PeerJ
type: channel
link: https://peerj.com/articles/
description: Articles published in PeerJ
publisher: PeerJ Inc.
publication name: PeerJ
issn: 2167-8359
items: Co-expression analysis and ceRNA network reveal eight novel potential lncRNA biomarkers in hepatocellular carcinoma
items: The impact of storage conditions on human stool 16S rRNA microbiome composition and diversity
items: Propofol inhibits stromatoxin-1-sensitive voltage-dependent K+ channels in pancreatic β-cells and enhances insulin secretion
items: Global transcriptome analysis of different stages of preimplantation embryo development in river buffalo
items: Brain structural and functional changes in patients with major depressive disorder: a literature review
items: Stress-induced changes in the expression of antioxidant system genes for rice (Oryza sativa L.) and bread wheat (Triticum aestivum L.)
items: Taxonomic assessment of species of the genus Octopus from the northeastern Pacific via morphological, molecular and morphometric analyses
items: Relationship between the Dark Triad and depressive symptoms
items: Identification of prognostic gene signature associated with microenvironment of lung adenocarcinoma
items: Characteristics of the vaginal microbiome in cross-border female sex workers in China: a case-control study

Co-expression analysis and ceRNA network reveal eight novel potential lncRNA biomarkers in hepatocellular carcinoma
type: item
type: AcademicArticle
description: Background Hepatocellular carcinoma (HCC) is the most common primary liver cancer in the world, with a high degree of malignancy and recurrence. The influence of the ceRNA network in tumor on the biological function of liver cancer is very important, It has been reported that many lncRNA play a key role in liver cancer development. In our study, integrated data analysis revealed potential eight novel lncRNA biomarkers in hepatocellular carcinoma. Methods Transcriptome data and clinical data were downloaded from the The Cancer Genome Atlas (TCGA) data portal. Weighted gene co-expression network analysis was performed to identify the expression pattern of genes in liver cancer. Then, the ceRNA network was constructed using transcriptome data. Results The integrated analysis of miRNA and RNAseq in the database show eight novel lncRNAs that may be involved in important biological pathways, including TNM and disease development in liver cancer. We performed function enrichment analysis of mRNAs affected by these lncRNAs. Conclusions By identifying the ceRNA network and the lncRNAs that affect liver cancer, we showed that eight novel lncRNAs play an important role in the development and progress of liver cancer.
format: application/pdf
format: text/html
creator: Ren-chao Zou
creator: Zhi-tian Shi
creator: Shu-feng Xiao
creator: Yang Ke
creator: Hao-ran Tang
creator: Tian-gen Wu
creator: Zhi-tang Guo
creator: Fan Ni
creator: Sanqi An
creator: Lin Wang
subject: Bioinformatics
subject: Gastroenterology and Hepatology
subject: Oncology
description: doi:10.7717/peerj.8101
publisher: PeerJ Inc.
rights: © 2019 Zou et al.
abstract: Background Hepatocellular carcinoma (HCC) is the most common primary liver cancer in the world, with a high degree of malignancy and recurrence. The influence of the ceRNA network in tumor on the biological function of liver cancer is very important, It has been reported that many lncRNA play a key role in liver cancer development. In our study, integrated data analysis revealed potential eight novel lncRNA biomarkers in hepatocellular carcinoma. Methods Transcriptome data and clinical data were downloaded from the The Cancer Genome Atlas (TCGA) data portal. Weighted gene co-expression network analysis was performed to identify the expression pattern of genes in liver cancer. Then, the ceRNA network was constructed using transcriptome data. Results The integrated analysis of miRNA and RNAseq in the database show eight novel lncRNAs that may be involved in important biological pathways, including TNM and disease development in liver cancer. We performed function enrichment analysis of mRNAs affected by these lncRNAs. Conclusions By identifying the ceRNA network and the lncRNAs that affect liver cancer, we showed that eight novel lncRNAs play an important role in the development and progress of liver cancer.
bibliographic citation: Zou et al. (2019) Co-expression analysis and ceRNA network reveal eight novel potential lncRNA biomarkers in hepatocellular carcinoma. PeerJ 7:e8101 https://doi.org/10.7717/peerj.8101
date submitted: 2019-04-16
date accepted: 2019-10-25
issued: 2019-12-02
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Zou
  given name: Ren-chao
author list: Agent
  family name: Shi
  given name: Zhi-tian
author list: Agent
  family name: Xiao
  given name: Shu-feng
author list: Agent
  family name: Ke
  given name: Yang
author list: Agent
  family name: Tang
  given name: Hao-ran
author list: Agent
  family name: Wu
  given name: Tian-gen
author list: Agent
  family name: Guo
  given name: Zhi-tang
author list: Agent
  family name: Ni
  given name: Fan
author list: Agent
  family name: An
  given name: Sanqi
author list: Agent
  family name: Wang
  given name: Lin
doi: 10.7717/peerj.8101
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-12-02
copyright: ©2019 Zou et al.
attribution name: Zou et al.

The impact of storage conditions on human stool 16S rRNA microbiome composition and diversity
type: item
type: AcademicArticle
description: Background Multiple factors can influence stool sample integrity upon sample collection. Preservation of faecal samples for microbiome studies is therefore an important step, particularly in tropical regions where resources are limited and high temperatures may significantly influence microbiota profiles. Freezing is the accepted standard to preserve faecal samples however, cold chain methods are often unfeasible in fieldwork scenarios particularly in low and middle-income countries and alternatives are required. This study therefore aimed to address the impact of different preservative methods, time-to-freezing at ambient tropical temperatures, and stool heterogeneity on stool microbiome diversity and composition under real-life physical environments found in resource-limited fieldwork conditions. Methods Inner and outer stool samples collected from one specimen obtained from three children were stored using different storage preservation methods (raw, ethanol and RNAlater) in a Ugandan field setting. Mixed stool was also stored using these techniques and frozen at different time-to-freezing intervals post-collection from 0–32 h. Metataxonomic profiling was used to profile samples, targeting the V1–V2 regions of 16S rRNA with samples run on a MiSeq platform. Reads were trimmed, combined and aligned to the Greengenes database. Microbial diversity and composition data were generated and analysed using Quantitative Insights Into Microbial Ecology and R software. Results Child donor was the greatest predictor of microbiome variation between the stool samples, with all samples remaining identifiable to their child of origin despite the stool being stored under a variety of conditions. However, significant differences were observed in composition and diversity between preservation techniques, but intra-preservation technique variation was minimal for all preservation methods, and across the time-to-freezing range (0–32 h) used. Stool heterogeneity yielded no apparent mic…
format: application/pdf
format: text/html
creator: Lauren V. Carruthers
creator: Arinaitwe Moses
creator: Moses Adriko
creator: Christina L. Faust
creator: Edridah M. Tukahebwa
creator: Lindsay J. Hall
creator: Lisa C. Ranford-Cartwright
creator: Poppy H.L. Lamberton
subject: Bioinformatics
subject: Genomics
subject: Microbiology
description: doi:10.7717/peerj.8133
publisher: PeerJ Inc.
rights: © 2019 Carruthers et al.
abstract: Background Multiple factors can influence stool sample integrity upon sample collection. Preservation of faecal samples for microbiome studies is therefore an important step, particularly in tropical regions where resources are limited and high temperatures may significantly influence microbiota profiles. Freezing is the accepted standard to preserve faecal samples however, cold chain methods are often unfeasible in fieldwork scenarios particularly in low and middle-income countries and alternatives are required. This study therefore aimed to address the impact of different preservative methods, time-to-freezing at ambient tropical temperatures, and stool heterogeneity on stool microbiome diversity and composition under real-life physical environments found in resource-limited fieldwork conditions. Methods Inner and outer stool samples collected from one specimen obtained from three children were stored using different storage preservation methods (raw, ethanol and RNAlater) in a Ugandan field setting. Mixed stool was also stored using these techniques and frozen at different time-to-freezing intervals post-collection from 0–32 h. Metataxonomic profiling was used to profile samples, targeting the V1–V2 regions of 16S rRNA with samples run on a MiSeq platform. Reads were trimmed, combined and aligned to the Greengenes database. Microbial diversity and composition data were generated and analysed using Quantitative Insights Into Microbial Ecology and R software. Results Child donor was the greatest predictor of microbiome variation between the stool samples, with all samples remaining identifiable to their child of origin despite the stool being stored under a variety of conditions. However, significant differences were observed in composition and diversity between preservation techniques, but intra-preservation technique variation was minimal for all preservation methods, and across the time-to-freezing range (0–32 h) used. Stool heterogeneity yielded no apparent mic…
bibliographic citation: Carruthers et al. (2019) The impact of storage conditions on human stool 16S rRNA microbiome composition and diversity. PeerJ 7:e8133 https://doi.org/10.7717/peerj.8133
date submitted: 2019-07-04
date accepted: 2019-11-01
issued: 2019-12-02
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Carruthers
  given name: Lauren V.
author list: Agent
  family name: Moses
  given name: Arinaitwe
author list: Agent
  family name: Adriko
  given name: Moses
author list: Agent
  family name: Faust
  given name: Christina L.
author list: Agent
  family name: Tukahebwa
  given name: Edridah M.
author list: Agent
  family name: Hall
  given name: Lindsay J.
author list: Agent
  family name: Ranford-Cartwright
  given name: Lisa C.
author list: Agent
  family name: Lamberton
  given name: Poppy H.L.
doi: 10.7717/peerj.8133
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-12-02
copyright: © 2019 Carruthers et al.
attribution name: Carruthers et al.

Propofol inhibits stromatoxin-1-sensitive voltage-dependent K+ channels in pancreatic β-cells and enhances insulin secretion
type: item
type: AcademicArticle
description: Background Proper glycemic control is an important goal of critical care medicine, including perioperative patient care that can influence patients’ prognosis. Insulin secretion from pancreatic β-cells is generally assumed to play a critical role in glycemic control in response to an elevated blood glucose concentration. Many animal and human studies have demonstrated that perioperative drugs, including volatile anesthetics, have an impact on glucose-stimulated insulin secretion (GSIS). However, the effects of the intravenous anesthetic propofol on glucose metabolism and insulin sensitivity are largely unknown at present. Methods The effect of propofol on insulin secretion under low glucose or high glucose was examined in mouse MIN6 cells, rat INS-1 cells, and mouse pancreatic β-cells/islets. Cellular oxygen or energy metabolism was measured by Extracellular Flux Analyzer. Expression of glucose transporter 2 (GLUT2), potassium channels, and insulin mRNA was assessed by qRT-PCR. Protein expression of voltage-dependent potassium channels (Kv2) was also assessed by immunoblot. Propofol’s effects on potassium channels including stromatoxin-1-sensitive Kv channels and cellular oxygen and energy metabolisms were also examined. Results We showed that propofol, at clinically relevant doses, facilitates insulin secretion under low glucose conditions and GSIS in MIN6, INS-1 cells, and pancreatic β-cells/islets. Propofol did not affect intracellular ATP or ADP concentrations and cellular oxygen or energy metabolism. The mRNA expression of GLUT2 and channels including the voltage-dependent calcium channels Cav1.2, Kir6.2, and SUR1 subunit of KATP, and Kv2 were not affected by glucose or propofol. Finally, we demonstrated that propofol specifically blocks Kv currents in β-cells, resulting in insulin secretion in the presence of glucose. Conclusions Our data support the hypothesis that glucose induces membrane depolarization at the distal site, leading to KATP channel closure, an…
format: application/pdf
format: text/html
creator: Munenori Kusunoki
creator: Mikio Hayashi
creator: Tomohiro Shoji
creator: Takeo Uba
creator: Hiromasa Tanaka
creator: Chisato Sumi
creator: Yoshiyuki Matsuo
creator: Kiichi Hirota
subject: Cell Biology
subject: Anesthesiology and Pain Management
subject: Diabetes and Endocrinology
subject: Pharmacology
description: doi:10.7717/peerj.8157
publisher: PeerJ Inc.
rights: © 2019 Kusunoki et al.
abstract: Background Proper glycemic control is an important goal of critical care medicine, including perioperative patient care that can influence patients’ prognosis. Insulin secretion from pancreatic β-cells is generally assumed to play a critical role in glycemic control in response to an elevated blood glucose concentration. Many animal and human studies have demonstrated that perioperative drugs, including volatile anesthetics, have an impact on glucose-stimulated insulin secretion (GSIS). However, the effects of the intravenous anesthetic propofol on glucose metabolism and insulin sensitivity are largely unknown at present. Methods The effect of propofol on insulin secretion under low glucose or high glucose was examined in mouse MIN6 cells, rat INS-1 cells, and mouse pancreatic β-cells/islets. Cellular oxygen or energy metabolism was measured by Extracellular Flux Analyzer. Expression of glucose transporter 2 (GLUT2), potassium channels, and insulin mRNA was assessed by qRT-PCR. Protein expression of voltage-dependent potassium channels (Kv2) was also assessed by immunoblot. Propofol’s effects on potassium channels including stromatoxin-1-sensitive Kv channels and cellular oxygen and energy metabolisms were also examined. Results We showed that propofol, at clinically relevant doses, facilitates insulin secretion under low glucose conditions and GSIS in MIN6, INS-1 cells, and pancreatic β-cells/islets. Propofol did not affect intracellular ATP or ADP concentrations and cellular oxygen or energy metabolism. The mRNA expression of GLUT2 and channels including the voltage-dependent calcium channels Cav1.2, Kir6.2, and SUR1 subunit of KATP, and Kv2 were not affected by glucose or propofol. Finally, we demonstrated that propofol specifically blocks Kv currents in β-cells, resulting in insulin secretion in the presence of glucose. Conclusions Our data support the hypothesis that glucose induces membrane depolarization at the distal site, leading to KATP channel closure, an…
bibliographic citation: Kusunoki et al. (2019) Propofol inhibits stromatoxin-1-sensitive voltage-dependent K+ channels in pancreatic β-cells and enhances insulin secretion. PeerJ 7:e8157 https://doi.org/10.7717/peerj.8157
date submitted: 2019-05-23
date accepted: 2019-11-04
issued: 2019-12-02
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Kusunoki
  given name: Munenori
author list: Agent
  family name: Hayashi
  given name: Mikio
author list: Agent
  family name: Shoji
  given name: Tomohiro
author list: Agent
  family name: Uba
  given name: Takeo
author list: Agent
  family name: Tanaka
  given name: Hiromasa
author list: Agent
  family name: Sumi
  given name: Chisato
author list: Agent
  family name: Matsuo
  given name: Yoshiyuki
author list: Agent
  family name: Hirota
  given name: Kiichi
doi: 10.7717/peerj.8157
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-12-02
copyright: ©2019 Kusunoki et al.
attribution name: Kusunoki et al.

Global transcriptome analysis of different stages of preimplantation embryo development in river buffalo
type: item
type: AcademicArticle
description: Background Water buffalo (Bubalus bubalis) are divided into river buffalo and swamp buffalo subspecies and are essential livestock for agriculture and the local economy. Studies on buffalo reproduction have primarily focused on optimal fertility and embryonic mortality. There is currently limited knowledge on buffalo embryonic development, especially during the preimplantation period. Assembly of the river buffalo genome offers a reference for omics studies and facilitates transcriptomic analysis of preimplantation embryo development (PED). Methods We revealed transcriptomic profile of four stages (2-cell, 8-cell, Morula and Blastocyst) of PED via RNA-seq (Illumina HiSeq4000). Each stage comprised three biological replicates. The data were analyzed according to the basic RNA-seq analysis process. Ingenuity analysis of cell lineage control, especially transcription factor (TF) regulatory networks, was also performed. Results A total of 21,519 expressed genes and 67,298 transcripts were predicted from approximately 81.94 Gb of raw data. Analysis of transcriptome-wide expression, gene coexpression networks, and differentially expressed genes (DEGs) allowed for the characterization of gene-specific expression levels and relationships for each stage. The expression patterns of TFs, such as POU5F1, TEAD4, CDX4 and GATAs, were elucidated across diverse time series; most TF expression levels were increased during the blastocyst stage, during which time cell differentiation is initiated. All of these TFs were involved in the composition of the regulatory networks that precisely specify cell fate. These findings offer a deeper understanding of PED at the transcriptional level in the river buffalo.
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format: text/html
creator: Chun-Ying Pang
creator: Ming-Zhou Bai
creator: Chi Zhang
creator: Junhui Chen
creator: Xing-Rong Lu
creator: Ting-Xian Deng
creator: Xiao-Ya Ma
creator: An-Qin Duan
creator: Sha-sha Liang
creator: Yun-Qi Huang
creator: Zhihui Xiu
creator: Xian-Wei Liang
subject: Agricultural Science
subject: Bioinformatics
subject: Developmental Biology
subject: Molecular Biology
subject: Zoology
description: doi:10.7717/peerj.8185
publisher: PeerJ Inc.
rights: © 2019 Pang et al.
abstract: Background Water buffalo (Bubalus bubalis) are divided into river buffalo and swamp buffalo subspecies and are essential livestock for agriculture and the local economy. Studies on buffalo reproduction have primarily focused on optimal fertility and embryonic mortality. There is currently limited knowledge on buffalo embryonic development, especially during the preimplantation period. Assembly of the river buffalo genome offers a reference for omics studies and facilitates transcriptomic analysis of preimplantation embryo development (PED). Methods We revealed transcriptomic profile of four stages (2-cell, 8-cell, Morula and Blastocyst) of PED via RNA-seq (Illumina HiSeq4000). Each stage comprised three biological replicates. The data were analyzed according to the basic RNA-seq analysis process. Ingenuity analysis of cell lineage control, especially transcription factor (TF) regulatory networks, was also performed. Results A total of 21,519 expressed genes and 67,298 transcripts were predicted from approximately 81.94 Gb of raw data. Analysis of transcriptome-wide expression, gene coexpression networks, and differentially expressed genes (DEGs) allowed for the characterization of gene-specific expression levels and relationships for each stage. The expression patterns of TFs, such as POU5F1, TEAD4, CDX4 and GATAs, were elucidated across diverse time series; most TF expression levels were increased during the blastocyst stage, during which time cell differentiation is initiated. All of these TFs were involved in the composition of the regulatory networks that precisely specify cell fate. These findings offer a deeper understanding of PED at the transcriptional level in the river buffalo.
bibliographic citation: Pang et al. (2019) Global transcriptome analysis of different stages of preimplantation embryo development in river buffalo. PeerJ 7:e8185 https://doi.org/10.7717/peerj.8185
date submitted: 2019-07-01
date accepted: 2019-11-10
issued: 2019-12-02
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Pang
  given name: Chun-Ying
author list: Agent
  family name: Bai
  given name: Ming-Zhou
author list: Agent
  family name: Zhang
  given name: Chi
author list: Agent
  family name: Chen
  given name: Junhui
author list: Agent
  family name: Lu
  given name: Xing-Rong
author list: Agent
  family name: Deng
  given name: Ting-Xian
author list: Agent
  family name: Ma
  given name: Xiao-Ya
author list: Agent
  family name: Duan
  given name: An-Qin
author list: Agent
  family name: Liang
  given name: Sha-sha
author list: Agent
  family name: Huang
  given name: Yun-Qi
author list: Agent
  family name: Xiu
  given name: Zhihui
author list: Agent
  family name: Liang
  given name: Xian-Wei
doi: 10.7717/peerj.8185
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-12-02
copyright: ©2019 Pang et al.
attribution name: Pang et al.

Brain structural and functional changes in patients with major depressive disorder: a literature review
type: item
type: AcademicArticle
description: Depression is a mental disorder characterized by low mood and anhedonia that involves abnormalities in multiple brain regions and networks. Epidemiological studies demonstrated that depression has become one of the most important diseases affecting human health and longevity. The pathogenesis of the disease has not been fully elucidated. The clinical effect of treatment is not satisfactory in many cases. Neuroimaging studies have provided rich and valuable evidence that psychological symptoms and behavioral deficits in patients with depression are closely related to structural and functional abnormalities in specific areas of the brain. There were morphological differences in several brain regions, including the frontal lobe, temporal lobe, and limbic system, in people with depression compared to healthy people. In addition, people with depression also had abnormal functional connectivity to the default mode network, the central executive network, and the salience network. These findings provide an opportunity to re-understand the biological mechanisms of depression. In the future, magnetic resonance imaging (MRI) may serve as an important auxiliary tool for psychiatrists in the process of early and accurate diagnosis of depression and finding the appropriate treatment target for each patient to optimize clinical response.
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creator: Lisong Dai
creator: Hongmei Zhou
creator: Xiangyang Xu
creator: Zhentao Zuo
subject: Psychiatry and Psychology
subject: Public Health
subject: Radiology and Medical Imaging
description: doi:10.7717/peerj.8170
publisher: PeerJ Inc.
rights: © 2019 Dai et al.
abstract: Depression is a mental disorder characterized by low mood and anhedonia that involves abnormalities in multiple brain regions and networks. Epidemiological studies demonstrated that depression has become one of the most important diseases affecting human health and longevity. The pathogenesis of the disease has not been fully elucidated. The clinical effect of treatment is not satisfactory in many cases. Neuroimaging studies have provided rich and valuable evidence that psychological symptoms and behavioral deficits in patients with depression are closely related to structural and functional abnormalities in specific areas of the brain. There were morphological differences in several brain regions, including the frontal lobe, temporal lobe, and limbic system, in people with depression compared to healthy people. In addition, people with depression also had abnormal functional connectivity to the default mode network, the central executive network, and the salience network. These findings provide an opportunity to re-understand the biological mechanisms of depression. In the future, magnetic resonance imaging (MRI) may serve as an important auxiliary tool for psychiatrists in the process of early and accurate diagnosis of depression and finding the appropriate treatment target for each patient to optimize clinical response.
bibliographic citation: Dai et al. (2019) Brain structural and functional changes in patients with major depressive disorder: a literature review. PeerJ 7:e8170 https://doi.org/10.7717/peerj.8170
date submitted: 2019-06-08
date accepted: 2019-11-06
issued: 2019-11-29
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Dai
  given name: Lisong
author list: Agent
  family name: Zhou
  given name: Hongmei
author list: Agent
  family name: Xu
  given name: Xiangyang
author list: Agent
  family name: Zuo
  given name: Zhentao
doi: 10.7717/peerj.8170
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-11-29
copyright: ©2019 Dai et al.
attribution name: Dai et al.

Stress-induced changes in the expression of antioxidant system genes for rice (Oryza sativa L.) and bread wheat (Triticum aestivum L.)
type: item
type: AcademicArticle
description: Background Plant cell metabolism inevitably forms reactive oxygen species (ROS), which can damage cells or lead to their death. The antioxidant system (AOS) evolved to eliminate a high concentration of ROS. For plants, this system consists of the seven classes of antioxidant enzymes and antioxidant compounds. Each enzymatic class contains a various number of genes which may vary from species to species. In such a multi-copy genetic system, the integration of evolutionary characteristics and expression data makes it possible to effectively predict promising breeding targets for the design of highly-yielding cultivars. In the plant cells, ROS production can increase as a result of abiotic stresses. Accordingly, AOS responds to stress by altering the expression of the genes of its components. Expression profiles of AOS enzymes, including their changes under stress, remains incomplete. A comprehensive study of the system behavior in response to stress for different species gives the key to identify the general mechanisms of AOS regulation. In this article, we studied stress-induced changes in the expression of AOS genes in photosynthetic tissues for rice and bread wheat. Methods A meta-analysis of genome-wide transcriptome data on stress-induced changes in expression profiles of antioxidant genes using microarray and next generation sequencing (NGS) experiments from the GEO NCBI database for rice and bread wheat was carried out. Experimental study of expression changes in short (6 h) and prolonged (24 h) cold stress responses for selected AOS genes of bread wheat cultivars Saratovskaya29 and Yanetzkis Probat was conducted using qPCR. Results The large-scale meta-transcriptome and complementary experimental analysis revealed a summary of fold changes in the AOS gene expression in response to cold and water deficiency for rice and bread wheat.
format: application/pdf
format: text/html
creator: Anton Ermakov
creator: Aleksandr Bobrovskikh
creator: Ulyana Zubairova
creator: Dmitrii Konstantinov
creator: Alexey Doroshkov
subject: Bioinformatics
subject: Computational Biology
subject: Genomics
subject: Plant Science
description: doi:10.7717/peerj.7791
publisher: PeerJ Inc.
rights: © 2019 Ermakov et al.
abstract: Background Plant cell metabolism inevitably forms reactive oxygen species (ROS), which can damage cells or lead to their death. The antioxidant system (AOS) evolved to eliminate a high concentration of ROS. For plants, this system consists of the seven classes of antioxidant enzymes and antioxidant compounds. Each enzymatic class contains a various number of genes which may vary from species to species. In such a multi-copy genetic system, the integration of evolutionary characteristics and expression data makes it possible to effectively predict promising breeding targets for the design of highly-yielding cultivars. In the plant cells, ROS production can increase as a result of abiotic stresses. Accordingly, AOS responds to stress by altering the expression of the genes of its components. Expression profiles of AOS enzymes, including their changes under stress, remains incomplete. A comprehensive study of the system behavior in response to stress for different species gives the key to identify the general mechanisms of AOS regulation. In this article, we studied stress-induced changes in the expression of AOS genes in photosynthetic tissues for rice and bread wheat. Methods A meta-analysis of genome-wide transcriptome data on stress-induced changes in expression profiles of antioxidant genes using microarray and next generation sequencing (NGS) experiments from the GEO NCBI database for rice and bread wheat was carried out. Experimental study of expression changes in short (6 h) and prolonged (24 h) cold stress responses for selected AOS genes of bread wheat cultivars Saratovskaya29 and Yanetzkis Probat was conducted using qPCR. Results The large-scale meta-transcriptome and complementary experimental analysis revealed a summary of fold changes in the AOS gene expression in response to cold and water deficiency for rice and bread wheat.
bibliographic citation: Ermakov et al. (2019) Stress-induced changes in the expression of antioxidant system genes for rice (Oryza sativa L.) and bread wheat (Triticum aestivum L.). PeerJ 7:e7791 https://doi.org/10.7717/peerj.7791
date submitted: 2019-05-02
date accepted: 2019-08-29
issued: 2019-11-29
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Ermakov
  given name: Anton
author list: Agent
  family name: Bobrovskikh
  given name: Aleksandr
author list: Agent
  family name: Zubairova
  given name: Ulyana
author list: Agent
  family name: Konstantinov
  given name: Dmitrii
author list: Agent
  family name: Doroshkov
  given name: Alexey
doi: 10.7717/peerj.7791
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-11-29
copyright: © 2019 Ermakov et al.
attribution name: Ermakov et al.

Taxonomic assessment of species of the genus Octopus from the northeastern Pacific via morphological, molecular and morphometric analyses
type: item
type: AcademicArticle
description: Species of the genus Octopus from the northeastern Pacific are ecologically and economically important; however, their taxonomy is confusing and has not been comprehensively assessed. In this study, we performed a taxonomic evaluation of these species considering the morphological characteristics of the original descriptions, a molecular analysis of partial COI-gene sequences, and a traditional morphometry analysis of nine body measurements. Several interesting findings were obtained with our results: for instance, we updated the diagnoses of some species by including characters such as the number of lamellae per demibranch and the presence of chromatophores in the visceral sac; we deposited partial COI-gene sequences of species that had not been incorporated into the GenBank repository; and according to the morphometric analysis, we confirmed that the lengths of arms I–IV are relevant to discriminate the species under study. The taxa evaluated were morphologically, molecularly and morphometrically well-delimited; however, features such as funnel organ shape and arm length proportions in regard to dorsal mantle length are either not included in the diagnosis of the genus Octopus or overlap with other genera. Hence, this information, combined with the results obtained from the molecular analysis, supports the generic re-assignation of two of the species evaluated.
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format: text/html
creator: Mariana Díaz-Santana-Iturrios
creator: César Augusto Salinas-Zavala
creator: Francisco Javier García-Rodríguez
creator: Jasmín Granados-Amores
subject: Aquaculture, Fisheries and Fish Science
subject: Biodiversity
subject: Marine Biology
subject: Taxonomy
subject: Zoology
description: doi:10.7717/peerj.8118
publisher: PeerJ Inc.
rights: © 2019 Díaz-Santana-Iturrios et al.
abstract: Species of the genus Octopus from the northeastern Pacific are ecologically and economically important; however, their taxonomy is confusing and has not been comprehensively assessed. In this study, we performed a taxonomic evaluation of these species considering the morphological characteristics of the original descriptions, a molecular analysis of partial COI-gene sequences, and a traditional morphometry analysis of nine body measurements. Several interesting findings were obtained with our results: for instance, we updated the diagnoses of some species by including characters such as the number of lamellae per demibranch and the presence of chromatophores in the visceral sac; we deposited partial COI-gene sequences of species that had not been incorporated into the GenBank repository; and according to the morphometric analysis, we confirmed that the lengths of arms I–IV are relevant to discriminate the species under study. The taxa evaluated were morphologically, molecularly and morphometrically well-delimited; however, features such as funnel organ shape and arm length proportions in regard to dorsal mantle length are either not included in the diagnosis of the genus Octopus or overlap with other genera. Hence, this information, combined with the results obtained from the molecular analysis, supports the generic re-assignation of two of the species evaluated.
bibliographic citation: Díaz-Santana-Iturrios et al. (2019) Taxonomic assessment of species of the genus Octopus from the northeastern Pacific via morphological, molecular and morphometric analyses. PeerJ 7:e8118 https://doi.org/10.7717/peerj.8118
date submitted: 2019-07-12
date accepted: 2019-10-29
issued: 2019-11-29
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Díaz-Santana-Iturrios
  given name: Mariana
author list: Agent
  family name: Salinas-Zavala
  given name: César Augusto
author list: Agent
  family name: García-Rodríguez
  given name: Francisco Javier
author list: Agent
  family name: Granados-Amores
  given name: Jasmín
doi: 10.7717/peerj.8118
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-11-29
copyright: © 2019 Díaz-Santana-Iturrios et al.
attribution name: Díaz-Santana-Iturrios et al.

Relationship between the Dark Triad and depressive symptoms
type: item
type: AcademicArticle
description: The Dark Triad (DT) is composed of three closely related personality traits: psychopathy, Machiavellianism and narcissism. These traits have been linked to emotional deficits. The aim of the present study was to analyze the relationship between the DT traits, including sub-dimensions, and depressive symptoms in order to identify those factors most strongly associated with the development of depression in individuals scoring high on DT. For these purposes, a total of 791 adults (M = 35.76 years; 24.91% males) completed a questionnaire battery including DT traits and depression measures. A positive significant correlation was found between psychopathy and Machiavellianism traits (total score and all sub-dimensions) and depressive symptoms. For narcissism, the direction of the correlation was dependent on the sub-dimension assessed. A model explaining 26.2% of the depressive symptoms scores was composed of the callous affect and criminal tendencies sub-dimensions of psychopathy, cynical view of human nature, which is a sub-dimension of Machiavellianism, and entitlement and self-sufficiency, which are sub-dimensions of narcissism. In addition, some of the relationships found between DT sub-dimensions and depressive symptoms appeared to depend on gender. Our results could have implications for detection and intervention programs aimed at decreasing the negative emotional consequences suffered by individuals with high DT scores. Limitations and future lines of research are discussed.
format: application/pdf
format: text/html
creator: Raquel Gómez-Leal
creator: Alberto Megías-Robles
creator: María José Gutiérrez-Cobo
creator: Rosario Cabello
creator: Enrique G. Fernández-Abascal
creator: Pablo Fernández-Berrocal
subject: Cognitive Disorders
subject: Public Health
description: doi:10.7717/peerj.8120
publisher: PeerJ Inc.
rights: © 2019 Gómez-Leal et al.
abstract: The Dark Triad (DT) is composed of three closely related personality traits: psychopathy, Machiavellianism and narcissism. These traits have been linked to emotional deficits. The aim of the present study was to analyze the relationship between the DT traits, including sub-dimensions, and depressive symptoms in order to identify those factors most strongly associated with the development of depression in individuals scoring high on DT. For these purposes, a total of 791 adults (M = 35.76 years; 24.91% males) completed a questionnaire battery including DT traits and depression measures. A positive significant correlation was found between psychopathy and Machiavellianism traits (total score and all sub-dimensions) and depressive symptoms. For narcissism, the direction of the correlation was dependent on the sub-dimension assessed. A model explaining 26.2% of the depressive symptoms scores was composed of the callous affect and criminal tendencies sub-dimensions of psychopathy, cynical view of human nature, which is a sub-dimension of Machiavellianism, and entitlement and self-sufficiency, which are sub-dimensions of narcissism. In addition, some of the relationships found between DT sub-dimensions and depressive symptoms appeared to depend on gender. Our results could have implications for detection and intervention programs aimed at decreasing the negative emotional consequences suffered by individuals with high DT scores. Limitations and future lines of research are discussed.
bibliographic citation: Gómez-Leal et al. (2019) Relationship between the Dark Triad and depressive symptoms. PeerJ 7:e8120 https://doi.org/10.7717/peerj.8120
date submitted: 2019-06-13
date accepted: 2019-10-30
issued: 2019-11-29
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Gómez-Leal
  given name: Raquel
author list: Agent
  family name: Megías-Robles
  given name: Alberto
author list: Agent
  family name: Gutiérrez-Cobo
  given name: María José
author list: Agent
  family name: Cabello
  given name: Rosario
author list: Agent
  family name: Fernández-Abascal
  given name: Enrique G.
author list: Agent
  family name: Fernández-Berrocal
  given name: Pablo
doi: 10.7717/peerj.8120
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-11-29
copyright: © 2019 Gómez-Leal et al.
attribution name: Gómez-Leal et al.

Identification of prognostic gene signature associated with microenvironment of lung adenocarcinoma
type: item
type: AcademicArticle
description: Background Lung cancer has the highest morbidity and mortality worldwide, and lung adenocarcinoma (LADC) is the most common pathological subtype. Accumulating evidence suggests the tumor microenvironment (TME) is correlated with the tumor progress and the patient’s outcome. As the major components of TME, the tumor-infiltrated immune cells and stromal cells have attracted more and more attention. In this study, differentially expressed immune and stromal signature genes were used to construct a TME-related prognostic model for predicting the outcomes of LADC patients. Methods The expression profiles of LADC samples with clinical information were obtained from The Cancer Genome Atlas (TCGA) and Gene Expression Omnibus (GEO). The differentially expressed genes (DEGs) related to the TME of LADC were identified using TCGA dataset by Wilcoxon rank sum test. The prognostic effects of TME-related DEGs were analyzed using univariate Cox regression. Then, the least absolute shrinkage and selection operator (LASSO) regression was performed to reduce the overfit and the number of genes for further analysis. Next, the prognostic model was constructed by step multivariate Cox regression and risk score of each sample was calculated. Then, survival and Receiver Operating Characteristic (ROC) analyses were conducted to validate the model using TCGA and GEO datasets, respectively. The Kyoto Encyclopedia of Genes and Genomes analysis of gene signature was performed using Gene Set Enrichment Analysis (GSEA). Finally, the overall immune status, tumor purity and the expression profiles of HLA genes of high- and low-risk samples was further analyzed to reveal the potential mechanisms of prognostic effects of the model. Results A total of 93 TME-related DEGs were identified, of which 23 DEGs were up-regulated and 70 DEGs were down-regulated. The univariate cox analysis indicated that 23 DEGs has the prognostic effects, the hazard ratio ranged from 0.65 to 1.25 (p < 0.05). Then, seven gene…
format: application/pdf
format: text/html
creator: Cheng Yue
creator: Hongtao Ma
creator: Yubai Zhou
subject: Bioinformatics
subject: Oncology
subject: Respiratory Medicine
subject: Data Mining and Machine Learning
description: doi:10.7717/peerj.8128
publisher: PeerJ Inc.
rights: © 2019 Yue et al.
abstract: Background Lung cancer has the highest morbidity and mortality worldwide, and lung adenocarcinoma (LADC) is the most common pathological subtype. Accumulating evidence suggests the tumor microenvironment (TME) is correlated with the tumor progress and the patient’s outcome. As the major components of TME, the tumor-infiltrated immune cells and stromal cells have attracted more and more attention. In this study, differentially expressed immune and stromal signature genes were used to construct a TME-related prognostic model for predicting the outcomes of LADC patients. Methods The expression profiles of LADC samples with clinical information were obtained from The Cancer Genome Atlas (TCGA) and Gene Expression Omnibus (GEO). The differentially expressed genes (DEGs) related to the TME of LADC were identified using TCGA dataset by Wilcoxon rank sum test. The prognostic effects of TME-related DEGs were analyzed using univariate Cox regression. Then, the least absolute shrinkage and selection operator (LASSO) regression was performed to reduce the overfit and the number of genes for further analysis. Next, the prognostic model was constructed by step multivariate Cox regression and risk score of each sample was calculated. Then, survival and Receiver Operating Characteristic (ROC) analyses were conducted to validate the model using TCGA and GEO datasets, respectively. The Kyoto Encyclopedia of Genes and Genomes analysis of gene signature was performed using Gene Set Enrichment Analysis (GSEA). Finally, the overall immune status, tumor purity and the expression profiles of HLA genes of high- and low-risk samples was further analyzed to reveal the potential mechanisms of prognostic effects of the model. Results A total of 93 TME-related DEGs were identified, of which 23 DEGs were up-regulated and 70 DEGs were down-regulated. The univariate cox analysis indicated that 23 DEGs has the prognostic effects, the hazard ratio ranged from 0.65 to 1.25 (p < 0.05). Then, seven gene…
bibliographic citation: Yue et al. (2019) Identification of prognostic gene signature associated with microenvironment of lung adenocarcinoma. PeerJ 7:e8128 https://doi.org/10.7717/peerj.8128
date submitted: 2019-07-24
date accepted: 2019-10-31
issued: 2019-11-29
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Yue
  given name: Cheng
author list: Agent
  family name: Ma
  given name: Hongtao
author list: Agent
  family name: Zhou
  given name: Yubai
doi: 10.7717/peerj.8128
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-11-29
copyright: © 2019 Yue et al.
attribution name: Yue et al.

Characteristics of the vaginal microbiome in cross-border female sex workers in China: a case-control study
type: item
type: AcademicArticle
description: Background Female sex workers (FSWs) are key groups in the transmission of sexual transmitted infections (STI), and vaginal microbiome variations play an important role in transmission. We aimed to explore the characteristics of vaginal microbiome among FSWs. Materials and Methods A total of 24 cross-border FSWs were randomly selected from a cross-sectional survey for female sex workers in southwest China. Thirty-seven female non-sex workers (FNSWs) were randomly selected from the gynecology clinic and health examination center. Vaginal swabs were collected, bacterial DNA extracted and 16S rRNA genes were sequenced. Differences in the vaginal microbiome between both groups were compared using bioinformatics analysis. Results One DNA sample was excluded due to unqualified concentration, therefore 60 samples were sequenced. FSWs had significantly different vaginal microbiota β diversity, but undifferentiated α diversity when compared with non-sex workers. The average relative abundance of Sneathia, Shigella, Neisseria, Chlamydia, Prevotella, Enterococcus and Ureaplasma among FSWs was higher than FNSWs, and relative abundance of Atopobium in FSWs was lower than FNSWs. The Lactobacillus genus was the major genus in both groups. At the species level, Lactobacllus crispatus, Lactobacllus gasseri and Lactobacllus jensenii, in female sex workers, were lower when compared to FNSWs. Conclusion There were distinct differences in vaginal bacteria variety between FSWs and FNSWs. Some disease-related genus were also more abundant in FSWs. Based on these observations, further research is required to identify microbiome communities related to high STI risks and other diseases in these cohorts.
format: application/pdf
format: text/html
creator: Xiang Hong
creator: Shenghao Fang
creator: Kaiping Huang
creator: Jiechen Yin
creator: Jianshuang Chen
creator: Yan Xuan
creator: Jing Zhu
creator: Jun Ma
creator: Pengfei Qin
creator: Danhong Peng
creator: Ning Wang
creator: Bei Wang
subject: Microbiology
subject: HIV
subject: Public Health
subject: Women’s Health
description: doi:10.7717/peerj.8131
publisher: PeerJ Inc.
rights: © 2019 Hong et al.
abstract: Background Female sex workers (FSWs) are key groups in the transmission of sexual transmitted infections (STI), and vaginal microbiome variations play an important role in transmission. We aimed to explore the characteristics of vaginal microbiome among FSWs. Materials and Methods A total of 24 cross-border FSWs were randomly selected from a cross-sectional survey for female sex workers in southwest China. Thirty-seven female non-sex workers (FNSWs) were randomly selected from the gynecology clinic and health examination center. Vaginal swabs were collected, bacterial DNA extracted and 16S rRNA genes were sequenced. Differences in the vaginal microbiome between both groups were compared using bioinformatics analysis. Results One DNA sample was excluded due to unqualified concentration, therefore 60 samples were sequenced. FSWs had significantly different vaginal microbiota β diversity, but undifferentiated α diversity when compared with non-sex workers. The average relative abundance of Sneathia, Shigella, Neisseria, Chlamydia, Prevotella, Enterococcus and Ureaplasma among FSWs was higher than FNSWs, and relative abundance of Atopobium in FSWs was lower than FNSWs. The Lactobacillus genus was the major genus in both groups. At the species level, Lactobacllus crispatus, Lactobacllus gasseri and Lactobacllus jensenii, in female sex workers, were lower when compared to FNSWs. Conclusion There were distinct differences in vaginal bacteria variety between FSWs and FNSWs. Some disease-related genus were also more abundant in FSWs. Based on these observations, further research is required to identify microbiome communities related to high STI risks and other diseases in these cohorts.
bibliographic citation: Hong et al. (2019) Characteristics of the vaginal microbiome in cross-border female sex workers in China: a case-control study. PeerJ 7:e8131 https://doi.org/10.7717/peerj.8131
date submitted: 2019-07-03
date accepted: 2019-10-31
issued: 2019-11-29
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Hong
  given name: Xiang
author list: Agent
  family name: Fang
  given name: Shenghao
author list: Agent
  family name: Huang
  given name: Kaiping
author list: Agent
  family name: Yin
  given name: Jiechen
author list: Agent
  family name: Chen
  given name: Jianshuang
author list: Agent
  family name: Xuan
  given name: Yan
author list: Agent
  family name: Zhu
  given name: Jing
author list: Agent
  family name: Ma
  given name: Jun
author list: Agent
  family name: Qin
  given name: Pengfei
author list: Agent
  family name: Peng
  given name: Danhong
author list: Agent
  family name: Wang
  given name: Ning
author list: Agent
  family name: Wang
  given name: Bei
doi: 10.7717/peerj.8131
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-11-29
copyright: © 2019 Hong et al.
attribution name: Hong et al.

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