PeerJ
type: channel
link: https://peerj.com/articles/
description: Articles published in PeerJ
publisher: PeerJ Inc.
publication name: PeerJ
issn: 2167-8359
items: Effects of BRD4 inhibitor JQ1 on the expression profile of super-enhancer related lncRNAs and mRNAs in cervical cancer HeLa cells
items: AMMI and GGE biplot analysis for genotype × environment interactions affecting the yield and quality characteristics of sugar beet
items: The association between urbanization and adolescent depression in China
items: https://peerj.com/articles/16905
items: Color components determination and full-length comparative transcriptomic analyses reveal the potential mechanism of carotenoid synthesis during Paphiopedilum armeniacum flowering
items: Hypoxic bone marrow mesenchymal stem cell exosomes promote angiogenesis and enhance endometrial injury repair through the miR-424-5p-mediated DLL4/Notch signaling pathway
items: Beneficial endophytic fungi improve the yield and quality of Salvia miltiorrhiza by performing different ecological functions
items: miR-138-5p ameliorates intestinal barrier disruption caused by acute superior mesenteric vein thrombosis injury by inhibiting the NLRP3/HMGB1 axis
items: Identification of quantitative trait loci (QTLs) regulating leaf SPAD value and trichome density in mungbean (Vigna radiata L.) using genotyping-by-sequencing (GBS) approach
items: Proteomic study on nintedanib in gastric cancer cells

Effects of BRD4 inhibitor JQ1 on the expression profile of super-enhancer related lncRNAs and mRNAs in cervical cancer HeLa cells
type: item
type: AcademicArticle
description: Objective To investigate the effects of bromine domain protein 4 (BRD4) inhibitor JQ1 on the expression profile of super-enhancer-related lncRNAs (SE-lncRNAs) and mRNAs in cervical cancer (CC) HeLa-cells. Methods The CCK8 method was implemented to detect the inhibitory effect of JQ1 on HeLa cells and explore the best inhibitory concentration. Whole transcriptome sequencing was performed to detect the changes of lncRNAs and mRNAs expression profiles in cells of the JQ1 treatment group and control group, respectively. The differentially expressed SE-lncRNAs were obtained by matching, while the co-expressed mRNAs were obtained by Pearson correlation analysis. Results The inhibitory effect of JQ1 on HeLa cell proliferation increased significantly with increasing concentration and treatment time (P < 0.05). Under the experimental conditions of three concentrations of 0.01, 0.1 and 1 μmol/L of JQ1 on HeLa cells at 24, 48, 72 and 120 h, 1 μmol/L of JQ1 at 72 and 120 h had the same cell viability and the strongest cell proliferation inhibition. In order to understand the inhibitory mechanism of JQ1 on HeLa cells, this study analyzed the expression profile differences from the perspective of SE-lncRNAs and mRNAs. A total of 162 SE-lncRNAs were identified, of which 8 SE-lncRNAs were down-regulated and seven SE-lncRNAs were up-regulated. A total of 418 differentially expressed mRNAs related to SE-lncRNAs were identified, of which 395 mRNAs had positive correlation with 12 SE-lncRNAs and 408 mRNAs had negative correlation with 15 SE-lncRNAs. Conclusion JQ1 can significantly inhibit the proliferation of HeLa cells and affect the expression profile of SE-lncRNAs and mRNAs.
format: application/pdf
format: text/html
creator: Jianqing Zheng
creator: Bifen Huang
creator: Lihua Xiao
creator: Min Wu
subject: Cell Biology
subject: Gynecology and Obstetrics
subject: Oncology
subject: Women’s Health
subject: Medical Genetics
description: doi:10.7717/peerj.17035
publisher: PeerJ Inc.
rights: © 2024 Zheng et al.
abstract: Objective To investigate the effects of bromine domain protein 4 (BRD4) inhibitor JQ1 on the expression profile of super-enhancer-related lncRNAs (SE-lncRNAs) and mRNAs in cervical cancer (CC) HeLa-cells. Methods The CCK8 method was implemented to detect the inhibitory effect of JQ1 on HeLa cells and explore the best inhibitory concentration. Whole transcriptome sequencing was performed to detect the changes of lncRNAs and mRNAs expression profiles in cells of the JQ1 treatment group and control group, respectively. The differentially expressed SE-lncRNAs were obtained by matching, while the co-expressed mRNAs were obtained by Pearson correlation analysis. Results The inhibitory effect of JQ1 on HeLa cell proliferation increased significantly with increasing concentration and treatment time (P < 0.05). Under the experimental conditions of three concentrations of 0.01, 0.1 and 1 μmol/L of JQ1 on HeLa cells at 24, 48, 72 and 120 h, 1 μmol/L of JQ1 at 72 and 120 h had the same cell viability and the strongest cell proliferation inhibition. In order to understand the inhibitory mechanism of JQ1 on HeLa cells, this study analyzed the expression profile differences from the perspective of SE-lncRNAs and mRNAs. A total of 162 SE-lncRNAs were identified, of which 8 SE-lncRNAs were down-regulated and seven SE-lncRNAs were up-regulated. A total of 418 differentially expressed mRNAs related to SE-lncRNAs were identified, of which 395 mRNAs had positive correlation with 12 SE-lncRNAs and 408 mRNAs had negative correlation with 15 SE-lncRNAs. Conclusion JQ1 can significantly inhibit the proliferation of HeLa cells and affect the expression profile of SE-lncRNAs and mRNAs.
bibliographic citation: Zheng et al. (2024) Effects of BRD4 inhibitor JQ1 on the expression profile of super-enhancer related lncRNAs and mRNAs in cervical cancer HeLa cells. PeerJ 12:e17035 https://doi.org/10.7717/peerj.17035
date submitted: 2023-06-19
date accepted: 2024-02-09
issued: 2024-02-23
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Zheng
  given name: Jianqing
author list: Agent
  family name: Huang
  given name: Bifen
author list: Agent
  family name: Xiao
  given name: Lihua
author list: Agent
  family name: Wu
  given name: Min
doi: 10.7717/peerj.17035
volume: 12
issn: 2167-8359
publication name: PeerJ
publication date: 2024-02-23
copyright: © 2024 Zheng et al.
attribution name: Zheng et al.

AMMI and GGE biplot analysis for genotype × environment interactions affecting the yield and quality characteristics of sugar beet
type: item
type: AcademicArticle
description: Sugar beet, an important sugar crop, contributes significantly to the world’s sugar production. However, genotype–environment interactions (GEI) often affect the quality characteristics of sugar beet. Hence, understanding the effects of GEI on sugar beet quality can aid in identifying high-quality genotypes that can adapt to different environments. Traditional variance analysis can only be used to examine the yield of a variety and not its specific adaptability to specific conditions. Therefore, more comprehensive analytical methods are required to evaluate the characteristics of the variety under specific environments. Additive main effects and multiplicative interaction (AMMI) and genotype main effect and genotype × environment interaction (GGE) biplot models can be employed to comprehensively evaluate different varieties and address the drawbacks associated with a single evaluation method. Moreover, these models also allow us to explore new varieties more objectively and comprehensively. In this study, the adaptability and stability of 16 sugar beet varieties, in terms of yield and sugar content, were evaluated using AMMI and GGE biplot analysis in seven pilot projects undertaken in 2022. In the assessment of a small but significant proportion of the total GEI variance for the two qualitative traits (yield and sugar content), 80.58% of the variance was explained by the cumulative contribution of IPC1, IPC2, and IPC3. AMMI and GGE biplots clearly highlighted that KWS4207 (G3) exhibited high and stable quality. They also demonstrated that the experiments in Jalaid Banner (Inner Mongolia) (E7) were the most representative. Together, the results suggested that the comprehensive application of AMMI and GGE biplot analysis allowed for a more comprehensive, scientific, and effective evaluation of sugar beet varieties across different regions. The findings offer a theoretical basis for sugar beet breeding and could guide the rational design of experiments for testing new…
format: application/pdf
format: text/html
creator: Xinwang Dang
creator: Xiaohang Hu
creator: Yahuai Ma
creator: Yanli Li
creator: Wenliang Kan
creator: Xinjiu Dong
subject: Agricultural Science
subject: Plant Science
description: doi:10.7717/peerj.16882
publisher: PeerJ Inc.
rights: © 2024 Dang et al.
abstract: Sugar beet, an important sugar crop, contributes significantly to the world’s sugar production. However, genotype–environment interactions (GEI) often affect the quality characteristics of sugar beet. Hence, understanding the effects of GEI on sugar beet quality can aid in identifying high-quality genotypes that can adapt to different environments. Traditional variance analysis can only be used to examine the yield of a variety and not its specific adaptability to specific conditions. Therefore, more comprehensive analytical methods are required to evaluate the characteristics of the variety under specific environments. Additive main effects and multiplicative interaction (AMMI) and genotype main effect and genotype × environment interaction (GGE) biplot models can be employed to comprehensively evaluate different varieties and address the drawbacks associated with a single evaluation method. Moreover, these models also allow us to explore new varieties more objectively and comprehensively. In this study, the adaptability and stability of 16 sugar beet varieties, in terms of yield and sugar content, were evaluated using AMMI and GGE biplot analysis in seven pilot projects undertaken in 2022. In the assessment of a small but significant proportion of the total GEI variance for the two qualitative traits (yield and sugar content), 80.58% of the variance was explained by the cumulative contribution of IPC1, IPC2, and IPC3. AMMI and GGE biplots clearly highlighted that KWS4207 (G3) exhibited high and stable quality. They also demonstrated that the experiments in Jalaid Banner (Inner Mongolia) (E7) were the most representative. Together, the results suggested that the comprehensive application of AMMI and GGE biplot analysis allowed for a more comprehensive, scientific, and effective evaluation of sugar beet varieties across different regions. The findings offer a theoretical basis for sugar beet breeding and could guide the rational design of experiments for testing new…
bibliographic citation: Dang et al. (2024) AMMI and GGE biplot analysis for genotype × environment interactions affecting the yield and quality characteristics of sugar beet. PeerJ 12:e16882 https://doi.org/10.7717/peerj.16882
date submitted: 2023-08-30
date accepted: 2024-01-12
issued: 2024-02-22
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Dang
  given name: Xinwang
author list: Agent
  family name: Hu
  given name: Xiaohang
author list: Agent
  family name: Ma
  given name: Yahuai
author list: Agent
  family name: Li
  given name: Yanli
author list: Agent
  family name: Kan
  given name: Wenliang
author list: Agent
  family name: Dong
  given name: Xinjiu
doi: 10.7717/peerj.16882
volume: 12
issn: 2167-8359
publication name: PeerJ
publication date: 2024-02-22
copyright: © 2024 Dang et al.
attribution name: Dang et al.

The association between urbanization and adolescent depression in China
type: item
type: AcademicArticle
description: Background With the rapid urbanization in many countries, more attention is being paid to the relationship between urbanization and mental health, especially depression. However, in countries with rapid urbanization, few empirical studies exist on the relationship between urbanization and adolescent depression. Methods Nationally representative survey data from the China Family Panel Studies in 2012, 2016 and 2018 were used. Data of 1,588 adolescents were obtained from 25 provinces. Depression was measured using the Center for Epidemiology Studies of Depression 20-item score. The urbanization rate was obtained from the National Bureau of Statistics of China. The generalized estimating equation was used to estimate the statistical relationship. Results The participants’ mean age at baseline was 15 years, and 51.2% (813/1,588) of participants were male. After adjusting for all covariates (gender, age, ethnicity, level of education, marital status, urban/rural areas, body mass index, self-rated health, academic pressure, smoking, drinking and exercise), the rate of urbanization was monotonically and negatively associated with adolescent depression (odds ratio 0.34, 95% CI [0.14–0.79]). Compared with female adolescents, male adolescents had a lower risk of depression (odds ratio 0.80, 95% CI [0.67–0.97]). Conclusion In the context of China, urbanization has a positive effect on the mental health of adolescents. Female adolescents are more likely to experience depression than male adolescents.
format: application/pdf
format: text/html
creator: Degong Pan
creator: Ning Yan
creator: Lining Pu
creator: Xiaoxue He
creator: Huihui Wang
creator: Xue Zhang
creator: Xiaojuan Shi
creator: Jing Wen
creator: Jiangping Li
subject: Psychiatry and Psychology
subject: Public Health
subject: Mental Health
description: doi:10.7717/peerj.16888
publisher: PeerJ Inc.
rights: © 2024 Pan et al.
abstract: Background With the rapid urbanization in many countries, more attention is being paid to the relationship between urbanization and mental health, especially depression. However, in countries with rapid urbanization, few empirical studies exist on the relationship between urbanization and adolescent depression. Methods Nationally representative survey data from the China Family Panel Studies in 2012, 2016 and 2018 were used. Data of 1,588 adolescents were obtained from 25 provinces. Depression was measured using the Center for Epidemiology Studies of Depression 20-item score. The urbanization rate was obtained from the National Bureau of Statistics of China. The generalized estimating equation was used to estimate the statistical relationship. Results The participants’ mean age at baseline was 15 years, and 51.2% (813/1,588) of participants were male. After adjusting for all covariates (gender, age, ethnicity, level of education, marital status, urban/rural areas, body mass index, self-rated health, academic pressure, smoking, drinking and exercise), the rate of urbanization was monotonically and negatively associated with adolescent depression (odds ratio 0.34, 95% CI [0.14–0.79]). Compared with female adolescents, male adolescents had a lower risk of depression (odds ratio 0.80, 95% CI [0.67–0.97]). Conclusion In the context of China, urbanization has a positive effect on the mental health of adolescents. Female adolescents are more likely to experience depression than male adolescents.
bibliographic citation: Pan et al. (2024) The association between urbanization and adolescent depression in China. PeerJ 12:e16888 https://doi.org/10.7717/peerj.16888
date submitted: 2023-08-11
date accepted: 2024-01-15
issued: 2024-02-22
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Pan
  given name: Degong
author list: Agent
  family name: Yan
  given name: Ning
author list: Agent
  family name: Pu
  given name: Lining
author list: Agent
  family name: He
  given name: Xiaoxue
author list: Agent
  family name: Wang
  given name: Huihui
author list: Agent
  family name: Zhang
  given name: Xue
author list: Agent
  family name: Shi
  given name: Xiaojuan
author list: Agent
  family name: Wen
  given name: Jing
author list: Agent
  family name: Li
  given name: Jiangping
doi: 10.7717/peerj.16888
volume: 12
issn: 2167-8359
publication name: PeerJ
publication date: 2024-02-22
copyright: ©2024 Pan et al.
attribution name: Pan et al.

https://peerj.com/articles/16905
type: item
type: AcademicArticle
title: Exploratory study to characterise the individual types of health literacy and beliefs and their associations with infection prevention behaviours amid the COVID-19 pandemic in Japan: a longitudinal study
description: Background During a global infectious disease pandemic such as the coronavirus disease 2019 (COVID-19), individuals’ infection prevention/risk-taking behaviours are likely to differ depending on their health literacy and beliefs regarding the disease. To effectively promote infection prevention behaviours, it is necessary to enable information dissemination and risk communication that consider individuals’ health literacy and beliefs. In this study, we exploratorily characterised segments based on individual health literacy and beliefs regarding COVID-19 among the Japanese during the early stage of the COVID-19 pandemic, and investigated whether infection prevention/risk-taking behaviours and fear of COVID-19 differed among these segments. Methods In this study, we conducted two web-based longitudinal surveys in Japan (PHASE 1, 1–30 November 2020, 6,000 participants; PHASE 2, 1–31 December 2020, 3,800 participants). We characterised segments of the target population using cluster analysis on health literacy and beliefs regarding COVID-19 obtained in PHASE 1. We further investigated the associations between the clusters and infection prevention/risk-taking behaviours and fear of COVID-19, obtained from PHASE 2. Results Five clusters were identified: ‘Calm/hoax denial’, ‘Hoax affinity/threat denial’, ‘Minority/indifference’, ‘Over vigilance’, and ‘Optimism’. There were significant differences in infection prevention/risk-taking behaviours and fear of COVID-19 among the five clusters. The belief in susceptibility to infection, rather than affinity for hoaxes and conspiracy theories, was coherently associated with infection prevention/risk-taking behaviours and fear of infection across clusters. This study provides foundational knowledge for creating segment-specific public messages and developing interactive risk communication to encourage infection prevention behaviours.
format: application/pdf
format: text/html
creator: Mao Yagihashi
creator: Michio Murakami
creator: Mai Kato
creator: Asayo Yamamura
creator: Asako Miura
creator: Kei Hirai
subject: Infectious Diseases
subject: Psychiatry and Psychology
subject: Public Health
subject: COVID-19
description: doi:10.7717/peerj.16905
publisher: PeerJ Inc.
rights: © 2024 Yagihashi et al.
abstract: Background During a global infectious disease pandemic such as the coronavirus disease 2019 (COVID-19), individuals’ infection prevention/risk-taking behaviours are likely to differ depending on their health literacy and beliefs regarding the disease. To effectively promote infection prevention behaviours, it is necessary to enable information dissemination and risk communication that consider individuals’ health literacy and beliefs. In this study, we exploratorily characterised segments based on individual health literacy and beliefs regarding COVID-19 among the Japanese during the early stage of the COVID-19 pandemic, and investigated whether infection prevention/risk-taking behaviours and fear of COVID-19 differed among these segments. Methods In this study, we conducted two web-based longitudinal surveys in Japan (PHASE 1, 1–30 November 2020, 6,000 participants; PHASE 2, 1–31 December 2020, 3,800 participants). We characterised segments of the target population using cluster analysis on health literacy and beliefs regarding COVID-19 obtained in PHASE 1. We further investigated the associations between the clusters and infection prevention/risk-taking behaviours and fear of COVID-19, obtained from PHASE 2. Results Five clusters were identified: ‘Calm/hoax denial’, ‘Hoax affinity/threat denial’, ‘Minority/indifference’, ‘Over vigilance’, and ‘Optimism’. There were significant differences in infection prevention/risk-taking behaviours and fear of COVID-19 among the five clusters. The belief in susceptibility to infection, rather than affinity for hoaxes and conspiracy theories, was coherently associated with infection prevention/risk-taking behaviours and fear of infection across clusters. This study provides foundational knowledge for creating segment-specific public messages and developing interactive risk communication to encourage infection prevention behaviours.
bibliographic citation: Yagihashi et al. (2024) Exploratory study to characterise the individual types of health literacy and beliefs and their associations with infection prevention behaviours amid the COVID-19 pandemic in Japan: a longitudinal study. PeerJ 12:e16905 https://doi.org/10.7717/peerj.16905
date submitted: 2023-04-24
date accepted: 2024-01-17
issued: 2024-02-22
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Yagihashi
  given name: Mao
author list: Agent
  family name: Murakami
  given name: Michio
author list: Agent
  family name: Kato
  given name: Mai
author list: Agent
  family name: Yamamura
  given name: Asayo
author list: Agent
  family name: Miura
  given name: Asako
author list: Agent
  family name: Hirai
  given name: Kei
doi: 10.7717/peerj.16905
volume: 12
issn: 2167-8359
publication name: PeerJ
publication date: 2024-02-22
copyright: ©2024 Yagihashi et al.
attribution name: Yagihashi et al.

Color components determination and full-length comparative transcriptomic analyses reveal the potential mechanism of carotenoid synthesis during Paphiopedilum armeniacum flowering
type: item
type: AcademicArticle
description: Background Paphiopedilum armeniacum (P. armeniacum), an ornamental plant native to China, is known for its distinctive yellow blossoms. However, the mechanisms underlying P. armeniacum flower coloration remain unclear. Methods We selected P. armeniacum samples from different flowering stages and conducted rigorous physicochemical analyses. The specimens were differentiated based on their chemical properties, specifically their solubilities in polar solvents. This key step enabled us to identify the main metabolite of flower color development of P. armeniacum, and to complete the identification by High-performance liquid chromatography (HPLC) based on the results. Additionally, we employed a combined approach, integrating both third-generation full-length transcriptome sequencing and second-generation high-throughput transcriptome sequencing, to comprehensively explore the molecular components involved. Results We combined physical and chemical analysis with transcriptome sequencing to reveal that carotenoid is the main pigment of P. armeniacum flower color. Extraction colorimetric method and HPLC were used to explore the characteristics of carotenoid accumulation during flowering. We identified 28 differentially expressed carotenoid biosynthesis genes throughout the flowering process, validated their expression through fluorescence quantification, and discovered 19 potential positive regulators involved in carotenoid synthesis. Among these candidates, three RCP2 genes showed a strong potential for governing the PDS and ZDS gene families. In summary, our study elucidates the fundamental mechanisms governing carotenoid synthesis during P. armeniacum flowering, enhancing our understanding of this process and providing a foundation for future research on the molecular mechanisms driving P. armeniacum flowering.
format: application/pdf
format: text/html
creator: Yiwei Bai
creator: Jiping Ma
creator: Yanjun Ma
creator: Yanting Chang
creator: Wenbo Zhang
creator: Yayun Deng
creator: Na Zhang
creator: Xue Zhang
creator: Keke Fan
creator: Xiaomeng Hu
creator: Shuhua Wang
creator: Zehui Jiang
creator: Tao Hu
subject: Bioinformatics
subject: Molecular Biology
subject: Plant Science
description: doi:10.7717/peerj.16914
publisher: PeerJ Inc.
rights: © 2024 Bai et al.
abstract: Background Paphiopedilum armeniacum (P. armeniacum), an ornamental plant native to China, is known for its distinctive yellow blossoms. However, the mechanisms underlying P. armeniacum flower coloration remain unclear. Methods We selected P. armeniacum samples from different flowering stages and conducted rigorous physicochemical analyses. The specimens were differentiated based on their chemical properties, specifically their solubilities in polar solvents. This key step enabled us to identify the main metabolite of flower color development of P. armeniacum, and to complete the identification by High-performance liquid chromatography (HPLC) based on the results. Additionally, we employed a combined approach, integrating both third-generation full-length transcriptome sequencing and second-generation high-throughput transcriptome sequencing, to comprehensively explore the molecular components involved. Results We combined physical and chemical analysis with transcriptome sequencing to reveal that carotenoid is the main pigment of P. armeniacum flower color. Extraction colorimetric method and HPLC were used to explore the characteristics of carotenoid accumulation during flowering. We identified 28 differentially expressed carotenoid biosynthesis genes throughout the flowering process, validated their expression through fluorescence quantification, and discovered 19 potential positive regulators involved in carotenoid synthesis. Among these candidates, three RCP2 genes showed a strong potential for governing the PDS and ZDS gene families. In summary, our study elucidates the fundamental mechanisms governing carotenoid synthesis during P. armeniacum flowering, enhancing our understanding of this process and providing a foundation for future research on the molecular mechanisms driving P. armeniacum flowering.
bibliographic citation: Bai et al. (2024) Color components determination and full-length comparative transcriptomic analyses reveal the potential mechanism of carotenoid synthesis during Paphiopedilum armeniacum flowering. PeerJ 12:e16914 https://doi.org/10.7717/peerj.16914
date submitted: 2023-09-21
date accepted: 2024-01-18
issued: 2024-02-22
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Bai
  given name: Yiwei
author list: Agent
  family name: Ma
  given name: Jiping
author list: Agent
  family name: Ma
  given name: Yanjun
author list: Agent
  family name: Chang
  given name: Yanting
author list: Agent
  family name: Zhang
  given name: Wenbo
author list: Agent
  family name: Deng
  given name: Yayun
author list: Agent
  family name: Zhang
  given name: Na
author list: Agent
  family name: Zhang
  given name: Xue
author list: Agent
  family name: Fan
  given name: Keke
author list: Agent
  family name: Hu
  given name: Xiaomeng
author list: Agent
  family name: Wang
  given name: Shuhua
author list: Agent
  family name: Jiang
  given name: Zehui
author list: Agent
  family name: Hu
  given name: Tao
doi: 10.7717/peerj.16914
volume: 12
issn: 2167-8359
publication name: PeerJ
publication date: 2024-02-22
copyright: ©2024 Bai et al.
attribution name: Bai et al.

Hypoxic bone marrow mesenchymal stem cell exosomes promote angiogenesis and enhance endometrial injury repair through the miR-424-5p-mediated DLL4/Notch signaling pathway
type: item
type: AcademicArticle
description: Background Currently, bone marrow mesenchymal stem cells (BMSCs) have been reported to promote endometrial regeneration in rat models of mechanically injury-induced uterine adhesions (IUAs), but the therapeutic effects and mechanisms of hypoxic BMSC-derived exosomes on IUAs have not been elucidated. Objective To investigate the potential mechanism by which the BMSCS-derived exosomal miR-424-5p regulates IUA angiogenesis through the DLL4/Notch signaling pathway under hypoxic conditions and promotes endometrial injury repair. Methods The morphology of the exosomes was observed via transmission electron microscopy, and the expression of exosome markers (CD9, CD63, CD81, and HSP70) was detected via flow cytometry and Western blotting. The expression of angiogenesis-related genes (Ang1, Flk1, Vash1, and TSP1) was detected via RT‒qPCR, and the expression of DLL4/Notch signaling pathway-related proteins (DLL4, Notch1, and Notch2) was detected via Western blotting. Cell proliferation was detected by a CCK-8 assay, and angiogenesis was assessed via an angiogenesis assay. The expression of CD3 was detected by immunofluorescence. The endometrial lesions of IUA rats were observed via HE staining, and the expression of CD3 and VEGFA was detected via immunohistochemistry. Results Compared with those in exosomes from normoxic conditions, miR-424-5p was more highly expressed in the exosomes from hypoxic BMSCs. Compared with those in normoxic BMSC-derived exosomes, the proliferation and angiogenesis of HUVECs were significantly enhanced after treatment with hypoxic BMSC-derived exosomes, and these effects were weakened after inhibition of miR-424-5p. miR-424-5p can target and negatively regulate the expression of DLL4, promote the expression of the proangiogenic genes Ang1 and Flk1, and inhibit the expression of the antiangiogenic genes Vash1 and TSP1. The effect of miR-424-5p can be reversed by overexpression of DLL4. In IUA rats, treatment with hypoxic BMSC exosomes and the miR-42…
format: application/pdf
format: text/html
creator: Zhenghua Xiong
creator: Yong Hu
creator: Min Jiang
creator: Beibei Liu
creator: Wenjiao Jin
creator: Huiqin Chen
creator: Linjuan Yang
creator: Xuesong Han
subject: Gynecology and Obstetrics
subject: Women’s Health
description: doi:10.7717/peerj.16953
publisher: PeerJ Inc.
rights: © 2024 Xiong et al.
abstract: Background Currently, bone marrow mesenchymal stem cells (BMSCs) have been reported to promote endometrial regeneration in rat models of mechanically injury-induced uterine adhesions (IUAs), but the therapeutic effects and mechanisms of hypoxic BMSC-derived exosomes on IUAs have not been elucidated. Objective To investigate the potential mechanism by which the BMSCS-derived exosomal miR-424-5p regulates IUA angiogenesis through the DLL4/Notch signaling pathway under hypoxic conditions and promotes endometrial injury repair. Methods The morphology of the exosomes was observed via transmission electron microscopy, and the expression of exosome markers (CD9, CD63, CD81, and HSP70) was detected via flow cytometry and Western blotting. The expression of angiogenesis-related genes (Ang1, Flk1, Vash1, and TSP1) was detected via RT‒qPCR, and the expression of DLL4/Notch signaling pathway-related proteins (DLL4, Notch1, and Notch2) was detected via Western blotting. Cell proliferation was detected by a CCK-8 assay, and angiogenesis was assessed via an angiogenesis assay. The expression of CD3 was detected by immunofluorescence. The endometrial lesions of IUA rats were observed via HE staining, and the expression of CD3 and VEGFA was detected via immunohistochemistry. Results Compared with those in exosomes from normoxic conditions, miR-424-5p was more highly expressed in the exosomes from hypoxic BMSCs. Compared with those in normoxic BMSC-derived exosomes, the proliferation and angiogenesis of HUVECs were significantly enhanced after treatment with hypoxic BMSC-derived exosomes, and these effects were weakened after inhibition of miR-424-5p. miR-424-5p can target and negatively regulate the expression of DLL4, promote the expression of the proangiogenic genes Ang1 and Flk1, and inhibit the expression of the antiangiogenic genes Vash1 and TSP1. The effect of miR-424-5p can be reversed by overexpression of DLL4. In IUA rats, treatment with hypoxic BMSC exosomes and the miR-42…
bibliographic citation: Xiong et al. (2024) Hypoxic bone marrow mesenchymal stem cell exosomes promote angiogenesis and enhance endometrial injury repair through the miR-424-5p-mediated DLL4/Notch signaling pathway. PeerJ 12:e16953 https://doi.org/10.7717/peerj.16953
date submitted: 2023-08-07
date accepted: 2024-01-25
issued: 2024-02-22
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Xiong
  given name: Zhenghua
author list: Agent
  family name: Hu
  given name: Yong
author list: Agent
  family name: Jiang
  given name: Min
author list: Agent
  family name: Liu
  given name: Beibei
author list: Agent
  family name: Jin
  given name: Wenjiao
author list: Agent
  family name: Chen
  given name: Huiqin
author list: Agent
  family name: Yang
  given name: Linjuan
author list: Agent
  family name: Han
  given name: Xuesong
doi: 10.7717/peerj.16953
volume: 12
issn: 2167-8359
publication name: PeerJ
publication date: 2024-02-22
copyright: © 2024 Xiong et al.
attribution name: Xiong et al.

Beneficial endophytic fungi improve the yield and quality of Salvia miltiorrhiza by performing different ecological functions
type: item
type: AcademicArticle
description: Background Endophytic fungi can enhance the growth and synthesis of secondary metabolites in medicinal plants. Salvia miltiorrhiza Bunge is frequently employed for treating cardiovascular and cerebrovascular ailments, with the primary bioactive components being salvianolic acid and tanshinone. However, their levels in cultivated S. miltiorrhiza are inferior to that of the wild herbs, so the production of high-quality medicinal herbs is sharply declining. Consequently, the utilization of beneficial endophytic fungi to improve the yield and quality of S. miltiorrhiza holds great significance for the cultivation of medicinal plants. Methods In this study, nine non-pathogenic, endophytic fungal strains were introduced into sterile S. miltiorrhiza seedlings and cultivated both in vitro and in situ (the greenhouse). The effects of these strains on the growth indices, C and N metabolism, antioxidant activity, photosynthesis, and content of bioactive ingredients in S. miltiorrhiza were then evaluated. Results The results showed that the different genera, species, or strains of endophytic fungi regulated the growth and metabolism of S. miltiorrhiza in unique ways. These endophytic fungi primarily exerted their growth-promoting effects by increasing the net photosynthetic rate, intercellular CO2 concentration, and the activities of sucrose synthase, sucrose phosphate synthase, nitrate reductase, and glutamine synthetase. They also enhanced the adaptability and resistance to environmental stresses by improving the synthesis of osmoregulatory compounds and the activity of antioxidant enzymes. However, their regulatory effects on the growth and development of S. miltiorrhiza were affected by environmental changes. Moreover, the strains that significantly promoted the synthesis and accumulation of phenolic acids inhibited the accumulation of tanshinones components, and vice versa. The endophytic fungal strains Penicillium meloforme DS8, Berkeleyomyces basicola DS10, and Acremoniu…
format: application/pdf
format: text/html
creator: Xiaoyu Li
creator: Yali Lin
creator: Yong Qin
creator: Guiqi Han
creator: Hai Wang
creator: Zhuyun Yan
subject: Agricultural Science
subject: Microbiology
subject: Mycology
subject: Plant Science
description: doi:10.7717/peerj.16959
publisher: PeerJ Inc.
rights: © 2024 Li et al.
abstract: Background Endophytic fungi can enhance the growth and synthesis of secondary metabolites in medicinal plants. Salvia miltiorrhiza Bunge is frequently employed for treating cardiovascular and cerebrovascular ailments, with the primary bioactive components being salvianolic acid and tanshinone. However, their levels in cultivated S. miltiorrhiza are inferior to that of the wild herbs, so the production of high-quality medicinal herbs is sharply declining. Consequently, the utilization of beneficial endophytic fungi to improve the yield and quality of S. miltiorrhiza holds great significance for the cultivation of medicinal plants. Methods In this study, nine non-pathogenic, endophytic fungal strains were introduced into sterile S. miltiorrhiza seedlings and cultivated both in vitro and in situ (the greenhouse). The effects of these strains on the growth indices, C and N metabolism, antioxidant activity, photosynthesis, and content of bioactive ingredients in S. miltiorrhiza were then evaluated. Results The results showed that the different genera, species, or strains of endophytic fungi regulated the growth and metabolism of S. miltiorrhiza in unique ways. These endophytic fungi primarily exerted their growth-promoting effects by increasing the net photosynthetic rate, intercellular CO2 concentration, and the activities of sucrose synthase, sucrose phosphate synthase, nitrate reductase, and glutamine synthetase. They also enhanced the adaptability and resistance to environmental stresses by improving the synthesis of osmoregulatory compounds and the activity of antioxidant enzymes. However, their regulatory effects on the growth and development of S. miltiorrhiza were affected by environmental changes. Moreover, the strains that significantly promoted the synthesis and accumulation of phenolic acids inhibited the accumulation of tanshinones components, and vice versa. The endophytic fungal strains Penicillium meloforme DS8, Berkeleyomyces basicola DS10, and Acremoniu…
bibliographic citation: Li et al. (2024) Beneficial endophytic fungi improve the yield and quality of Salvia miltiorrhiza by performing different ecological functions. PeerJ 12:e16959 https://doi.org/10.7717/peerj.16959
date submitted: 2023-10-02
date accepted: 2024-01-25
issued: 2024-02-22
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Li
  given name: Xiaoyu
author list: Agent
  family name: Lin
  given name: Yali
author list: Agent
  family name: Qin
  given name: Yong
author list: Agent
  family name: Han
  given name: Guiqi
author list: Agent
  family name: Wang
  given name: Hai
author list: Agent
  family name: Yan
  given name: Zhuyun
doi: 10.7717/peerj.16959
volume: 12
issn: 2167-8359
publication name: PeerJ
publication date: 2024-02-22
copyright: ©2024 Li et al.
attribution name: Li et al.

miR-138-5p ameliorates intestinal barrier disruption caused by acute superior mesenteric vein thrombosis injury by inhibiting the NLRP3/HMGB1 axis
type: item
type: AcademicArticle
description: Background Acute superior mesenteric venous thrombosis (ASMVT) decreases junction-associated protein expression and intestinal epithelial cell numbers, leading to intestinal epithelial barrier disruption. Pyroptosis has also recently been found to be one of the important causes of mucosal barrier defects. However, the role and mechanism of pyroptosis in ASMVT are not fully understood. Methods Differentially expressed microRNAs (miRNAs) in the intestinal tissues of ASMVT mice were detected by transcriptome sequencing (RNA-Seq). Gene expression levels were determined by RNA extraction and reverse transcription-quantitative PCR (RT–qPCR). Western blot and immunofluorescence staining analysis were used to analyze protein expression. H&E staining was used to observe the intestinal tissue structure. Cell Counting Kit-8 (CCK-8) and fluorescein isothiocyanate/propidine iodide (FITC/PI) were used to detect cell viability and apoptosis, respectively. Dual-luciferase reporter assays prove that miR-138-5p targets NLRP3. Results miR-138-5p expression was downregulated in ASMVT-induced intestinal tissues. Inhibition of miR-138-5p promoted NLRP3-related pyroptosis and destroyed tight junctions between IEC-6 cells, ameliorating ASMVT injury. miR-138-5p targeted to downregulate NLRP3. Knockdown of NLRP3 reversed the inhibition of proliferation, apoptosis, and pyroptosis and the decrease in tight junction proteins caused by suppression of miR-138-5p; however, this effect was later inhibited by overexpressing HMGB1. miR-138-5p inhibited pyroptosis, promoted intestinal epithelial tight junctions and alleviated ASMVT injury-induced intestinal barrier disruption via the NLRP3/HMGB1 axis.
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format: text/html
creator: Yuejin Li
creator: Ping Ling
creator: Yu Li
creator: Yongzhi Wang
creator: Guosan Li
creator: Changtao Qiu
creator: Jianghui Wang
creator: Kunmei Gong
subject: Biochemistry
subject: Cell Biology
subject: Molecular Biology
description: doi:10.7717/peerj.16692
publisher: PeerJ Inc.
rights: © 2024 Li et al.
abstract: Background Acute superior mesenteric venous thrombosis (ASMVT) decreases junction-associated protein expression and intestinal epithelial cell numbers, leading to intestinal epithelial barrier disruption. Pyroptosis has also recently been found to be one of the important causes of mucosal barrier defects. However, the role and mechanism of pyroptosis in ASMVT are not fully understood. Methods Differentially expressed microRNAs (miRNAs) in the intestinal tissues of ASMVT mice were detected by transcriptome sequencing (RNA-Seq). Gene expression levels were determined by RNA extraction and reverse transcription-quantitative PCR (RT–qPCR). Western blot and immunofluorescence staining analysis were used to analyze protein expression. H&E staining was used to observe the intestinal tissue structure. Cell Counting Kit-8 (CCK-8) and fluorescein isothiocyanate/propidine iodide (FITC/PI) were used to detect cell viability and apoptosis, respectively. Dual-luciferase reporter assays prove that miR-138-5p targets NLRP3. Results miR-138-5p expression was downregulated in ASMVT-induced intestinal tissues. Inhibition of miR-138-5p promoted NLRP3-related pyroptosis and destroyed tight junctions between IEC-6 cells, ameliorating ASMVT injury. miR-138-5p targeted to downregulate NLRP3. Knockdown of NLRP3 reversed the inhibition of proliferation, apoptosis, and pyroptosis and the decrease in tight junction proteins caused by suppression of miR-138-5p; however, this effect was later inhibited by overexpressing HMGB1. miR-138-5p inhibited pyroptosis, promoted intestinal epithelial tight junctions and alleviated ASMVT injury-induced intestinal barrier disruption via the NLRP3/HMGB1 axis.
bibliographic citation: Li et al. (2024) miR-138-5p ameliorates intestinal barrier disruption caused by acute superior mesenteric vein thrombosis injury by inhibiting the NLRP3/HMGB1 axis. PeerJ 12:e16692 https://doi.org/10.7717/peerj.16692
date submitted: 2023-08-25
date accepted: 2023-11-28
issued: 2024-02-21
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Li
  given name: Yuejin
author list: Agent
  family name: Ling
  given name: Ping
author list: Agent
  family name: Li
  given name: Yu
author list: Agent
  family name: Wang
  given name: Yongzhi
author list: Agent
  family name: Li
  given name: Guosan
author list: Agent
  family name: Qiu
  given name: Changtao
author list: Agent
  family name: Wang
  given name: Jianghui
author list: Agent
  family name: Gong
  given name: Kunmei
doi: 10.7717/peerj.16692
volume: 12
issn: 2167-8359
publication name: PeerJ
publication date: 2024-02-21
copyright: ©2024 Li et al.
attribution name: Li et al.

Identification of quantitative trait loci (QTLs) regulating leaf SPAD value and trichome density in mungbean (Vigna radiata L.) using genotyping-by-sequencing (GBS) approach
type: item
type: AcademicArticle
description: Quantitative trait loci (QTL) mapping is used for the precise localization of genomic regions regulating various traits in plants. Two major QTLs regulating Soil Plant Analysis Development (SPAD) value (qSPAD-7-1) and trichome density (qTric-7-2) in mungbean were identified using recombinant inbred line (RIL) populations (PMR-1×Pusa Baisakhi) on chromosome 7. Functional analysis of QTL region identified 35 candidate genes for SPAD value (16 No) and trichome (19 No) traits. The candidate genes regulating trichome density on the dorsal leaf surface of the mungbean include VRADI07G24840, VRADI07G17780, and VRADI07G15650, which encodes for ZFP6, TFs bHLH DNA-binding superfamily protein, and MYB102, respectively. Also, candidate genes having vital roles in chlorophyll biosynthesis are VRADIO7G29860, VRADIO7G29450, and VRADIO7G28520, which encodes for s-adenosyl-L-methionine, FTSHI1 protein, and CRS2-associated factor, respectively. The findings unfolded the opportunity for the development of customized genotypes having high SPAD value and high trichome density having a possible role in yield and mungbean yellow vein mosaic India virus (MYMIV) resistance in mungbean.
format: application/pdf
format: text/html
creator: Nikki Kumari
creator: Gyan Prakash Mishra
creator: Harsh Kumar Dikshit
creator: Soma Gupta
creator: Anirban Roy
creator: Subodh Kumar Sinha
creator: Dwijesh C. Mishra
creator: Shouvik Das
creator: Ranjeet R. Kumar
creator: Ramakrishnan Madhavan Nair
creator: Muraleedhar Aski
subject: Agricultural Science
subject: Bioinformatics
subject: Genomics
subject: Molecular Biology
subject: Plant Science
description: doi:10.7717/peerj.16722
publisher: PeerJ Inc.
rights: © 2024 Kumari et al.
abstract: Quantitative trait loci (QTL) mapping is used for the precise localization of genomic regions regulating various traits in plants. Two major QTLs regulating Soil Plant Analysis Development (SPAD) value (qSPAD-7-1) and trichome density (qTric-7-2) in mungbean were identified using recombinant inbred line (RIL) populations (PMR-1×Pusa Baisakhi) on chromosome 7. Functional analysis of QTL region identified 35 candidate genes for SPAD value (16 No) and trichome (19 No) traits. The candidate genes regulating trichome density on the dorsal leaf surface of the mungbean include VRADI07G24840, VRADI07G17780, and VRADI07G15650, which encodes for ZFP6, TFs bHLH DNA-binding superfamily protein, and MYB102, respectively. Also, candidate genes having vital roles in chlorophyll biosynthesis are VRADIO7G29860, VRADIO7G29450, and VRADIO7G28520, which encodes for s-adenosyl-L-methionine, FTSHI1 protein, and CRS2-associated factor, respectively. The findings unfolded the opportunity for the development of customized genotypes having high SPAD value and high trichome density having a possible role in yield and mungbean yellow vein mosaic India virus (MYMIV) resistance in mungbean.
bibliographic citation: Kumari et al. (2024) Identification of quantitative trait loci (QTLs) regulating leaf SPAD value and trichome density in mungbean (Vigna radiata L.) using genotyping-by-sequencing (GBS) approach. PeerJ 12:e16722 https://doi.org/10.7717/peerj.16722
date submitted: 2023-08-29
date accepted: 2023-12-04
issued: 2024-02-21
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Kumari
  given name: Nikki
author list: Agent
  family name: Mishra
  given name: Gyan Prakash
author list: Agent
  family name: Dikshit
  given name: Harsh Kumar
author list: Agent
  family name: Gupta
  given name: Soma
author list: Agent
  family name: Roy
  given name: Anirban
author list: Agent
  family name: Sinha
  given name: Subodh Kumar
author list: Agent
  family name: Mishra
  given name: Dwijesh C.
author list: Agent
  family name: Das
  given name: Shouvik
author list: Agent
  family name: Kumar
  given name: Ranjeet R.
author list: Agent
  family name: Nair
  given name: Ramakrishnan Madhavan
author list: Agent
  family name: Aski
  given name: Muraleedhar
doi: 10.7717/peerj.16722
volume: 12
issn: 2167-8359
publication name: PeerJ
publication date: 2024-02-21
copyright: ©2024 Kumari et al.
attribution name: Kumari et al.

Proteomic study on nintedanib in gastric cancer cells
type: item
type: AcademicArticle
description: Background Gastric cancer is a very common gastrointestinal tumor with a high mortality rate. Nintedanib has been shown to significantly reduce tumor cell proliferation and increase apoptosis in gastric cancer cells in vitro. However, its systemic action mechanism on gastric cancer cells remains unclear. A high-throughput proteomic approach should help identify the potential mechanisms and targets of nintedanib on gastric cancer cells. Methods The effects of nintedanib on the biological behavior of gastric cancer cells were evaluated. A cytotoxic proliferation assay was performed to estimate the half maximal inhibitory concentration (IC50). AGS cells were divided into control, and nintedanib-treated groups (5 µM, 48 h), and differential protein expression was investigated using tandem mass tags (TMT) proteomics. The molecular mechanisms of these differentially expressed proteins and their network interactions were then analyzed using bioinformatics, and potential nintedanib targets were identified. Results This study identified 845 differentially expressed proteins in the nintedanib-treated group (compared to the control group), comprising 526 up-regulated and 319 down-regulated proteins. Bioinformatics analysis revealed that the differentially expressed proteins were primarily enriched in biological pathways for branched-chain amino acid metabolism, steroid biosynthesis, propionate metabolism, fatty acid metabolism, lysosome, peroxisome, and ferroptosis. Key driver analysis revealed that proteins, such as enoyl-CoA hydratase and 3-hydroxyacyl CoA dehydrogenase (EHHADH), isocitrate dehydrogenase 1 (IDH1), acyl-CoA oxidase 1 (ACOX1), acyl-CoA oxidase 2 (ACOX2), acyl-CoA oxidase 3 (ACOX3), and acetyl-CoA acyltransferase 1 (ACAA1) could be linked with nintedanib action. Conclusion Nintedanib inhibits the proliferation, invasion, and metastasis of gastric cancer cells. The crossover pathways and protein networks predicted by proteomics should provide more detailed molec…
format: application/pdf
format: text/html
creator: Xiaohua Dong
creator: Liuli Wang
creator: Da Wang
creator: Miao Yu
creator: Xiao jun Yang
creator: Hui Cai
subject: Biochemistry
subject: Cell Biology
subject: Molecular Biology
description: doi:10.7717/peerj.16771
publisher: PeerJ Inc.
rights: © 2024 Dong et al.
abstract: Background Gastric cancer is a very common gastrointestinal tumor with a high mortality rate. Nintedanib has been shown to significantly reduce tumor cell proliferation and increase apoptosis in gastric cancer cells in vitro. However, its systemic action mechanism on gastric cancer cells remains unclear. A high-throughput proteomic approach should help identify the potential mechanisms and targets of nintedanib on gastric cancer cells. Methods The effects of nintedanib on the biological behavior of gastric cancer cells were evaluated. A cytotoxic proliferation assay was performed to estimate the half maximal inhibitory concentration (IC50). AGS cells were divided into control, and nintedanib-treated groups (5 µM, 48 h), and differential protein expression was investigated using tandem mass tags (TMT) proteomics. The molecular mechanisms of these differentially expressed proteins and their network interactions were then analyzed using bioinformatics, and potential nintedanib targets were identified. Results This study identified 845 differentially expressed proteins in the nintedanib-treated group (compared to the control group), comprising 526 up-regulated and 319 down-regulated proteins. Bioinformatics analysis revealed that the differentially expressed proteins were primarily enriched in biological pathways for branched-chain amino acid metabolism, steroid biosynthesis, propionate metabolism, fatty acid metabolism, lysosome, peroxisome, and ferroptosis. Key driver analysis revealed that proteins, such as enoyl-CoA hydratase and 3-hydroxyacyl CoA dehydrogenase (EHHADH), isocitrate dehydrogenase 1 (IDH1), acyl-CoA oxidase 1 (ACOX1), acyl-CoA oxidase 2 (ACOX2), acyl-CoA oxidase 3 (ACOX3), and acetyl-CoA acyltransferase 1 (ACAA1) could be linked with nintedanib action. Conclusion Nintedanib inhibits the proliferation, invasion, and metastasis of gastric cancer cells. The crossover pathways and protein networks predicted by proteomics should provide more detailed molec…
bibliographic citation: Dong et al. (2024) Proteomic study on nintedanib in gastric cancer cells. PeerJ 12:e16771 https://doi.org/10.7717/peerj.16771
date submitted: 2023-08-02
date accepted: 2023-12-18
issued: 2024-02-21
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Dong
  given name: Xiaohua
author list: Agent
  family name: Wang
  given name: Liuli
author list: Agent
  family name: Wang
  given name: Da
author list: Agent
  family name: Yu
  given name: Miao
author list: Agent
  family name: Yang
  given name: Xiao jun
author list: Agent
  family name: Cai
  given name: Hui
doi: 10.7717/peerj.16771
volume: 12
issn: 2167-8359
publication name: PeerJ
publication date: 2024-02-21
copyright: ©2024 Dong et al.
attribution name: Dong et al.

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