historical bottleneck effects and recent expansions in the northwestern sublineage and the southeastern sublineage. SDMs depicted that stable suitable habitats had existed in the upper-middle streams of the Yellow River, Dadu River, Jinsha River and Yalong River. These regions were also recognized as the ancestral areas of different lineages. In conclusion, Nanorana pleskei lineages have probably experienced long-term separations. Stable suitable habitats existing in upper-middle streams of major rivers on the eastern Tibetan Plateau and distinct demographic dynamics of different lineages indicated that the lineages possessed independent evolutionary processes in multiple glacial refugia. The findings verified the profound effects of Pleistocene climatic fluctuations on the plateau endemic species.
format: application/pdf
format: text/html
creator: Bin Wang
creator: Feng Xie
creator: Jiannan Li
creator: Gang Wang
creator: Cheng Li
creator: Jianping Jiang
subject: Biogeography
subject: Evolutionary Studies
subject: Zoology
description: doi:10.7717/peerj.3770
publisher: PeerJ Inc.
rights: © 2017 Wang et al.
abstract: The largest plateau Tibetan Plateau supplied an excellent opportunity to investigate the influence of the Pleistocene events on the high-elevation species. To test for the alternative hypotheses of Pleistocene glacial refugia, we used partial sequences of two mitochondrial genes and one nuclear gene to examine the phylogeographic patterns of the endemic frog species Nanorana pleskei across its known range in the eastern Tibetan Plateau, and conducted species distribution modelling (SDM) to explore changes of its distribution range through current and paleo periods. In all data sets, the species was divided into lineage north occupying open plateau platform and lineage south colonizing the mountainous plateau. The divergence of two major clades was estimated at the early Pleistocene. In mtDNA, lineage north contained northeastern and northwestern sublineages, and lineage south had two overlapping-distributed sublineages. Different lineages possessed distinct demographic characteristics, i.e., subdivision in the northeastern sublineage, historical bottleneck effects and recent expansions in the northwestern sublineage and the southeastern sublineage. SDMs depicted that stable suitable habitats had existed in the upper-middle streams of the Yellow River, Dadu River, Jinsha River and Yalong River. These regions were also recognized as the ancestral areas of different lineages. In conclusion, Nanorana pleskei lineages have probably experienced long-term separations. Stable suitable habitats existing in upper-middle streams of major rivers on the eastern Tibetan Plateau and distinct demographic dynamics of different lineages indicated that the lineages possessed independent evolutionary processes in multiple glacial refugia. The findings verified the profound effects of Pleistocene climatic fluctuations on the plateau endemic species.
bibliographic citation: Wang et al. (2017) Phylogeographic investigation and ecological niche modelling of the endemic frog species Nanorana pleskei revealed multiple refugia in the eastern Tibetan Plateau. PeerJ 5:e3770 https://doi.org/10.7717/peerj.3770
date submitted: 2016-11-10
date accepted: 2017-08-16
issued: 2017-09-11
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Wang
  given name: Bin
author list: Agent
  family name: Xie
  given name: Feng
author list: Agent
  family name: Li
  given name: Jiannan
author list: Agent
  family name: Wang
  given name: Gang
author list: Agent
  family name: Li
  given name: Cheng
author list: Agent
  family name: Jiang
  given name: Jianping
doi: 10.7717/peerj.3770
volume: 5
issn: 2167-8359
publication name: PeerJ
publication date: 2017-09-11
copyright: © 2017 Wang et al.
attribution name: Wang et al.

Genomic and functional analysis of Romboutsia ilealis CRIBT reveals adaptation to the small intestine
type: item
type: AcademicArticle
description: Background The microbiota in the small intestine relies on their capacity to rapidly import and ferment available carbohydrates to survive in a complex and highly competitive ecosystem. Understanding how these communities function requires elucidating the role of its key players, the interactions among them and with their environment/host. Methods The genome of the gut bacterium Romboutsia ilealis CRIBT was sequenced with multiple technologies (Illumina paired-end, mate-pair and PacBio). The transcriptome was sequenced (Illumina HiSeq) after growth on three different carbohydrate sources, and short chain fatty acids were measured via HPLC. Results We present the complete genome of Romboutsia ilealis CRIBT, a natural inhabitant and key player of the small intestine of rats. R. ilealis CRIBT possesses a circular chromosome of 2,581,778 bp and a plasmid of 6,145 bp, carrying 2,351 and eight predicted protein coding sequences, respectively. Analysis of the genome revealed limited capacity to synthesize amino acids and vitamins, whereas multiple and partially redundant pathways for the utilization of different relatively simple carbohydrates are present. Transcriptome analysis allowed identification of the key components in the degradation of glucose, L-fucose and fructo-oligosaccharides. Discussion This revealed that R. ilealis CRIBT is adapted to a nutrient-rich environment where carbohydrates, amino acids and vitamins are abundantly available.
format: application/pdf
format: text/html
creator: Jacoline Gerritsen
creator: Bastian Hornung
creator: Bernadette Renckens
creator: Sacha A.F.T. van Hijum
creator: Vitor A.P. Martins dos Santos
creator: Ger T. Rijkers
creator: Peter J. Schaap
creator: Willem M. de Vos
creator: Hauke Smidt
subject: Genomics
subject: Microbiology
description: doi:10.7717/peerj.3698
publisher: PeerJ Inc.
rights: © 2017 Gerritsen et al.
abstract: Background The microbiota in the small intestine relies on their capacity to rapidly import and ferment available carbohydrates to survive in a complex and highly competitive ecosystem. Understanding how these communities function requires elucidating the role of its key players, the interactions among them and with their environment/host. Methods The genome of the gut bacterium Romboutsia ilealis CRIBT was sequenced with multiple technologies (Illumina paired-end, mate-pair and PacBio). The transcriptome was sequenced (Illumina HiSeq) after growth on three different carbohydrate sources, and short chain fatty acids were measured via HPLC. Results We present the complete genome of Romboutsia ilealis CRIBT, a natural inhabitant and key player of the small intestine of rats. R. ilealis CRIBT possesses a circular chromosome of 2,581,778 bp and a plasmid of 6,145 bp, carrying 2,351 and eight predicted protein coding sequences, respectively. Analysis of the genome revealed limited capacity to synthesize amino acids and vitamins, whereas multiple and partially redundant pathways for the utilization of different relatively simple carbohydrates are present. Transcriptome analysis allowed identification of the key components in the degradation of glucose, L-fucose and fructo-oligosaccharides. Discussion This revealed that R. ilealis CRIBT is adapted to a nutrient-rich environment where carbohydrates, amino acids and vitamins are abundantly available.
bibliographic citation: Gerritsen et al. (2017) Genomic and functional analysis of Romboutsia ilealis CRIBT reveals adaptation to the small intestine. PeerJ 5:e3698 https://doi.org/10.7717/peerj.3698
date submitted: 2017-04-06
date accepted: 2017-07-26
issued: 2017-09-11
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Gerritsen
  given name: Jacoline
author list: Agent
  family name: Hornung
  given name: Bastian
author list: Agent
  family name: Renckens
  given name: Bernadette
author list: Agent
  family name: van Hijum
  given name: Sacha A.F.T.
author list: Agent
  family name: Martins dos Santos
  given name: Vitor A.P.
author list: Agent
  family name: Rijkers
  given name: Ger T.
author list: Agent
  family name: Schaap
  given name: Peter J.
author list: Agent
  family name: de Vos
  given name: Willem M.
author list: Agent
  family name: Smidt
  given name: Hauke
doi: 10.7717/peerj.3698
volume: 5
issn: 2167-8359
publication name: PeerJ
publication date: 2017-09-11
copyright: ©2017 Gerritsen et al.
attribution name: Gerritsen et al.

Development and evaluation of rapid novel isothermal amplification assays for important veterinary pathogens: Chlamydia psittaci and Chlamydia pecorum
type: item
type: AcademicArticle
description: Background Chlamydia psittaci and Chlamydia pecorum are important veterinary pathogens, with the former also being responsible for zoonoses, and the latter adversely affecting koala populations in Australia and livestock globally. The rapid detection of these organisms is still challenging, particularly at the point-of-care (POC). In the present study, we developed and evaluated rapid, sensitive and robust C. psittaci-specific and C. pecorum-specific Loop Mediated Isothermal Amplification (LAMP) assays for detection of these pathogens. Methods and Materials The LAMP assays, performed in a Genie III real-time fluorometer, targeted a 263 bp region of the C. psittaci-specific Cps_0607 gene or a 209 bp region of a C. pecorum-specific conserved gene CpecG_0573, and were evaluated using a range of samples previously screened using species-specific quantitative PCRs (qPCRs). Species-specificity for C. psittaci and C. pecorum LAMP targets was tested against DNA samples from related chlamydial species and a range of other bacteria. In order to evaluate pathogen detection in clinical samples, C. psittaci LAMP was evaluated using a total of 26 DNA extracts from clinical samples from equine and avian hosts, while for C. pecorum LAMP, we tested a total of 63 DNA extracts from clinical samples from koala, sheep and cattle hosts. A subset of 36 C. pecorum samples was also tested in a thermal cycler (instead of a real-time fluorometer) using newly developed LAMP and results were determined as an end point detection. We also evaluated rapid swab processing (without DNA extraction) to assess the robustness of these assays. Results Both LAMP assays were demonstrated to species-specific, highly reproducible and to be able to detect as little as 10 genome copy number/reaction, with a mean amplification time of 14 and 24 min for C. psittaci and C. pecorum, respectively. When testing clinical samples, the overall congruence between the newly developed LAMP assays and qPCR was 92.3% for C.…
format: application/pdf
format: text/html
creator: Martina Jelocnik
creator: Md. Mominul Islam
creator: Danielle Madden
creator: Cheryl Jenkins
creator: James Branley
creator: Scott Carver
creator: Adam Polkinghorne
subject: Microbiology
subject: Veterinary Medicine
subject: Public Health
description: doi:10.7717/peerj.3799
publisher: PeerJ Inc.
rights: © 2017 Jelocnik et al.
abstract: Background Chlamydia psittaci and Chlamydia pecorum are important veterinary pathogens, with the former also being responsible for zoonoses, and the latter adversely affecting koala populations in Australia and livestock globally. The rapid detection of these organisms is still challenging, particularly at the point-of-care (POC). In the present study, we developed and evaluated rapid, sensitive and robust C. psittaci-specific and C. pecorum-specific Loop Mediated Isothermal Amplification (LAMP) assays for detection of these pathogens. Methods and Materials The LAMP assays, performed in a Genie III real-time fluorometer, targeted a 263 bp region of the C. psittaci-specific Cps_0607 gene or a 209 bp region of a C. pecorum-specific conserved gene CpecG_0573, and were evaluated using a range of samples previously screened using species-specific quantitative PCRs (qPCRs). Species-specificity for C. psittaci and C. pecorum LAMP targets was tested against DNA samples from related chlamydial species and a range of other bacteria. In order to evaluate pathogen detection in clinical samples, C. psittaci LAMP was evaluated using a total of 26 DNA extracts from clinical samples from equine and avian hosts, while for C. pecorum LAMP, we tested a total of 63 DNA extracts from clinical samples from koala, sheep and cattle hosts. A subset of 36 C. pecorum samples was also tested in a thermal cycler (instead of a real-time fluorometer) using newly developed LAMP and results were determined as an end point detection. We also evaluated rapid swab processing (without DNA extraction) to assess the robustness of these assays. Results Both LAMP assays were demonstrated to species-specific, highly reproducible and to be able to detect as little as 10 genome copy number/reaction, with a mean amplification time of 14 and 24 min for C. psittaci and C. pecorum, respectively. When testing clinical samples, the overall congruence between the newly developed LAMP assays and qPCR was 92.3% for C.…
bibliographic citation: Jelocnik et al. (2017) Development and evaluation of rapid novel isothermal amplification assays for important veterinary pathogens: Chlamydia psittaci and Chlamydia pecorum. PeerJ 5:e3799 https://doi.org/10.7717/peerj.3799
date submitted: 2017-07-20
date accepted: 2017-08-22
issued: 2017-09-08
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Jelocnik
  given name: Martina
author list: Agent
  family name: Islam
  given name: Md. Mominul
author list: Agent
  family name: Madden
  given name: Danielle
author list: Agent
  family name: Jenkins
  given name: Cheryl
author list: Agent
  family name: Branley
  given name: James
author list: Agent
  family name: Carver
  given name: Scott
author list: Agent
  family name: Polkinghorne
  given name: Adam
doi: 10.7717/peerj.3799
volume: 5
issn: 2167-8359
publication name: PeerJ
publication date: 2017-09-08
copyright: ©2017 Jelocnik et al.
attribution name: Jelocnik et al.

Variance component testing for identifying differentially expressed genes in RNA-seq data
type: item
type: AcademicArticle
description: RNA sequencing (RNA-Seq) enables the measurement and comparison of gene expression with isoform-level quantification. Differences in the effect of each isoform may make traditional methods, which aggregate isoforms, ineffective. Here, we introduce a variance component-based test that can jointly test multiple isoforms of one gene to identify differentially expressed (DE) genes, especially those with isoforms that have differential effects. We model isoform-level expression data from RNA-Seq using a negative binomial distribution and consider the baseline abundance of isoforms and their effects as two random terms. Our approach tests the global null hypothesis of no difference in any of the isoforms. The null distribution of the derived score statistic is investigated using empirical and theoretical methods. The results of simulations suggest that the performance of the proposed set test is superior to that of traditional algorithms and almost reaches optimal power when the variance of covariates is large. This method is also applied to analyze real data. Our algorithm, as a supplement to traditional algorithms, is superior at selecting DE genes with sparse or opposite effects for isoforms.
format: application/pdf
format: text/html
creator: Sheng Yang
creator: Fang Shao
creator: Weiwei Duan
creator: Yang Zhao
creator: Feng Chen
subject: Bioinformatics
subject: Statistics
description: doi:10.7717/peerj.3797
publisher: PeerJ Inc.
rights: © 2017 Yang et al.
abstract: RNA sequencing (RNA-Seq) enables the measurement and comparison of gene expression with isoform-level quantification. Differences in the effect of each isoform may make traditional methods, which aggregate isoforms, ineffective. Here, we introduce a variance component-based test that can jointly test multiple isoforms of one gene to identify differentially expressed (DE) genes, especially those with isoforms that have differential effects. We model isoform-level expression data from RNA-Seq using a negative binomial distribution and consider the baseline abundance of isoforms and their effects as two random terms. Our approach tests the global null hypothesis of no difference in any of the isoforms. The null distribution of the derived score statistic is investigated using empirical and theoretical methods. The results of simulations suggest that the performance of the proposed set test is superior to that of traditional algorithms and almost reaches optimal power when the variance of covariates is large. This method is also applied to analyze real data. Our algorithm, as a supplement to traditional algorithms, is superior at selecting DE genes with sparse or opposite effects for isoforms.
bibliographic citation: Yang et al. (2017) Variance component testing for identifying differentially expressed genes in RNA-seq data. PeerJ 5:e3797 https://doi.org/10.7717/peerj.3797
date submitted: 2017-04-13
date accepted: 2017-08-21
issued: 2017-09-08
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Yang
  given name: Sheng
author list: Agent
  family name: Shao
  given name: Fang
author list: Agent
  family name: Duan
  given name: Weiwei
author list: Agent
  family name: Zhao
  given name: Yang
author list: Agent
  family name: Chen
  given name: Feng
doi: 10.7717/peerj.3797
volume: 5
issn: 2167-8359
publication name: PeerJ
publication date: 2017-09-08
copyright: ©2017 Yang et al.
attribution name: Yang et al.

Age, growth, mortality and reproductive seasonality of jolthead porgy, Calamus bajonado, from Florida waters
type: item
type: AcademicArticle
description: Ages of jolthead porgy (Calamus bajonado Schneider 1801) (n = 635) from Florida commercial and recreational fisheries from 2008–2016 were determined using sectioned sagittal otoliths. We determined, using edge-type analysis, that opaque zones were annular, forming March–June (peaking in April). Jolthead porgy ranged from 1–13 years, and the largest fish measured 680 mm TL (total length, mm). Body size relationships for jolthead porgy were TL = 1.09FL + 20.44 (n = 622, r2 = 0.99), FL = 0.90 TL –14.26 (n = 622, r2 = 0.99), and W = 1.1 × 10−5 TL3.06 (n = 577), where W is total weight (grams, g) and FL is fork length (mm). The von Bertalanffy growth equation for jolthead porgy was Lt = 737(1 − e−0.14(t+2.02)) (n = 635). Point estimate of natural mortality was M = 0.32, while age-specific estimates of M ranged from 0.58–0.17 y−1 for ages 1–13. Catch curve analysis estimated the instantaneous rate of total mortality Z = 0.70, while instantaneous rate of fishing mortality F was 0.38. Macroscopic staging of female gonads indicated the presence of hydrated oocytes from December–March, and GSI data indicates that peak spawning in females occurs during March. This study presents the first published findings of life history parameters for jolthead porgy from the Atlantic waters off the southeastern United States.
format: application/pdf
format: text/html
creator: Michael L. Burton
creator: Jennifer C. Potts
creator: Jordan Page
creator: Ariel Poholek
subject: Aquaculture, Fisheries and Fish Science
subject: Environmental Sciences
subject: Marine Biology
subject: Natural Resource Management
description: doi:10.7717/peerj.3774
publisher: PeerJ Inc.
rights: © 2017 Burton et al.
abstract: Ages of jolthead porgy (Calamus bajonado Schneider 1801) (n = 635) from Florida commercial and recreational fisheries from 2008–2016 were determined using sectioned sagittal otoliths. We determined, using edge-type analysis, that opaque zones were annular, forming March–June (peaking in April). Jolthead porgy ranged from 1–13 years, and the largest fish measured 680 mm TL (total length, mm). Body size relationships for jolthead porgy were TL = 1.09FL + 20.44 (n = 622, r2 = 0.99), FL = 0.90 TL –14.26 (n = 622, r2 = 0.99), and W = 1.1 × 10−5 TL3.06 (n = 577), where W is total weight (grams, g) and FL is fork length (mm). The von Bertalanffy growth equation for jolthead porgy was Lt = 737(1 − e−0.14(t+2.02)) (n = 635). Point estimate of natural mortality was M = 0.32, while age-specific estimates of M ranged from 0.58–0.17 y−1 for ages 1–13. Catch curve analysis estimated the instantaneous rate of total mortality Z = 0.70, while instantaneous rate of fishing mortality F was 0.38. Macroscopic staging of female gonads indicated the presence of hydrated oocytes from December–March, and GSI data indicates that peak spawning in females occurs during March. This study presents the first published findings of life history parameters for jolthead porgy from the Atlantic waters off the southeastern United States.
bibliographic citation: Burton et al. (2017) Age, growth, mortality and reproductive seasonality of jolthead porgy, Calamus bajonado, from Florida waters. PeerJ 5:e3774 https://doi.org/10.7717/peerj.3774
date submitted: 2017-07-04
date accepted: 2017-08-16
issued: 2017-09-08
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Burton
  given name: Michael L.
author list: Agent
  family name: Potts
  given name: Jennifer C.
author list: Agent
  family name: Page
  given name: Jordan
author list: Agent
  family name: Poholek
  given name: Ariel
doi: 10.7717/peerj.3774
volume: 5
issn: 2167-8359
publication name: PeerJ
publication date: 2017-09-08
copyright: ©2017 Burton et al.
attribution name: Burton et al.

Current practice in the management of new-onset atrial fibrillation in critically ill patients: a UK-wide survey
type: item
type: AcademicArticle
description: Background New-onset atrial fibrillation (AF) is the most common arrhythmia in critically ill patients. Although evidence base and expert consensus opinion for management have been summarised in several international guidelines, no specific considerations for critically ill patients have been included. We aimed to establish current practice of management of critically ill patients with new-onset AF. Methods We designed a short user-friendly online questionnaire. All members of the Intensive Care Society were invited via email containing a link to the questionnaire, which comprised 21 questions. The online survey was conducted between November 2016 and December 2016. Results The response rate was 397/3152 (12.6%). The majority of respondents (81.1%) worked in mixed Intensive Care Units and were consultants (71.8%). Most respondents (39.5%) would start intervention on patients with fast new-onset AF and stable blood pressure at a heart rate between 120 and 139 beats/min. However, 34.8% of participants would treat all patients who developed new-onset fast AF. Amiodarone and beta-blockers (80.9% and 11.6% of answers) were the most commonly used anti-arrhythmics. A total of 63.8% of respondents do not regularly anti-coagulate critically ill patients with new-onset fast AF, while 30.8% anti-coagulate within 72 hours. A total of 68.0% of survey respondents do not routinely use stroke risk scores in critically ill patients with new-onset AF. A total of 85.4% of participants would consider taking part in a clinical trial investigating treatment of new-onset fast AF in the critically ill. Discussion Our results suggest a considerable disparity between contemporary practice of management of new-onset AF in critical illness and treatment recommendations for the general patient population suffering from AF, particularly with regard to anti-arrhythmics and anti-coagulation used. Amongst intensivists, there is a substantial interest in research for management of new-onset AF in cr…
format: application/pdf
format: text/html
creator: Chung Shen Chean
creator: Daniel McAuley
creator: Anthony Gordon
creator: Ingeborg Dorothea Welters
subject: Anesthesiology and Pain Management
subject: Cardiology
subject: Emergency and Critical Care
description: doi:10.7717/peerj.3716
publisher: PeerJ Inc.
rights: © 2017 Chean et al.
abstract: Background New-onset atrial fibrillation (AF) is the most common arrhythmia in critically ill patients. Although evidence base and expert consensus opinion for management have been summarised in several international guidelines, no specific considerations for critically ill patients have been included. We aimed to establish current practice of management of critically ill patients with new-onset AF. Methods We designed a short user-friendly online questionnaire. All members of the Intensive Care Society were invited via email containing a link to the questionnaire, which comprised 21 questions. The online survey was conducted between November 2016 and December 2016. Results The response rate was 397/3152 (12.6%). The majority of respondents (81.1%) worked in mixed Intensive Care Units and were consultants (71.8%). Most respondents (39.5%) would start intervention on patients with fast new-onset AF and stable blood pressure at a heart rate between 120 and 139 beats/min. However, 34.8% of participants would treat all patients who developed new-onset fast AF. Amiodarone and beta-blockers (80.9% and 11.6% of answers) were the most commonly used anti-arrhythmics. A total of 63.8% of respondents do not regularly anti-coagulate critically ill patients with new-onset fast AF, while 30.8% anti-coagulate within 72 hours. A total of 68.0% of survey respondents do not routinely use stroke risk scores in critically ill patients with new-onset AF. A total of 85.4% of participants would consider taking part in a clinical trial investigating treatment of new-onset fast AF in the critically ill. Discussion Our results suggest a considerable disparity between contemporary practice of management of new-onset AF in critical illness and treatment recommendations for the general patient population suffering from AF, particularly with regard to anti-arrhythmics and anti-coagulation used. Amongst intensivists, there is a substantial interest in research for management of new-onset AF in cr…
bibliographic citation: Chean et al. (2017) Current practice in the management of new-onset atrial fibrillation in critically ill patients: a UK-wide survey. PeerJ 5:e3716 https://doi.org/10.7717/peerj.3716
date submitted: 2017-05-29
date accepted: 2017-07-29
issued: 2017-09-08
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Chean
  given name: Chung Shen
author list: Agent
  family name: McAuley
  given name: Daniel
author list: Agent
  family name: Gordon
  given name: Anthony
author list: Agent
  family name: Welters
  given name: Ingeborg Dorothea
doi: 10.7717/peerj.3716
volume: 5
issn: 2167-8359
publication name: PeerJ
publication date: 2017-09-08
copyright: ©2017 Chean et al.
attribution name: Chean et al.

Early-branching euteleost relationships: areas of congruence between concatenation and coalescent model inferences
type: item
type: AcademicArticle
description: Phylogenetic inference based on evidence from DNA sequences has led to significant strides in the development of a stable and robustly supported framework for the vertebrate tree of life. To date, the bulk of those advances have relied on sequence data from a small number of genome regions that have proven unable to produce satisfactory answers to consistently recalcitrant phylogenetic questions. Here, we re-examine phylogenetic relationships among early-branching euteleostean fish lineages classically grouped in the Protacanthopterygii using DNA sequence data surrounding ultraconserved elements. We report and examine a dataset of thirty-four OTUs with 17,957 aligned characters from fifty-three nuclear loci. Phylogenetic analysis is conducted in concatenated, joint gene trees and species tree estimation and summary coalescent frameworks. All analytical frameworks yield supporting evidence for existing hypotheses of relationship for the placement of Lepidogalaxias salamandroides, monophyly of the Stomiatii and the presence of an esociform + salmonid clade. Lepidogalaxias salamandroides and the Esociformes + Salmoniformes are successive sister lineages to all other euteleosts in the majority of analyses. The concatenated and joint gene trees and species tree analysis types produce high support values for this arrangement. However, inter-relationships of Argentiniformes, Stomiatii and Neoteleostei remain uncertain as they varied by analysis type while receiving strong and contradictory indices of support. Topological differences between analysis types are also apparent within the otomorph and the percomorph taxa in the data set. Our results identify concordant areas with strong support for relationships within and between early-branching euteleost lineages but they also reveal limitations in the ability of larger datasets to conclusively resolve other aspects of that phylogeny.
format: application/pdf
format: text/html
creator: Matthew A. Campbell
creator: Michael E. Alfaro
creator: Max Belasco
creator: J. Andrés López
subject: Aquaculture, Fisheries and Fish Science
subject: Evolutionary Studies
subject: Zoology
description: doi:10.7717/peerj.3548
publisher: PeerJ Inc.
rights: © 2017 Campbell et al.
abstract: Phylogenetic inference based on evidence from DNA sequences has led to significant strides in the development of a stable and robustly supported framework for the vertebrate tree of life. To date, the bulk of those advances have relied on sequence data from a small number of genome regions that have proven unable to produce satisfactory answers to consistently recalcitrant phylogenetic questions. Here, we re-examine phylogenetic relationships among early-branching euteleostean fish lineages classically grouped in the Protacanthopterygii using DNA sequence data surrounding ultraconserved elements. We report and examine a dataset of thirty-four OTUs with 17,957 aligned characters from fifty-three nuclear loci. Phylogenetic analysis is conducted in concatenated, joint gene trees and species tree estimation and summary coalescent frameworks. All analytical frameworks yield supporting evidence for existing hypotheses of relationship for the placement of Lepidogalaxias salamandroides, monophyly of the Stomiatii and the presence of an esociform + salmonid clade. Lepidogalaxias salamandroides and the Esociformes + Salmoniformes are successive sister lineages to all other euteleosts in the majority of analyses. The concatenated and joint gene trees and species tree analysis types produce high support values for this arrangement. However, inter-relationships of Argentiniformes, Stomiatii and Neoteleostei remain uncertain as they varied by analysis type while receiving strong and contradictory indices of support. Topological differences between analysis types are also apparent within the otomorph and the percomorph taxa in the data set. Our results identify concordant areas with strong support for relationships within and between early-branching euteleost lineages but they also reveal limitations in the ability of larger datasets to conclusively resolve other aspects of that phylogeny.
bibliographic citation: Campbell et al. (2017) Early-branching euteleost relationships: areas of congruence between concatenation and coalescent model inferences. PeerJ 5:e3548 https://doi.org/10.7717/peerj.3548
date submitted: 2017-03-31
date accepted: 2017-06-15
issued: 2017-09-08
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Campbell
  given name: Matthew A.
author list: Agent
  family name: Alfaro
  given name: Michael E.
author list: Agent
  family name: Belasco
  given name: Max
author list: Agent
  family name: López
  given name: J. Andrés
doi: 10.7717/peerj.3548
volume: 5
issn: 2167-8359
publication name: PeerJ
publication date: 2017-09-08
copyright: ©2017 Campbell et al.
attribution name: Campbell et al.

A comparison of the morphological and biochemical characteristics of Chlorella sorokiniana and Chlorella zofingiensis cultured under photoautotrophic and mixotrophic conditions
type: item
type: AcademicArticle
description: The responses of two species of microalgae, Chlorella sorokiniana and Chlorella zofingiensis, were compared regarding their morphological and biochemical properties under photoautotrophic and mixotrophic conditions. These microalgae were cultured under both conditions, and their crude ethanolic extracts were examined for their pigment and total phenolic contents. In addition, the microalgae’s antioxidant activities were determined using a DPPH radical scavenging assay and a ferric reducing antioxidant power (FRAP) assay. Both strains showed increases in cell size due to the accumulation of lipid bodies and other cell contents, especially carotenoids, under the mixotrophic condition. Notably, reductions in phenolic and chlorophyll contents were observed to be associated with lower antioxidant activity. C. zofingiensis compared with C. sorokiniana, demonstrated higher antioxidant activity and carotenoid content. This study showed that different species of microalgae responded differently to varying conditions by producing different types of metabolites, as evidenced by the production of higher levels of phenolic compounds under the photoautotrophic condition and the production of the same levels of carotenoids under both photoautotrophic and mixotrophic conditions.
format: application/pdf
format: text/html
creator: Siti Nor Ani Azaman
creator: Norio Nagao
creator: Fatimah M. Yusoff
creator: Sheau Wei Tan
creator: Swee Keong Yeap
subject: Aquaculture, Fisheries and Fish Science
subject: Freshwater Biology
subject: Natural Resource Management
description: doi:10.7717/peerj.3473
publisher: PeerJ Inc.
rights: © 2017 Azaman et al.
abstract: The responses of two species of microalgae, Chlorella sorokiniana and Chlorella zofingiensis, were compared regarding their morphological and biochemical properties under photoautotrophic and mixotrophic conditions. These microalgae were cultured under both conditions, and their crude ethanolic extracts were examined for their pigment and total phenolic contents. In addition, the microalgae’s antioxidant activities were determined using a DPPH radical scavenging assay and a ferric reducing antioxidant power (FRAP) assay. Both strains showed increases in cell size due to the accumulation of lipid bodies and other cell contents, especially carotenoids, under the mixotrophic condition. Notably, reductions in phenolic and chlorophyll contents were observed to be associated with lower antioxidant activity. C. zofingiensis compared with C. sorokiniana, demonstrated higher antioxidant activity and carotenoid content. This study showed that different species of microalgae responded differently to varying conditions by producing different types of metabolites, as evidenced by the production of higher levels of phenolic compounds under the photoautotrophic condition and the production of the same levels of carotenoids under both photoautotrophic and mixotrophic conditions.
bibliographic citation: Azaman et al. (2017) A comparison of the morphological and biochemical characteristics of Chlorella sorokiniana and Chlorella zofingiensis cultured under photoautotrophic and mixotrophic conditions. PeerJ 5:e3473 https://doi.org/10.7717/peerj.3473
date submitted: 2016-04-21
date accepted: 2017-05-27
issued: 2017-09-08
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Azaman
  given name: Siti Nor Ani
author list: Agent
  family name: Nagao
  given name: Norio
author list: Agent
  family name: Yusoff
  given name: Fatimah M.
author list: Agent
  family name: Tan
  given name: Sheau Wei
author list: Agent
  family name: Yeap
  given name: Swee Keong
doi: 10.7717/peerj.3473
volume: 5
issn: 2167-8359
publication name: PeerJ
publication date: 2017-09-08
copyright: ©2017 Azaman et al.
attribution name: Azaman et al.

MetaCRAST: reference-guided extraction of CRISPR spacers from unassembled metagenomes
type: item
type: AcademicArticle
description: Clustered regularly interspaced short palindromic repeat (CRISPR) systems are the adaptive immune systems of bacteria and archaea against viral infection. While CRISPRs have been exploited as a tool for genetic engineering, their spacer sequences can also provide valuable insights into microbial ecology by linking environmental viruses to their microbial hosts. Despite this importance, metagenomic CRISPR detection remains a major challenge. Here we present a reference-guided CRISPR spacer detection tool (Metagenomic CRISPR Reference-Aided Search Tool—MetaCRAST) that constrains searches based on user-specified direct repeats (DRs). These DRs could be expected from assembly or taxonomic profiles of metagenomes. We compared the performance of MetaCRAST to those of two existing metagenomic CRISPR detection tools—Crass and MinCED—using both real and simulated acid mine drainage (AMD) and enhanced biological phosphorus removal (EBPR) metagenomes. Our evaluation shows MetaCRAST improves CRISPR spacer detection in real metagenomes compared to the de novo CRISPR detection methods Crass and MinCED. Evaluation on simulated metagenomes show it performs better than de novo tools for Illumina metagenomes and comparably for 454 metagenomes. It also has comparable performance dependence on read length and community composition, run time, and accuracy to these tools. MetaCRAST is implemented in Perl, parallelizable through the Many Core Engine (MCE), and takes metagenomic sequence reads and direct repeat queries (FASTA or FASTQ) as input. It is freely available for download at https://github.com/molleraj/MetaCRAST.
format: application/pdf
format: text/html
creator: Abraham G. Moller
creator: Chun Liang
subject: Bioinformatics
subject: Computational Biology
subject: Ecology
subject: Genomics
subject: Microbiology
description: doi:10.7717/peerj.3788
publisher: PeerJ Inc.
rights: © 2017 Moller and Liang
abstract: Clustered regularly interspaced short palindromic repeat (CRISPR) systems are the adaptive immune systems of bacteria and archaea against viral infection. While CRISPRs have been exploited as a tool for genetic engineering, their spacer sequences can also provide valuable insights into microbial ecology by linking environmental viruses to their microbial hosts. Despite this importance, metagenomic CRISPR detection remains a major challenge. Here we present a reference-guided CRISPR spacer detection tool (Metagenomic CRISPR Reference-Aided Search Tool—MetaCRAST) that constrains searches based on user-specified direct repeats (DRs). These DRs could be expected from assembly or taxonomic profiles of metagenomes. We compared the performance of MetaCRAST to those of two existing metagenomic CRISPR detection tools—Crass and MinCED—using both real and simulated acid mine drainage (AMD) and enhanced biological phosphorus removal (EBPR) metagenomes. Our evaluation shows MetaCRAST improves CRISPR spacer detection in real metagenomes compared to the de novo CRISPR detection methods Crass and MinCED. Evaluation on simulated metagenomes show it performs better than de novo tools for Illumina metagenomes and comparably for 454 metagenomes. It also has comparable performance dependence on read length and community composition, run time, and accuracy to these tools. MetaCRAST is implemented in Perl, parallelizable through the Many Core Engine (MCE), and takes metagenomic sequence reads and direct repeat queries (FASTA or FASTQ) as input. It is freely available for download at https://github.com/molleraj/MetaCRAST.
bibliographic citation: Moller et al. (2017) MetaCRAST: reference-guided extraction of CRISPR spacers from unassembled metagenomes. PeerJ 5:e3788 https://doi.org/10.7717/peerj.3788
date submitted: 2017-01-26
date accepted: 2017-08-18
issued: 2017-09-07
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Moller
  given name: Abraham G.
author list: Agent
  family name: Liang
  given name: Chun
doi: 10.7717/peerj.3788
volume: 5
issn: 2167-8359
publication name: PeerJ
publication date: 2017-09-07
copyright: ©2017 Moller and Liang
attribution name: Moller and Liang

Lectins: an effective tool for screening of potential cancer biomarkers
type: item
type: AcademicArticle
description: In recent years, the use of lectins for screening of potential biomarkers has gained increased importance in cancer research, given the development in glycobiology that highlights altered structural changes of glycans in cancer associated processes. Lectins, having the properties of recognizing specific carbohydrate moieties of glycoconjugates, have become an effective tool for detection of new cancer biomarkers in complex bodily fluids and tissues. The specificity of lectins provides an added advantage of selecting peptides that are differently glycosylated and aberrantly expressed in cancer patients, many of which are not possibly detected using conventional methods because of their low abundance in bodily fluids. When coupled with mass spectrometry, research utilizing lectins, which are mainly from plants and fungi, has led to identification of numerous potential cancer biomarkers that may be used in the future. This article reviews lectin-based methods that are commonly adopted in cancer biomarker discovery research.
format: application/pdf
format: text/html
creator: Onn Haji Hashim
creator: Jaime Jacqueline Jayapalan
creator: Cheng-Siang Lee
subject: Biochemistry
subject: Biotechnology
subject: Oncology
description: doi:10.7717/peerj.3784
publisher: PeerJ Inc.
rights: © 2017 Hashim et al.
abstract: In recent years, the use of lectins for screening of potential biomarkers has gained increased importance in cancer research, given the development in glycobiology that highlights altered structural changes of glycans in cancer associated processes. Lectins, having the properties of recognizing specific carbohydrate moieties of glycoconjugates, have become an effective tool for detection of new cancer biomarkers in complex bodily fluids and tissues. The specificity of lectins provides an added advantage of selecting peptides that are differently glycosylated and aberrantly expressed in cancer patients, many of which are not possibly detected using conventional methods because of their low abundance in bodily fluids. When coupled with mass spectrometry, research utilizing lectins, which are mainly from plants and fungi, has led to identification of numerous potential cancer biomarkers that may be used in the future. This article reviews lectin-based methods that are commonly adopted in cancer biomarker discovery research.
bibliographic citation: Hashim et al. (2017) Lectins: an effective tool for screening of potential cancer biomarkers. PeerJ 5:e3784 https://doi.org/10.7717/peerj.3784
date submitted: 2017-06-19
date accepted: 2017-08-18
issued: 2017-09-07
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Hashim
  given name: Onn Haji
author list: Agent
  family name: Jayapalan
  given name: Jaime Jacqueline
author list: Agent
  family name: Lee
  given name: Cheng-Siang
doi: 10.7717/peerj.3784
volume: 5
issn: 2167-8359
publication name: PeerJ
publication date: 2017-09-07
copyright: ©2017 Hashim et al.
attribution name: Hashim et al.

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