PeerJ
type: channel
link: https://peerj.com/articles/
description: Articles published in PeerJ
publisher: PeerJ Inc.
publication name: PeerJ
issn: 2167-8359
items: De novo species identification using 16S rRNA gene nanopore sequencing
items: Small-scale distribution of microbes and biogeochemistry in the Great Barrier Reef
items: Comparison of the diversity of cultured and total bacterial communities in marine sediment using culture-dependent and sequencing methods
items: Functional characterization of quorum sensing LuxR-type transcriptional regulator, EasR in Enterobacter asburiae strain L1
items: Morphological and molecular systematic review of Marphysa Quatrefages, 1865 (Annelida: Eunicidae) species from South Africa
items: Vegetation drives the structure of active microbial communities on an acidogenic mine tailings deposit
items: Immunoglobulin superfamily member 10 is a novel prognostic biomarker for breast cancer
items: Genomics versus mtDNA for resolving stock structure in the silky shark (Carcharhinus falciformis)
items: DNA barcoding for identification of anuran species in the central region of South America
items: Structure and functions of Yellow-breasted Boubou (Laniarius atroflavus) solos and duets

De novo species identification using 16S rRNA gene nanopore sequencing
type: item
type: AcademicArticle
description: Nanopore sequencing is rapidly becoming more popular for use in various microbiota-based applications. Major limitations of current approaches are that they do not enable de novo species identification and that they cannot be used to verify species assignments. This severely limits applicability of the nanopore sequencing technology in taxonomic applications. Here, we demonstrate the possibility of de novo species identification and verification using hexamer frequencies in combination with k-means clustering for nanopore sequencing data. The approach was tested on the human infant gut microbiota of 3-month-old infants. Using the hexamer k-means approach we identified two new low abundant species associated with vaginal delivery. In addition, we confirmed both the vaginal delivery association for two previously identified species and the overall high levels of bifidobacteria. Taxonomic assignments were further verified by mock community analyses. Therefore, we believe our de novo species identification approach will have widespread application in analyzing microbial communities in the future.
format: application/pdf
format: text/html
creator: Inga Leena Angell
creator: Morten Nilsen
creator: Karin C. Lødrup Carlsen
creator: Kai-Håkon Carlsen
creator: Gunilla Hedlin
creator: Christine M. Jonassen
creator: Benjamin Marsland
creator: Björn Nordlund
creator: Eva Maria Rehbinder
creator: Carina Saunders
creator: Håvard Ove Skjerven
creator: Anne Cathrine Staff
creator: Cilla Söderhäll
creator: Riyas Vettukattil
creator: Knut Rudi
subject: Bioinformatics
subject: Ecology
subject: Microbiology
subject: Molecular Biology
description: doi:10.7717/peerj.10029
publisher: PeerJ Inc.
rights: © 2020 Angell et al.
abstract: Nanopore sequencing is rapidly becoming more popular for use in various microbiota-based applications. Major limitations of current approaches are that they do not enable de novo species identification and that they cannot be used to verify species assignments. This severely limits applicability of the nanopore sequencing technology in taxonomic applications. Here, we demonstrate the possibility of de novo species identification and verification using hexamer frequencies in combination with k-means clustering for nanopore sequencing data. The approach was tested on the human infant gut microbiota of 3-month-old infants. Using the hexamer k-means approach we identified two new low abundant species associated with vaginal delivery. In addition, we confirmed both the vaginal delivery association for two previously identified species and the overall high levels of bifidobacteria. Taxonomic assignments were further verified by mock community analyses. Therefore, we believe our de novo species identification approach will have widespread application in analyzing microbial communities in the future.
bibliographic citation: Angell et al. (2020) De novo species identification using 16S rRNA gene nanopore sequencing. PeerJ 8:e10029 https://doi.org/10.7717/peerj.10029
date submitted: 2020-03-13
date accepted: 2020-09-03
issued: 2020-10-21
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Angell
  given name: Inga Leena
author list: Agent
  family name: Nilsen
  given name: Morten
author list: Agent
  family name: Carlsen
  given name: Karin C. Lødrup
author list: Agent
  family name: Carlsen
  given name: Kai-Håkon
author list: Agent
  family name: Hedlin
  given name: Gunilla
author list: Agent
  family name: Jonassen
  given name: Christine M.
author list: Agent
  family name: Marsland
  given name: Benjamin
author list: Agent
  family name: Nordlund
  given name: Björn
author list: Agent
  family name: Rehbinder
  given name: Eva Maria
author list: Agent
  family name: Saunders
  given name: Carina
author list: Agent
  family name: Skjerven
  given name: Håvard Ove
author list: Agent
  family name: Staff
  given name: Anne Cathrine
author list: Agent
  family name: Söderhäll
  given name: Cilla
author list: Agent
  family name: Vettukattil
  given name: Riyas
author list: Agent
  family name: Rudi
  given name: Knut
doi: 10.7717/peerj.10029
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-10-21
copyright: ©2020 Angell et al.
attribution name: Angell et al.

Small-scale distribution of microbes and biogeochemistry in the Great Barrier Reef
type: item
type: AcademicArticle
description: Microbial communities distribute heterogeneously at small-scales (mm-cm) due to physical, chemical and biological processes. To understand microbial processes and functions it is necessary to appreciate microbes and matter at small scales, however, few studies have determined microbial, viral, and biogeochemical distribution over space and time at these scales. In this study, the small-scale spatial and temporal distribution of microbes (bacteria and chlorophyll a), viruses, dissolved inorganic nutrients and dissolved organic carbon were determined at five locations (spatial) along the Great Barrier Reef (Australia), and over 4 consecutive days (temporal) at a coastal location. Our results show that: (1) the parameters show high small-scale heterogeneity; (2) none of the parameters measured explained the bacterial abundance distributions at these scales spatially or temporally; (3) chemical (ammonium, nitrate/nitrite, phosphate, dissolved organic carbon, and total dissolved nitrogen) and biological (chl a, and bacterial and viral abundances) measurements did not reveal significant relationships at the small scale; and (4) statistically significant differences were found between sites/days for all parameter measured but without a clear pattern.
format: application/pdf
format: text/html
creator: Cátia Carreira
creator: Júlia Porto Silva Carvalho
creator: Samantha Talbot
creator: Isabel Pereira
creator: Christian Lønborg
subject: Ecology
subject: Microbiology
subject: Aquatic and Marine Chemistry
subject: Biological Oceanography
description: doi:10.7717/peerj.10049
publisher: PeerJ Inc.
rights: © 2020 Carreira et al.
abstract: Microbial communities distribute heterogeneously at small-scales (mm-cm) due to physical, chemical and biological processes. To understand microbial processes and functions it is necessary to appreciate microbes and matter at small scales, however, few studies have determined microbial, viral, and biogeochemical distribution over space and time at these scales. In this study, the small-scale spatial and temporal distribution of microbes (bacteria and chlorophyll a), viruses, dissolved inorganic nutrients and dissolved organic carbon were determined at five locations (spatial) along the Great Barrier Reef (Australia), and over 4 consecutive days (temporal) at a coastal location. Our results show that: (1) the parameters show high small-scale heterogeneity; (2) none of the parameters measured explained the bacterial abundance distributions at these scales spatially or temporally; (3) chemical (ammonium, nitrate/nitrite, phosphate, dissolved organic carbon, and total dissolved nitrogen) and biological (chl a, and bacterial and viral abundances) measurements did not reveal significant relationships at the small scale; and (4) statistically significant differences were found between sites/days for all parameter measured but without a clear pattern.
bibliographic citation: Carreira et al. (2020) Small-scale distribution of microbes and biogeochemistry in the Great Barrier Reef. PeerJ 8:e10049 https://doi.org/10.7717/peerj.10049
date submitted: 2020-04-08
date accepted: 2020-09-06
issued: 2020-10-21
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Carreira
  given name: Cátia
author list: Agent
  family name: Carvalho
  given name: Júlia Porto Silva
author list: Agent
  family name: Talbot
  given name: Samantha
author list: Agent
  family name: Pereira
  given name: Isabel
author list: Agent
  family name: Lønborg
  given name: Christian
doi: 10.7717/peerj.10049
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-10-21
copyright: ©2020 Carreira et al.
attribution name: Carreira et al.

Comparison of the diversity of cultured and total bacterial communities in marine sediment using culture-dependent and sequencing methods
type: item
type: AcademicArticle
description: Despite recent great advances in microbial culture, most microbes have not yet been cultured, and the impact of medium composition on the isolation of microbes from natural systems has not been elucidated. To optimize media for culturing marine microbes, microbial communities in three sediment samples were described using high-throughput sequencing (HTS) and culture-dependent techniques. HTS revealed communities dominated by Gammaproteobacteria, and culture-based methods revealed communities dominated by Actinobacteria. Among the total operational taxonomic units (OTUs) from the HTS dataset, 6% were recovered in the culture collection. Four potentially novel bacterial strains belonging to Oceaniovalibus, Psychrobacter and Salegentibacter were isolated. The combination of media cultured more taxa than any single medium. Nutrient-rich and single-carbon/nitrogen-source media supported the growth of relatively few taxa, and the quality of nitrogen strongly influenced the types of bacteria isolated.
format: application/pdf
format: text/html
creator: Meng Wang
creator: Samina Noor
creator: Ran Huan
creator: Congling Liu
creator: JiaYi Li
creator: Qingxin Shi
creator: Yan-Jiao Zhang
creator: Cuiling Wu
creator: Hailun He
subject: Biotechnology
subject: Marine Biology
subject: Microbiology
subject: Molecular Biology
description: doi:10.7717/peerj.10060
publisher: PeerJ Inc.
rights: © 2020 Wang et al.
abstract: Despite recent great advances in microbial culture, most microbes have not yet been cultured, and the impact of medium composition on the isolation of microbes from natural systems has not been elucidated. To optimize media for culturing marine microbes, microbial communities in three sediment samples were described using high-throughput sequencing (HTS) and culture-dependent techniques. HTS revealed communities dominated by Gammaproteobacteria, and culture-based methods revealed communities dominated by Actinobacteria. Among the total operational taxonomic units (OTUs) from the HTS dataset, 6% were recovered in the culture collection. Four potentially novel bacterial strains belonging to Oceaniovalibus, Psychrobacter and Salegentibacter were isolated. The combination of media cultured more taxa than any single medium. Nutrient-rich and single-carbon/nitrogen-source media supported the growth of relatively few taxa, and the quality of nitrogen strongly influenced the types of bacteria isolated.
bibliographic citation: Wang et al. (2020) Comparison of the diversity of cultured and total bacterial communities in marine sediment using culture-dependent and sequencing methods. PeerJ 8:e10060 https://doi.org/10.7717/peerj.10060
date submitted: 2020-01-29
date accepted: 2020-09-07
issued: 2020-10-21
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Wang
  given name: Meng
author list: Agent
  family name: Noor
  given name: Samina
author list: Agent
  family name: Huan
  given name: Ran
author list: Agent
  family name: Liu
  given name: Congling
author list: Agent
  family name: Li
  given name: JiaYi
author list: Agent
  family name: Shi
  given name: Qingxin
author list: Agent
  family name: Zhang
  given name: Yan-Jiao
author list: Agent
  family name: Wu
  given name: Cuiling
author list: Agent
  family name: He
  given name: Hailun
doi: 10.7717/peerj.10060
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-10-21
copyright: ©2020 Wang et al.
attribution name: Wang et al.

Functional characterization of quorum sensing LuxR-type transcriptional regulator, EasR in Enterobacter asburiae strain L1
type: item
type: AcademicArticle
description: Over the past decades, Enterobacter spp. have been identified as challenging and important pathogens. The emergence of multidrug-resistant Enterobacteria especially those that produce Klebsiella pneumoniae carbapenemase has been a very worrying health crisis. Although efforts have been made to unravel the complex mechanisms that contribute to the pathogenicity of different Enterobacter spp., there is very little information associated with AHL-type QS mechanism in Enterobacter spp. Signaling via N-acyl homoserine lactone (AHL) is the most common quorum sensing (QS) mechanism utilized by Proteobacteria. A typical AHL-based QS system involves two key players: a luxI gene homolog to synthesize AHLs and a luxR gene homolog, an AHL-dependent transcriptional regulator. These signaling molecules enable inter-species and intra-species interaction in response to external stimuli according to population density. In our recent study, we reported the genome of AHL-producing bacterium, Enterobacter asburiae strain L1. Whole genome sequencing and in silico analysis revealed the presence of a pair of luxI/R genes responsible for AHL-type QS, designated as easI/R, in strain L1. In a QS system, a LuxR transcriptional protein detects and responds to the concentration of a specific AHL controlling gene expression. In E. asburiae strain L1, EasR protein binds to its cognate AHLs, N-butanoyl homoserine lactone (C4-HSL) and N–hexanoyl homoserine lactone (C6-HSL), modulating the expression of targeted genes. In this current work, we have cloned the 693 bp luxR homolog of strain L1 for further characterization. The functionality and specificity of EasR protein in response to different AHL signaling molecules to activate gene transcription were tested and validated with β-galactosidase assays. Higher β-galactosidase activities were detected for cells harboring EasR, indicating EasR is a functional transcriptional regulator. This is the first report documenting the cloning and characterizati…
format: application/pdf
format: text/html
creator: Yin Yin Lau
creator: Kah Yan How
creator: Wai-Fong Yin
creator: Kok-Gan Chan
subject: Genomics
subject: Microbiology
subject: Molecular Biology
description: doi:10.7717/peerj.10068
publisher: PeerJ Inc.
rights: © 2020 Lau et al.
abstract: Over the past decades, Enterobacter spp. have been identified as challenging and important pathogens. The emergence of multidrug-resistant Enterobacteria especially those that produce Klebsiella pneumoniae carbapenemase has been a very worrying health crisis. Although efforts have been made to unravel the complex mechanisms that contribute to the pathogenicity of different Enterobacter spp., there is very little information associated with AHL-type QS mechanism in Enterobacter spp. Signaling via N-acyl homoserine lactone (AHL) is the most common quorum sensing (QS) mechanism utilized by Proteobacteria. A typical AHL-based QS system involves two key players: a luxI gene homolog to synthesize AHLs and a luxR gene homolog, an AHL-dependent transcriptional regulator. These signaling molecules enable inter-species and intra-species interaction in response to external stimuli according to population density. In our recent study, we reported the genome of AHL-producing bacterium, Enterobacter asburiae strain L1. Whole genome sequencing and in silico analysis revealed the presence of a pair of luxI/R genes responsible for AHL-type QS, designated as easI/R, in strain L1. In a QS system, a LuxR transcriptional protein detects and responds to the concentration of a specific AHL controlling gene expression. In E. asburiae strain L1, EasR protein binds to its cognate AHLs, N-butanoyl homoserine lactone (C4-HSL) and N–hexanoyl homoserine lactone (C6-HSL), modulating the expression of targeted genes. In this current work, we have cloned the 693 bp luxR homolog of strain L1 for further characterization. The functionality and specificity of EasR protein in response to different AHL signaling molecules to activate gene transcription were tested and validated with β-galactosidase assays. Higher β-galactosidase activities were detected for cells harboring EasR, indicating EasR is a functional transcriptional regulator. This is the first report documenting the cloning and characterizati…
bibliographic citation: Lau et al. (2020) Functional characterization of quorum sensing LuxR-type transcriptional regulator, EasR in Enterobacter asburiae strain L1. PeerJ 8:e10068 https://doi.org/10.7717/peerj.10068
date submitted: 2019-11-26
date accepted: 2020-09-08
issued: 2020-10-21
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Lau
  given name: Yin Yin
author list: Agent
  family name: How
  given name: Kah Yan
author list: Agent
  family name: Yin
  given name: Wai-Fong
author list: Agent
  family name: Chan
  given name: Kok-Gan
doi: 10.7717/peerj.10068
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-10-21
copyright: © 2020 Lau et al.
attribution name: Lau et al.

Morphological and molecular systematic review of Marphysa Quatrefages, 1865 (Annelida: Eunicidae) species from South Africa
type: item
type: AcademicArticle
description: A vast polychaete fauna is hidden behind complexes of cryptic and pseudo-cryptic species, which has greatly hindered our understanding of species diversity in several regions worldwide. Among the eunicids, Marphysa sanguinea Montagu, 1813 is a typical example, recorded in three oceans and with various species considered its junior synonyms. In South Africa, specimens previously misidentified as M. sanguinea are now known as Marphysa elityeni Lewis & Karageorgopoulos, 2008. Of the six Marphysa Quatrefages, 1865a species recorded from the same region, three have their distributions restricted to South Africa while the others are considered to have worldwide distributions. Here, we evaluated the taxonomic status of the indigenous M. elityeni and investigated the presence of the widespread species Marphysa macintoshi Crossland, 1903 and Marphysa depressa Schmarda, 1861 in South Africa using morphological and molecular data. Our results reveal that M. elityeni is a junior synonym of Marphysa haemasoma, a species previously described from South Africa which is herein reinstated as a valid species. Both M. macintoshi and M. depressa are not present in South Africa and their status as being distributed worldwide deserves further investigation. Marphysa durbanensis Day, 1934 and the new species described here, M. sherlockae n. sp., had been misidentified as M. macintoshi and M. depressa respectively. Thus, the number of Marphysa species with distributions restricted to South Africa increased from three to five. This study reiterates the importance of implementing an integrated taxonomic framework to unravel local biodiversity.
format: application/pdf
format: text/html
creator: Jyothi Kara
creator: Isabel C. Molina-Acevedo
creator: Joana Zanol
creator: Carol Simon
creator: Izwandy Idris
subject: Biodiversity
subject: Marine Biology
subject: Molecular Biology
subject: Taxonomy
subject: Zoology
description: doi:10.7717/peerj.10076
publisher: PeerJ Inc.
rights: © 2020 Kara et al.
abstract: A vast polychaete fauna is hidden behind complexes of cryptic and pseudo-cryptic species, which has greatly hindered our understanding of species diversity in several regions worldwide. Among the eunicids, Marphysa sanguinea Montagu, 1813 is a typical example, recorded in three oceans and with various species considered its junior synonyms. In South Africa, specimens previously misidentified as M. sanguinea are now known as Marphysa elityeni Lewis & Karageorgopoulos, 2008. Of the six Marphysa Quatrefages, 1865a species recorded from the same region, three have their distributions restricted to South Africa while the others are considered to have worldwide distributions. Here, we evaluated the taxonomic status of the indigenous M. elityeni and investigated the presence of the widespread species Marphysa macintoshi Crossland, 1903 and Marphysa depressa Schmarda, 1861 in South Africa using morphological and molecular data. Our results reveal that M. elityeni is a junior synonym of Marphysa haemasoma, a species previously described from South Africa which is herein reinstated as a valid species. Both M. macintoshi and M. depressa are not present in South Africa and their status as being distributed worldwide deserves further investigation. Marphysa durbanensis Day, 1934 and the new species described here, M. sherlockae n. sp., had been misidentified as M. macintoshi and M. depressa respectively. Thus, the number of Marphysa species with distributions restricted to South Africa increased from three to five. This study reiterates the importance of implementing an integrated taxonomic framework to unravel local biodiversity.
bibliographic citation: Kara et al. (2020) Morphological and molecular systematic review of Marphysa Quatrefages, 1865 (Annelida: Eunicidae) species from South Africa. PeerJ 8:e10076 https://doi.org/10.7717/peerj.10076
date submitted: 2020-05-19
date accepted: 2020-09-10
issued: 2020-10-21
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Kara
  given name: Jyothi
author list: Agent
  family name: Molina-Acevedo
  given name: Isabel C.
author list: Agent
  family name: Zanol
  given name: Joana
author list: Agent
  family name: Simon
  given name: Carol
author list: Agent
  family name: Idris
  given name: Izwandy
doi: 10.7717/peerj.10076
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-10-21
copyright: ©2020 Kara et al.
attribution name: Kara et al.

Vegetation drives the structure of active microbial communities on an acidogenic mine tailings deposit
type: item
type: AcademicArticle
description: Plant-microbe associations are increasingly recognized as an inextricable part of plant biology and biogeochemistry. Microbes play an essential role in the survival and development of plants, allowing them to thrive in diverse environments. The composition of the rhizosphere soil microbial communities is largely influenced by edaphic conditions and plant species. In order to decipher how environmental conditions on a mine site can influence the dynamics of microbial communities, we characterized the rhizosphere soil microbial communities associated with paper birch, speckled alder, and spruce that had naturally colonized an acidogenic mine tailings deposit containing heavy metals. The study site, which had been largely undisturbed for five decades, had highly variable vegetation density; with some areas remaining almost barren, and others having a few stands or large thickets of mature trees. Using Illumina sequencing and ordination analyses (redundancy analysis and principal coordinate analysis), our study showed that soil bacterial and fungal community structures correlated mainly with vegetation density, and plant species. Tailings without any vegetation were the most different in bacterial community structure, compared to all other areas on the mine site, as well as an adjacent natural forest (comparison plot). The bacterial genera Acidiferrobacter and Leptospirillum were more abundant in tailings without vegetation than in any of the other sites, while Bradyrhizobium sp. were more abundant in areas of the tailings deposit having higher vegetation density. Frankia sp. is equally represented in each of the vegetation densities and Pseudomonas sp. present a greater relative abundance in boreal forest. Furthermore, alder rhizosphere showed a greater relative abundance of Bradyrhizobium sp. (in comparison with birch and spruce) as well as Haliangium sp. (in comparison with birch). In contrast, fungal community structures were similar across the tailings deposit rega…
format: application/pdf
format: text/html
creator: Vanessa Gagnon
creator: Michaël Rodrigue-Morin
creator: Julien Tremblay
creator: Jessica Wasserscheid
creator: Julie Champagne
creator: Jean-Philippe Bellenger
creator: Charles W. Greer
creator: Sébastien Roy
subject: Microbiology
subject: Biogeochemistry
subject: Environmental Contamination and Remediation
subject: Environmental Impacts
description: doi:10.7717/peerj.10109
publisher: PeerJ Inc.
rights: © 2020 Gagnon et al.
abstract: Plant-microbe associations are increasingly recognized as an inextricable part of plant biology and biogeochemistry. Microbes play an essential role in the survival and development of plants, allowing them to thrive in diverse environments. The composition of the rhizosphere soil microbial communities is largely influenced by edaphic conditions and plant species. In order to decipher how environmental conditions on a mine site can influence the dynamics of microbial communities, we characterized the rhizosphere soil microbial communities associated with paper birch, speckled alder, and spruce that had naturally colonized an acidogenic mine tailings deposit containing heavy metals. The study site, which had been largely undisturbed for five decades, had highly variable vegetation density; with some areas remaining almost barren, and others having a few stands or large thickets of mature trees. Using Illumina sequencing and ordination analyses (redundancy analysis and principal coordinate analysis), our study showed that soil bacterial and fungal community structures correlated mainly with vegetation density, and plant species. Tailings without any vegetation were the most different in bacterial community structure, compared to all other areas on the mine site, as well as an adjacent natural forest (comparison plot). The bacterial genera Acidiferrobacter and Leptospirillum were more abundant in tailings without vegetation than in any of the other sites, while Bradyrhizobium sp. were more abundant in areas of the tailings deposit having higher vegetation density. Frankia sp. is equally represented in each of the vegetation densities and Pseudomonas sp. present a greater relative abundance in boreal forest. Furthermore, alder rhizosphere showed a greater relative abundance of Bradyrhizobium sp. (in comparison with birch and spruce) as well as Haliangium sp. (in comparison with birch). In contrast, fungal community structures were similar across the tailings deposit rega…
bibliographic citation: Gagnon et al. (2020) Vegetation drives the structure of active microbial communities on an acidogenic mine tailings deposit. PeerJ 8:e10109 https://doi.org/10.7717/peerj.10109
date submitted: 2020-03-05
date accepted: 2020-09-16
issued: 2020-10-21
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Gagnon
  given name: Vanessa
author list: Agent
  family name: Rodrigue-Morin
  given name: Michaël
author list: Agent
  family name: Tremblay
  given name: Julien
author list: Agent
  family name: Wasserscheid
  given name: Jessica
author list: Agent
  family name: Champagne
  given name: Julie
author list: Agent
  family name: Bellenger
  given name: Jean-Philippe
author list: Agent
  family name: Greer
  given name: Charles W.
author list: Agent
  family name: Roy
  given name: Sébastien
doi: 10.7717/peerj.10109
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-10-21
copyright: ©2020 Gagnon et al.
attribution name: Gagnon et al.

Immunoglobulin superfamily member 10 is a novel prognostic biomarker for breast cancer
type: item
type: AcademicArticle
description: Background Immunoglobulin superfamily member 10 (IGSF10) is a member of the immunoglobulin superfamily that is expressed at high levels in both the gallbladder and ovary. Currently, the role and possible mechanism of IGSF10 in breast cancer remain unclear. Method By applying real-time quantitative polymerase chain reaction (qRT-PCR) and immunohistochemistry (IHC), the expression of IGSF10 in breast cancer cells and tissues was detected. We collected the clinical information from 700 patients with breast cancer in The Cancer Genome Atlas (TCGA), and analyzed the relationship between IGSF10 expression and the clinicopathological features and survival outcomes of these patients. The potential mechanisms and pathways associated with IGSF10 in breast cancer were explored by performing a gene set enrichment analysis (GSEA). Results According to TCGA data, qRT-PCR and IHC experiments, levels of the IGSF10 mRNA and protein were significantly decreased in breast cancer tissues. IGSF10 expression was significantly correlated with age, tumor size, and tumor stage. Moreover, shorter overall survival (OS) and relapse-free survival (RFS) correlated with lower IGSF10 expression, according to the survival analysis. The multivariate analysis identified that IGSF10 as an independent prognostic factor for the OS (hazard ratio (HR) = 1.793, 95% confidence interval (CI) [1.141–2.815], P = 0.011) and RFS (HR = 2.298, 95% CI [1.317–4.010], P = 0.003) of patients with breast cancer. Based on the GSEA, IGSF10 was involved in DNA repair, cell cycle, and glycolysis. IGSF10 was also associated with the PI3K/Akt/mTOR and mTORC1 signaling pathways. Conclusions This study revealed a clear relationship between IGSF10 expression and the tumorigenesis of breast cancer for the first time. Therefore, further studies are needed to understand the mechanism of IGSF10 in breast cancer.
format: application/pdf
format: text/html
creator: Mengxue Wang
creator: Meng Dai
creator: Yu-shen Wu
creator: Ziying Yi
creator: Yunhai Li
creator: Guosheng Ren
subject: Bioinformatics
subject: Genomics
subject: Oncology
description: doi:10.7717/peerj.10128
publisher: PeerJ Inc.
rights: © 2020 Wang et al.
abstract: Background Immunoglobulin superfamily member 10 (IGSF10) is a member of the immunoglobulin superfamily that is expressed at high levels in both the gallbladder and ovary. Currently, the role and possible mechanism of IGSF10 in breast cancer remain unclear. Method By applying real-time quantitative polymerase chain reaction (qRT-PCR) and immunohistochemistry (IHC), the expression of IGSF10 in breast cancer cells and tissues was detected. We collected the clinical information from 700 patients with breast cancer in The Cancer Genome Atlas (TCGA), and analyzed the relationship between IGSF10 expression and the clinicopathological features and survival outcomes of these patients. The potential mechanisms and pathways associated with IGSF10 in breast cancer were explored by performing a gene set enrichment analysis (GSEA). Results According to TCGA data, qRT-PCR and IHC experiments, levels of the IGSF10 mRNA and protein were significantly decreased in breast cancer tissues. IGSF10 expression was significantly correlated with age, tumor size, and tumor stage. Moreover, shorter overall survival (OS) and relapse-free survival (RFS) correlated with lower IGSF10 expression, according to the survival analysis. The multivariate analysis identified that IGSF10 as an independent prognostic factor for the OS (hazard ratio (HR) = 1.793, 95% confidence interval (CI) [1.141–2.815], P = 0.011) and RFS (HR = 2.298, 95% CI [1.317–4.010], P = 0.003) of patients with breast cancer. Based on the GSEA, IGSF10 was involved in DNA repair, cell cycle, and glycolysis. IGSF10 was also associated with the PI3K/Akt/mTOR and mTORC1 signaling pathways. Conclusions This study revealed a clear relationship between IGSF10 expression and the tumorigenesis of breast cancer for the first time. Therefore, further studies are needed to understand the mechanism of IGSF10 in breast cancer.
bibliographic citation: Wang et al. (2020) Immunoglobulin superfamily member 10 is a novel prognostic biomarker for breast cancer. PeerJ 8:e10128 https://doi.org/10.7717/peerj.10128
date submitted: 2020-02-24
date accepted: 2020-09-17
issued: 2020-10-21
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Wang
  given name: Mengxue
author list: Agent
  family name: Dai
  given name: Meng
author list: Agent
  family name: Wu
  given name: Yu-shen
author list: Agent
  family name: Yi
  given name: Ziying
author list: Agent
  family name: Li
  given name: Yunhai
author list: Agent
  family name: Ren
  given name: Guosheng
doi: 10.7717/peerj.10128
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-10-21
copyright: © 2020 Wang et al.
attribution name: Wang et al.

Genomics versus mtDNA for resolving stock structure in the silky shark (Carcharhinus falciformis)
type: item
type: AcademicArticle
description: Conservation genetic approaches for elasmobranchs have focused on regions of the mitochondrial genome or a handful of nuclear microsatellites. High-throughput sequencing offers a powerful alternative for examining population structure using many loci distributed across the nuclear and mitochondrial genomes. These single nucleotide polymorphisms are expected to provide finer scale and more accurate population level data; however, there have been few genomic studies applied to elasmobranch species. The desire to apply next-generation sequencing approaches is often tempered by the costs, which can be offset by pooling specimens prior to sequencing (pool-seq). In this study, we assess the utility of pool-seq by applying this method to the same individual silky sharks, Carcharhinus falciformis, previously surveyed with the mtDNA control region in the Atlantic and Indian Oceans. Pool-seq methods were able to recover the entire mitochondrial genome as well as thousands of nuclear markers. This volume of sequence data enabled the detection of population structure between regions of the Atlantic Ocean populations, undetected in the previous study (inter-Atlantic mitochondrial SNPs FST values comparison ranging from 0.029 to 0.135 and nuclear SNPs from 0.015 to 0.025). Our results reinforce the conclusion that sampling the mitochondrial control region alone may fail to detect fine-scale population structure, and additional sampling across the genome may increase resolution for some species. Additionally, this study shows that the costs of analyzing 4,988 loci using pool-seq methods are equivalent to the standard Sanger-sequenced markers and become less expensive when large numbers of individuals (>300) are analyzed.
format: application/pdf
format: text/html
creator: Derek W. Kraft
creator: Emily E. Conklin
creator: Evan W. Barba
creator: Melanie Hutchinson
creator: Robert J. Toonen
creator: Zac H. Forsman
creator: Brian W. Bowen
subject: Biogeography
subject: Genetics
subject: Genomics
subject: Molecular Biology
subject: Natural Resource Management
description: doi:10.7717/peerj.10186
publisher: PeerJ Inc.
rights: © 2020 Kraft et al.
abstract: Conservation genetic approaches for elasmobranchs have focused on regions of the mitochondrial genome or a handful of nuclear microsatellites. High-throughput sequencing offers a powerful alternative for examining population structure using many loci distributed across the nuclear and mitochondrial genomes. These single nucleotide polymorphisms are expected to provide finer scale and more accurate population level data; however, there have been few genomic studies applied to elasmobranch species. The desire to apply next-generation sequencing approaches is often tempered by the costs, which can be offset by pooling specimens prior to sequencing (pool-seq). In this study, we assess the utility of pool-seq by applying this method to the same individual silky sharks, Carcharhinus falciformis, previously surveyed with the mtDNA control region in the Atlantic and Indian Oceans. Pool-seq methods were able to recover the entire mitochondrial genome as well as thousands of nuclear markers. This volume of sequence data enabled the detection of population structure between regions of the Atlantic Ocean populations, undetected in the previous study (inter-Atlantic mitochondrial SNPs FST values comparison ranging from 0.029 to 0.135 and nuclear SNPs from 0.015 to 0.025). Our results reinforce the conclusion that sampling the mitochondrial control region alone may fail to detect fine-scale population structure, and additional sampling across the genome may increase resolution for some species. Additionally, this study shows that the costs of analyzing 4,988 loci using pool-seq methods are equivalent to the standard Sanger-sequenced markers and become less expensive when large numbers of individuals (>300) are analyzed.
bibliographic citation: Kraft et al. (2020) Genomics versus mtDNA for resolving stock structure in the silky shark (Carcharhinus falciformis). PeerJ 8:e10186 https://doi.org/10.7717/peerj.10186
date submitted: 2020-07-27
date accepted: 2020-09-24
issued: 2020-10-21
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Kraft
  given name: Derek W.
author list: Agent
  family name: Conklin
  given name: Emily E.
author list: Agent
  family name: Barba
  given name: Evan W.
author list: Agent
  family name: Hutchinson
  given name: Melanie
author list: Agent
  family name: Toonen
  given name: Robert J.
author list: Agent
  family name: Forsman
  given name: Zac H.
author list: Agent
  family name: Bowen
  given name: Brian W.
doi: 10.7717/peerj.10186
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-10-21
copyright: © 2020 Kraft et al.
attribution name: Kraft et al.

DNA barcoding for identification of anuran species in the central region of South America
type: item
type: AcademicArticle
description: The use of COI barcodes for specimen identification and species discovery has been a useful molecular approach for the study of Anura. Here, we establish a comprehensive amphibian barcode reference database in a central area of South America, in particular for specimens collected in Mato Grosso do Sul state (Brazil), and to evaluate the applicability of the COI gene for species-level identification. Both distance- and tree-based methods were applied for assessing species boundaries and the accuracy of specimen identification was evaluated. A total of 204 mitochondrial COI barcode sequences were evaluated from 22 genera and 59 species (19 newly barcoded species). Our results indicate that morphological and molecular identifications converge for most species, however, some species may present cryptic species due to high intraspecific variation, and there is a high efficiency of specimen identification. Thus, we show that COI sequencing can be used to identify anuran species present in this region.
format: application/pdf
format: text/html
creator: Ricardo Koroiva
creator: Luís Reginaldo Ribeiro Rodrigues
creator: Diego José Santana
subject: Conservation Biology
subject: Genetics
subject: Molecular Biology
subject: Zoology
description: doi:10.7717/peerj.10189
publisher: PeerJ Inc.
rights: © 2020 Koroiva et al.
abstract: The use of COI barcodes for specimen identification and species discovery has been a useful molecular approach for the study of Anura. Here, we establish a comprehensive amphibian barcode reference database in a central area of South America, in particular for specimens collected in Mato Grosso do Sul state (Brazil), and to evaluate the applicability of the COI gene for species-level identification. Both distance- and tree-based methods were applied for assessing species boundaries and the accuracy of specimen identification was evaluated. A total of 204 mitochondrial COI barcode sequences were evaluated from 22 genera and 59 species (19 newly barcoded species). Our results indicate that morphological and molecular identifications converge for most species, however, some species may present cryptic species due to high intraspecific variation, and there is a high efficiency of specimen identification. Thus, we show that COI sequencing can be used to identify anuran species present in this region.
bibliographic citation: Koroiva et al. (2020) DNA barcoding for identification of anuran species in the central region of South America. PeerJ 8:e10189 https://doi.org/10.7717/peerj.10189
date submitted: 2020-06-26
date accepted: 2020-09-24
issued: 2020-10-21
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Koroiva
  given name: Ricardo
author list: Agent
  family name: Rodrigues
  given name: Luís Reginaldo Ribeiro
author list: Agent
  family name: Santana
  given name: Diego José
doi: 10.7717/peerj.10189
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-10-21
copyright: ©2020 Koroiva et al.
attribution name: Koroiva et al.

Structure and functions of Yellow-breasted Boubou (Laniarius atroflavus) solos and duets
type: item
type: AcademicArticle
description: Background Birds have extremely well-developed acoustic communication and have become popular in bioacoustics research. The majority of studies on bird song have been conducted in the temperate zones where usually males of birds sing to attract females and defend territories. In over 360 bird species mostly inhabiting the tropics both males and females sing together in duets. Avian duets are usually formed when a male and female coordinate their songs. We focused on a species with relatively weakly coordinated duets, with male solo as the prevailing vocalisation type. Methods Instead of analysing a set of recordings spread over a long time, we analysed whole day microphone-array recordings of the Yellow-breasted Boubou (Laniarius atroflavus), a species endemic to West African montane rainforests. We described the structure of the solo and duet vocalisations and temporal characteristics of daily activity based on 5,934 vocal bouts of 18 focal pairs and their neighbours. Results Birds had small, sex specific repertoires. All males shared three types of loud whistles functioning as song type repertoires in both solos and duets. Females vocalised with five types of harsh, atonal notes with a more variable and usually lower amplitude. Three of them were produced both as solos and in duets, while two seem to function as alarm and excitement calls given almost exclusively as a solo. Solos were the most common vocalisation mode (75.4%), with males being more vocally active than females. Duets accounted for 24.6% of all vocalisations and in most cases were initiated by males (81%). The majority of duets were simple (85.1%) consisting of a single male and female song type, but altogether 38 unique duet combinations were described. Males usually initiated singing at dawn and for this used one particular song type more often than expected by chance. Male solo and duet activities peaked around dawn, while female solos were produced evenly throughout the day. Discussion Yellow-br…
format: application/pdf
format: text/html
creator: Amie Wheeldon
creator: Paweł Szymański
creator: Michał Budka
creator: Tomasz S. Osiejuk
subject: Animal Behavior
subject: Ecology
subject: Zoology
description: doi:10.7717/peerj.10214
publisher: PeerJ Inc.
rights: © 2020 Wheeldon et al.
abstract: Background Birds have extremely well-developed acoustic communication and have become popular in bioacoustics research. The majority of studies on bird song have been conducted in the temperate zones where usually males of birds sing to attract females and defend territories. In over 360 bird species mostly inhabiting the tropics both males and females sing together in duets. Avian duets are usually formed when a male and female coordinate their songs. We focused on a species with relatively weakly coordinated duets, with male solo as the prevailing vocalisation type. Methods Instead of analysing a set of recordings spread over a long time, we analysed whole day microphone-array recordings of the Yellow-breasted Boubou (Laniarius atroflavus), a species endemic to West African montane rainforests. We described the structure of the solo and duet vocalisations and temporal characteristics of daily activity based on 5,934 vocal bouts of 18 focal pairs and their neighbours. Results Birds had small, sex specific repertoires. All males shared three types of loud whistles functioning as song type repertoires in both solos and duets. Females vocalised with five types of harsh, atonal notes with a more variable and usually lower amplitude. Three of them were produced both as solos and in duets, while two seem to function as alarm and excitement calls given almost exclusively as a solo. Solos were the most common vocalisation mode (75.4%), with males being more vocally active than females. Duets accounted for 24.6% of all vocalisations and in most cases were initiated by males (81%). The majority of duets were simple (85.1%) consisting of a single male and female song type, but altogether 38 unique duet combinations were described. Males usually initiated singing at dawn and for this used one particular song type more often than expected by chance. Male solo and duet activities peaked around dawn, while female solos were produced evenly throughout the day. Discussion Yellow-br…
bibliographic citation: Wheeldon et al. (2020) Structure and functions of Yellow-breasted Boubou (Laniarius atroflavus) solos and duets. PeerJ 8:e10214 https://doi.org/10.7717/peerj.10214
date submitted: 2020-06-29
date accepted: 2020-09-28
issued: 2020-10-21
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Wheeldon
  given name: Amie
author list: Agent
  family name: Szymański
  given name: Paweł
author list: Agent
  family name: Budka
  given name: Michał
author list: Agent
  family name: Osiejuk
  given name: Tomasz S.
doi: 10.7717/peerj.10214
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-10-21
copyright: ©2020 Wheeldon et al.
attribution name: Wheeldon et al.

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