PeerJ
type: channel
link: https://peerj.com/articles/
description: Articles published in PeerJ
publisher: PeerJ Inc.
publication name: PeerJ
issn: 2167-8359
items: Multi-scale analysis of the characteristics of the changing landscape of the typical mountainous region of Southwest China over the past 40 years
items: Consequences of herbal mixture supplementation on milk performance, ruminal fermentation, and bacterial diversity in water buffaloes
items: The multi metal-resistant bacterium Cupriavidus metallidurans CH34 affects growth and metal mobilization in Arabidopsis thaliana plants exposed to copper
items: DZNep, an inhibitor of the histone methyltransferase EZH2, suppresses hepatic fibrosis through regulating miR-199a-5p/SOCS7 pathway
items: Oxidative stress induces cell death partially by decreasing both mRNA and protein levels of nicotinamide phosphoribosyltransferase in differentiated PC12 cells
items: The relationship between PLOD1 expression level and glioma prognosis investigated using public databases
items: DNA barcoding of Austrian snow scorpionflies (Mecoptera, Boreidae) reveals potential cryptic diversity in Boreus westwoodi
items: Identification of diagnostic genes and vital microRNAs involved in rheumatoid arthritis: based on data mining and experimental verification
items: EGFR mutation status yield from bronchoalveolar lavage in patients with primary pulmonary adenocarcinoma compared to a venous blood sample and tissue biopsy
items: Seasonal variation of 25-Hydroxyvitamin D and indices of carbohydrate and lipid metabolism in postmenopausal women

Multi-scale analysis of the characteristics of the changing landscape of the typical mountainous region of Southwest China over the past 40 years
type: item
type: AcademicArticle
description: Context Yunnan Province is an important ecological security barrier in China. This study investigated the temporal and spatial changes to landscape ecology and is of great significance for guiding landscape protection and future socio-economic development. Objectives To analyze the temporal and spatial changes of the landscape patterns at the county, river basin, and provincial levels, and clarify and describe the temporal and spatial differentiation characteristics of the landscape patterns in Yunnan Province. Methods Based on landscape ecology, GIS spatial analysis, and spatio-temporal change analysis, nine landscape pattern indices, and spatial autocorrelation for different years, were calculated. Results The landscape of Yunnan Province has evolved as a whole toward isolation. The indices of separation and fragmentation changed significantly from 2010 to 2015. From 2015 to 2018 the rate of fragmentation decreased. Fragmentation in the Nu Jiang and Irrawaddy River basins was less than in other basins. The landscape patterns of the Jinsha and Pearl River basins were relatively fragmented due to human activity, socioeconomic development, and utilization. The differences between the Lancang and Red River Basins were relatively small and at an intermediate level. Conclusions Spatial autocorrelation analysis indicated that there are three areas with typical clusters, namely the Hengduan Mountains where the degree of fragmentation of the landscape was low, while landscape connectivity and aggregation were high. The subtropical region of Southern Yunnan displayed high landscape heterogeneity, a complex shape index, and high connectivity and sprawl. Central Yunnan exhibited a fragmented landscape with poor connectivity and aggregation. These three regions correspond with “the three screens and two belts” in the Main Functional Planning Area of Yunnan Province.
format: application/pdf
format: text/html
creator: Fang Liu
creator: Wanbin Wang
creator: Jinliang Wang
creator: Xingzi Zhang
creator: Jing Ren
creator: Yuexiong Liu
subject: Ecology
subject: Spatial and Geographic Information Science
description: doi:10.7717/peerj.10923
publisher: PeerJ Inc.
rights: © 2021 Liu et al.
abstract: Context Yunnan Province is an important ecological security barrier in China. This study investigated the temporal and spatial changes to landscape ecology and is of great significance for guiding landscape protection and future socio-economic development. Objectives To analyze the temporal and spatial changes of the landscape patterns at the county, river basin, and provincial levels, and clarify and describe the temporal and spatial differentiation characteristics of the landscape patterns in Yunnan Province. Methods Based on landscape ecology, GIS spatial analysis, and spatio-temporal change analysis, nine landscape pattern indices, and spatial autocorrelation for different years, were calculated. Results The landscape of Yunnan Province has evolved as a whole toward isolation. The indices of separation and fragmentation changed significantly from 2010 to 2015. From 2015 to 2018 the rate of fragmentation decreased. Fragmentation in the Nu Jiang and Irrawaddy River basins was less than in other basins. The landscape patterns of the Jinsha and Pearl River basins were relatively fragmented due to human activity, socioeconomic development, and utilization. The differences between the Lancang and Red River Basins were relatively small and at an intermediate level. Conclusions Spatial autocorrelation analysis indicated that there are three areas with typical clusters, namely the Hengduan Mountains where the degree of fragmentation of the landscape was low, while landscape connectivity and aggregation were high. The subtropical region of Southern Yunnan displayed high landscape heterogeneity, a complex shape index, and high connectivity and sprawl. Central Yunnan exhibited a fragmented landscape with poor connectivity and aggregation. These three regions correspond with “the three screens and two belts” in the Main Functional Planning Area of Yunnan Province.
bibliographic citation: Liu et al. (2021) Multi-scale analysis of the characteristics of the changing landscape of the typical mountainous region of Southwest China over the past 40 years. PeerJ 9:e10923 https://doi.org/10.7717/peerj.10923
date submitted: 2020-09-08
date accepted: 2021-01-19
issued: 2021-05-14
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Liu
  given name: Fang
author list: Agent
  family name: Wang
  given name: Wanbin
author list: Agent
  family name: Wang
  given name: Jinliang
author list: Agent
  family name: Zhang
  given name: Xingzi
author list: Agent
  family name: Ren
  given name: Jing
author list: Agent
  family name: Liu
  given name: Yuexiong
doi: 10.7717/peerj.10923
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-05-14
copyright: ©2021 Liu et al.
attribution name: Liu et al.

Consequences of herbal mixture supplementation on milk performance, ruminal fermentation, and bacterial diversity in water buffaloes
type: item
type: AcademicArticle
description: This study was aimed to evaluate the potential of a herbal mixture (HM) to improve production performance, rumen fermentation, and milk fatty acid profile in water buffaloes. Sixteen Murrah buffaloes (in four groups) were fed for 10 weeks with the same basal diet supplemented with 0 (control); 20 (HM20), 30 (HM30), and 40 (HM40) g/buffalo per day. The herbal mixture contained an equal quantity of black pepper (fruit), ginger (tubers), cinnamon (bark), peppermint (leaves), ajwain (seeds) and garlic (bulbs). After two weeks of adaptation, daily milk yield, and weekly milk composition were recorded. On the last day of the experiment, rumen contents were collected to determine rumen fermentation parameters and bacterial diversity through 16S rRNA sequencing. Results revealed no effect of treatment on dry matter intake (DMI), rumen fermentation parameters, and daily milk yield. However, milk fat (%) showed a tendency to increase (p = 0.07) in HM20 as compared with the control group. A significant increase in mono and polyunsaturated fatty acids (C14:1, C16:1, C18:2n6 and C18:3) whereas a decrease in saturated fatty acids (C18:0) in milk was observed in HM20 as compared with the control group. No significant change in bacterial diversity parameters (alpha and beta diversity) was observed in response to the treatment. Despite the substantial variation observed in the relative abundance of bacteria among treatment groups, no significant effect of treatment was observed when compared with the control group. Correlation analysis revealed several positive and negative correlations of rumen bacteria with rumen volatile fatty acids (VFA) and milk yield traits. Bacterial genera including Succinivibrionaceae, Butyrivibrio, Pseudobutyrivibrio, and Lachnospiraceae showed a positive correlation with VFA and milk yield traits. Overall, we observed 52 positive and 10 negative correlations of rumen bacteria with milk fatty acid contents. Our study revealed the potential of the herbal mi…
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format: text/html
creator: Faizul Hassan
creator: Zhenhua Tang
creator: Hossam M. Ebeid
creator: Mengwei Li
creator: Kaiping Peng
creator: Xin Liang
creator: Chengjian Yang
subject: Agricultural Science
subject: Microbiology
subject: Veterinary Medicine
subject: Zoology
description: doi:10.7717/peerj.11241
publisher: PeerJ Inc.
rights: © 2021 Hassan et al.
abstract: This study was aimed to evaluate the potential of a herbal mixture (HM) to improve production performance, rumen fermentation, and milk fatty acid profile in water buffaloes. Sixteen Murrah buffaloes (in four groups) were fed for 10 weeks with the same basal diet supplemented with 0 (control); 20 (HM20), 30 (HM30), and 40 (HM40) g/buffalo per day. The herbal mixture contained an equal quantity of black pepper (fruit), ginger (tubers), cinnamon (bark), peppermint (leaves), ajwain (seeds) and garlic (bulbs). After two weeks of adaptation, daily milk yield, and weekly milk composition were recorded. On the last day of the experiment, rumen contents were collected to determine rumen fermentation parameters and bacterial diversity through 16S rRNA sequencing. Results revealed no effect of treatment on dry matter intake (DMI), rumen fermentation parameters, and daily milk yield. However, milk fat (%) showed a tendency to increase (p = 0.07) in HM20 as compared with the control group. A significant increase in mono and polyunsaturated fatty acids (C14:1, C16:1, C18:2n6 and C18:3) whereas a decrease in saturated fatty acids (C18:0) in milk was observed in HM20 as compared with the control group. No significant change in bacterial diversity parameters (alpha and beta diversity) was observed in response to the treatment. Despite the substantial variation observed in the relative abundance of bacteria among treatment groups, no significant effect of treatment was observed when compared with the control group. Correlation analysis revealed several positive and negative correlations of rumen bacteria with rumen volatile fatty acids (VFA) and milk yield traits. Bacterial genera including Succinivibrionaceae, Butyrivibrio, Pseudobutyrivibrio, and Lachnospiraceae showed a positive correlation with VFA and milk yield traits. Overall, we observed 52 positive and 10 negative correlations of rumen bacteria with milk fatty acid contents. Our study revealed the potential of the herbal mi…
bibliographic citation: Hassan et al. (2021) Consequences of herbal mixture supplementation on milk performance, ruminal fermentation, and bacterial diversity in water buffaloes. PeerJ 9:e11241 https://doi.org/10.7717/peerj.11241
date submitted: 2020-09-14
date accepted: 2021-03-17
issued: 2021-05-14
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Hassan
  given name: Faizul
author list: Agent
  family name: Tang
  given name: Zhenhua
author list: Agent
  family name: Ebeid
  given name: Hossam M.
author list: Agent
  family name: Li
  given name: Mengwei
author list: Agent
  family name: Peng
  given name: Kaiping
author list: Agent
  family name: Liang
  given name: Xin
author list: Agent
  family name: Yang
  given name: Chengjian
doi: 10.7717/peerj.11241
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-05-14
copyright: ©2021 Hassan et al.
attribution name: Hassan et al.

The multi metal-resistant bacterium Cupriavidus metallidurans CH34 affects growth and metal mobilization in Arabidopsis thaliana plants exposed to copper
type: item
type: AcademicArticle
description: Copper (Cu) is important for plant growth, but high concentrations can lead to detrimental effects such as primary root length inhibition, vegetative tissue chlorosis, and even plant death. The interaction between plant-soil microbiota and roots can potentially affect metal mobility and availability, and, therefore, overall plant metal concentration. Cupriavidus metallidurans CH34 is a multi metal-resistant bacterial model that alters metal mobility and bioavailability through ion pumping, metal complexation, and reduction processes. The interactions between strain CH34 and plants may affect the growth, metal uptake, and translocation of Arabidopsis thaliana plants that are exposed to or not exposed to Cu. In this study, we looked also at the specific gene expression changes in C. metallidurans when co-cultured with Cu-exposed A. thaliana. We found that A. thaliana’s rosette area, primary and secondary root growth, and dry weight were affected by strain CH34, and that beneficial or detrimental effects depended on Cu concentration. An increase in some plant growth parameters was observed at copper concentrations lower than 50 µM and significant detrimental effects were found at concentrations higher than 50 µM Cu. We also observed up to a 90% increase and 60% decrease in metal accumulation and mobilization in inoculated A. thaliana. In turn, copper-stressed A. thaliana altered C. metallidurans colonization, and cop genes that encoded copper resistance in strain CH34 were induced by the combination of A. thaliana and Cu. These results reveal the complexity of the plant-bacteria-metal triad and will contribute to our understanding of their applications in plant growth promotion, protection, and phytoremediation strategies.
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format: text/html
creator: Claudia Clavero-León
creator: Daniela Ruiz
creator: Javier Cillero
creator: Julieta Orlando
creator: Bernardo González
subject: Agricultural Science
subject: Microbiology
subject: Plant Science
subject: Environmental Contamination and Remediation
description: doi:10.7717/peerj.11373
publisher: PeerJ Inc.
rights: © 2021 Clavero-León et al.
abstract: Copper (Cu) is important for plant growth, but high concentrations can lead to detrimental effects such as primary root length inhibition, vegetative tissue chlorosis, and even plant death. The interaction between plant-soil microbiota and roots can potentially affect metal mobility and availability, and, therefore, overall plant metal concentration. Cupriavidus metallidurans CH34 is a multi metal-resistant bacterial model that alters metal mobility and bioavailability through ion pumping, metal complexation, and reduction processes. The interactions between strain CH34 and plants may affect the growth, metal uptake, and translocation of Arabidopsis thaliana plants that are exposed to or not exposed to Cu. In this study, we looked also at the specific gene expression changes in C. metallidurans when co-cultured with Cu-exposed A. thaliana. We found that A. thaliana’s rosette area, primary and secondary root growth, and dry weight were affected by strain CH34, and that beneficial or detrimental effects depended on Cu concentration. An increase in some plant growth parameters was observed at copper concentrations lower than 50 µM and significant detrimental effects were found at concentrations higher than 50 µM Cu. We also observed up to a 90% increase and 60% decrease in metal accumulation and mobilization in inoculated A. thaliana. In turn, copper-stressed A. thaliana altered C. metallidurans colonization, and cop genes that encoded copper resistance in strain CH34 were induced by the combination of A. thaliana and Cu. These results reveal the complexity of the plant-bacteria-metal triad and will contribute to our understanding of their applications in plant growth promotion, protection, and phytoremediation strategies.
bibliographic citation: Clavero-León et al. (2021) The multi metal-resistant bacterium Cupriavidus metallidurans CH34 affects growth and metal mobilization in Arabidopsis thaliana plants exposed to copper. PeerJ 9:e11373 https://doi.org/10.7717/peerj.11373
date submitted: 2020-09-10
date accepted: 2021-04-07
issued: 2021-05-14
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Clavero-León
  given name: Claudia
author list: Agent
  family name: Ruiz
  given name: Daniela
author list: Agent
  family name: Cillero
  given name: Javier
author list: Agent
  family name: Orlando
  given name: Julieta
author list: Agent
  family name: González
  given name: Bernardo
doi: 10.7717/peerj.11373
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-05-14
copyright: ©2021 Clavero-León et al.
attribution name: Clavero-León et al.

DZNep, an inhibitor of the histone methyltransferase EZH2, suppresses hepatic fibrosis through regulating miR-199a-5p/SOCS7 pathway
type: item
type: AcademicArticle
description: Background Hepatic fibrosis is a common response to chronic liver injury. Recently, the role of DZNep (a histone methyltransferase EZH2 inhibitor) in repressing pulmonary and renal fibrosis was verified. However, the potential effect of DZNep on hepatic fibrosis has not been elucidated. Methods The hepatic fibrosis model was established in rats treated with CCl4 and in hepatic stellate cells (HSCs) treated with TGF-β1. The liver tissues were stained with H&E and Masson’s trichrome. The expression of EZH2, SOCS7, collagen I, αSMA mRNA and miR-199-5p was assessed using qPCR, immunohistochemical or western blot analysis. A dual-luciferase reporter assay was carried out to validate the regulatory relationship of miR-199a-5p with SOCS7. Results The EZH2 level was increased in CCl4-treated rats and in TGF-β1-treated HSCs, whereas DZNep treatment significantly inhibited EZH2 expression. DZNep repressed hepatic fibrosis in vivo and in vitro, as evidenced by the decrease of hepatic fibrosis markers (α-SMA and Collagen I). Moreover, miR-199a-5p expression was repressed by DZNep in TGF-β1-activated HSCs. Notably, downregulation of miR-199a-5p decreased TGF-β1-induced expression of fibrosis markers. SOCS7 was identified as a direct target of miR-199a-5p. The expression of SOCS7 was decreased in TGF-β1-activated HSCs, but DZNep treatment restore d SOCS7 expression. More importantly, SOCS7 knockdown decreased the effect of DZNep on collagen I and α SMA expression in TGF-β1-activated HSCs. Conclusions DZNep suppresses hepatic fibrosis through regulating miR-199a-5p/SOCS7 axis, suggesting that DZNep may represent a novel treatment for fibrosis.
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format: text/html
creator: Rongrong Ding
creator: Jianming Zheng
creator: Ning Li
creator: Qi Cheng
creator: Mengqi Zhu
creator: Yanbing Wang
creator: Xinlan Zhou
creator: Zhanqing Zhang
creator: Guangfeng Shi
subject: Biochemistry
subject: Cell Biology
subject: Molecular Biology
subject: Gastroenterology and Hepatology
description: doi:10.7717/peerj.11374
publisher: PeerJ Inc.
rights: © 2021 Ding et al.
abstract: Background Hepatic fibrosis is a common response to chronic liver injury. Recently, the role of DZNep (a histone methyltransferase EZH2 inhibitor) in repressing pulmonary and renal fibrosis was verified. However, the potential effect of DZNep on hepatic fibrosis has not been elucidated. Methods The hepatic fibrosis model was established in rats treated with CCl4 and in hepatic stellate cells (HSCs) treated with TGF-β1. The liver tissues were stained with H&E and Masson’s trichrome. The expression of EZH2, SOCS7, collagen I, αSMA mRNA and miR-199-5p was assessed using qPCR, immunohistochemical or western blot analysis. A dual-luciferase reporter assay was carried out to validate the regulatory relationship of miR-199a-5p with SOCS7. Results The EZH2 level was increased in CCl4-treated rats and in TGF-β1-treated HSCs, whereas DZNep treatment significantly inhibited EZH2 expression. DZNep repressed hepatic fibrosis in vivo and in vitro, as evidenced by the decrease of hepatic fibrosis markers (α-SMA and Collagen I). Moreover, miR-199a-5p expression was repressed by DZNep in TGF-β1-activated HSCs. Notably, downregulation of miR-199a-5p decreased TGF-β1-induced expression of fibrosis markers. SOCS7 was identified as a direct target of miR-199a-5p. The expression of SOCS7 was decreased in TGF-β1-activated HSCs, but DZNep treatment restore d SOCS7 expression. More importantly, SOCS7 knockdown decreased the effect of DZNep on collagen I and α SMA expression in TGF-β1-activated HSCs. Conclusions DZNep suppresses hepatic fibrosis through regulating miR-199a-5p/SOCS7 axis, suggesting that DZNep may represent a novel treatment for fibrosis.
bibliographic citation: Ding et al. (2021) DZNep, an inhibitor of the histone methyltransferase EZH2, suppresses hepatic fibrosis through regulating miR-199a-5p/SOCS7 pathway. PeerJ 9:e11374 https://doi.org/10.7717/peerj.11374
date submitted: 2020-10-12
date accepted: 2021-04-07
issued: 2021-05-14
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Ding
  given name: Rongrong
author list: Agent
  family name: Zheng
  given name: Jianming
author list: Agent
  family name: Li
  given name: Ning
author list: Agent
  family name: Cheng
  given name: Qi
author list: Agent
  family name: Zhu
  given name: Mengqi
author list: Agent
  family name: Wang
  given name: Yanbing
author list: Agent
  family name: Zhou
  given name: Xinlan
author list: Agent
  family name: Zhang
  given name: Zhanqing
author list: Agent
  family name: Shi
  given name: Guangfeng
doi: 10.7717/peerj.11374
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-05-14
copyright: ©2021 Ding et al.
attribution name: Ding et al.

Oxidative stress induces cell death partially by decreasing both mRNA and protein levels of nicotinamide phosphoribosyltransferase in differentiated PC12 cells
type: item
type: AcademicArticle
description: Background. Multiple studies have indicated crucial roles of NAD+ deficiency in several neurological diseases and aging. It is critical to discover the mechanisms underlying the NAD+ deficiency. A decreased level of Nicotinamide phosphoribosyltransferase (Nampt)—an important enzyme in the salvage pathway of NAD+ synthesis—has been found under certain pathological conditions, while the mechanisms underlying the Nampt decrease are unclear. The purpose of this study is to test the hypothesis that oxidative stress can produce decreased Nampt, and to investigate the biological effects of Nampt on NAD+ synthesis and cell survival under both basal and oxidative stress conditions. Methods. We used differentiated PC12 cells as a cellular model to investigate the effects of oxidative stress on the levels of Nampt. Multiple assays, including flow cytometry-based cell death assays and NAD+ assays were conducted. Results. First, oxidative stress can decrease the levels of Nampt mRNA and Nampt protein; second, Nampt plays significant roles in NAD+ synthesis under both basal conditions and oxidative stress conditions; third, Nampt plays critical roles in cell survival under both basal conditions and oxidative stress conditions; and fourth, oxidative stress produced decreased NAD+ levels and cell survival partially by decreasing Nampt. Collectively, our study has indicated that oxidative stress is a pathological factor leading to decreased Nampt, which plays important roles in oxidative stress-produced decreases in NAD+ levels and cell survival. Our findings have indicated major roles of Nampt in maintaining NAD+ levels and cell survival under both basal and oxidative stress conditions.
format: application/pdf
format: text/html
creator: Cuiyan Zhou
creator: Weihai Ying
subject: Biochemistry
subject: Cell Biology
description: doi:10.7717/peerj.11401
publisher: PeerJ Inc.
rights: © 2021 Zhou and Ying
abstract: Background. Multiple studies have indicated crucial roles of NAD+ deficiency in several neurological diseases and aging. It is critical to discover the mechanisms underlying the NAD+ deficiency. A decreased level of Nicotinamide phosphoribosyltransferase (Nampt)—an important enzyme in the salvage pathway of NAD+ synthesis—has been found under certain pathological conditions, while the mechanisms underlying the Nampt decrease are unclear. The purpose of this study is to test the hypothesis that oxidative stress can produce decreased Nampt, and to investigate the biological effects of Nampt on NAD+ synthesis and cell survival under both basal and oxidative stress conditions. Methods. We used differentiated PC12 cells as a cellular model to investigate the effects of oxidative stress on the levels of Nampt. Multiple assays, including flow cytometry-based cell death assays and NAD+ assays were conducted. Results. First, oxidative stress can decrease the levels of Nampt mRNA and Nampt protein; second, Nampt plays significant roles in NAD+ synthesis under both basal conditions and oxidative stress conditions; third, Nampt plays critical roles in cell survival under both basal conditions and oxidative stress conditions; and fourth, oxidative stress produced decreased NAD+ levels and cell survival partially by decreasing Nampt. Collectively, our study has indicated that oxidative stress is a pathological factor leading to decreased Nampt, which plays important roles in oxidative stress-produced decreases in NAD+ levels and cell survival. Our findings have indicated major roles of Nampt in maintaining NAD+ levels and cell survival under both basal and oxidative stress conditions.
bibliographic citation: Zhou et al. (2021) Oxidative stress induces cell death partially by decreasing both mRNA and protein levels of nicotinamide phosphoribosyltransferase in differentiated PC12 cells. PeerJ 9:e11401 https://doi.org/10.7717/peerj.11401
date submitted: 2020-11-26
date accepted: 2021-04-13
issued: 2021-05-14
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Zhou
  given name: Cuiyan
author list: Agent
  family name: Ying
  given name: Weihai
doi: 10.7717/peerj.11401
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-05-14
copyright: © 2021 Zhou and Ying
attribution name: Zhou and Ying

The relationship between PLOD1 expression level and glioma prognosis investigated using public databases
type: item
type: AcademicArticle
description: Background Glioma is the most common type of intracranial tumor with high malignancy and poor prognosis despite the use of various aggressive treatments. Targeted therapy and immunotherapy are not effective and new biomarkers need to be explored. Some Procollagen-lysine 2-oxyglutarate 5-dioxygenase (PLOD) family members have been found to be involved in the metastasis and progression of tumors. Both PLOD2 and PLOD3 had been reported to be highly expressed in gliomas, while the prognostic value of PLOD1 remains to be further illustrated, so we want to investigate the PLOD1 expression in glioma and its clinical implication. Methods We collected gene expression and corresponding clinical data of glioma from the Chinese Glioma Genome Atlas (CGGA) database, The Cancer Genome Atlas (TCGA) database and the Gene Expression Omnibus (GEO) database. First, we analyzed the expression and mutation of PLOD1 in gliomas and its relationship with clinicopathologic characteristics. Then, we conducted survival analysis, prognostic analysis and nomogram construction of the PLOD1 gene. Finally, we conducted gene ontology (GO) enrichment analysis and gene set enrichment analysis (GSEA) to explore possible mechanisms and gene co-expression analysis was also be performed. Results The results showed that the expression level of PLOD1 was higher in gliomas than normal tissues, and high expression of PLOD1 was related to poor survival which can serve as an oncogenic factor and an independent prognostic indicator for glioma patients. Both the GO and GSEA analysis showed high expression of PLOD1 were enriched in Extracellular matrix (ECM) related pathways, the co-expression analysis revealed that PLOD1 was positively related to HSPG2, COL6A2, COL4A2, FN1, COL1A1, COL4A1, CD44, COL3A1, COL1A2 and SPP1, and high expression of these genes were also correlated to poor prognosis of glioma. Conclusions The results showed that high expression of PLOD1 leads to poor prognosis, and PLOD1 is an independe…
format: application/pdf
format: text/html
creator: Lei Tian
creator: Huandi Zhou
creator: Guohui Wang
creator: Wen yan Wang
creator: Yuehong Li
creator: Xiaoying Xue
subject: Bioinformatics
subject: Neurology
subject: Oncology
subject: Medical Genetics
description: doi:10.7717/peerj.11422
publisher: PeerJ Inc.
rights: © 2021 Tian et al.
abstract: Background Glioma is the most common type of intracranial tumor with high malignancy and poor prognosis despite the use of various aggressive treatments. Targeted therapy and immunotherapy are not effective and new biomarkers need to be explored. Some Procollagen-lysine 2-oxyglutarate 5-dioxygenase (PLOD) family members have been found to be involved in the metastasis and progression of tumors. Both PLOD2 and PLOD3 had been reported to be highly expressed in gliomas, while the prognostic value of PLOD1 remains to be further illustrated, so we want to investigate the PLOD1 expression in glioma and its clinical implication. Methods We collected gene expression and corresponding clinical data of glioma from the Chinese Glioma Genome Atlas (CGGA) database, The Cancer Genome Atlas (TCGA) database and the Gene Expression Omnibus (GEO) database. First, we analyzed the expression and mutation of PLOD1 in gliomas and its relationship with clinicopathologic characteristics. Then, we conducted survival analysis, prognostic analysis and nomogram construction of the PLOD1 gene. Finally, we conducted gene ontology (GO) enrichment analysis and gene set enrichment analysis (GSEA) to explore possible mechanisms and gene co-expression analysis was also be performed. Results The results showed that the expression level of PLOD1 was higher in gliomas than normal tissues, and high expression of PLOD1 was related to poor survival which can serve as an oncogenic factor and an independent prognostic indicator for glioma patients. Both the GO and GSEA analysis showed high expression of PLOD1 were enriched in Extracellular matrix (ECM) related pathways, the co-expression analysis revealed that PLOD1 was positively related to HSPG2, COL6A2, COL4A2, FN1, COL1A1, COL4A1, CD44, COL3A1, COL1A2 and SPP1, and high expression of these genes were also correlated to poor prognosis of glioma. Conclusions The results showed that high expression of PLOD1 leads to poor prognosis, and PLOD1 is an independe…
bibliographic citation: Tian et al. (2021) The relationship between PLOD1 expression level and glioma prognosis investigated using public databases. PeerJ 9:e11422 https://doi.org/10.7717/peerj.11422
date submitted: 2021-02-08
date accepted: 2021-04-16
issued: 2021-05-14
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Tian
  given name: Lei
author list: Agent
  family name: Zhou
  given name: Huandi
author list: Agent
  family name: Wang
  given name: Guohui
author list: Agent
  family name: Wang
  given name: Wen yan
author list: Agent
  family name: Li
  given name: Yuehong
author list: Agent
  family name: Xue
  given name: Xiaoying
doi: 10.7717/peerj.11422
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-05-14
copyright: ©2021 Tian et al.
attribution name: Tian et al.

DNA barcoding of Austrian snow scorpionflies (Mecoptera, Boreidae) reveals potential cryptic diversity in Boreus westwoodi
type: item
type: AcademicArticle
description: Background Snow scorpionflies (genus Boreus) belong to a family of Mecoptera, Boreidae, that has been vastly neglected by entomological researchers due to their shift in seasonality to the winter months. Their activity during this time is regarded as a strategy for predator avoidance and regular sightings on snow fields suggest that this also facilitates dispersal. However, many aspects about snow scorpionflies, especially systematics, taxonomy, distribution of species, phylogenetics and phylogeography have remained fairly unexplored until today. In this study, we fill some of these gaps by generating a reference DNA barcode database for Austrian snow scorpionflies in the frame of the Austrian Barcode of Life initiative and by characterising morphological diversity in the study region. Methods Initial species assignment of all 67 specimens was based on male morphological characters previously reported to differ between Boreus species and, for females, the shape of the ovipositor. DNA barcoding of the mitochondrial cytochrome c oxidase subunit 1 (COI) gene was carried out for all 67 samples and served as a basis for BIN assignment, genetic distance calculations, as well as alternative species delimitation analyses (ABGD, GMYC, bGMYC, bPTP) and a statistical parsimony network to infer phylogenetic relationships among individual samples/sampling sites. Results Morphological investigations suggested the presence of both Boreus hyemalis and Boreus westwoodi in Austria. DNA barcoding also separated the two species, but resulted in several divergent clades, the paraphyly of B. westwoodi in Austria, and high levels of phylogeographic structure on a small geographic scale. Even though the different molecular species delimitation methods disagreed on the exact number of species, they unequivocally suggested the presence of more than the traditionally recognized two Boreus species in Austria, thus indicating potential cryptic species within the genus Boreus in general and espe…
format: application/pdf
format: text/html
creator: Lukas Zangl
creator: Elisabeth Glatzhofer
creator: Raphael Schmid
creator: Susanne Randolf
creator: Stephan Koblmüller
subject: Biodiversity
subject: Entomology
subject: Evolutionary Studies
subject: Genetics
subject: Zoology
description: doi:10.7717/peerj.11424
publisher: PeerJ Inc.
rights: © 2021 Zangl et al.
abstract: Background Snow scorpionflies (genus Boreus) belong to a family of Mecoptera, Boreidae, that has been vastly neglected by entomological researchers due to their shift in seasonality to the winter months. Their activity during this time is regarded as a strategy for predator avoidance and regular sightings on snow fields suggest that this also facilitates dispersal. However, many aspects about snow scorpionflies, especially systematics, taxonomy, distribution of species, phylogenetics and phylogeography have remained fairly unexplored until today. In this study, we fill some of these gaps by generating a reference DNA barcode database for Austrian snow scorpionflies in the frame of the Austrian Barcode of Life initiative and by characterising morphological diversity in the study region. Methods Initial species assignment of all 67 specimens was based on male morphological characters previously reported to differ between Boreus species and, for females, the shape of the ovipositor. DNA barcoding of the mitochondrial cytochrome c oxidase subunit 1 (COI) gene was carried out for all 67 samples and served as a basis for BIN assignment, genetic distance calculations, as well as alternative species delimitation analyses (ABGD, GMYC, bGMYC, bPTP) and a statistical parsimony network to infer phylogenetic relationships among individual samples/sampling sites. Results Morphological investigations suggested the presence of both Boreus hyemalis and Boreus westwoodi in Austria. DNA barcoding also separated the two species, but resulted in several divergent clades, the paraphyly of B. westwoodi in Austria, and high levels of phylogeographic structure on a small geographic scale. Even though the different molecular species delimitation methods disagreed on the exact number of species, they unequivocally suggested the presence of more than the traditionally recognized two Boreus species in Austria, thus indicating potential cryptic species within the genus Boreus in general and espe…
bibliographic citation: Zangl et al. (2021) DNA barcoding of Austrian snow scorpionflies (Mecoptera, Boreidae) reveals potential cryptic diversity in Boreus westwoodi. PeerJ 9:e11424 https://doi.org/10.7717/peerj.11424
date submitted: 2021-01-20
date accepted: 2021-04-17
issued: 2021-05-14
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Zangl
  given name: Lukas
author list: Agent
  family name: Glatzhofer
  given name: Elisabeth
author list: Agent
  family name: Schmid
  given name: Raphael
author list: Agent
  family name: Randolf
  given name: Susanne
author list: Agent
  family name: Koblmüller
  given name: Stephan
doi: 10.7717/peerj.11424
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-05-14
copyright: ©2021 Zangl et al.
attribution name: Zangl et al.

Identification of diagnostic genes and vital microRNAs involved in rheumatoid arthritis: based on data mining and experimental verification
type: item
type: AcademicArticle
description: Background The pathogenesis of rheumatoid arthritis (RA) is complex. This study aimed to identify diagnostic biomarkers and transcriptional regulators that underlie RA based on bioinformatics analysis and experimental verification. Material and Methods We applied weighted gene co-expression network analysis (WGCNA) to analyze dataset GSE55457 and obtained the key module most relevant to the RA phenotype. We then conducted gene function annotation, gene set enrichment analysis (GSEA) and immunocytes quantitative analysis (CIBERSORT). Moreover, the intersection of differentially expressed genes (DEGs) and genes within the key module were entered into the STRING database to construct an interaction network and to mine hub genes. We predicted microRNA (miRNA) using a web-based tool (miRDB). Finally, hub genes and vital miRNAs were validated with independent GEO datasets, RT-qPCR and Western blot. Results A total of 367 DEGs were characterized by differential expression analysis. The WGCNA method divided genes into 14 modules, and we focused on the turquoise module containing 845 genes. Gene function annotation and GSEA suggested that immune response and inflammatory signaling pathways are the molecular mechanisms behind RA. Nine hub genes were screened from the network and seven vital regulators were obtained using miRNA prediction. CIBERSORT analysis identified five cell types enriched in RA samples, which were closely related to the expression of hub genes. Through ROC curve and RT-qPCR validation, we confirmed five genes that were specific for RA, including CCL25, CXCL9, CXCL10, CXCL11, and CXCL13. Moreover, we selected a representative gene (CXCL10) for Western blot validation. Vital miRNAs verification showed that only the differences in has-miR-573 and has-miR-34a were statistically significant. Conclusion Our study reveals diagnostic genes and vital microRNAs highly related to RA, which could help improve our understanding of the molecular mechanisms underlying t…
format: application/pdf
format: text/html
creator: Conglin Ren
creator: Mingshuang Li
creator: Yang Zheng
creator: Fengqing Wu
creator: Weibin Du
creator: Renfu Quan
subject: Bioinformatics
subject: Molecular Biology
subject: Rheumatology
subject: Data Mining and Machine Learning
description: doi:10.7717/peerj.11427
publisher: PeerJ Inc.
rights: © 2021 Ren et al.
abstract: Background The pathogenesis of rheumatoid arthritis (RA) is complex. This study aimed to identify diagnostic biomarkers and transcriptional regulators that underlie RA based on bioinformatics analysis and experimental verification. Material and Methods We applied weighted gene co-expression network analysis (WGCNA) to analyze dataset GSE55457 and obtained the key module most relevant to the RA phenotype. We then conducted gene function annotation, gene set enrichment analysis (GSEA) and immunocytes quantitative analysis (CIBERSORT). Moreover, the intersection of differentially expressed genes (DEGs) and genes within the key module were entered into the STRING database to construct an interaction network and to mine hub genes. We predicted microRNA (miRNA) using a web-based tool (miRDB). Finally, hub genes and vital miRNAs were validated with independent GEO datasets, RT-qPCR and Western blot. Results A total of 367 DEGs were characterized by differential expression analysis. The WGCNA method divided genes into 14 modules, and we focused on the turquoise module containing 845 genes. Gene function annotation and GSEA suggested that immune response and inflammatory signaling pathways are the molecular mechanisms behind RA. Nine hub genes were screened from the network and seven vital regulators were obtained using miRNA prediction. CIBERSORT analysis identified five cell types enriched in RA samples, which were closely related to the expression of hub genes. Through ROC curve and RT-qPCR validation, we confirmed five genes that were specific for RA, including CCL25, CXCL9, CXCL10, CXCL11, and CXCL13. Moreover, we selected a representative gene (CXCL10) for Western blot validation. Vital miRNAs verification showed that only the differences in has-miR-573 and has-miR-34a were statistically significant. Conclusion Our study reveals diagnostic genes and vital microRNAs highly related to RA, which could help improve our understanding of the molecular mechanisms underlying t…
bibliographic citation: Ren et al. (2021) Identification of diagnostic genes and vital microRNAs involved in rheumatoid arthritis: based on data mining and experimental verification. PeerJ 9:e11427 https://doi.org/10.7717/peerj.11427
date submitted: 2020-11-28
date accepted: 2021-04-18
issued: 2021-05-14
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Ren
  given name: Conglin
author list: Agent
  family name: Li
  given name: Mingshuang
author list: Agent
  family name: Zheng
  given name: Yang
author list: Agent
  family name: Wu
  given name: Fengqing
author list: Agent
  family name: Du
  given name: Weibin
author list: Agent
  family name: Quan
  given name: Renfu
doi: 10.7717/peerj.11427
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-05-14
copyright: ©2021 Ren et al.
attribution name: Ren et al.

EGFR mutation status yield from bronchoalveolar lavage in patients with primary pulmonary adenocarcinoma compared to a venous blood sample and tissue biopsy
type: item
type: AcademicArticle
description: Background In recent years, there has been a revolution in the genomic profiling and molecular typing of lung cancer. A key oncogene is the epidermal growth factor receptor (EGFR). The gold standard for determining EGFR mutation status is tissue biopsy, where a histological specimen is taken by a bronchoscopic or surgical method (transbronchial biopsy, forceps biopsy, etc.). However, in clinical practice the tissue sample is often insufficient for morphological and molecular analysis. Bronchoalveolar lavage is a validated diagnostic method for pathogenic infections in the lower respiratory tract, yet its diagnostic value for oncogenic mutation testing in lung cancer has not been extensively investigated. This study aims to compare the prevalence of EGFR mutation status in bronchoalveolar lavage and peripheral blood referring to the gold standard - tissue biopsy in patients with primary lung adenocarcinoma. Methods Twenty-six patients with adenocarcinoma were examined for EGFR mutation from tissue biopsy, peripheral blood sample and bronchoalveolar lavage. Results Thirteen patients had wild type EGFR and the other 13 had EGFR mutation. EGFR mutation from a peripheral blood sample was identified in 38.5% (5/13) of patients, whereas EGFR mutation obtained from bronchoalveolar lavage (BAL) was identified in 92.3% (12/13). This study demonstrates that a liquid biopsy sample for EGFR status from BAL has a higher sensitivity compared to a venous blood sample.
format: application/pdf
format: text/html
creator: Nikolay Yanev
creator: Evgeni Mekov
creator: Dinko Valev
creator: Georgi Yankov
creator: Vladimir Milanov
creator: Stoyan Bichev
creator: Natalia Gabrovska
creator: Dimitar Kostadinov
subject: Genetics
subject: Oncology
subject: Respiratory Medicine
description: doi:10.7717/peerj.11448
publisher: PeerJ Inc.
rights: © 2021 Yanev et al.
abstract: Background In recent years, there has been a revolution in the genomic profiling and molecular typing of lung cancer. A key oncogene is the epidermal growth factor receptor (EGFR). The gold standard for determining EGFR mutation status is tissue biopsy, where a histological specimen is taken by a bronchoscopic or surgical method (transbronchial biopsy, forceps biopsy, etc.). However, in clinical practice the tissue sample is often insufficient for morphological and molecular analysis. Bronchoalveolar lavage is a validated diagnostic method for pathogenic infections in the lower respiratory tract, yet its diagnostic value for oncogenic mutation testing in lung cancer has not been extensively investigated. This study aims to compare the prevalence of EGFR mutation status in bronchoalveolar lavage and peripheral blood referring to the gold standard - tissue biopsy in patients with primary lung adenocarcinoma. Methods Twenty-six patients with adenocarcinoma were examined for EGFR mutation from tissue biopsy, peripheral blood sample and bronchoalveolar lavage. Results Thirteen patients had wild type EGFR and the other 13 had EGFR mutation. EGFR mutation from a peripheral blood sample was identified in 38.5% (5/13) of patients, whereas EGFR mutation obtained from bronchoalveolar lavage (BAL) was identified in 92.3% (12/13). This study demonstrates that a liquid biopsy sample for EGFR status from BAL has a higher sensitivity compared to a venous blood sample.
bibliographic citation: Yanev et al. (2021) EGFR mutation status yield from bronchoalveolar lavage in patients with primary pulmonary adenocarcinoma compared to a venous blood sample and tissue biopsy. PeerJ 9:e11448 https://doi.org/10.7717/peerj.11448
date submitted: 2020-09-09
date accepted: 2021-04-22
issued: 2021-05-14
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Yanev
  given name: Nikolay
author list: Agent
  family name: Mekov
  given name: Evgeni
author list: Agent
  family name: Valev
  given name: Dinko
author list: Agent
  family name: Yankov
  given name: Georgi
author list: Agent
  family name: Milanov
  given name: Vladimir
author list: Agent
  family name: Bichev
  given name: Stoyan
author list: Agent
  family name: Gabrovska
  given name: Natalia
author list: Agent
  family name: Kostadinov
  given name: Dimitar
doi: 10.7717/peerj.11448
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-05-14
copyright: ©2021 Yanev et al.
attribution name: Yanev et al.

Seasonal variation of 25-Hydroxyvitamin D and indices of carbohydrate and lipid metabolism in postmenopausal women
type: item
type: AcademicArticle
description: Background Some studies indicate vitamin D’s significant contribution to metabolic processess. Therefore, the purpose of this study was to evaluate the level of carbohydrate and lipid metabolism indices in relation to seasonal changes in 25-hydroxyvitamin D (25(OH)D) concentration in postmenopausal women. Methods Sixteen postmenopausal women meeting health criteria and not using vitamin D supplementation were included in the study. Seasonal variation of somatic features and the serum concentration of 25(OH)D, glucose, insulin, parathormon, sclerostin and lipid profile were determined on two terms (autumn-winter). Results Comparative analysis of the variables between the study terms revealed a marked decrease in the concentration of 25(OH)D (p ≤ 0.0001), insulin (p < 0.05), insulin resistance index (HOMA-IR), (p < 0.05). The significant positive correlations of changes (Δ) between autumn and winter in 25(OH)D with body mass (p < 0.05), and fat mass (p ≤ 0.01), measured in the first study term, in the group of women with normal body mass index (BMI), and negative correlation with fat mass (p < 0.05) in women with a BMI value above the reference values, were found. The relationship analysis showed that in women with normal BMI, the decrease in 25(OH)D concentrations was greater when the body fat percentage was higher, whereas in women with a BMI value above the reference values, the higher the fat percentage, the smaller was the decrease in 25(OH)D concentration. Conclusions Seasonal changes in 25(OH)D concentration did not significantly affect the concentration of carbohydrate and lipid metabolism indices. The magnitude of decline in 25(OH)D levels depends on the fat mass. We suppose that environmental or lifestyle-related factors, e.g., nutritional behaviours, may have had more influence on metabolic indices than changes in 25(OH)D.
format: application/pdf
format: text/html
creator: Anna Huta-Osiecka
creator: Krystian Wochna
creator: Zbigniew Kasprzak
creator: Alicja Nowak
subject: Biochemistry
subject: Geriatrics
subject: Women’s Health
subject: Metabolic Sciences
description: doi:10.7717/peerj.11341
publisher: PeerJ Inc.
rights: © 2021 Huta-Osiecka et al.
abstract: Background Some studies indicate vitamin D’s significant contribution to metabolic processess. Therefore, the purpose of this study was to evaluate the level of carbohydrate and lipid metabolism indices in relation to seasonal changes in 25-hydroxyvitamin D (25(OH)D) concentration in postmenopausal women. Methods Sixteen postmenopausal women meeting health criteria and not using vitamin D supplementation were included in the study. Seasonal variation of somatic features and the serum concentration of 25(OH)D, glucose, insulin, parathormon, sclerostin and lipid profile were determined on two terms (autumn-winter). Results Comparative analysis of the variables between the study terms revealed a marked decrease in the concentration of 25(OH)D (p ≤ 0.0001), insulin (p < 0.05), insulin resistance index (HOMA-IR), (p < 0.05). The significant positive correlations of changes (Δ) between autumn and winter in 25(OH)D with body mass (p < 0.05), and fat mass (p ≤ 0.01), measured in the first study term, in the group of women with normal body mass index (BMI), and negative correlation with fat mass (p < 0.05) in women with a BMI value above the reference values, were found. The relationship analysis showed that in women with normal BMI, the decrease in 25(OH)D concentrations was greater when the body fat percentage was higher, whereas in women with a BMI value above the reference values, the higher the fat percentage, the smaller was the decrease in 25(OH)D concentration. Conclusions Seasonal changes in 25(OH)D concentration did not significantly affect the concentration of carbohydrate and lipid metabolism indices. The magnitude of decline in 25(OH)D levels depends on the fat mass. We suppose that environmental or lifestyle-related factors, e.g., nutritional behaviours, may have had more influence on metabolic indices than changes in 25(OH)D.
bibliographic citation: Huta-Osiecka et al. (2021) Seasonal variation of 25-Hydroxyvitamin D and indices of carbohydrate and lipid metabolism in postmenopausal women. PeerJ 9:e11341 https://doi.org/10.7717/peerj.11341
date submitted: 2020-12-18
date accepted: 2021-04-03
issued: 2021-05-13
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Huta-Osiecka
  given name: Anna
author list: Agent
  family name: Wochna
  given name: Krystian
author list: Agent
  family name: Kasprzak
  given name: Zbigniew
author list: Agent
  family name: Nowak
  given name: Alicja
doi: 10.7717/peerj.11341
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-05-13
copyright: ©2021 Huta-Osiecka et al.
attribution name: Huta-Osiecka et al.

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