PeerJ
type: channel
link: https://peerj.com/articles/
description: Articles published in PeerJ
publisher: PeerJ Inc.
publication name: PeerJ
issn: 2167-8359
items: Genomic characterization of a new endophytic Streptomyces kebangsaanensis identifies biosynthetic pathway gene clusters for novel phenazine antibiotic production
items: Geological duration of ammonoids controlled their geographical range of fossil distribution
items: Denitrifying metabolism of the methylotrophic marine bacterium Methylophaga nitratireducenticrescens strain JAM1
items: The presence of genes encoding enzymes that digest carbohydrates in coral genomes and analysis of their activities
items: Evaluation of potential reference genes for real-time qPCR analysis in a biparental beetle, Lethrus apterus (Coleoptera: Geotrupidae)
items: Phylogeographic and population insights of the Asian common toad (Bufo gargarizans) in Korea and China: population isolation and expansions as response to the ice ages
items: Impacts of diarrhea on the immune system, intestinal environment, and expression of PGRPs in New Zealand rabbits
items: Diagnostic value of serum procalcitonin, lactate, and high-sensitivity C-reactive protein for predicting bacteremia in adult patients in the emergency department
items: The zebrafish as a model system for analyzing mammalian and native α-crystallin promoter function
items: The relationship between egg size and helper number in cooperative breeders: a meta-analysis across species

Genomic characterization of a new endophytic Streptomyces kebangsaanensis identifies biosynthetic pathway gene clusters for novel phenazine antibiotic production
type: item
type: AcademicArticle
description: Background Streptomyces are well known for their capability to produce many bioactive secondary metabolites with medical and industrial importance. Here we report a novel bioactive phenazine compound, 6-((2-hydroxy-4-methoxyphenoxy) carbonyl) phenazine-1-carboxylic acid (HCPCA) extracted from Streptomyces kebangsaanensis, an endophyte isolated from the ethnomedicinal Portulaca oleracea. Methods The HCPCA chemical structure was determined using nuclear magnetic resonance spectroscopy. We conducted whole genome sequencing for the identification of the gene cluster(s) believed to be responsible for phenazine biosynthesis in order to map its corresponding pathway, in addition to bioinformatics analysis to assess the potential of S. kebangsaanensis in producing other useful secondary metabolites. Results The S. kebangsaanensis genome comprises an 8,328,719 bp linear chromosome with high GC content (71.35%) consisting of 12 rRNA operons, 81 tRNA, and 7,558 protein coding genes. We identified 24 gene clusters involved in polyketide, nonribosomal peptide, terpene, bacteriocin, and siderophore biosynthesis, as well as a gene cluster predicted to be responsible for phenazine biosynthesis. Discussion The HCPCA phenazine structure was hypothesized to derive from the combination of two biosynthetic pathways, phenazine-1,6-dicarboxylic acid and 4-methoxybenzene-1,2-diol, originated from the shikimic acid pathway. The identification of a biosynthesis pathway gene cluster for phenazine antibiotics might facilitate future genetic engineering design of new synthetic phenazine antibiotics. Additionally, these findings confirm the potential of S. kebangsaanensis for producing various antibiotics and secondary metabolites.
format: application/pdf
format: text/html
creator: Juwairiah Remali
creator: Nurul ‘Izzah Mohd Sarmin
creator: Chyan Leong Ng
creator: John J.L. Tiong
creator: Wan M. Aizat
creator: Loke Kok Keong
creator: Noraziah Mohamad Zin
subject: Bioinformatics
subject: Biotechnology
subject: Genomics
subject: Drugs and Devices
description: doi:10.7717/peerj.3738
publisher: PeerJ Inc.
rights: © 2017 Remali et al.
abstract: Background Streptomyces are well known for their capability to produce many bioactive secondary metabolites with medical and industrial importance. Here we report a novel bioactive phenazine compound, 6-((2-hydroxy-4-methoxyphenoxy) carbonyl) phenazine-1-carboxylic acid (HCPCA) extracted from Streptomyces kebangsaanensis, an endophyte isolated from the ethnomedicinal Portulaca oleracea. Methods The HCPCA chemical structure was determined using nuclear magnetic resonance spectroscopy. We conducted whole genome sequencing for the identification of the gene cluster(s) believed to be responsible for phenazine biosynthesis in order to map its corresponding pathway, in addition to bioinformatics analysis to assess the potential of S. kebangsaanensis in producing other useful secondary metabolites. Results The S. kebangsaanensis genome comprises an 8,328,719 bp linear chromosome with high GC content (71.35%) consisting of 12 rRNA operons, 81 tRNA, and 7,558 protein coding genes. We identified 24 gene clusters involved in polyketide, nonribosomal peptide, terpene, bacteriocin, and siderophore biosynthesis, as well as a gene cluster predicted to be responsible for phenazine biosynthesis. Discussion The HCPCA phenazine structure was hypothesized to derive from the combination of two biosynthetic pathways, phenazine-1,6-dicarboxylic acid and 4-methoxybenzene-1,2-diol, originated from the shikimic acid pathway. The identification of a biosynthesis pathway gene cluster for phenazine antibiotics might facilitate future genetic engineering design of new synthetic phenazine antibiotics. Additionally, these findings confirm the potential of S. kebangsaanensis for producing various antibiotics and secondary metabolites.
bibliographic citation: Remali et al. (2017) Genomic characterization of a new endophytic Streptomyces kebangsaanensis identifies biosynthetic pathway gene clusters for novel phenazine antibiotic production. PeerJ 5:e3738 https://doi.org/10.7717/peerj.3738
date submitted: 2017-05-08
date accepted: 2017-08-04
issued: 2017-11-29
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Remali
  given name: Juwairiah
author list: Agent
  family name: Sarmin
  given name: Nurul ‘Izzah Mohd
author list: Agent
  family name: Ng
  given name: Chyan Leong
author list: Agent
  family name: Tiong
  given name: John J.L.
author list: Agent
  family name: Aizat
  given name: Wan M.
author list: Agent
  family name: Keong
  given name: Loke Kok
author list: Agent
  family name: Zin
  given name: Noraziah Mohamad
doi: 10.7717/peerj.3738
volume: 5
issn: 2167-8359
publication name: PeerJ
publication date: 2017-11-29
copyright: ©2017 Remali et al.
attribution name: Remali et al.

Geological duration of ammonoids controlled their geographical range of fossil distribution
type: item
type: AcademicArticle
description: The latitudinal distributions in Devonian–Cretaceous ammonoids were analyzed at the genus level, and were compared with the hatchling sizes (i.e., ammonitella diameters) and the geological durations. The results show that (1) length of temporal ranges of ammonoids effected broader ranges of fossil distribution and paleobiogeography of ammonoids, and (2) the hatchling size was not related to the geographical range of fossil distribution of ammonoids. Reducing the influence of geological duration in this analysis implies that hatchling size was one of the controlling factors that determined the distribution of ammonoid habitats at any given period in time: ammonoids with smaller hatchling sizes tended to have broader ammonoid habitat ranges. These relationships were somewhat blurred in the Devonian, Carboniferous, Triassic, and Jurassic, which is possibly due to (1) the course of development of a reproductive strategy with smaller hatchling sizes in the Devonian and (2) the high origination rates after the mass extinction events.
format: application/pdf
format: text/html
creator: Ryoji Wani
subject: Evolutionary Studies
subject: Marine Biology
subject: Paleontology
subject: Zoology
description: doi:10.7717/peerj.4108
publisher: PeerJ Inc.
rights: © 2017 Wani
abstract: The latitudinal distributions in Devonian–Cretaceous ammonoids were analyzed at the genus level, and were compared with the hatchling sizes (i.e., ammonitella diameters) and the geological durations. The results show that (1) length of temporal ranges of ammonoids effected broader ranges of fossil distribution and paleobiogeography of ammonoids, and (2) the hatchling size was not related to the geographical range of fossil distribution of ammonoids. Reducing the influence of geological duration in this analysis implies that hatchling size was one of the controlling factors that determined the distribution of ammonoid habitats at any given period in time: ammonoids with smaller hatchling sizes tended to have broader ammonoid habitat ranges. These relationships were somewhat blurred in the Devonian, Carboniferous, Triassic, and Jurassic, which is possibly due to (1) the course of development of a reproductive strategy with smaller hatchling sizes in the Devonian and (2) the high origination rates after the mass extinction events.
bibliographic citation: Wani (2017) Geological duration of ammonoids controlled their geographical range of fossil distribution. PeerJ 5:e4108 https://doi.org/10.7717/peerj.4108
date submitted: 2017-08-22
date accepted: 2017-11-08
issued: 2017-11-28
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Wani
  given name: Ryoji
doi: 10.7717/peerj.4108
volume: 5
issn: 2167-8359
publication name: PeerJ
publication date: 2017-11-28
copyright: ©2017 Wani
attribution name: Wani

Denitrifying metabolism of the methylotrophic marine bacterium Methylophaga nitratireducenticrescens strain JAM1
type: item
type: AcademicArticle
description: Background Methylophaga nitratireducenticrescens strain JAM1 is a methylotrophic, marine bacterium that was isolated from a denitrification reactor treating a closed-circuit seawater aquarium. It can sustain growth under anoxic conditions by reducing nitrate ( ${\mathrm{NO}}_{3}^{-}$ NO 3 − ) to nitrite ( ${\mathrm{NO}}_{2}^{-}$ NO 2 − ). These physiological traits are attributed to gene clusters that encode two dissimilatory nitrate reductases (Nar). Strain JAM1 also contains gene clusters encoding two nitric oxide (NO) reductases and one nitrous oxide (N2O) reductase, suggesting that NO and N2O can be reduced by strain JAM1. Here we characterized further the denitrifying activities of M. nitratireducenticrescens JAM1. Methods Series of oxic and anoxic cultures of strain JAM1 were performed with N2O, ${\mathrm{NO}}_{3}^{-}$ NO 3 − or sodium nitroprusside, and growth and N2O, ${\mathrm{NO}}_{3}^{-}$ NO 3 − , ${\mathrm{NO}}_{2}^{-}$ NO 2 − and N2 concentrations were measured. Ammonium ( ${\mathrm{NH}}_{4}^{+}$ NH 4 + )-free cultures were also tested to assess the dynamics of N2O, ${\mathrm{NO}}_{3}^{-}$ NO 3 − and ${\mathrm{NO}}_{2}^{-}$ NO 2 − . Isotopic labeling of N2O was performed in 15NH4+-amended cultures. Cultures with the JAM1ΔnarG1narG2 double mutant were performed to assess the involvement of the Nar systems on N2O production. Finally, RT-qPCR was used to measure the gene expression levels of the denitrification genes cytochrome bc-type nitric oxide reductase (cnorB1 and cnorB2) and nitrous oxide reductase (nosZ), and also nnrS and norR that encode NO-sensitive regulators. Results Strain JAM1 can reduce NO to N2O and N2O to N2 and can sustain growth under anoxic conditions by reducing N2O as the sole electron acceptor. Although strain JAM1 lacks a gene encoding a dissimilatory ${\mathrm{NO}}_{2}^{-}$ NO 2 − reductase, ${\mathrm{NO}}_{3}^{-}$ NO 3 − -amended cultures produce N2O, representing up to 6% of the N-input. ${\mathrm{NO}}_{2}^{-}$ NO 2 − was shown …
format: application/pdf
format: text/html
creator: Florian Mauffrey
creator: Alexandra Cucaita
creator: Philippe Constant
creator: Richard Villemur
subject: Environmental Sciences
subject: Microbiology
subject: Molecular Biology
subject: Biogeochemistry
description: doi:10.7717/peerj.4098
publisher: PeerJ Inc.
rights: © 2017 Mauffrey et al.
abstract: Background Methylophaga nitratireducenticrescens strain JAM1 is a methylotrophic, marine bacterium that was isolated from a denitrification reactor treating a closed-circuit seawater aquarium. It can sustain growth under anoxic conditions by reducing nitrate ( ${\mathrm{NO}}_{3}^{-}$ NO 3 − ) to nitrite ( ${\mathrm{NO}}_{2}^{-}$ NO 2 − ). These physiological traits are attributed to gene clusters that encode two dissimilatory nitrate reductases (Nar). Strain JAM1 also contains gene clusters encoding two nitric oxide (NO) reductases and one nitrous oxide (N2O) reductase, suggesting that NO and N2O can be reduced by strain JAM1. Here we characterized further the denitrifying activities of M. nitratireducenticrescens JAM1. Methods Series of oxic and anoxic cultures of strain JAM1 were performed with N2O, ${\mathrm{NO}}_{3}^{-}$ NO 3 − or sodium nitroprusside, and growth and N2O, ${\mathrm{NO}}_{3}^{-}$ NO 3 − , ${\mathrm{NO}}_{2}^{-}$ NO 2 − and N2 concentrations were measured. Ammonium ( ${\mathrm{NH}}_{4}^{+}$ NH 4 + )-free cultures were also tested to assess the dynamics of N2O, ${\mathrm{NO}}_{3}^{-}$ NO 3 − and ${\mathrm{NO}}_{2}^{-}$ NO 2 − . Isotopic labeling of N2O was performed in 15NH4+-amended cultures. Cultures with the JAM1ΔnarG1narG2 double mutant were performed to assess the involvement of the Nar systems on N2O production. Finally, RT-qPCR was used to measure the gene expression levels of the denitrification genes cytochrome bc-type nitric oxide reductase (cnorB1 and cnorB2) and nitrous oxide reductase (nosZ), and also nnrS and norR that encode NO-sensitive regulators. Results Strain JAM1 can reduce NO to N2O and N2O to N2 and can sustain growth under anoxic conditions by reducing N2O as the sole electron acceptor. Although strain JAM1 lacks a gene encoding a dissimilatory ${\mathrm{NO}}_{2}^{-}$ NO 2 − reductase, ${\mathrm{NO}}_{3}^{-}$ NO 3 − -amended cultures produce N2O, representing up to 6% of the N-input. ${\mathrm{NO}}_{2}^{-}$ NO 2 − was shown …
bibliographic citation: Mauffrey et al. (2017) Denitrifying metabolism of the methylotrophic marine bacterium Methylophaga nitratireducenticrescens strain JAM1. PeerJ 5:e4098 https://doi.org/10.7717/peerj.4098
date submitted: 2017-09-15
date accepted: 2017-11-06
issued: 2017-11-28
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Mauffrey
  given name: Florian
author list: Agent
  family name: Cucaita
  given name: Alexandra
author list: Agent
  family name: Constant
  given name: Philippe
author list: Agent
  family name: Villemur
  given name: Richard
doi: 10.7717/peerj.4098
volume: 5
issn: 2167-8359
publication name: PeerJ
publication date: 2017-11-28
copyright: ©2017 Mauffrey et al.
attribution name: Mauffrey et al.

The presence of genes encoding enzymes that digest carbohydrates in coral genomes and analysis of their activities
type: item
type: AcademicArticle
description: Numerous enzymes that digest carbohydrates, such as cellulases and chitinases, are present in various organisms (e.g., termites, nematodes, and so on). Recently, the presence of cellulases and chitinases has been reported in marine organisms such as urchin and bivalves, and their several roles in marine ecosystems have been proposed. In this study, we reported the presence of genes predicted to encode proteins similar to cellulases and chitinases in the genome of the coral Acropora digitifera, their gene expression patterns at various life stages, and cellulose- and chitin-degrading enzyme activities in several coral species (A. digitifera, Galaxea fascicularis, Goniastrea aspera, Montipora digitata, Pavona divaricata, Pocillopora damicornis, and Porites australiensis). Our gene expression analysis demonstrated the expressions of these cellulase- and chitinase-like genes during various life stages, including unfertilized eggs, fertilized eggs, zygotes, planula larvae, primary polyps and adults of A. digitifera. Agar plate assays confirmed cellulase and chitinase activities in the tissues extracted from adult branches of several coral species. These results suggested that corals are able to utilize cellulases and chitinases in their life histories.
format: application/pdf
format: text/html
creator: Yuki Yoshioka
creator: Toshiaki Tanabe
creator: Akira Iguchi
subject: Marine Biology
description: doi:10.7717/peerj.4087
publisher: PeerJ Inc.
rights: © 2017 Yoshioka et al.
abstract: Numerous enzymes that digest carbohydrates, such as cellulases and chitinases, are present in various organisms (e.g., termites, nematodes, and so on). Recently, the presence of cellulases and chitinases has been reported in marine organisms such as urchin and bivalves, and their several roles in marine ecosystems have been proposed. In this study, we reported the presence of genes predicted to encode proteins similar to cellulases and chitinases in the genome of the coral Acropora digitifera, their gene expression patterns at various life stages, and cellulose- and chitin-degrading enzyme activities in several coral species (A. digitifera, Galaxea fascicularis, Goniastrea aspera, Montipora digitata, Pavona divaricata, Pocillopora damicornis, and Porites australiensis). Our gene expression analysis demonstrated the expressions of these cellulase- and chitinase-like genes during various life stages, including unfertilized eggs, fertilized eggs, zygotes, planula larvae, primary polyps and adults of A. digitifera. Agar plate assays confirmed cellulase and chitinase activities in the tissues extracted from adult branches of several coral species. These results suggested that corals are able to utilize cellulases and chitinases in their life histories.
bibliographic citation: Yoshioka et al. (2017) The presence of genes encoding enzymes that digest carbohydrates in coral genomes and analysis of their activities. PeerJ 5:e4087 https://doi.org/10.7717/peerj.4087
date submitted: 2017-06-20
date accepted: 2017-11-02
issued: 2017-11-28
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Yoshioka
  given name: Yuki
author list: Agent
  family name: Tanabe
  given name: Toshiaki
author list: Agent
  family name: Iguchi
  given name: Akira
doi: 10.7717/peerj.4087
volume: 5
issn: 2167-8359
publication name: PeerJ
publication date: 2017-11-28
copyright: ©2017 Yoshioka et al.
attribution name: Yoshioka et al.

Evaluation of potential reference genes for real-time qPCR analysis in a biparental beetle, Lethrus apterus (Coleoptera: Geotrupidae)
type: item
type: AcademicArticle
description: Hormones play an important role in the regulation of physiological, developmental and behavioural processes. Many of these mechanisms in insects, however, are still not well understood. One way to investigate hormonal regulation is to analyse gene expression patterns of hormones and their receptors by real-time quantitative polymerase chain reaction (RT-qPCR). This method, however, requires stably expressed reference genes for normalisation. In the present study, we evaluated 11 candidate housekeeping genes as reference genes in samples of Lethrus apterus, an earth-boring beetle with biparental care, collected from a natural population. For identifying the most stable genes we used the following computational methods: geNorm, NormFinder, BestKeeper, comparative delta Ct method and RefFinder. Based on our results, the two body regions sampled (head and thorax) differ in which genes are most stably expressed. We identified two candidate reference genes for each region investigated: ribosomal protein L7A and RP18 in samples extracted from the head, and ribosomal protein L7A and RP4 extracted from the muscles of the thorax. Additionally, L7A and RP18 appear to be the best reference genes for normalisation in all samples irrespective of body region. These reference genes can be used to study the hormonal regulation of reproduction and parental care in Lethrus apterus in the future.
format: application/pdf
format: text/html
creator: Nikoletta A. Nagy
creator: Zoltán Németh
creator: Edit Juhász
creator: Szilárd Póliska
creator: Rita Rácz
creator: András Kosztolányi
creator: Zoltán Barta
subject: Entomology
subject: Genetics
subject: Molecular Biology
description: doi:10.7717/peerj.4047
publisher: PeerJ Inc.
rights: © 2017 Nagy et al.
abstract: Hormones play an important role in the regulation of physiological, developmental and behavioural processes. Many of these mechanisms in insects, however, are still not well understood. One way to investigate hormonal regulation is to analyse gene expression patterns of hormones and their receptors by real-time quantitative polymerase chain reaction (RT-qPCR). This method, however, requires stably expressed reference genes for normalisation. In the present study, we evaluated 11 candidate housekeeping genes as reference genes in samples of Lethrus apterus, an earth-boring beetle with biparental care, collected from a natural population. For identifying the most stable genes we used the following computational methods: geNorm, NormFinder, BestKeeper, comparative delta Ct method and RefFinder. Based on our results, the two body regions sampled (head and thorax) differ in which genes are most stably expressed. We identified two candidate reference genes for each region investigated: ribosomal protein L7A and RP18 in samples extracted from the head, and ribosomal protein L7A and RP4 extracted from the muscles of the thorax. Additionally, L7A and RP18 appear to be the best reference genes for normalisation in all samples irrespective of body region. These reference genes can be used to study the hormonal regulation of reproduction and parental care in Lethrus apterus in the future.
bibliographic citation: Nagy et al. (2017) Evaluation of potential reference genes for real-time qPCR analysis in a biparental beetle, Lethrus apterus (Coleoptera: Geotrupidae). PeerJ 5:e4047 https://doi.org/10.7717/peerj.4047
date submitted: 2017-07-29
date accepted: 2017-10-26
issued: 2017-11-28
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Nagy
  given name: Nikoletta A.
author list: Agent
  family name: Németh
  given name: Zoltán
author list: Agent
  family name: Juhász
  given name: Edit
author list: Agent
  family name: Póliska
  given name: Szilárd
author list: Agent
  family name: Rácz
  given name: Rita
author list: Agent
  family name: Kosztolányi
  given name: András
author list: Agent
  family name: Barta
  given name: Zoltán
doi: 10.7717/peerj.4047
volume: 5
issn: 2167-8359
publication name: PeerJ
publication date: 2017-11-28
copyright: ©2017 Nagy et al.
attribution name: Nagy et al.

Phylogeographic and population insights of the Asian common toad (Bufo gargarizans) in Korea and China: population isolation and expansions as response to the ice ages
type: item
type: AcademicArticle
description: The effects of ice ages on speciation have been well documented for many European and North American taxa. In contrast, very few studies have addressed the consequences of such environmental and topographical changes in North East Asian species. More precisely, the Korean Peninsula offers a unique model to assess patterns and processes of speciation as it hosts the northern- and eastern-most distribution limit of some widespread Asian taxa. Despite this, studies addressing phylogeographic patterns and population genetics in the peninsula and surrounding countries are few and studies for most families are lacking. Here we inferred the phylogenetic relationships of the common toad (Bufo gargarizans) from South Korea and their North East Asian counterpart populations, based on mitochondrial data. Korean B. gargarizans GenBank BLASTs matched few individuals from nearby China, but the presence of a Korean clade suggests isolation on the Korean Peninsula, previous to the last glacial maximum, linked to sea level resurgence. Molecular clock calibrations within this group were used to date the divergence between clades and their relationship to paleo-climatic events in the area. Lack of genetic structure among South Korean populations and strong homogeneity between the Korean and some Chinese localities suggest weak isolation and recent expansion. Geographical projection of continuous coalescent maximum-clade-credibility trees shows an original Chinese expansion towards the Korean Peninsula through the Yellow Sea circa two million years ago with colonisation events dating circa 800 thousand years ago (K. y. a.). Following this colonisation, the data point to outgoing Korean Peninsula dispersal events throughout different periods, towards the North through land, and West through land bridge formations over the Yellow Sea during sea level falls. In accordance, demographic analyses revealed a population expansion in the Koran Peninsula circa 300 K. y. a., likely attributed to …
format: application/pdf
format: text/html
creator: Amaël Borzée
creator: Joana L. Santos
creator: Santiago Sánchez-RamÍrez
creator: Yoonhyuk Bae
creator: Kyongman Heo
creator: Yikweon Jang
creator: Michael Joseph Jowers
subject: Biodiversity
subject: Biogeography
subject: Zoology
description: doi:10.7717/peerj.4044
publisher: PeerJ Inc.
rights: © 2017 Borzee et al.
abstract: The effects of ice ages on speciation have been well documented for many European and North American taxa. In contrast, very few studies have addressed the consequences of such environmental and topographical changes in North East Asian species. More precisely, the Korean Peninsula offers a unique model to assess patterns and processes of speciation as it hosts the northern- and eastern-most distribution limit of some widespread Asian taxa. Despite this, studies addressing phylogeographic patterns and population genetics in the peninsula and surrounding countries are few and studies for most families are lacking. Here we inferred the phylogenetic relationships of the common toad (Bufo gargarizans) from South Korea and their North East Asian counterpart populations, based on mitochondrial data. Korean B. gargarizans GenBank BLASTs matched few individuals from nearby China, but the presence of a Korean clade suggests isolation on the Korean Peninsula, previous to the last glacial maximum, linked to sea level resurgence. Molecular clock calibrations within this group were used to date the divergence between clades and their relationship to paleo-climatic events in the area. Lack of genetic structure among South Korean populations and strong homogeneity between the Korean and some Chinese localities suggest weak isolation and recent expansion. Geographical projection of continuous coalescent maximum-clade-credibility trees shows an original Chinese expansion towards the Korean Peninsula through the Yellow Sea circa two million years ago with colonisation events dating circa 800 thousand years ago (K. y. a.). Following this colonisation, the data point to outgoing Korean Peninsula dispersal events throughout different periods, towards the North through land, and West through land bridge formations over the Yellow Sea during sea level falls. In accordance, demographic analyses revealed a population expansion in the Koran Peninsula circa 300 K. y. a., likely attributed to …
bibliographic citation: Borzée et al. (2017) Phylogeographic and population insights of the Asian common toad (Bufo gargarizans) in Korea and China: population isolation and expansions as response to the ice ages. PeerJ 5:e4044 https://doi.org/10.7717/peerj.4044
date submitted: 2017-03-01
date accepted: 2017-10-25
issued: 2017-11-28
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Borzée
  given name: Amaël
author list: Agent
  family name: Santos
  given name: Joana L.
author list: Agent
  family name: Sánchez-RamÍrez
  given name: Santiago
author list: Agent
  family name: Bae
  given name: Yoonhyuk
author list: Agent
  family name: Heo
  given name: Kyongman
author list: Agent
  family name: Jang
  given name: Yikweon
author list: Agent
  family name: Jowers
  given name: Michael Joseph
doi: 10.7717/peerj.4044
volume: 5
issn: 2167-8359
publication name: PeerJ
publication date: 2017-11-28
copyright: © 2017 Borzée et al.
attribution name: Borzee et al.

Impacts of diarrhea on the immune system, intestinal environment, and expression of PGRPs in New Zealand rabbits
type: item
type: AcademicArticle
description: Diarrhea is a syndrome of digestive disorders in young rabbits and may lead to secondary infections resulting in reduced immunity and higher mortality in baby rabbits, with serious impacts on rabbit farming. In this study, we investigated the effects of diarrhea on the health of baby rabbits in terms of intestinal mucosal development, immune function, and intestinal microbial diversity. We found that the duodenal villus length and the villus/crypt ratio in rabbits with diarrhea were significantly reduced compared with those in healthy rabbits (P < 0.01). Rabbits with diarrhea had significantly lower concentrations of acetic acid (P < 0.05), higher pH levels (P < 0.05), and higher levels of ammonia nitrogen (P < 0.01) in the cecum. Moreover, diarrhea in baby rabbits led to significantly reduced levels of total serum protein (P < 0.05) and markedly increased levels of alkaline phosphatase, urea nitrogen, TNF-α, and IL-6 (P < 0.05). Transcriptional analysis of peptidoglycan recognition proteins (PGRPs, including PGLYRP-1, PGLYRP-2, and PGLYRP-3) using real-time PCR revealed that diarrhea induced the upregulation of PGRPs in the cecum and duodenum. Furthermore, through pyrosequencing of the 16S rRNA V4 region in cecum samples, we found that the total number and diversity of microbes were not significantly different between healthy rabbits and those with diarrhea, though there were noticeable differences in the prevalences of Clostridium, Roseburia, and Alistipes. Our results will contribute to a better understanding of the pathological mechanisms of diarrhea in young rabbits.
format: application/pdf
format: text/html
creator: Yang Chen
creator: Bohao Zhao
creator: Yuwei Wu
creator: Shuaishuai Hu
creator: Lin Mu
creator: Cigen Zhu
creator: Yulai Pan
creator: Xinsheng Wu
subject: Agricultural Science
subject: Genetics
description: doi:10.7717/peerj.4100
publisher: PeerJ Inc.
rights: © 2017 Chen et al.
abstract: Diarrhea is a syndrome of digestive disorders in young rabbits and may lead to secondary infections resulting in reduced immunity and higher mortality in baby rabbits, with serious impacts on rabbit farming. In this study, we investigated the effects of diarrhea on the health of baby rabbits in terms of intestinal mucosal development, immune function, and intestinal microbial diversity. We found that the duodenal villus length and the villus/crypt ratio in rabbits with diarrhea were significantly reduced compared with those in healthy rabbits (P < 0.01). Rabbits with diarrhea had significantly lower concentrations of acetic acid (P < 0.05), higher pH levels (P < 0.05), and higher levels of ammonia nitrogen (P < 0.01) in the cecum. Moreover, diarrhea in baby rabbits led to significantly reduced levels of total serum protein (P < 0.05) and markedly increased levels of alkaline phosphatase, urea nitrogen, TNF-α, and IL-6 (P < 0.05). Transcriptional analysis of peptidoglycan recognition proteins (PGRPs, including PGLYRP-1, PGLYRP-2, and PGLYRP-3) using real-time PCR revealed that diarrhea induced the upregulation of PGRPs in the cecum and duodenum. Furthermore, through pyrosequencing of the 16S rRNA V4 region in cecum samples, we found that the total number and diversity of microbes were not significantly different between healthy rabbits and those with diarrhea, though there were noticeable differences in the prevalences of Clostridium, Roseburia, and Alistipes. Our results will contribute to a better understanding of the pathological mechanisms of diarrhea in young rabbits.
bibliographic citation: Chen et al. (2017) Impacts of diarrhea on the immune system, intestinal environment, and expression of PGRPs in New Zealand rabbits. PeerJ 5:e4100 https://doi.org/10.7717/peerj.4100
date submitted: 2017-08-08
date accepted: 2017-11-06
issued: 2017-11-27
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Chen
  given name: Yang
author list: Agent
  family name: Zhao
  given name: Bohao
author list: Agent
  family name: Wu
  given name: Yuwei
author list: Agent
  family name: Hu
  given name: Shuaishuai
author list: Agent
  family name: Mu
  given name: Lin
author list: Agent
  family name: Zhu
  given name: Cigen
author list: Agent
  family name: Pan
  given name: Yulai
author list: Agent
  family name: Wu
  given name: Xinsheng
doi: 10.7717/peerj.4100
volume: 5
issn: 2167-8359
publication name: PeerJ
publication date: 2017-11-27
copyright: ©2017 Chen et al.
attribution name: Chen et al.

Diagnostic value of serum procalcitonin, lactate, and high-sensitivity C-reactive protein for predicting bacteremia in adult patients in the emergency department
type: item
type: AcademicArticle
description: Background Few studies compared the diagnostic value of procalcitonin with a combination of other tests including lactate and high-sensitivity C-reactive protein in the prediction of pathogenic bacteremia in emergency department adult patients. Methods We performed a retrospective study assessing the differences in performances of procalcitonin at a cutoff of 0.5 ng/mL, lactate at a cutoff of 19.8 mg/dL, high-sensitivity C-reactive protein at a cutoff of 0.8 mg/dL and their combinations for predicting bacteremia in emergency department adult patients. Sensitivity, specificity, overall accuracy, positive-test and negative-test likelihood, and diagnostic odds ratio with 95% confidence interval for each test combination were calculated for comparison. The receiver operating characteristic curve for every single test were compared using DeLong’s method. We also performed a sensitivity analysis in two expanded patient cohorts to assess the discriminative ability of procalcitonin or test combination. Results A total of 886 patients formed the initial patient cohort. The area under the receiver operating characteristic curve for discriminating positive blood culture was: procalcitonin = 0.72 (95% CI [0.69–0.75]) with a derived optimal cutoff at 3.9 ng/mL; lactate 0.69 (0.66–0.72) with an optimal cutoff at 17.9 mg/dL; high-sensitivity C-reactive protein 0.56 (0.53–0.59) with an optimal cutoff of 13 mg/dL; with pairwise comparisons showing statistically significant better performance of either procalcitonin or lactate outperforming high-sensitivity C-reactive protein. To predict positive blood cultures, the diagnostic odds ratio for procalcitonin was 3.64 (95% CI [2.46–5.51]), lactate 2.93 (2.09–4.14), and high-sensitivity C-reactive protein 0.91 (0.55–1.55; P = 0.79). About combined tests, the diagnostic odds ratio for procalcitonin and lactate increases were 3.98 (95% CI [2.81–5.63]) for positive blood culture prediction. Elevated procalcitonin level rendered a six-fold in…
format: application/pdf
format: text/html
creator: Chiung-Tsung Lin
creator: Jang-Jih Lu
creator: Yu-Ching Chen
creator: Victor C. Kok
creator: Jorng-Tzong Horng
subject: Emergency and Critical Care
subject: Infectious Diseases
subject: Internal Medicine
subject: Pathology
description: doi:10.7717/peerj.4094
publisher: PeerJ Inc.
rights: © 2017 Lin et al.
abstract: Background Few studies compared the diagnostic value of procalcitonin with a combination of other tests including lactate and high-sensitivity C-reactive protein in the prediction of pathogenic bacteremia in emergency department adult patients. Methods We performed a retrospective study assessing the differences in performances of procalcitonin at a cutoff of 0.5 ng/mL, lactate at a cutoff of 19.8 mg/dL, high-sensitivity C-reactive protein at a cutoff of 0.8 mg/dL and their combinations for predicting bacteremia in emergency department adult patients. Sensitivity, specificity, overall accuracy, positive-test and negative-test likelihood, and diagnostic odds ratio with 95% confidence interval for each test combination were calculated for comparison. The receiver operating characteristic curve for every single test were compared using DeLong’s method. We also performed a sensitivity analysis in two expanded patient cohorts to assess the discriminative ability of procalcitonin or test combination. Results A total of 886 patients formed the initial patient cohort. The area under the receiver operating characteristic curve for discriminating positive blood culture was: procalcitonin = 0.72 (95% CI [0.69–0.75]) with a derived optimal cutoff at 3.9 ng/mL; lactate 0.69 (0.66–0.72) with an optimal cutoff at 17.9 mg/dL; high-sensitivity C-reactive protein 0.56 (0.53–0.59) with an optimal cutoff of 13 mg/dL; with pairwise comparisons showing statistically significant better performance of either procalcitonin or lactate outperforming high-sensitivity C-reactive protein. To predict positive blood cultures, the diagnostic odds ratio for procalcitonin was 3.64 (95% CI [2.46–5.51]), lactate 2.93 (2.09–4.14), and high-sensitivity C-reactive protein 0.91 (0.55–1.55; P = 0.79). About combined tests, the diagnostic odds ratio for procalcitonin and lactate increases were 3.98 (95% CI [2.81–5.63]) for positive blood culture prediction. Elevated procalcitonin level rendered a six-fold in…
bibliographic citation: Lin et al. (2017) Diagnostic value of serum procalcitonin, lactate, and high-sensitivity C-reactive protein for predicting bacteremia in adult patients in the emergency department. PeerJ 5:e4094 https://doi.org/10.7717/peerj.4094
date submitted: 2017-08-03
date accepted: 2017-11-06
issued: 2017-11-27
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Lin
  given name: Chiung-Tsung
author list: Agent
  family name: Lu
  given name: Jang-Jih
author list: Agent
  family name: Chen
  given name: Yu-Ching
author list: Agent
  family name: Kok
  given name: Victor C.
author list: Agent
  family name: Horng
  given name: Jorng-Tzong
doi: 10.7717/peerj.4094
volume: 5
issn: 2167-8359
publication name: PeerJ
publication date: 2017-11-27
copyright: ©2017 Lin et al.
attribution name: Lin et al.

The zebrafish as a model system for analyzing mammalian and native α-crystallin promoter function
type: item
type: AcademicArticle
description: Previous studies have used the zebrafish to investigate the biology of lens crystallin proteins and their roles in development and disease. However, little is known about zebrafish α-crystallin promoter function, how it compares to that of mammals, or whether mammalian α-crystallin promoter activity can be assessed using zebrafish embryos. We injected a variety of α-crystallin promoter fragments from each species combined with the coding sequence for green fluorescent protein (GFP) into zebrafish zygotes to determine the resulting spatiotemporal expression patterns in the developing embryo. We also measured mRNA levels and protein abundance for all three zebrafish α-crystallins. Our data showed that mouse and zebrafish αA-crystallin promoters generated similar GFP expression in the lens, but with earlier onset when using mouse promoters. Expression was also found in notochord and skeletal muscle in a smaller percentage of embryos. Mouse αB-crystallin promoter fragments drove GFP expression primarily in zebrafish skeletal muscle, with less common expression in notochord, lens, heart and in extraocular regions of the eye. A short fragment containing only a lens-specific enhancer region increased lens and notochord GFP expression while decreasing muscle expression, suggesting that the influence of mouse promoter control regions carries over into zebrafish embryos. The two paralogous zebrafish αB-crystallin promoters produced subtly different expression profiles, with the aBa promoter driving expression equally in notochord and skeletal muscle while the αBb promoter resulted primarily in skeletal muscle expression. Messenger RNA for zebrafish αA increased between 1 and 2 days post fertilization (dpf), αBa increased between 4 and 5 dpf, but αBb remained at baseline levels through 5 dpf. Parallel reaction monitoring (PRM) mass spectrometry was used to detect αA, aBa, and αBb peptides in digests of zebrafish embryos. In whole embryos, αA-crystallin was first detected by 2 …
format: application/pdf
format: text/html
creator: Mason Posner
creator: Kelly L. Murray
creator: Matthew S. McDonald
creator: Hayden Eighinger
creator: Brandon Andrew
creator: Amy Drossman
creator: Zachary Haley
creator: Justin Nussbaum
creator: Larry L. David
creator: Kirsten J. Lampi
subject: Developmental Biology
subject: Molecular Biology
subject: Neuroscience
subject: Ophthalmology
description: doi:10.7717/peerj.4093
publisher: PeerJ Inc.
rights: © 2017 Posner et al.
abstract: Previous studies have used the zebrafish to investigate the biology of lens crystallin proteins and their roles in development and disease. However, little is known about zebrafish α-crystallin promoter function, how it compares to that of mammals, or whether mammalian α-crystallin promoter activity can be assessed using zebrafish embryos. We injected a variety of α-crystallin promoter fragments from each species combined with the coding sequence for green fluorescent protein (GFP) into zebrafish zygotes to determine the resulting spatiotemporal expression patterns in the developing embryo. We also measured mRNA levels and protein abundance for all three zebrafish α-crystallins. Our data showed that mouse and zebrafish αA-crystallin promoters generated similar GFP expression in the lens, but with earlier onset when using mouse promoters. Expression was also found in notochord and skeletal muscle in a smaller percentage of embryos. Mouse αB-crystallin promoter fragments drove GFP expression primarily in zebrafish skeletal muscle, with less common expression in notochord, lens, heart and in extraocular regions of the eye. A short fragment containing only a lens-specific enhancer region increased lens and notochord GFP expression while decreasing muscle expression, suggesting that the influence of mouse promoter control regions carries over into zebrafish embryos. The two paralogous zebrafish αB-crystallin promoters produced subtly different expression profiles, with the aBa promoter driving expression equally in notochord and skeletal muscle while the αBb promoter resulted primarily in skeletal muscle expression. Messenger RNA for zebrafish αA increased between 1 and 2 days post fertilization (dpf), αBa increased between 4 and 5 dpf, but αBb remained at baseline levels through 5 dpf. Parallel reaction monitoring (PRM) mass spectrometry was used to detect αA, aBa, and αBb peptides in digests of zebrafish embryos. In whole embryos, αA-crystallin was first detected by 2 …
bibliographic citation: Posner et al. (2017) The zebrafish as a model system for analyzing mammalian and native α-crystallin promoter function. PeerJ 5:e4093 https://doi.org/10.7717/peerj.4093
date submitted: 2017-03-20
date accepted: 2017-11-04
issued: 2017-11-27
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Posner
  given name: Mason
author list: Agent
  family name: Murray
  given name: Kelly L.
author list: Agent
  family name: McDonald
  given name: Matthew S.
author list: Agent
  family name: Eighinger
  given name: Hayden
author list: Agent
  family name: Andrew
  given name: Brandon
author list: Agent
  family name: Drossman
  given name: Amy
author list: Agent
  family name: Haley
  given name: Zachary
author list: Agent
  family name: Nussbaum
  given name: Justin
author list: Agent
  family name: David
  given name: Larry L.
author list: Agent
  family name: Lampi
  given name: Kirsten J.
doi: 10.7717/peerj.4093
volume: 5
issn: 2167-8359
publication name: PeerJ
publication date: 2017-11-27
copyright: ©2017 Posner et al.
attribution name: Posner et al.

The relationship between egg size and helper number in cooperative breeders: a meta-analysis across species
type: item
type: AcademicArticle
description: Background Life history theory predicts that mothers should adjust reproductive investment depending on benefits of current reproduction and costs of reduced future reproductive success. These costs and benefits may in turn depend on the breeding female’s social environment. Cooperative breeders provide an ideal system to test whether changes in maternal investment are associated with the social conditions mothers experience. As alloparental helpers assist in offspring care, larger groups might reduce reproductive costs for mothers or alternatively indicate attractive conditions for reproduction. Thus, mothers may show reduced (load-lightening) or increased (differential allocation) reproductive investment in relation to group size. A growing number of studies have investigated how cooperatively breeding mothers adjust pre-natal investment depending on group size. Our aim was to survey these studies to assess, first, whether mothers consistently reduce or increase pre-natal investment when in larger groups and, second, whether these changes relate to variation in post-natal investment. Methods We extracted data on the relationship between helper number and maternal pre-natal investment (egg size) from 12 studies on 10 species of cooperatively breeding vertebrates. We performed meta-analyses to calculate the overall estimated relationship between egg size and helper number, and to quantify variation among species. We also tested whether these relationships are stronger in species in which the addition of helpers is associated with significant changes in maternal and helper post-natal investment. Results Across studies, there is a significant negative relationship between helper number and egg size, suggesting that in most instances mothers show reduced reproductive investment in larger groups, in particular in species in which mothers also show a significant reduction in post-natal investment. However, even in this limited sample, substantial variation exists in the …
format: application/pdf
format: text/html
creator: Tanmay Dixit
creator: Sinead English
creator: Dieter Lukas
subject: Animal Behavior
subject: Ecology
subject: Evolutionary Studies
subject: Zoology
description: doi:10.7717/peerj.4028
publisher: PeerJ Inc.
rights: © 2017 Dixit et al.
abstract: Background Life history theory predicts that mothers should adjust reproductive investment depending on benefits of current reproduction and costs of reduced future reproductive success. These costs and benefits may in turn depend on the breeding female’s social environment. Cooperative breeders provide an ideal system to test whether changes in maternal investment are associated with the social conditions mothers experience. As alloparental helpers assist in offspring care, larger groups might reduce reproductive costs for mothers or alternatively indicate attractive conditions for reproduction. Thus, mothers may show reduced (load-lightening) or increased (differential allocation) reproductive investment in relation to group size. A growing number of studies have investigated how cooperatively breeding mothers adjust pre-natal investment depending on group size. Our aim was to survey these studies to assess, first, whether mothers consistently reduce or increase pre-natal investment when in larger groups and, second, whether these changes relate to variation in post-natal investment. Methods We extracted data on the relationship between helper number and maternal pre-natal investment (egg size) from 12 studies on 10 species of cooperatively breeding vertebrates. We performed meta-analyses to calculate the overall estimated relationship between egg size and helper number, and to quantify variation among species. We also tested whether these relationships are stronger in species in which the addition of helpers is associated with significant changes in maternal and helper post-natal investment. Results Across studies, there is a significant negative relationship between helper number and egg size, suggesting that in most instances mothers show reduced reproductive investment in larger groups, in particular in species in which mothers also show a significant reduction in post-natal investment. However, even in this limited sample, substantial variation exists in the …
bibliographic citation: Dixit et al. (2017) The relationship between egg size and helper number in cooperative breeders: a meta-analysis across species. PeerJ 5:e4028 https://doi.org/10.7717/peerj.4028
date submitted: 2017-04-04
date accepted: 2017-10-23
issued: 2017-11-24
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Dixit
  given name: Tanmay
author list: Agent
  family name: English
  given name: Sinead
author list: Agent
  family name: Lukas
  given name: Dieter
doi: 10.7717/peerj.4028
volume: 5
issn: 2167-8359
publication name: PeerJ
publication date: 2017-11-24
copyright: ©2017 Dixit et al.
attribution name: Dixit et al.

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