PeerJ
type: channel
link: https://peerj.com/articles/
description: Articles published in PeerJ
publisher: PeerJ Inc.
publication name: PeerJ
issn: 2167-8359
items: The co-expression networks of differentially expressed RBPs with TFs and LncRNAs related to clinical TNM stages of cancers
items: Characteristics and prognosis of pelvic Ewing sarcoma: a SEER population-based study
items: MYB transcription factors in alfalfa (Medicago sativa): genome-wide identification and expression analysis under abiotic stresses
items: Ecological networks reveal contrasting patterns of bacterial and fungal communities in glacier-fed streams in Central Asia
items: Urine proteome changes in rats subcutaneously inoculated with approximately ten tumor cells
items: Effects of shokyo (Zingiberis Rhizoma) and kankyo (Zingiberis Processum Rhizoma) on prostaglandin E2 production in lipopolysaccharide-treated mouse macrophage RAW264.7 cells
items: Identification of lncRNAs associated with lung squamous cell carcinoma prognosis in the competitive endogenous RNA network
items: Liver slice culture as a model for lipid metabolism in fish
items: Engrailed 1 overexpression as a potential prognostic marker in Lower Grade Glioma
items: Seasonal and inter-annual community structure characteristics of zooplankton driven by water environment factors in a sub-lake of Lake Poyang, China

The co-expression networks of differentially expressed RBPs with TFs and LncRNAs related to clinical TNM stages of cancers
type: item
type: AcademicArticle
description: Background RNA-binding proteins (RBPs) play important roles in cellular homeostasis by regulating the expression of thousands of transcripts, which have been reported to be involved in human tumorigenesis. Despite previous reports of the dysregulation of RBPs in cancers, the degree of dysregulation of RBPs in cancers and the intrinsic relevance between dysregulated RBPs and clinical TNM information remains unknown. Furthermore, the co-expressed networks of dysregulated RBPs with transcriptional factors and lncRNAs also require further investigation. Results Here, we firstly analyzed the deviations of expression levels of 1,542 RBPs from 20 cancer types and found that (1) RBPs are dysregulated in almost all 20 cancer types, especially in BLCA, COAD, READ, STAD, LUAD, LUSC and GBM with proportion of deviation larger than 300% compared with non-RBPs in normal tissues. (2) Up- and down-regulated RBPs also show opposed patterns of differential expression in cancers and normal tissues. In addition, down-regulated RBPs show a greater degree of dysregulated expression than up-regulated RBPs do. Secondly, we analyzed the intrinsic relevance between dysregulated RBPs and clinical TNM information and found that (3) Clinical TNM information for two cancer types—CHOL and KICH—is shown to be closely related to patterns of differentially expressed RBPs (DE RBPs) by co-expression cluster analysis. Thirdly, we identified ten key RBPs (seven down-regulated and three up-regulated) in CHOL and seven key RBPs (five down-regulated and two up-regulated) in KICH by analyzing co-expression correlation networks. Fourthly, we constructed the co-expression networks of key RBPs between 1,570 TFs and 4,147 lncRNAs for CHOL and KICH, respectively. Conclusions These results may provide an insight into the understanding of the functions of RBPs in human carcinogenesis. Furthermore, key RBPs and the co-expressed networks offer useful information for potential prognostic biomarkers and therapeutic ta…
format: application/pdf
format: text/html
creator: Shuaibin Lian
creator: Liansheng Li
creator: Yongjie Zhou
creator: Zixiao Liu
creator: Lei Wang
subject: Bioinformatics
subject: Genomics
description: doi:10.7717/peerj.7696
publisher: PeerJ Inc.
rights: © 2019 Lian et al.
abstract: Background RNA-binding proteins (RBPs) play important roles in cellular homeostasis by regulating the expression of thousands of transcripts, which have been reported to be involved in human tumorigenesis. Despite previous reports of the dysregulation of RBPs in cancers, the degree of dysregulation of RBPs in cancers and the intrinsic relevance between dysregulated RBPs and clinical TNM information remains unknown. Furthermore, the co-expressed networks of dysregulated RBPs with transcriptional factors and lncRNAs also require further investigation. Results Here, we firstly analyzed the deviations of expression levels of 1,542 RBPs from 20 cancer types and found that (1) RBPs are dysregulated in almost all 20 cancer types, especially in BLCA, COAD, READ, STAD, LUAD, LUSC and GBM with proportion of deviation larger than 300% compared with non-RBPs in normal tissues. (2) Up- and down-regulated RBPs also show opposed patterns of differential expression in cancers and normal tissues. In addition, down-regulated RBPs show a greater degree of dysregulated expression than up-regulated RBPs do. Secondly, we analyzed the intrinsic relevance between dysregulated RBPs and clinical TNM information and found that (3) Clinical TNM information for two cancer types—CHOL and KICH—is shown to be closely related to patterns of differentially expressed RBPs (DE RBPs) by co-expression cluster analysis. Thirdly, we identified ten key RBPs (seven down-regulated and three up-regulated) in CHOL and seven key RBPs (five down-regulated and two up-regulated) in KICH by analyzing co-expression correlation networks. Fourthly, we constructed the co-expression networks of key RBPs between 1,570 TFs and 4,147 lncRNAs for CHOL and KICH, respectively. Conclusions These results may provide an insight into the understanding of the functions of RBPs in human carcinogenesis. Furthermore, key RBPs and the co-expressed networks offer useful information for potential prognostic biomarkers and therapeutic ta…
bibliographic citation: Lian et al. (2019) The co-expression networks of differentially expressed RBPs with TFs and LncRNAs related to clinical TNM stages of cancers. PeerJ 7:e7696 https://doi.org/10.7717/peerj.7696
date submitted: 2019-05-22
date accepted: 2019-08-19
issued: 2019-09-17
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Lian
  given name: Shuaibin
author list: Agent
  family name: Li
  given name: Liansheng
author list: Agent
  family name: Zhou
  given name: Yongjie
author list: Agent
  family name: Liu
  given name: Zixiao
author list: Agent
  family name: Wang
  given name: Lei
doi: 10.7717/peerj.7696
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-09-17
copyright: ©2019 Lian et al.
attribution name: Lian et al.

Characteristics and prognosis of pelvic Ewing sarcoma: a SEER population-based study
type: item
type: AcademicArticle
description: Background The pelvis is one of the primary sites of Ewing sarcoma (ES) and is associated with poorer prognoses than the extremities. Due to the rarity of this disease and limited data available, the prognostic factors of pelvic ES remain controversial. Thus, this study aimed to identify independent prognostic factors, and develop a nomogram for predicting survival rates in patients with pelvic ES. Methods Using data provided by the Surveillance, Epidemiology, and End Results (SEER) database, variables including age, sex, race, tumor size, tumor stage, surgery, and radiotherapy were analyzed using the Kaplan–Meier method and Cox proportional hazards regression. Based on the results of multivariate analyses, a nomogram was built to predict the overall survival (OS) of patients with pelvic ES. The performance of the nomogram was evaluated by the concordance index (C-index). Results A total of 267 cases diagnosed between 2004 and 2016 were included in the study. Univariate and multivariate analyses showed that patients who were younger, white, had a localized tumor stage, or underwent surgery were associated with improved prognoses, while no significant differences were observed in OS based on sex, tumor size, or radiotherapy. A nomogram was developed and the C-index was 0.728, indicating adequate performance for survival prediction. Conclusions Age, race, tumor stage, and surgery were identified as independent prognostic factors for the OS of pelvic ES. The nomogram developed in this study can individually predict 3- and 5-year OS in patients with pelvic ES.
format: application/pdf
format: text/html
creator: Li Chen
creator: Cheng Long
creator: Jiaxin Liu
creator: Fei Xing
creator: Xin Duan
subject: Oncology
subject: Orthopedics
subject: Surgery and Surgical Specialties
description: doi:10.7717/peerj.7710
publisher: PeerJ Inc.
rights: © 2019 Chen et al.
abstract: Background The pelvis is one of the primary sites of Ewing sarcoma (ES) and is associated with poorer prognoses than the extremities. Due to the rarity of this disease and limited data available, the prognostic factors of pelvic ES remain controversial. Thus, this study aimed to identify independent prognostic factors, and develop a nomogram for predicting survival rates in patients with pelvic ES. Methods Using data provided by the Surveillance, Epidemiology, and End Results (SEER) database, variables including age, sex, race, tumor size, tumor stage, surgery, and radiotherapy were analyzed using the Kaplan–Meier method and Cox proportional hazards regression. Based on the results of multivariate analyses, a nomogram was built to predict the overall survival (OS) of patients with pelvic ES. The performance of the nomogram was evaluated by the concordance index (C-index). Results A total of 267 cases diagnosed between 2004 and 2016 were included in the study. Univariate and multivariate analyses showed that patients who were younger, white, had a localized tumor stage, or underwent surgery were associated with improved prognoses, while no significant differences were observed in OS based on sex, tumor size, or radiotherapy. A nomogram was developed and the C-index was 0.728, indicating adequate performance for survival prediction. Conclusions Age, race, tumor stage, and surgery were identified as independent prognostic factors for the OS of pelvic ES. The nomogram developed in this study can individually predict 3- and 5-year OS in patients with pelvic ES.
bibliographic citation: Chen et al. (2019) Characteristics and prognosis of pelvic Ewing sarcoma: a SEER population-based study. PeerJ 7:e7710 https://doi.org/10.7717/peerj.7710
date submitted: 2019-07-02
date accepted: 2019-08-20
issued: 2019-09-17
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Chen
  given name: Li
author list: Agent
  family name: Long
  given name: Cheng
author list: Agent
  family name: Liu
  given name: Jiaxin
author list: Agent
  family name: Xing
  given name: Fei
author list: Agent
  family name: Duan
  given name: Xin
doi: 10.7717/peerj.7710
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-09-17
copyright: © 2019 Chen et al.
attribution name: Chen et al.

MYB transcription factors in alfalfa (Medicago sativa): genome-wide identification and expression analysis under abiotic stresses
type: item
type: AcademicArticle
description: Background Alfalfa is the most widely cultivated forage legume and one of the most economically valuable crops in the world. Its survival and production are often hampered by environmental changes. However, there are few studies on stress-resistance genes in alfalfa because of its incomplete genomic information and rare expression profile data. The MYB proteins are characterized by a highly conserved DNA-binding domain, which is large, functionally diverse, and represented in all eukaryotes. The role of MYB proteins in plant development is essential; they function in diverse biological processes, including stress and defense responses, and seed and floral development. Studies on the MYB gene family have been reported in several species, but they have not been comprehensively analyzed in alfalfa. Methods To identify more comprehensive MYB transcription factor family genes, the sequences of 168 Arabidopsis thaliana, 430 Glycine max, 185 Medicago truncatula, and 130 Oryza sativa MYB proteins were downloaded from the Plant Transcription Factor Database. These sequences were used as queries in a BLAST search against the M. sativa proteome sequences provided by the Noble Research Institute. Results In the present study, a total of 265 MsMYB proteins were obtained, including 50 R1-MYB, 186 R2R3-MYB, 26 R1R2R3-MYB, and three atypical-MYB proteins. These predicted MsMYB proteins were divided into 12 subgroups by phylogenetic analysis, and gene ontology (GO) analysis indicated that most of the MsMYB genes are involved in various biological processes. The expression profiles and quantitative real-time PCR analysis indicated that some MsMYB genes might play a crucial role in the response to abiotic stresses. Additionally, a total of 170 and 914 predicted protein–protein and protein-DNA interactions were obtained, respectively. The interactions between MsMYB043 and MSAD320162, MsMYB253 and MSAD320162, and MsMYB253 and MSAD308489 were confirmed by a yeast two-hybrid system. This …
format: application/pdf
format: text/html
creator: Qiang Zhou
creator: Chenglin Jia
creator: Wenxue Ma
creator: Yue Cui
creator: Xiaoyu Jin
creator: Dong Luo
creator: Xueyang Min
creator: Zhipeng Liu
subject: Agricultural Science
subject: Molecular Biology
subject: Plant Science
description: doi:10.7717/peerj.7714
publisher: PeerJ Inc.
rights: © 2019 Zhou et al.
abstract: Background Alfalfa is the most widely cultivated forage legume and one of the most economically valuable crops in the world. Its survival and production are often hampered by environmental changes. However, there are few studies on stress-resistance genes in alfalfa because of its incomplete genomic information and rare expression profile data. The MYB proteins are characterized by a highly conserved DNA-binding domain, which is large, functionally diverse, and represented in all eukaryotes. The role of MYB proteins in plant development is essential; they function in diverse biological processes, including stress and defense responses, and seed and floral development. Studies on the MYB gene family have been reported in several species, but they have not been comprehensively analyzed in alfalfa. Methods To identify more comprehensive MYB transcription factor family genes, the sequences of 168 Arabidopsis thaliana, 430 Glycine max, 185 Medicago truncatula, and 130 Oryza sativa MYB proteins were downloaded from the Plant Transcription Factor Database. These sequences were used as queries in a BLAST search against the M. sativa proteome sequences provided by the Noble Research Institute. Results In the present study, a total of 265 MsMYB proteins were obtained, including 50 R1-MYB, 186 R2R3-MYB, 26 R1R2R3-MYB, and three atypical-MYB proteins. These predicted MsMYB proteins were divided into 12 subgroups by phylogenetic analysis, and gene ontology (GO) analysis indicated that most of the MsMYB genes are involved in various biological processes. The expression profiles and quantitative real-time PCR analysis indicated that some MsMYB genes might play a crucial role in the response to abiotic stresses. Additionally, a total of 170 and 914 predicted protein–protein and protein-DNA interactions were obtained, respectively. The interactions between MsMYB043 and MSAD320162, MsMYB253 and MSAD320162, and MsMYB253 and MSAD308489 were confirmed by a yeast two-hybrid system. This …
bibliographic citation: Zhou et al. (2019) MYB transcription factors in alfalfa (Medicago sativa): genome-wide identification and expression analysis under abiotic stresses. PeerJ 7:e7714 https://doi.org/10.7717/peerj.7714
date submitted: 2019-04-18
date accepted: 2019-08-21
issued: 2019-09-17
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Zhou
  given name: Qiang
author list: Agent
  family name: Jia
  given name: Chenglin
author list: Agent
  family name: Ma
  given name: Wenxue
author list: Agent
  family name: Cui
  given name: Yue
author list: Agent
  family name: Jin
  given name: Xiaoyu
author list: Agent
  family name: Luo
  given name: Dong
author list: Agent
  family name: Min
  given name: Xueyang
author list: Agent
  family name: Liu
  given name: Zhipeng
doi: 10.7717/peerj.7714
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-09-17
copyright: © 2019 Zhou et al.
attribution name: Zhou et al.

Ecological networks reveal contrasting patterns of bacterial and fungal communities in glacier-fed streams in Central Asia
type: item
type: AcademicArticle
description: Bacterial and fungal communities in biofilms are important components in driving biogeochemical processes in stream ecosystems. Previous studies have well documented the patterns of bacterial alpha diversity in stream biofilms in glacier-fed streams, where, however, beta diversity of the microbial communities has received much less attention especially considering both bacterial and fungal communities. A focus on beta diversity can provide insights into the mechanisms driving community changes associated to large environmental fluctuations and disturbances, such as in glacier-fed streams. Moreover, modularity of co-occurrence networks can reveal more ecological and evolutionary properties of microbial communities beyond taxonomic groups. Here, integrating beta diversity and co-occurrence approach, we explored the network topology and modularity of the bacterial and fungal communities with consideration of environmental variation in glacier-fed streams in Central Asia. Combining results from hydrological modeling and normalized difference of vegetation index, this study highlighted that hydrological variables and vegetation status are major variables determining the environmental heterogeneity of glacier-fed streams. Bacterial communities formed a more complex and connected network, while the fungal communities formed a more clustered network. Moreover, the strong interrelations among the taxonomic dissimilarities of bacterial community (BC) and modules suggest they had common processes in driving diversity and taxonomic compositions across the heterogeneous environment. In contrast, fungal community (FC) and modules generally showed distinct driving processes to each other. Moreover, bacterial and fungal communities also had different driving processes. Furthermore, the variation of BC and modules were strongly correlated with hydrological properties and vegetation status but not with nutrients, while FC and modules (except one module) were not associated with envir…
format: application/pdf
format: text/html
creator: Ze Ren
creator: Hongkai Gao
subject: Biogeography
subject: Ecology
subject: Microbiology
subject: Freshwater Biology
description: doi:10.7717/peerj.7715
publisher: PeerJ Inc.
rights: © 2019 Ren and Gao
abstract: Bacterial and fungal communities in biofilms are important components in driving biogeochemical processes in stream ecosystems. Previous studies have well documented the patterns of bacterial alpha diversity in stream biofilms in glacier-fed streams, where, however, beta diversity of the microbial communities has received much less attention especially considering both bacterial and fungal communities. A focus on beta diversity can provide insights into the mechanisms driving community changes associated to large environmental fluctuations and disturbances, such as in glacier-fed streams. Moreover, modularity of co-occurrence networks can reveal more ecological and evolutionary properties of microbial communities beyond taxonomic groups. Here, integrating beta diversity and co-occurrence approach, we explored the network topology and modularity of the bacterial and fungal communities with consideration of environmental variation in glacier-fed streams in Central Asia. Combining results from hydrological modeling and normalized difference of vegetation index, this study highlighted that hydrological variables and vegetation status are major variables determining the environmental heterogeneity of glacier-fed streams. Bacterial communities formed a more complex and connected network, while the fungal communities formed a more clustered network. Moreover, the strong interrelations among the taxonomic dissimilarities of bacterial community (BC) and modules suggest they had common processes in driving diversity and taxonomic compositions across the heterogeneous environment. In contrast, fungal community (FC) and modules generally showed distinct driving processes to each other. Moreover, bacterial and fungal communities also had different driving processes. Furthermore, the variation of BC and modules were strongly correlated with hydrological properties and vegetation status but not with nutrients, while FC and modules (except one module) were not associated with envir…
bibliographic citation: Ren et al. (2019) Ecological networks reveal contrasting patterns of bacterial and fungal communities in glacier-fed streams in Central Asia. PeerJ 7:e7715 https://doi.org/10.7717/peerj.7715
date submitted: 2019-04-03
date accepted: 2019-08-21
issued: 2019-09-17
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Ren
  given name: Ze
author list: Agent
  family name: Gao
  given name: Hongkai
doi: 10.7717/peerj.7715
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-09-17
copyright: © 2019 Ren and Gao
attribution name: Ren and Gao

Urine proteome changes in rats subcutaneously inoculated with approximately ten tumor cells
type: item
type: AcademicArticle
description: Background Biomarkers are changes associated with the disease. Urine is not subject to homeostatic control and therefore accumulates very early changes, making it an ideal biomarker source. Usually, we have performed urinary biomarker studies involving at least thousands of tumor cells. However, no tumor starts from a thousand tumor cells. We therefore examined urine proteome changes in rats subcutaneously inoculated with approximately ten tumor cells. Methods Here, we serially diluted Walker-256 carcinosarcoma cells to a concentration of 102/mL and subcutaneously inoculated 0.1 mL of these cells into nine rats. The urine proteomes on days 0, 13 and 21 were analyzed by liquid chromatography coupled with tandem mass spectrometry. Results Hierarchical clustering analysis showed that the urine proteome of each sample at three time points were clustered into three clusters, indicating the good consistency of these nine rats when inoculated with the same limited tumor cells. Differential proteins on days 13 and 21 were mainly associated with cell adhesion, autophagic cell death, changes in extracellular matrix organization, angiogenesis, and the pentose phosphate pathway. All of these enriched functional processes were reported to contribute to tumor progression and could not be enriched through random allocation analysis. Conclusions Our results indicated that (1) the urine proteome reflects changes associated with cancer even with only approximately ten tumor cells in the body and that (2) the urine proteome reflects pathophysiological changes in the body with extremely high sensitivity and provides potential for a very early screening process of clinical patients.
format: application/pdf
format: text/html
creator: Jing Wei
creator: Wenshu Meng
creator: Youhe Gao
subject: Animal Behavior
subject: Biochemistry
subject: Bioinformatics
subject: Oncology
description: doi:10.7717/peerj.7717
publisher: PeerJ Inc.
rights: © 2019 Wei et al.
abstract: Background Biomarkers are changes associated with the disease. Urine is not subject to homeostatic control and therefore accumulates very early changes, making it an ideal biomarker source. Usually, we have performed urinary biomarker studies involving at least thousands of tumor cells. However, no tumor starts from a thousand tumor cells. We therefore examined urine proteome changes in rats subcutaneously inoculated with approximately ten tumor cells. Methods Here, we serially diluted Walker-256 carcinosarcoma cells to a concentration of 102/mL and subcutaneously inoculated 0.1 mL of these cells into nine rats. The urine proteomes on days 0, 13 and 21 were analyzed by liquid chromatography coupled with tandem mass spectrometry. Results Hierarchical clustering analysis showed that the urine proteome of each sample at three time points were clustered into three clusters, indicating the good consistency of these nine rats when inoculated with the same limited tumor cells. Differential proteins on days 13 and 21 were mainly associated with cell adhesion, autophagic cell death, changes in extracellular matrix organization, angiogenesis, and the pentose phosphate pathway. All of these enriched functional processes were reported to contribute to tumor progression and could not be enriched through random allocation analysis. Conclusions Our results indicated that (1) the urine proteome reflects changes associated with cancer even with only approximately ten tumor cells in the body and that (2) the urine proteome reflects pathophysiological changes in the body with extremely high sensitivity and provides potential for a very early screening process of clinical patients.
bibliographic citation: Wei et al. (2019) Urine proteome changes in rats subcutaneously inoculated with approximately ten tumor cells. PeerJ 7:e7717 https://doi.org/10.7717/peerj.7717
date submitted: 2019-05-20
date accepted: 2019-08-21
issued: 2019-09-17
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Wei
  given name: Jing
author list: Agent
  family name: Meng
  given name: Wenshu
author list: Agent
  family name: Gao
  given name: Youhe
doi: 10.7717/peerj.7717
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-09-17
copyright: ©2019 Wei et al.
attribution name: Wei et al.

Effects of shokyo (Zingiberis Rhizoma) and kankyo (Zingiberis Processum Rhizoma) on prostaglandin E2 production in lipopolysaccharide-treated mouse macrophage RAW264.7 cells
type: item
type: AcademicArticle
description: We previously reported that shokyo and kankyo, which are water-extracted fractions of ginger, reduced LPS-induced PGE2 production in human gingival fibroblasts. In this study, we examined the effects of these herbs on LPS-treated mouse macrophage RAW264.7 cells. Both shokyo and kankyo reduced LPS-induced PGE2 production in a concentration-dependent manner. Shokyo and kankyo did not inhibit cyclooxygenase (COX) activity, nor did they alter the expression of molecules in the arachidonic acid cascade. In addition, these herbs did not alter NF-κB p65 translocation into nucleus, or phosphorylation of p65 or ERK. These results suggest that shokyo and kankyo inhibit cPLA2 activity. Although 6-shogaol produced similar results to those of shokyo and kankyo, the concentration of 6-shogaol required for the reduction of PGE2 production were higher than those of 6-shogaol in shokyo and kankyo. Therefore, several gingerols and shogaols other than 6-shogaol may play a role in the reduction of LPS-induced PGE2 production. Thus, 6-shogaol, and other gingerols and shogaols inhibit cPLA2 activity and reduce LPS-induced PGE2 production via a different mechanism from traditional anti-inflammatory drugs. Moreover, kampo medicines that contain shokyo or kankyo are considered to be effective for inflammatory diseases.
format: application/pdf
format: text/html
creator: Toshiaki Ara
creator: Masanori Koide
creator: Hiroyuki Kitamura
creator: Norio Sogawa
subject: Molecular Biology
subject: Pharmacology
description: doi:10.7717/peerj.7725
publisher: PeerJ Inc.
rights: © 2019 Ara et al.
abstract: We previously reported that shokyo and kankyo, which are water-extracted fractions of ginger, reduced LPS-induced PGE2 production in human gingival fibroblasts. In this study, we examined the effects of these herbs on LPS-treated mouse macrophage RAW264.7 cells. Both shokyo and kankyo reduced LPS-induced PGE2 production in a concentration-dependent manner. Shokyo and kankyo did not inhibit cyclooxygenase (COX) activity, nor did they alter the expression of molecules in the arachidonic acid cascade. In addition, these herbs did not alter NF-κB p65 translocation into nucleus, or phosphorylation of p65 or ERK. These results suggest that shokyo and kankyo inhibit cPLA2 activity. Although 6-shogaol produced similar results to those of shokyo and kankyo, the concentration of 6-shogaol required for the reduction of PGE2 production were higher than those of 6-shogaol in shokyo and kankyo. Therefore, several gingerols and shogaols other than 6-shogaol may play a role in the reduction of LPS-induced PGE2 production. Thus, 6-shogaol, and other gingerols and shogaols inhibit cPLA2 activity and reduce LPS-induced PGE2 production via a different mechanism from traditional anti-inflammatory drugs. Moreover, kampo medicines that contain shokyo or kankyo are considered to be effective for inflammatory diseases.
bibliographic citation: Ara et al. (2019) Effects of shokyo (Zingiberis Rhizoma) and kankyo (Zingiberis Processum Rhizoma) on prostaglandin E2 production in lipopolysaccharide-treated mouse macrophage RAW264.7 cells. PeerJ 7:e7725 https://doi.org/10.7717/peerj.7725
date submitted: 2019-04-13
date accepted: 2019-08-22
issued: 2019-09-17
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Ara
  given name: Toshiaki
author list: Agent
  family name: Koide
  given name: Masanori
author list: Agent
  family name: Kitamura
  given name: Hiroyuki
author list: Agent
  family name: Sogawa
  given name: Norio
doi: 10.7717/peerj.7725
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-09-17
copyright: ©2019 Ara et al.
attribution name: Ara et al.

Identification of lncRNAs associated with lung squamous cell carcinoma prognosis in the competitive endogenous RNA network
type: item
type: AcademicArticle
description: Background Long noncoding RNAs (lncRNAs) play a role in the formation, development, and prognosis of various cancers. Our study aimed to identify prognostic-related lncRNAs in lung squamous cell carcinoma (LUSC), which may provide new perspectives for individualized treatment of patients. Materials and Methods The RNA sequencing (lncRNA, microRNA (miRNA), mRNA) data and clinical information related to LUSC were obtained from The Cancer Genome Atlas (TCGA) database. Differentially expressed RNA sequences were used to construct the competitive endogenous RNA (ceRNA) network. In present study, we mainly used two prognostic verification methods, Cox analysis and survival analysis, to identify the prognostic relevance of specific lncRNAs and construct prognostic model of lncRNA. Results Datasets on 551 samples of lncRNA and mRNA and 523 miRNA samples were retrieved from the TCGA database. Analysis of the normal and LUSC samples identified 170 DElncRNAs, 331 DEmiRNAs, and 417 DEmRNAs differentially expressed RNAs. The ceRNA network contained 27 lncRNAs, 43 miRNAs, and 11 mRNAs. Furthermore, we identified seven specific lncRNAs (ERVH48-1, HCG9, SEC62-AS1, AC022148.1, LINC00460, C5orf17, LINC00261) as potential prognostic factors after correlation analysis, and five of the seven lncRNAs (AC022148.1, HCG9, LINC00460, C5orf17, LINC00261) constructed a prognostic model of LUSC. Conclusion In present study, we identified seven lncRNAs in the ceRNA network that are associated with potential prognosis in LUSC patients, and constructed a prognostic model of LUSC which can be used to assess the prognosis risk of clinical patients. Further biological experiments are needed to elucidate the specific molecular mechanisms underlying them.
format: application/pdf
format: text/html
creator: Lingyu Qi
creator: Tingting Zhang
creator: Yan Yao
creator: Jing Zhuang
creator: Cun Liu
creator: Ruijuan Liu
creator: Changgang Sun
subject: Bioinformatics
subject: Oncology
subject: Respiratory Medicine
description: doi:10.7717/peerj.7727
publisher: PeerJ Inc.
rights: © 2019 Qi et al.
abstract: Background Long noncoding RNAs (lncRNAs) play a role in the formation, development, and prognosis of various cancers. Our study aimed to identify prognostic-related lncRNAs in lung squamous cell carcinoma (LUSC), which may provide new perspectives for individualized treatment of patients. Materials and Methods The RNA sequencing (lncRNA, microRNA (miRNA), mRNA) data and clinical information related to LUSC were obtained from The Cancer Genome Atlas (TCGA) database. Differentially expressed RNA sequences were used to construct the competitive endogenous RNA (ceRNA) network. In present study, we mainly used two prognostic verification methods, Cox analysis and survival analysis, to identify the prognostic relevance of specific lncRNAs and construct prognostic model of lncRNA. Results Datasets on 551 samples of lncRNA and mRNA and 523 miRNA samples were retrieved from the TCGA database. Analysis of the normal and LUSC samples identified 170 DElncRNAs, 331 DEmiRNAs, and 417 DEmRNAs differentially expressed RNAs. The ceRNA network contained 27 lncRNAs, 43 miRNAs, and 11 mRNAs. Furthermore, we identified seven specific lncRNAs (ERVH48-1, HCG9, SEC62-AS1, AC022148.1, LINC00460, C5orf17, LINC00261) as potential prognostic factors after correlation analysis, and five of the seven lncRNAs (AC022148.1, HCG9, LINC00460, C5orf17, LINC00261) constructed a prognostic model of LUSC. Conclusion In present study, we identified seven lncRNAs in the ceRNA network that are associated with potential prognosis in LUSC patients, and constructed a prognostic model of LUSC which can be used to assess the prognosis risk of clinical patients. Further biological experiments are needed to elucidate the specific molecular mechanisms underlying them.
bibliographic citation: Qi et al. (2019) Identification of lncRNAs associated with lung squamous cell carcinoma prognosis in the competitive endogenous RNA network. PeerJ 7:e7727 https://doi.org/10.7717/peerj.7727
date submitted: 2019-06-03
date accepted: 2019-08-22
issued: 2019-09-17
is part of: PeerJ
license: https://creativecommons.org/licenses/by-nc/4.0
author list: Agent
  family name: Qi
  given name: Lingyu
author list: Agent
  family name: Zhang
  given name: Tingting
author list: Agent
  family name: Yao
  given name: Yan
author list: Agent
  family name: Zhuang
  given name: Jing
author list: Agent
  family name: Liu
  given name: Cun
author list: Agent
  family name: Liu
  given name: Ruijuan
author list: Agent
  family name: Sun
  given name: Changgang
doi: 10.7717/peerj.7727
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-09-17
copyright: © 2019 Qi et al.
attribution name: Qi et al.

Liver slice culture as a model for lipid metabolism in fish
type: item
type: AcademicArticle
description: Hepatic lipid metabolism is traditionally investigated in vitro using hepatocyte monocultures lacking the complex three-dimensional structure and interacting cell types essential liver function. Precision cut liver slice (PCLS) culture represents an alternative in vitro system, which benefits from retention of tissue architecture. Here, we present the first comprehensive evaluation of the PCLS method in fish (Atlantic salmon, Salmo salar L.) and validate it in the context of lipid metabolism using feeding trials, extensive transcriptomic data, and fatty acid measurements. We observe an initial period of post-slicing global transcriptome adjustment, which plateaued after 3 days in major metabolic pathways and stabilized through 9 days. PCLS fed alpha-linolenic acid (ALA) and insulin responded in a liver-like manner, increasing lipid biosynthesis gene expression. We identify interactions between insulin and ALA, where two PUFA biosynthesis genes that were induced by insulin or ALA alone, were highly down-regulated when insulin and ALA were combined. We also find that transcriptomic profiles of liver slices are exceedingly more similar to whole liver than hepatocyte monocultures, both for lipid metabolism and liver marker genes. PCLS culture opens new avenues for high throughput experimentation on the effect of “novel feed composition” and represent a promising new strategy for studying genotype-specific molecular features of metabolism.
format: application/pdf
format: text/html
creator: Thomas N. Harvey
creator: Simen R. Sandve
creator: Yang Jin
creator: Jon Olav Vik
creator: Jacob S. Torgersen
subject: Aquaculture, Fisheries and Fish Science
subject: Cell Biology
subject: Genomics
subject: Molecular Biology
description: doi:10.7717/peerj.7732
publisher: PeerJ Inc.
rights: © 2019 Harvey et al.
abstract: Hepatic lipid metabolism is traditionally investigated in vitro using hepatocyte monocultures lacking the complex three-dimensional structure and interacting cell types essential liver function. Precision cut liver slice (PCLS) culture represents an alternative in vitro system, which benefits from retention of tissue architecture. Here, we present the first comprehensive evaluation of the PCLS method in fish (Atlantic salmon, Salmo salar L.) and validate it in the context of lipid metabolism using feeding trials, extensive transcriptomic data, and fatty acid measurements. We observe an initial period of post-slicing global transcriptome adjustment, which plateaued after 3 days in major metabolic pathways and stabilized through 9 days. PCLS fed alpha-linolenic acid (ALA) and insulin responded in a liver-like manner, increasing lipid biosynthesis gene expression. We identify interactions between insulin and ALA, where two PUFA biosynthesis genes that were induced by insulin or ALA alone, were highly down-regulated when insulin and ALA were combined. We also find that transcriptomic profiles of liver slices are exceedingly more similar to whole liver than hepatocyte monocultures, both for lipid metabolism and liver marker genes. PCLS culture opens new avenues for high throughput experimentation on the effect of “novel feed composition” and represent a promising new strategy for studying genotype-specific molecular features of metabolism.
bibliographic citation: Harvey et al. (2019) Liver slice culture as a model for lipid metabolism in fish. PeerJ 7:e7732 https://doi.org/10.7717/peerj.7732
date submitted: 2019-01-31
date accepted: 2019-08-23
issued: 2019-09-17
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Harvey
  given name: Thomas N.
author list: Agent
  family name: Sandve
  given name: Simen R.
author list: Agent
  family name: Jin
  given name: Yang
author list: Agent
  family name: Vik
  given name: Jon Olav
author list: Agent
  family name: Torgersen
  given name: Jacob S.
doi: 10.7717/peerj.7732
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-09-17
copyright: © 2019 Harvey et al.
attribution name: Harvey et al.

Engrailed 1 overexpression as a potential prognostic marker in Lower Grade Glioma
type: item
type: AcademicArticle
description: Background Engrailed 1 (EN1), as a member of homeobox-containing transcription factors, participates in the development of the brain. High expressions of EN1 exist in various tumors. However, the role of EN1 in lower grade glioma (LGG) is still unknown. Methods Coefficients of Cox regression were examined by data mining among 13 cancer types using OncoLnc to validate EN1 expressions in LGG patients from The Cancer Genome Atlas database (TCGA). Bioinformatic analysis was performed by using R2 and the UCSC Xena browser based on the data from 273 glioma cases in GSE16011 from GEO datasets and 530 cases of LGG patients in TCGA. Cases in GSE16011 were divided into two groups according to IDH1 mutation status. Cases in TCGA-LGG were classified to subtypes according to histopathological results, IDH1 mutation status and 1p19q status. The Kaplan–Meier survival curves were performed to analyze the relationship between EN1 expressions and clinicopathological characteristics and survival time respectively. Results Cox regression results showed that LGG was ranked statistically first among 13 different cancer types according to the false discovery rate (FDR) correction. Results from GSE16011 showed that: glioma, LGG and LGG with IDH1 mutation patients with high EN1 expressions had significantly shorter 5, 10, and 15-year overall survival time (OS) (p < 0.001). Similar results from TCGA-LGG showed that LGG patients with high EN1 expressions had significantly shorter 15-year OS, irrespective of IDH1 mutation and 1p19q co-deletion (p < 0.001). The astrocytoma subgroup showed highest levels of EN1 expression and shortest 5, 10 and 15-year OS compared with oligoastrocytoma and oligodendroglioma (p < 0.05). Conclusion EN1 can be used as a prognostic marker in LGG patients, combined with IDH1 mutation and 1p19q co-deletion.
format: application/pdf
format: text/html
creator: Jin Zhu
creator: Yu-Qi Zhang
subject: Bioinformatics
subject: Genomics
subject: Molecular Biology
description: doi:10.7717/peerj.7414
publisher: PeerJ Inc.
rights: © 2019 Zhu and and Zhang
abstract: Background Engrailed 1 (EN1), as a member of homeobox-containing transcription factors, participates in the development of the brain. High expressions of EN1 exist in various tumors. However, the role of EN1 in lower grade glioma (LGG) is still unknown. Methods Coefficients of Cox regression were examined by data mining among 13 cancer types using OncoLnc to validate EN1 expressions in LGG patients from The Cancer Genome Atlas database (TCGA). Bioinformatic analysis was performed by using R2 and the UCSC Xena browser based on the data from 273 glioma cases in GSE16011 from GEO datasets and 530 cases of LGG patients in TCGA. Cases in GSE16011 were divided into two groups according to IDH1 mutation status. Cases in TCGA-LGG were classified to subtypes according to histopathological results, IDH1 mutation status and 1p19q status. The Kaplan–Meier survival curves were performed to analyze the relationship between EN1 expressions and clinicopathological characteristics and survival time respectively. Results Cox regression results showed that LGG was ranked statistically first among 13 different cancer types according to the false discovery rate (FDR) correction. Results from GSE16011 showed that: glioma, LGG and LGG with IDH1 mutation patients with high EN1 expressions had significantly shorter 5, 10, and 15-year overall survival time (OS) (p < 0.001). Similar results from TCGA-LGG showed that LGG patients with high EN1 expressions had significantly shorter 15-year OS, irrespective of IDH1 mutation and 1p19q co-deletion (p < 0.001). The astrocytoma subgroup showed highest levels of EN1 expression and shortest 5, 10 and 15-year OS compared with oligoastrocytoma and oligodendroglioma (p < 0.05). Conclusion EN1 can be used as a prognostic marker in LGG patients, combined with IDH1 mutation and 1p19q co-deletion.
bibliographic citation: Zhu et al. (2019) Engrailed 1 overexpression as a potential prognostic marker in Lower Grade Glioma. PeerJ 7:e7414 https://doi.org/10.7717/peerj.7414
date submitted: 2019-03-25
date accepted: 2019-07-04
issued: 2019-09-16
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Zhu
  given name: Jin
author list: Agent
  family name: Zhang
  given name: Yu-Qi
doi: 10.7717/peerj.7414
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-09-16
copyright: ©2019 Zhu and and Zhang
attribution name: Zhu and and Zhang

Seasonal and inter-annual community structure characteristics of zooplankton driven by water environment factors in a sub-lake of Lake Poyang, China
type: item
type: AcademicArticle
description: Background Sub-lakes are important for the maintenance of the ecosystem integrity of Lake Poyang, and zooplankton play an important role in its substance and energy flow. Methods A seasonal investigation of zooplankton was conducted in spring (April), summer (July), autumn (October) and winter (January of the following year) from 2012 to 2016 in a sub-lake of Lake Poyang. The aim of the present study was to understand the seasonal dynamics and interannual variation of zooplankton communities and their relationship to environmental factors. Results A total of 115 species were identified in all samples in the four years, which comprised of 87 Rotifera, 13 Cladocera and 15 Copepoda. Rotifera was the dominant group in terms of quantity, and its species richness and abundance were significantly higher when compared to Cladocera and Copepoda (P < 0.05), while Cladocera dominated in terms of biomass. The species richness of Rotifera exhibited a significant seasonal difference (P < 0.05). Both the density and biomass of zooplankton revealed significant seasonal differences (P < 0.05). In general, the density and biomass of zooplankton were higher in summer and autumn, when compared to winter and spring. Biodiversity indices were dramatically lower in spring than in the other seasons. The non-metric multidimensional scaling (NMDS) analysis suggested that these zooplankton communities can be divided into three groups: spring community, summer-autumn community, and winter community. The seasonal succession of zooplankton communities did not have interannual reproducibility. In high water level years, the dominant species of zooplankton (Cladocerans and Copepods) in the wet season had a lower density, and the result in low water level years was exactly the opposite. The redundancy analysis revealed that water temperature (WT), conductivity, pH and dissolved oxygen (DO) had significant effects on the zooplankton community. Conclusions The community structure of zooplankton has a…
format: application/pdf
format: text/html
creator: Beijuan Hu
creator: Xuren Hu
creator: Xue Nie
creator: Xiaoke Zhang
creator: Naicheng Wu
creator: Yijiang Hong
creator: Hai Ming Qin
subject: Biodiversity
subject: Ecology
subject: Zoology
subject: Freshwater Biology
description: doi:10.7717/peerj.7590
publisher: PeerJ Inc.
rights: © 2019 Hu et al.
abstract: Background Sub-lakes are important for the maintenance of the ecosystem integrity of Lake Poyang, and zooplankton play an important role in its substance and energy flow. Methods A seasonal investigation of zooplankton was conducted in spring (April), summer (July), autumn (October) and winter (January of the following year) from 2012 to 2016 in a sub-lake of Lake Poyang. The aim of the present study was to understand the seasonal dynamics and interannual variation of zooplankton communities and their relationship to environmental factors. Results A total of 115 species were identified in all samples in the four years, which comprised of 87 Rotifera, 13 Cladocera and 15 Copepoda. Rotifera was the dominant group in terms of quantity, and its species richness and abundance were significantly higher when compared to Cladocera and Copepoda (P < 0.05), while Cladocera dominated in terms of biomass. The species richness of Rotifera exhibited a significant seasonal difference (P < 0.05). Both the density and biomass of zooplankton revealed significant seasonal differences (P < 0.05). In general, the density and biomass of zooplankton were higher in summer and autumn, when compared to winter and spring. Biodiversity indices were dramatically lower in spring than in the other seasons. The non-metric multidimensional scaling (NMDS) analysis suggested that these zooplankton communities can be divided into three groups: spring community, summer-autumn community, and winter community. The seasonal succession of zooplankton communities did not have interannual reproducibility. In high water level years, the dominant species of zooplankton (Cladocerans and Copepods) in the wet season had a lower density, and the result in low water level years was exactly the opposite. The redundancy analysis revealed that water temperature (WT), conductivity, pH and dissolved oxygen (DO) had significant effects on the zooplankton community. Conclusions The community structure of zooplankton has a…
bibliographic citation: Hu et al. (2019) Seasonal and inter-annual community structure characteristics of zooplankton driven by water environment factors in a sub-lake of Lake Poyang, China. PeerJ 7:e7590 https://doi.org/10.7717/peerj.7590
date submitted: 2019-02-04
date accepted: 2019-07-30
issued: 2019-09-16
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Hu
  given name: Beijuan
author list: Agent
  family name: Hu
  given name: Xuren
author list: Agent
  family name: Nie
  given name: Xue
author list: Agent
  family name: Zhang
  given name: Xiaoke
author list: Agent
  family name: Wu
  given name: Naicheng
author list: Agent
  family name: Hong
  given name: Yijiang
author list: Agent
  family name: Qin
  given name: Hai Ming
doi: 10.7717/peerj.7590
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-09-16
copyright: ©2019 Hu et al.
attribution name: Hu et al.

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