PeerJ
type: channel
link: https://peerj.com/articles/
description: Articles published in PeerJ
publisher: PeerJ Inc.
publication name: PeerJ
issn: 2167-8359
items: Gut microbiota of obese and diabetic Thai subjects and interplay with dietary habits and blood profiles
items: Classification of genomic components and prediction of genes of Begomovirus based on subsequence natural vector and support vector machine
items: Molecular mechanism underlying the effect of illumination time on the growth performance of broilers via changes in the intestinal bacterial community
items: Comparative transcriptomic analysis of Lactiplantibacillus plantarum RS66CD biofilm in high-salt conditions and planktonic cells
items: Increasing methane (CH4) emissions and altering rhizosphere microbial diversity in paddy soil by combining Chinese milk vetch and rice straw
items: Identification of DNA methylation patterns and biomarkers for clear-cell renal cell carcinoma by multi-omics data analysis
items: Characterization of two myostatin genes in pufferfish Takifugu bimaculatus: sequence, genomic structure, and expression
items: Measurement properties of the Knee Injury and Osteoarthritis Outcome Score Patello-Femoral questionnaire in Saudi Arabians
items: Distribution of deep-water scleractinian and stylasterid corals across abiotic environmental gradients on three seamounts in the Anegada Passage
items: Relationship between iron status markers and insulin resistance: an exploratory study in subjects with excess body weight

Gut microbiota of obese and diabetic Thai subjects and interplay with dietary habits and blood profiles
type: item
type: AcademicArticle
description: Obesity and type 2 diabetes mellitus (T2DM) have become major public health issues globally. Recent research indicates that intestinal microbiota play roles in metabolic disorders. Though there are numerous studies focusing on gut microbiota of health and obesity states, those are primarily focused on Western countries. Comparatively, only a few investigations exist on gut microbiota of people from Asian countries. In this study, the fecal microbiota of 30 adult volunteers living in Chiang Rai Province, Thailand were examined using next-generation sequencing (NGS) in association with blood profiles and dietary habits. Subjects were categorized by body mass index (BMI) and health status as follows; lean (L) = 8, overweight (OV) = 8, obese (OB) = 7 and diagnosed T2DM = 7. Members of T2DM group showed differences in dietary consumption and fasting glucose level compared to BMI groups. A low level of high-density cholesterol (HDL) was observed in the OB group. Principal coordinate analysis (PCoA) revealed that microbial communities of T2DM subjects were clearly distinct from those of OB. An analogous pattern was additionally illustrated by multiple factor analysis (MFA) based on dietary habits, blood profiles, and fecal gut microbiota in BMI and T2DM groups. In all four groups, Bacteroidetes and Firmicutes were the predominant phyla. Abundance of Faecalibacterium prausnitzii, a butyrate-producing bacterium, was significantly higher in OB than that in other groups. This study is the first to examine the gut microbiota of adult Thais in association with dietary intake and blood profiles and will provide the platform for future investigations.
format: application/pdf
format: text/html
creator: Lucsame Gruneck
creator: Niwed Kullawong
creator: Kongkiat Kespechara
creator: Siam Popluechai
subject: Microbiology
subject: Diabetes and Endocrinology
subject: Gastroenterology and Hepatology
subject: Hematology
description: doi:10.7717/peerj.9622
publisher: PeerJ Inc.
rights: © 2020 Gruneck et al.
abstract: Obesity and type 2 diabetes mellitus (T2DM) have become major public health issues globally. Recent research indicates that intestinal microbiota play roles in metabolic disorders. Though there are numerous studies focusing on gut microbiota of health and obesity states, those are primarily focused on Western countries. Comparatively, only a few investigations exist on gut microbiota of people from Asian countries. In this study, the fecal microbiota of 30 adult volunteers living in Chiang Rai Province, Thailand were examined using next-generation sequencing (NGS) in association with blood profiles and dietary habits. Subjects were categorized by body mass index (BMI) and health status as follows; lean (L) = 8, overweight (OV) = 8, obese (OB) = 7 and diagnosed T2DM = 7. Members of T2DM group showed differences in dietary consumption and fasting glucose level compared to BMI groups. A low level of high-density cholesterol (HDL) was observed in the OB group. Principal coordinate analysis (PCoA) revealed that microbial communities of T2DM subjects were clearly distinct from those of OB. An analogous pattern was additionally illustrated by multiple factor analysis (MFA) based on dietary habits, blood profiles, and fecal gut microbiota in BMI and T2DM groups. In all four groups, Bacteroidetes and Firmicutes were the predominant phyla. Abundance of Faecalibacterium prausnitzii, a butyrate-producing bacterium, was significantly higher in OB than that in other groups. This study is the first to examine the gut microbiota of adult Thais in association with dietary intake and blood profiles and will provide the platform for future investigations.
bibliographic citation: Gruneck et al. (2020) Gut microbiota of obese and diabetic Thai subjects and interplay with dietary habits and blood profiles. PeerJ 8:e9622 https://doi.org/10.7717/peerj.9622
date submitted: 2020-03-12
date accepted: 2020-07-07
issued: 2020-08-03
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Gruneck
  given name: Lucsame
author list: Agent
  family name: Kullawong
  given name: Niwed
author list: Agent
  family name: Kespechara
  given name: Kongkiat
author list: Agent
  family name: Popluechai
  given name: Siam
doi: 10.7717/peerj.9622
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-08-03
copyright: © 2020 Gruneck et al.
attribution name: Gruneck et al.

Classification of genomic components and prediction of genes of Begomovirus based on subsequence natural vector and support vector machine
type: item
type: AcademicArticle
description: Background Begomoviruses are widely distributed and causing devastating diseases in many crops. According to the number of genomic components, a begomovirus is known as either monopartite or bipartite begomovirus. Both the monopartite and bipartite begomoviruses have the DNA-A component which encodes all essential proteins for virus functions, while the bipartite begomoviruses still contain the DNA-B component. The satellite molecules, known as betasatellites, alphasatellites or deltasatellites, sometimes exist in the begomoviruses. So, the genomic components of begomoviruses are complex and varied. Different genomic components have different gene structures and functions. Classifying the components of begomoviruses is important for studying the virus origin and pathogenic mechanism. Methods We propose a model combining Subsequence Natural Vector (SNV) method with Support Vector Machine (SVM) algorithm, to classify the genomic components of begomoviruses and predict the genes of begomoviruses. First, the genome sequence is represented as a vector numerically by the SNV method. Then SVM is applied on the datasets to build the classification model. At last, recursive feature elimination (RFE) is used to select essential features of the subsequence natural vectors based on the importance of features. Results In the investigation, DNA-A, DNA-B, and different satellite DNAs are selected to build the model. To evaluate our model, the homology-based method BLAST and two machine learning algorithms Random Forest and Naive Bayes method are used to compare with our model. According to the results, our classification model can classify DNA-A, DNA-B, and different satellites with high accuracy. Especially, we can distinguish whether a DNA-A component is from a monopartite or a bipartite begomovirus. Then, based on the results of classification, we can also predict the genes of different genomic components. According to the selected features, we find that the content of four nuc…
format: application/pdf
format: text/html
creator: Shaojun Pei
creator: Rui Dong
creator: Yiming Bao
creator: Rong Lucy He
creator: Stephen S.-T. Yau
subject: Bioinformatics
subject: Genetics
subject: Mathematical Biology
subject: Virology
subject: Data Mining and Machine Learning
description: doi:10.7717/peerj.9625
publisher: PeerJ Inc.
rights: © 2020 Pei et al.
abstract: Background Begomoviruses are widely distributed and causing devastating diseases in many crops. According to the number of genomic components, a begomovirus is known as either monopartite or bipartite begomovirus. Both the monopartite and bipartite begomoviruses have the DNA-A component which encodes all essential proteins for virus functions, while the bipartite begomoviruses still contain the DNA-B component. The satellite molecules, known as betasatellites, alphasatellites or deltasatellites, sometimes exist in the begomoviruses. So, the genomic components of begomoviruses are complex and varied. Different genomic components have different gene structures and functions. Classifying the components of begomoviruses is important for studying the virus origin and pathogenic mechanism. Methods We propose a model combining Subsequence Natural Vector (SNV) method with Support Vector Machine (SVM) algorithm, to classify the genomic components of begomoviruses and predict the genes of begomoviruses. First, the genome sequence is represented as a vector numerically by the SNV method. Then SVM is applied on the datasets to build the classification model. At last, recursive feature elimination (RFE) is used to select essential features of the subsequence natural vectors based on the importance of features. Results In the investigation, DNA-A, DNA-B, and different satellite DNAs are selected to build the model. To evaluate our model, the homology-based method BLAST and two machine learning algorithms Random Forest and Naive Bayes method are used to compare with our model. According to the results, our classification model can classify DNA-A, DNA-B, and different satellites with high accuracy. Especially, we can distinguish whether a DNA-A component is from a monopartite or a bipartite begomovirus. Then, based on the results of classification, we can also predict the genes of different genomic components. According to the selected features, we find that the content of four nuc…
bibliographic citation: Pei et al. (2020) Classification of genomic components and prediction of genes of Begomovirus based on subsequence natural vector and support vector machine. PeerJ 8:e9625 https://doi.org/10.7717/peerj.9625
date submitted: 2020-04-02
date accepted: 2020-07-08
issued: 2020-08-03
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Pei
  given name: Shaojun
author list: Agent
  family name: Dong
  given name: Rui
author list: Agent
  family name: Bao
  given name: Yiming
author list: Agent
  family name: He
  given name: Rong Lucy
author list: Agent
  family name: Yau
  given name: Stephen S.-T.
doi: 10.7717/peerj.9625
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-08-03
copyright: ©2020 Pei et al.
attribution name: Pei et al.

Molecular mechanism underlying the effect of illumination time on the growth performance of broilers via changes in the intestinal bacterial community
type: item
type: AcademicArticle
description: The circadian rhythms associated with light have important effects on the growth, metabolism, immunity and reproduction of broilers. However, there is a lack of systematic evaluations of the effect of the light cycle on intestinal microbes and the nutritional metabolism of these microbes in broilers. This study was designed to study the effects of the light cycle on the intestinal bacterial community structure and growth of broilers. In this study, Arbor Acre (AA) broilers were fed under a short photoperiod (1L:23D), a long photoperiod (23L:1D), and a normal photoperiod (16L:8D), respectively. The feed conversion ratio of the broilers was calculated, and the levels of endocrine hormones, such as melatonin, insulin and glucagon, were determined. Intestinal contents were collected from the small intestines of the broilers after slaughtering, and the V3+V4 region of the 16s rDNA gene was sequenced. The results demonstrated that changes in the light cycle could affect the synthetic rhythms of melatonin, insulin and glucagon. Compared to short and normal photoperiod, long photoperiod significantly increased the abundances of Barnesiella species in intestinal microbes and decreased the abundances of Bacteroides and Alistipes species. Cluster of Orthologous Groups of proteins analysis indicated that prolongation of the illumination increased the abundances of bacterial genes with glycometabolic and membrane transport functions in intestinal microorganisms. A model was established in this study, and our results showed that prolonged illumination altered the intestinal microbial community structures of broilers, increased the absorption and utilization of polysaccharides in broilers, and reduced the feed-to-meat ratios. To the best of our knowledge, this is also the first study to describe the molecular mechanism underlying the effects of the light cycle on the uptake and utilization of nutrients that occur via modification of the intestinal microbial community structure in …
format: application/pdf
format: text/html
creator: Yongfen Wang
creator: Zhen Zhang
creator: Pengkun Yang
creator: Miaorui Zhang
creator: Lei Xi
creator: Qiong Liu
creator: Jingang Li
subject: Microbiology
subject: Molecular Biology
subject: Zoology
description: doi:10.7717/peerj.9638
publisher: PeerJ Inc.
rights: © 2020 Wang et al.
abstract: The circadian rhythms associated with light have important effects on the growth, metabolism, immunity and reproduction of broilers. However, there is a lack of systematic evaluations of the effect of the light cycle on intestinal microbes and the nutritional metabolism of these microbes in broilers. This study was designed to study the effects of the light cycle on the intestinal bacterial community structure and growth of broilers. In this study, Arbor Acre (AA) broilers were fed under a short photoperiod (1L:23D), a long photoperiod (23L:1D), and a normal photoperiod (16L:8D), respectively. The feed conversion ratio of the broilers was calculated, and the levels of endocrine hormones, such as melatonin, insulin and glucagon, were determined. Intestinal contents were collected from the small intestines of the broilers after slaughtering, and the V3+V4 region of the 16s rDNA gene was sequenced. The results demonstrated that changes in the light cycle could affect the synthetic rhythms of melatonin, insulin and glucagon. Compared to short and normal photoperiod, long photoperiod significantly increased the abundances of Barnesiella species in intestinal microbes and decreased the abundances of Bacteroides and Alistipes species. Cluster of Orthologous Groups of proteins analysis indicated that prolongation of the illumination increased the abundances of bacterial genes with glycometabolic and membrane transport functions in intestinal microorganisms. A model was established in this study, and our results showed that prolonged illumination altered the intestinal microbial community structures of broilers, increased the absorption and utilization of polysaccharides in broilers, and reduced the feed-to-meat ratios. To the best of our knowledge, this is also the first study to describe the molecular mechanism underlying the effects of the light cycle on the uptake and utilization of nutrients that occur via modification of the intestinal microbial community structure in …
bibliographic citation: Wang et al. (2020) Molecular mechanism underlying the effect of illumination time on the growth performance of broilers via changes in the intestinal bacterial community. PeerJ 8:e9638 https://doi.org/10.7717/peerj.9638
date submitted: 2020-02-24
date accepted: 2020-07-09
issued: 2020-08-03
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Wang
  given name: Yongfen
author list: Agent
  family name: Zhang
  given name: Zhen
author list: Agent
  family name: Yang
  given name: Pengkun
author list: Agent
  family name: Zhang
  given name: Miaorui
author list: Agent
  family name: Xi
  given name: Lei
author list: Agent
  family name: Liu
  given name: Qiong
author list: Agent
  family name: Li
  given name: Jingang
doi: 10.7717/peerj.9638
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-08-03
copyright: © 2020 Wang et al.
attribution name: Wang et al.

Comparative transcriptomic analysis of Lactiplantibacillus plantarum RS66CD biofilm in high-salt conditions and planktonic cells
type: item
type: AcademicArticle
description: Background Lactiplantibacillus plantarum (L. plantarum), a dominant strain in traditional fermented foods, is widely used in fermentation industry because of its fast acid production. However, L. plantarum is easily inactivated due to acidity, high temperature and other factors. The formation of biofilm by bacteria can effectively increase environmental tolerance. Therefore, it is important to improve the environmental tolerance of L. plantarum by studying its biofilm formation conditions and regulatory mechanisms. Methods After determining a suitable NaCl concentration for promoting biofilm formation, L. plantarum was grown with 48 g L−1 NaCl. Differential gene expressions in L. plantarum biofilm vs. planktonic cells were analyzed using RNA sequencing and validated using qPCR. Result L. plantarum RS66CD biofilm formation formed highest amount of when grown at 48 g L−1 NaCl. Altogether 447 genes were up-regulated and 426 genes were down-regulated in the biofilm. KEGG pathway analysis showed that genes coding for D-Alanine metabolism, peptidoglycan biosynthesis, two-component system, carbon metabolism, bacterial secretion system, lysine biosynthesis and fatty acid metabolism were crucial for biofilm formation. In addition, eight other genes related to biofilm formation were differentially expressed. Our results provide insights into the differential gene expression involved in biofilm formation, which can help to reveal gene regulation during L. plantarum biofilm formation.
format: application/pdf
format: text/html
creator: Xiaolin Ao
creator: Jiawei Zhao
creator: Junling Yan
creator: Shuliang Liu
creator: Ke Zhao
subject: Food Science and Technology
subject: Genomics
subject: Microbiology
subject: Molecular Biology
description: doi:10.7717/peerj.9639
publisher: PeerJ Inc.
rights: © 2020 Ao et al.
abstract: Background Lactiplantibacillus plantarum (L. plantarum), a dominant strain in traditional fermented foods, is widely used in fermentation industry because of its fast acid production. However, L. plantarum is easily inactivated due to acidity, high temperature and other factors. The formation of biofilm by bacteria can effectively increase environmental tolerance. Therefore, it is important to improve the environmental tolerance of L. plantarum by studying its biofilm formation conditions and regulatory mechanisms. Methods After determining a suitable NaCl concentration for promoting biofilm formation, L. plantarum was grown with 48 g L−1 NaCl. Differential gene expressions in L. plantarum biofilm vs. planktonic cells were analyzed using RNA sequencing and validated using qPCR. Result L. plantarum RS66CD biofilm formation formed highest amount of when grown at 48 g L−1 NaCl. Altogether 447 genes were up-regulated and 426 genes were down-regulated in the biofilm. KEGG pathway analysis showed that genes coding for D-Alanine metabolism, peptidoglycan biosynthesis, two-component system, carbon metabolism, bacterial secretion system, lysine biosynthesis and fatty acid metabolism were crucial for biofilm formation. In addition, eight other genes related to biofilm formation were differentially expressed. Our results provide insights into the differential gene expression involved in biofilm formation, which can help to reveal gene regulation during L. plantarum biofilm formation.
bibliographic citation: Ao et al. (2020) Comparative transcriptomic analysis of Lactiplantibacillus plantarum RS66CD biofilm in high-salt conditions and planktonic cells. PeerJ 8:e9639 https://doi.org/10.7717/peerj.9639
date submitted: 2020-03-23
date accepted: 2020-07-09
issued: 2020-08-03
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Ao
  given name: Xiaolin
author list: Agent
  family name: Zhao
  given name: Jiawei
author list: Agent
  family name: Yan
  given name: Junling
author list: Agent
  family name: Liu
  given name: Shuliang
author list: Agent
  family name: Zhao
  given name: Ke
doi: 10.7717/peerj.9639
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-08-03
copyright: ©2020 Ao et al.
attribution name: Ao et al.

Increasing methane (CH4) emissions and altering rhizosphere microbial diversity in paddy soil by combining Chinese milk vetch and rice straw
type: item
type: AcademicArticle
description: Background Chinese milk vetch (Astragalus sinicus L.) can improve paddy soil fertility and ecology through nitrogen fixation, but it can also increase greenhouse gas emissions. Our primary objective was to investigate how Chinese milk vetch, rice straw, and nitrogen fertilization affect the methane and microbial components of the rice rhizosphere. Methods We examined the rhizosphere’s methane emissions and microbial abundance and diversity after incorporating Chinese milk vetch and rice straw into paddy soil. We used high-throughput sequencing of the 16s rRNA and ITS1 genes to study changes in the bacterial and fungal communities, respectively. Over the course of our experiment, we applied seven different treatments to the paddy soil: conventional fertilization (the control treatment) for winter fallow crops, three levels of nitrogen in Chinese milk vetch, and three levels of nitrogen in Chinese milk vetch combined with rice straw. Results Rice yield and methane emissions increased during cultivation when the soil was treated with Chinese milk vetch with and without added straw. The nitrogen application also affected the methane fluxes. Alpha diversity measurements showed that Chinese milk vetch increased the diversity of the soil fungal community but did not significantly affect the bacterial community. Chinese milk vetch affected the rhizosphere microorganism communities by increasing the number of Methanomicrobia.
format: application/pdf
format: text/html
creator: Qiaoying Ma
creator: Jiwei Li
creator: Muhammad Aamer
creator: Guoqin Huang
subject: Agricultural Science
subject: Soil Science
subject: Climate Change Biology
description: doi:10.7717/peerj.9653
publisher: PeerJ Inc.
rights: © 2020 Ma et al.
abstract: Background Chinese milk vetch (Astragalus sinicus L.) can improve paddy soil fertility and ecology through nitrogen fixation, but it can also increase greenhouse gas emissions. Our primary objective was to investigate how Chinese milk vetch, rice straw, and nitrogen fertilization affect the methane and microbial components of the rice rhizosphere. Methods We examined the rhizosphere’s methane emissions and microbial abundance and diversity after incorporating Chinese milk vetch and rice straw into paddy soil. We used high-throughput sequencing of the 16s rRNA and ITS1 genes to study changes in the bacterial and fungal communities, respectively. Over the course of our experiment, we applied seven different treatments to the paddy soil: conventional fertilization (the control treatment) for winter fallow crops, three levels of nitrogen in Chinese milk vetch, and three levels of nitrogen in Chinese milk vetch combined with rice straw. Results Rice yield and methane emissions increased during cultivation when the soil was treated with Chinese milk vetch with and without added straw. The nitrogen application also affected the methane fluxes. Alpha diversity measurements showed that Chinese milk vetch increased the diversity of the soil fungal community but did not significantly affect the bacterial community. Chinese milk vetch affected the rhizosphere microorganism communities by increasing the number of Methanomicrobia.
bibliographic citation: Ma et al. (2020) Increasing methane (CH4) emissions and altering rhizosphere microbial diversity in paddy soil by combining Chinese milk vetch and rice straw. PeerJ 8:e9653 https://doi.org/10.7717/peerj.9653
date submitted: 2020-02-12
date accepted: 2020-07-13
issued: 2020-08-03
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Ma
  given name: Qiaoying
author list: Agent
  family name: Li
  given name: Jiwei
author list: Agent
  family name: Aamer
  given name: Muhammad
author list: Agent
  family name: Huang
  given name: Guoqin
doi: 10.7717/peerj.9653
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-08-03
copyright: ©2020 Ma et al.
attribution name: Ma et al.

Identification of DNA methylation patterns and biomarkers for clear-cell renal cell carcinoma by multi-omics data analysis
type: item
type: AcademicArticle
description: Background Tumorigenesis is highly heterogeneous, and using clinicopathological signatures only is not enough to effectively distinguish clear cell renal cell carcinoma (ccRCC) and improve risk stratification of patients. DNA methylation (DNAm) with the stability and reversibility often occurs in the early stage of tumorigenesis. Disorders of transcription and metabolism are also an important molecular mechanisms of tumorigenesis. Therefore, it is necessary to identify effective biomarkers involved in tumorigenesis through multi-omics analysis, and these biomarkers also provide new potential therapeutic targets. Method The discovery stage involved 160 pairs of ccRCC and matched normal tissues for investigation of DNAm and biomarkers as well as 318 cases of ccRCC including clinical signatures. Correlation analysis of epigenetic, transcriptomic and metabolomic data revealed the connection and discordance among multi-omics and the deregulated functional modules. Diagnostic or prognostic biomarkers were obtained by the correlation analysis, the Least Absolute Shrinkage and Selection Operator (LASSO) and the LASSO-Cox methods. Two classifiers were established based on random forest (RF) and LASSO-Cox algorithms in training datasets. Seven independent datasets were used to evaluate robustness and universality. The molecular biological function of biomarkers were investigated using DAVID and GeneMANIA. Results Based on multi-omics analysis, the epigenetic measurements uniquely identified DNAm dysregulation of cellular mechanisms resulting in transcriptomic alterations, including cell proliferation, immune response and inflammation. Combination of the gene co-expression network and metabolic network identified 134 CpG sites (CpGs) as potential biomarkers. Based on the LASSO and RF algorithms, five CpGs were obtained to build a diagnostic classifierwith better classification performance (AUC > 99%). A eight-CpG-based prognostic classifier was obtained to improve risk stratif…
format: application/pdf
format: text/html
creator: Pengfei Liu
creator: Weidong Tian
subject: Bioinformatics
subject: Genetics
subject: Nephrology
subject: Oncology
subject: Translational Medicine
description: doi:10.7717/peerj.9654
publisher: PeerJ Inc.
rights: © 2020 Liu and Tian
abstract: Background Tumorigenesis is highly heterogeneous, and using clinicopathological signatures only is not enough to effectively distinguish clear cell renal cell carcinoma (ccRCC) and improve risk stratification of patients. DNA methylation (DNAm) with the stability and reversibility often occurs in the early stage of tumorigenesis. Disorders of transcription and metabolism are also an important molecular mechanisms of tumorigenesis. Therefore, it is necessary to identify effective biomarkers involved in tumorigenesis through multi-omics analysis, and these biomarkers also provide new potential therapeutic targets. Method The discovery stage involved 160 pairs of ccRCC and matched normal tissues for investigation of DNAm and biomarkers as well as 318 cases of ccRCC including clinical signatures. Correlation analysis of epigenetic, transcriptomic and metabolomic data revealed the connection and discordance among multi-omics and the deregulated functional modules. Diagnostic or prognostic biomarkers were obtained by the correlation analysis, the Least Absolute Shrinkage and Selection Operator (LASSO) and the LASSO-Cox methods. Two classifiers were established based on random forest (RF) and LASSO-Cox algorithms in training datasets. Seven independent datasets were used to evaluate robustness and universality. The molecular biological function of biomarkers were investigated using DAVID and GeneMANIA. Results Based on multi-omics analysis, the epigenetic measurements uniquely identified DNAm dysregulation of cellular mechanisms resulting in transcriptomic alterations, including cell proliferation, immune response and inflammation. Combination of the gene co-expression network and metabolic network identified 134 CpG sites (CpGs) as potential biomarkers. Based on the LASSO and RF algorithms, five CpGs were obtained to build a diagnostic classifierwith better classification performance (AUC > 99%). A eight-CpG-based prognostic classifier was obtained to improve risk stratif…
bibliographic citation: Liu et al. (2020) Identification of DNA methylation patterns and biomarkers for clear-cell renal cell carcinoma by multi-omics data analysis. PeerJ 8:e9654 https://doi.org/10.7717/peerj.9654
date submitted: 2020-04-06
date accepted: 2020-07-13
issued: 2020-08-03
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Liu
  given name: Pengfei
author list: Agent
  family name: Tian
  given name: Weidong
doi: 10.7717/peerj.9654
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-08-03
copyright: © 2020 Liu and Tian
attribution name: Liu and Tian

Characterization of two myostatin genes in pufferfish Takifugu bimaculatus: sequence, genomic structure, and expression
type: item
type: AcademicArticle
description: Myostatin (MSTN) is a negative regulator of muscle growth, which restrains the proliferation and differentiation of myoblasts. To understand the role of two mstn genes of Takifugu bimaculatus, the full-length cDNAs of 1131 bp Tbmstn1 and 1,080 bp Tbmstn2 were obtained from the T. bimaculatus’ genomic database, which encodes 376 and 359 amino acids, respectively. The results of qRT-PCR showed that Tbmstn1 was expressed in the eye, kidney, spleen, skeletal muscle, gill, and brain, and the expression level in the skeletal muscle was extremely significantly higher than in other examined tissues. Tbmstn2 was expressed in the skin, skeletal muscle, gill, and brain, and had the highest expression in the skeletal muscle, followed by expression in the brain. Meanwhile, in different stages of embryonic development, the expression of Tbmstn1 started from the gastrula stage. Its expression in the eye-pigment formation stage and hatching stage was significantly higher than that in other stages. The Tbmstn2 was expressed in all examined embryonic stages with different levels, and the highest expression was detected in the eye-pigment formation stage. These results suggested that Tbmstn1 and Tbmstn2 may involve in the development of skeletal muscle, and Tbmstn2 may be related to the formation of nervous system.
format: application/pdf
format: text/html
creator: Yinzhen Sheng
creator: Yulong Sun
creator: Xin Zhang
creator: Haifu Wan
creator: Chengjie Yao
creator: Keying Liang
creator: Leibin Li
creator: Bo Liu
creator: Jianxing Zhong
creator: Ziping Zhang
creator: Yilei Wang
subject: Aquaculture, Fisheries and Fish Science
subject: Developmental Biology
subject: Genetics
subject: Molecular Biology
subject: Zoology
description: doi:10.7717/peerj.9655
publisher: PeerJ Inc.
rights: © 2020 Sheng et al.
abstract: Myostatin (MSTN) is a negative regulator of muscle growth, which restrains the proliferation and differentiation of myoblasts. To understand the role of two mstn genes of Takifugu bimaculatus, the full-length cDNAs of 1131 bp Tbmstn1 and 1,080 bp Tbmstn2 were obtained from the T. bimaculatus’ genomic database, which encodes 376 and 359 amino acids, respectively. The results of qRT-PCR showed that Tbmstn1 was expressed in the eye, kidney, spleen, skeletal muscle, gill, and brain, and the expression level in the skeletal muscle was extremely significantly higher than in other examined tissues. Tbmstn2 was expressed in the skin, skeletal muscle, gill, and brain, and had the highest expression in the skeletal muscle, followed by expression in the brain. Meanwhile, in different stages of embryonic development, the expression of Tbmstn1 started from the gastrula stage. Its expression in the eye-pigment formation stage and hatching stage was significantly higher than that in other stages. The Tbmstn2 was expressed in all examined embryonic stages with different levels, and the highest expression was detected in the eye-pigment formation stage. These results suggested that Tbmstn1 and Tbmstn2 may involve in the development of skeletal muscle, and Tbmstn2 may be related to the formation of nervous system.
bibliographic citation: Sheng et al. (2020) Characterization of two myostatin genes in pufferfish Takifugu bimaculatus: sequence, genomic structure, and expression. PeerJ 8:e9655 https://doi.org/10.7717/peerj.9655
date submitted: 2019-12-10
date accepted: 2020-07-13
issued: 2020-08-03
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Sheng
  given name: Yinzhen
author list: Agent
  family name: Sun
  given name: Yulong
author list: Agent
  family name: Zhang
  given name: Xin
author list: Agent
  family name: Wan
  given name: Haifu
author list: Agent
  family name: Yao
  given name: Chengjie
author list: Agent
  family name: Liang
  given name: Keying
author list: Agent
  family name: Li
  given name: Leibin
author list: Agent
  family name: Liu
  given name: Bo
author list: Agent
  family name: Zhong
  given name: Jianxing
author list: Agent
  family name: Zhang
  given name: Ziping
author list: Agent
  family name: Wang
  given name: Yilei
doi: 10.7717/peerj.9655
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-08-03
copyright: ©2020 Sheng et al.
attribution name: Sheng et al.

Measurement properties of the Knee Injury and Osteoarthritis Outcome Score Patello-Femoral questionnaire in Saudi Arabians
type: item
type: AcademicArticle
description: Background No Arabic or its dialect questionnaire is available to evaluate the anterior knee pain in the Saudi Arabian religious population. This study aims to translate, adapt, and psychometrically validate the Knee Injury and Osteoarthritis Outcome Score (KOOS-PF) Patellofemoral scale in the Arabic language in Saudi Arabic dialect. Method Translation has been done as per standard guidelines. The questionnaire was administered to 95 patients to determine the psychometric properties including on two different occasions, with a 48-hour gap in-between; to ensure that their answers were reliable; 84 patients (88.4% compliance rate) responded for test and retest reliability, ceiling-floor effects, validity and other psychometric criteria. Results Cronbach’s alpha (internal consistency) and test–retest reliability was good and excellent (∞ = 0.81; ICC > 0.95). None of the items showed >30% floor or ceiling effect and the minimal detectable change was within the acceptable range (<30%). The KOOS-PF subscale showed a moderate correlation (−0.568) with pain-visual analog scale for its construct validity. Conclusion The Arabic dialect of KOOS-PFis reliable and valid to be used to evaluate isolated knee pain of patellofemoral origin in Muslim patients in Saudi Arabia.
format: application/pdf
format: text/html
creator: Mahamed Ateef
subject: Orthopedics
subject: Rheumatology
description: doi:10.7717/peerj.9323
publisher: PeerJ Inc.
rights: © 2020 Ateef
abstract: Background No Arabic or its dialect questionnaire is available to evaluate the anterior knee pain in the Saudi Arabian religious population. This study aims to translate, adapt, and psychometrically validate the Knee Injury and Osteoarthritis Outcome Score (KOOS-PF) Patellofemoral scale in the Arabic language in Saudi Arabic dialect. Method Translation has been done as per standard guidelines. The questionnaire was administered to 95 patients to determine the psychometric properties including on two different occasions, with a 48-hour gap in-between; to ensure that their answers were reliable; 84 patients (88.4% compliance rate) responded for test and retest reliability, ceiling-floor effects, validity and other psychometric criteria. Results Cronbach’s alpha (internal consistency) and test–retest reliability was good and excellent (∞ = 0.81; ICC > 0.95). None of the items showed >30% floor or ceiling effect and the minimal detectable change was within the acceptable range (<30%). The KOOS-PF subscale showed a moderate correlation (−0.568) with pain-visual analog scale for its construct validity. Conclusion The Arabic dialect of KOOS-PFis reliable and valid to be used to evaluate isolated knee pain of patellofemoral origin in Muslim patients in Saudi Arabia.
bibliographic citation: Ateef (2020) Measurement properties of the Knee Injury and Osteoarthritis Outcome Score Patello-Femoral questionnaire in Saudi Arabians. PeerJ 8:e9323 https://doi.org/10.7717/peerj.9323
date submitted: 2020-02-19
date accepted: 2020-05-18
issued: 2020-07-31
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Ateef
  given name: Mahamed
doi: 10.7717/peerj.9323
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-07-31
copyright: ©2020 Ateef
attribution name: Ateef

Distribution of deep-water scleractinian and stylasterid corals across abiotic environmental gradients on three seamounts in the Anegada Passage
type: item
type: AcademicArticle
description: In the Caribbean Basin the distribution and diversity patterns of deep-sea scleractinian corals and stylasterid hydrocorals are poorly known compared to their shallow-water relatives. In this study, we examined species distribution and community assembly patterns of scleractinian and stylasterid corals on three high-profile seamounts within the Anegada Passage, a deep-water throughway linking the Caribbean Sea and western North Atlantic. Using remotely operated vehicle surveys conducted on the E/V Nautilus by the ROV Hercules in 2014, we characterized coral assemblages and seawater environmental variables between 162 and 2,157 m on Dog Seamount, Conrad Seamount, and Noroît Seamount. In all, 13 morphospecies of scleractinian and stylasterid corals were identified from video with stylasterids being numerically more abundant than both colonial and solitary scleractinians. Cosmopolitan framework-forming species including Madrepora oculata and Solenosmilia variabilis were present but occurred in patchy distributions among the three seamounts. Framework-forming species occurred at or above the depth of the aragonite saturation horizon with stylasterid hydrocorals being the only coral taxon observed below Ωarag values of 1. Coral assemblage variation was found to be strongly associated with depth and aragonite saturation state, while other environmental variables exerted less influence. This study enhances our understanding of the factors that regulate scleractinian and stylasterid coral distribution in an underreported marginal sea and establishes a baseline for monitoring future environmental changes due to ocean acidification and deoxygenation in the tropical western Atlantic.
format: application/pdf
format: text/html
creator: Steven R. Auscavitch
creator: Jay J. Lunden
creator: Alexandria Barkman
creator: Andrea M. Quattrini
creator: Amanda W.J. Demopoulos
creator: Erik E. Cordes
subject: Biodiversity
subject: Biogeography
subject: Marine Biology
subject: Aquatic and Marine Chemistry
subject: Biological Oceanography
description: doi:10.7717/peerj.9523
publisher: PeerJ Inc.
rights: © 2020 Auscavitch et al.
abstract: In the Caribbean Basin the distribution and diversity patterns of deep-sea scleractinian corals and stylasterid hydrocorals are poorly known compared to their shallow-water relatives. In this study, we examined species distribution and community assembly patterns of scleractinian and stylasterid corals on three high-profile seamounts within the Anegada Passage, a deep-water throughway linking the Caribbean Sea and western North Atlantic. Using remotely operated vehicle surveys conducted on the E/V Nautilus by the ROV Hercules in 2014, we characterized coral assemblages and seawater environmental variables between 162 and 2,157 m on Dog Seamount, Conrad Seamount, and Noroît Seamount. In all, 13 morphospecies of scleractinian and stylasterid corals were identified from video with stylasterids being numerically more abundant than both colonial and solitary scleractinians. Cosmopolitan framework-forming species including Madrepora oculata and Solenosmilia variabilis were present but occurred in patchy distributions among the three seamounts. Framework-forming species occurred at or above the depth of the aragonite saturation horizon with stylasterid hydrocorals being the only coral taxon observed below Ωarag values of 1. Coral assemblage variation was found to be strongly associated with depth and aragonite saturation state, while other environmental variables exerted less influence. This study enhances our understanding of the factors that regulate scleractinian and stylasterid coral distribution in an underreported marginal sea and establishes a baseline for monitoring future environmental changes due to ocean acidification and deoxygenation in the tropical western Atlantic.
bibliographic citation: Auscavitch et al. (2020) Distribution of deep-water scleractinian and stylasterid corals across abiotic environmental gradients on three seamounts in the Anegada Passage. PeerJ 8:e9523 https://doi.org/10.7717/peerj.9523
date submitted: 2020-01-27
date accepted: 2020-06-20
issued: 2020-07-31
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Auscavitch
  given name: Steven R.
author list: Agent
  family name: Lunden
  given name: Jay J.
author list: Agent
  family name: Barkman
  given name: Alexandria
author list: Agent
  family name: Quattrini
  given name: Andrea M.
author list: Agent
  family name: Demopoulos
  given name: Amanda W.J.
author list: Agent
  family name: Cordes
  given name: Erik E.
doi: 10.7717/peerj.9523
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-07-31
copyright: © 2020 Auscavitch et al.
attribution name: Auscavitch et al.

Relationship between iron status markers and insulin resistance: an exploratory study in subjects with excess body weight
type: item
type: AcademicArticle
description: Background Controversy exists on the relationship between iron metabolism and cardiometabolic risk. The aim of this study was to determine if there is a link between dysmetabolic iron and cardiometabolic markers in subjects with excess body weight. Methods Cross-sectional study with fifty participants presenting overweight or obesity and at least another metabolic syndrome factor. Determinations: anthropometry, body composition, blood pressure, lipids, glucose, insulin, leptin, areas under the curve (AUC) for glucose and insulin after an oral glucose tolerance test, hs-C reactive protein (hs-CRP), blood count, ferritin, transferrin, transferrin saturation (TSAT), soluble transferrin receptor (sTfR). Gender-adjusted linear correlations and two independent samples t tests were used. Results Ferritin was positively correlated with insulin-AUC (r = 0.547, p = 0.008) and TSAT was negatively correlated with waist-hip ratio (r = − 0.385, p = 0.008), insulin (r = − 0.551, p < 0.001), and insulin resistance (HOMA-IR, r = − 0.586, p < 0.001). Subjects with TSAT ≤ 20% had higher insulin (p = 0.012) and HOMA-IR (p = 0.003) compared to those with TSAT > 20%. In conclusion, the observed results suggest that iron transport and storage are altered in subjects with overweight/obesity, at the same time that they exhibit the characteristic features of insulin resistance. Nevertheless, this occurs without iron overload or deficiency. These results should be validated in wider cohorts since they suggest that iron transport and storage should be assessed when performing the clinical evaluation of subjects with excess body weight.
format: application/pdf
format: text/html
creator: M. Pilar Vaquero
creator: Daniel Martínez-Maqueda
creator: Angélica Gallego-Narbón
creator: Belén Zapatera
creator: Jara Pérez-Jiménez
subject: Biochemistry
subject: Diabetes and Endocrinology
subject: Nutrition
subject: Public Health
description: doi:10.7717/peerj.9528
publisher: PeerJ Inc.
rights: © 2020 Vaquero et al.
abstract: Background Controversy exists on the relationship between iron metabolism and cardiometabolic risk. The aim of this study was to determine if there is a link between dysmetabolic iron and cardiometabolic markers in subjects with excess body weight. Methods Cross-sectional study with fifty participants presenting overweight or obesity and at least another metabolic syndrome factor. Determinations: anthropometry, body composition, blood pressure, lipids, glucose, insulin, leptin, areas under the curve (AUC) for glucose and insulin after an oral glucose tolerance test, hs-C reactive protein (hs-CRP), blood count, ferritin, transferrin, transferrin saturation (TSAT), soluble transferrin receptor (sTfR). Gender-adjusted linear correlations and two independent samples t tests were used. Results Ferritin was positively correlated with insulin-AUC (r = 0.547, p = 0.008) and TSAT was negatively correlated with waist-hip ratio (r = − 0.385, p = 0.008), insulin (r = − 0.551, p < 0.001), and insulin resistance (HOMA-IR, r = − 0.586, p < 0.001). Subjects with TSAT ≤ 20% had higher insulin (p = 0.012) and HOMA-IR (p = 0.003) compared to those with TSAT > 20%. In conclusion, the observed results suggest that iron transport and storage are altered in subjects with overweight/obesity, at the same time that they exhibit the characteristic features of insulin resistance. Nevertheless, this occurs without iron overload or deficiency. These results should be validated in wider cohorts since they suggest that iron transport and storage should be assessed when performing the clinical evaluation of subjects with excess body weight.
bibliographic citation: Vaquero et al. (2020) Relationship between iron status markers and insulin resistance: an exploratory study in subjects with excess body weight. PeerJ 8:e9528 https://doi.org/10.7717/peerj.9528
date submitted: 2020-01-23
date accepted: 2020-06-21
issued: 2020-07-31
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Vaquero
  given name: M. Pilar
author list: Agent
  family name: Martínez-Maqueda
  given name: Daniel
author list: Agent
  family name: Gallego-Narbón
  given name: Angélica
author list: Agent
  family name: Zapatera
  given name: Belén
author list: Agent
  family name: Pérez-Jiménez
  given name: Jara
doi: 10.7717/peerj.9528
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-07-31
copyright: ©2020 Vaquero et al.
attribution name: Vaquero et al.

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