PeerJ
type: channel
link: https://peerj.com/articles/
description: Articles published in PeerJ
publisher: PeerJ Inc.
publication name: PeerJ
issn: 2167-8359
items: Group B Streptococcus and the vaginal microbiome among pregnant women: a systematic review
items: Machine learning in dental, oral and craniofacial imaging: a review of recent progress
items: The impact of COVID-19 pandemic on the level of depression among health care workers: cross-sectional study
items: Longer leisure walking time is associated with positive self-rated health among adults and older adults: a Brazilian nationwide study
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

Group B Streptococcus and the vaginal microbiome among pregnant women: a systematic review
type: item
type: AcademicArticle
description: Background Vaginal microbiome studies frequently report diversity metrics and communities of microbiomes associated with reproductive health outcomes. Reports of Streptococcus agalactiae (also known as Group B Streptococcus or GBS), the leading cause of neonatal infectious morbidity and mortality, are notably lacking from the studies of the vaginal microbiome, despite being a known contributor to preterm birth and other complications. Therefore, the purpose of this systematic review was to explore the frequency of GBS reporting in vaginal microbiome literature pertaining to pregnancy and to examine methodological bias that contributes to differences in species and genus-level microbiome reporting. Lack of identification of GBS via sequencing-based approaches due to methodologic or reporting bias may result incomplete understanding of bacterial composition during pregnancy and subsequent birth outcomes. Methodology A systematic review was conducted following the PRISMA guideline. Three databases (PubMed, CINAHL, and Web of Science) were used to identify papers for review based on the search terms “vaginal microbiome”, “pregnancy”, and “16S rRNA sequencing”. Articles were evaluated for methods of DNA extraction and sequencing, 16S region, taxonomy classification database, number of participants or vaginal specimens, and pregnancy trimester. Results Forty-five research articles reported employing a metagenomic approach or 16S approach for vaginal microbiome analysis during pregnancy that explicitly reported taxonomic composition and were included in this review. Less than 30% of articles reported the presence of GBS (N = 13). No significant differences in methodology were identified between articles that reported versus did not report GBS. However, there was large variability across research methods used for vaginal microbiome analysis and species-level bacterial community reporting. Conclusion Considerable differences in study design and data formatting methods may co…
format: application/pdf
format: text/html
creator: Sungju Lim
creator: Shilpa Rajagopal
creator: Ye Ryn Jeong
creator: Dumebi Nzegwu
creator: Michelle L. Wright
subject: Genomics
subject: Microbiology
subject: Molecular Biology
subject: Taxonomy
subject: Women’s Health
description: doi:10.7717/peerj.11437
publisher: PeerJ Inc.
rights: © 2021 Lim et al.
abstract: Background Vaginal microbiome studies frequently report diversity metrics and communities of microbiomes associated with reproductive health outcomes. Reports of Streptococcus agalactiae (also known as Group B Streptococcus or GBS), the leading cause of neonatal infectious morbidity and mortality, are notably lacking from the studies of the vaginal microbiome, despite being a known contributor to preterm birth and other complications. Therefore, the purpose of this systematic review was to explore the frequency of GBS reporting in vaginal microbiome literature pertaining to pregnancy and to examine methodological bias that contributes to differences in species and genus-level microbiome reporting. Lack of identification of GBS via sequencing-based approaches due to methodologic or reporting bias may result incomplete understanding of bacterial composition during pregnancy and subsequent birth outcomes. Methodology A systematic review was conducted following the PRISMA guideline. Three databases (PubMed, CINAHL, and Web of Science) were used to identify papers for review based on the search terms “vaginal microbiome”, “pregnancy”, and “16S rRNA sequencing”. Articles were evaluated for methods of DNA extraction and sequencing, 16S region, taxonomy classification database, number of participants or vaginal specimens, and pregnancy trimester. Results Forty-five research articles reported employing a metagenomic approach or 16S approach for vaginal microbiome analysis during pregnancy that explicitly reported taxonomic composition and were included in this review. Less than 30% of articles reported the presence of GBS (N = 13). No significant differences in methodology were identified between articles that reported versus did not report GBS. However, there was large variability across research methods used for vaginal microbiome analysis and species-level bacterial community reporting. Conclusion Considerable differences in study design and data formatting methods may co…
bibliographic citation: Lim et al. (2021) Group B Streptococcus and the vaginal microbiome among pregnant women: a systematic review. PeerJ 9:e11437 https://doi.org/10.7717/peerj.11437
date submitted: 2021-01-25
date accepted: 2021-04-20
issued: 2021-05-17
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Lim
  given name: Sungju
author list: Agent
  family name: Rajagopal
  given name: Shilpa
author list: Agent
  family name: Jeong
  given name: Ye Ryn
author list: Agent
  family name: Nzegwu
  given name: Dumebi
author list: Agent
  family name: Wright
  given name: Michelle L.
doi: 10.7717/peerj.11437
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-05-17
copyright: ©2021 Lim et al.
attribution name: Lim et al.

Machine learning in dental, oral and craniofacial imaging: a review of recent progress
type: item
type: AcademicArticle
description: Artificial intelligence has been emerging as an increasingly important aspect of our daily lives and is widely applied in medical science. One major application of artificial intelligence in medical science is medical imaging. As a major component of artificial intelligence, many machine learning models are applied in medical diagnosis and treatment with the advancement of technology and medical imaging facilities. The popularity of convolutional neural network in dental, oral and craniofacial imaging is heightening, as it has been continually applied to a broader spectrum of scientific studies. Our manuscript reviews the fundamental principles and rationales behind machine learning, and summarizes its research progress and its recent applications specifically in dental, oral and craniofacial imaging. It also reviews the problems that remain to be resolved and evaluates the prospect of the future development of this field of scientific study.
format: application/pdf
format: text/html
creator: Ruiyang Ren
creator: Haozhe Luo
creator: Chongying Su
creator: Yang Yao
creator: Wen Liao
subject: Dentistry
subject: Orthopedics
subject: Otorhinolaryngology
subject: Radiology and Medical Imaging
subject: Computational Science
description: doi:10.7717/peerj.11451
publisher: PeerJ Inc.
rights: © 2021 Ren et al.
abstract: Artificial intelligence has been emerging as an increasingly important aspect of our daily lives and is widely applied in medical science. One major application of artificial intelligence in medical science is medical imaging. As a major component of artificial intelligence, many machine learning models are applied in medical diagnosis and treatment with the advancement of technology and medical imaging facilities. The popularity of convolutional neural network in dental, oral and craniofacial imaging is heightening, as it has been continually applied to a broader spectrum of scientific studies. Our manuscript reviews the fundamental principles and rationales behind machine learning, and summarizes its research progress and its recent applications specifically in dental, oral and craniofacial imaging. It also reviews the problems that remain to be resolved and evaluates the prospect of the future development of this field of scientific study.
bibliographic citation: Ren et al. (2021) Machine learning in dental, oral and craniofacial imaging: a review of recent progress. PeerJ 9:e11451 https://doi.org/10.7717/peerj.11451
date submitted: 2020-10-02
date accepted: 2021-04-22
issued: 2021-05-17
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Ren
  given name: Ruiyang
author list: Agent
  family name: Luo
  given name: Haozhe
author list: Agent
  family name: Su
  given name: Chongying
author list: Agent
  family name: Yao
  given name: Yang
author list: Agent
  family name: Liao
  given name: Wen
doi: 10.7717/peerj.11451
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-05-17
copyright: © 2021 Ren et al.
attribution name: Ren et al.

The impact of COVID-19 pandemic on the level of depression among health care workers: cross-sectional study
type: item
type: AcademicArticle
description: Background The outbreak of the novel Corona Virus Infectious Disease 2019 (COVID-19) has spread rapidly to many countries leading to thousands of deaths globally. The burden of this pandemic has affected the physical and mental health of the frontline health care workers (HCWs) who are exposed to high risk of infection and psychological stressors. Aims The aim is to measure the level of depression among healthcare workers in Saudi Arabia during COVID-19 pandemic to establish interventional strategies. Method A descriptive cross-sectional study was used to conduct the current study. The data of this study was recruited between 15 June and 15 July 2020 from healthcare providers who work in both public and private healthcare sectors in Riyadh and Eastern province in Saudi Arabia utilizing a self-administered questionnaire. The study was approved by the Institutional Review Board at Dr. Sulaiman Al Habib Medical Group (IRB Log No. RC20.06.88-2). Data were collected by using The Zung Self-Rating Depression Scale SDS. A total of 900 healthcare providers working in the healthcare setting during COVID-19 pandemic were invited to participate in the study. A total of 650 healthcare providers participated in the study by completing and submitting the survey. Results Almost 30% suffered from depression which can be divided into three categories; mild depression (26.2%), moderate/major (2.5%) and severe/extreme (0.8%). The finding shows that the level of depression among respondents at the age range of 31–40 years old was significantly higher than the level of depression among respondents with the age above 50 years old. Non-Saudi healthcare workers experienced more depression than Saudi workers. It also shows how nurses suffered from depression compared to their physician colleagues. Those who did not suffer from sleeping disorder perceived more depression as compared to those who are having sleeping disorder. Conclusion It is recommended that health care facilities should impl…
format: application/pdf
format: text/html
creator: Abbas Al Mutair
creator: Alya Al Mutairi
creator: Zainab Ambani
creator: Abbas Shamsan
creator: Sana AlMahmoud
creator: Saad Alhumaid
subject: Evidence Based Medicine
subject: Global Health
subject: Psychiatry and Psychology
subject: Public Health
description: doi:10.7717/peerj.11469
publisher: PeerJ Inc.
rights: © 2021 Al Mutair et al.
abstract: Background The outbreak of the novel Corona Virus Infectious Disease 2019 (COVID-19) has spread rapidly to many countries leading to thousands of deaths globally. The burden of this pandemic has affected the physical and mental health of the frontline health care workers (HCWs) who are exposed to high risk of infection and psychological stressors. Aims The aim is to measure the level of depression among healthcare workers in Saudi Arabia during COVID-19 pandemic to establish interventional strategies. Method A descriptive cross-sectional study was used to conduct the current study. The data of this study was recruited between 15 June and 15 July 2020 from healthcare providers who work in both public and private healthcare sectors in Riyadh and Eastern province in Saudi Arabia utilizing a self-administered questionnaire. The study was approved by the Institutional Review Board at Dr. Sulaiman Al Habib Medical Group (IRB Log No. RC20.06.88-2). Data were collected by using The Zung Self-Rating Depression Scale SDS. A total of 900 healthcare providers working in the healthcare setting during COVID-19 pandemic were invited to participate in the study. A total of 650 healthcare providers participated in the study by completing and submitting the survey. Results Almost 30% suffered from depression which can be divided into three categories; mild depression (26.2%), moderate/major (2.5%) and severe/extreme (0.8%). The finding shows that the level of depression among respondents at the age range of 31–40 years old was significantly higher than the level of depression among respondents with the age above 50 years old. Non-Saudi healthcare workers experienced more depression than Saudi workers. It also shows how nurses suffered from depression compared to their physician colleagues. Those who did not suffer from sleeping disorder perceived more depression as compared to those who are having sleeping disorder. Conclusion It is recommended that health care facilities should impl…
bibliographic citation: Al Mutair et al. (2021) The impact of COVID-19 pandemic on the level of depression among health care workers: cross-sectional study. PeerJ 9:e11469 https://doi.org/10.7717/peerj.11469
date submitted: 2021-02-17
date accepted: 2021-04-26
issued: 2021-05-17
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Al Mutair
  given name: Abbas
author list: Agent
  family name: Al Mutairi
  given name: Alya
author list: Agent
  family name: Ambani
  given name: Zainab
author list: Agent
  family name: Shamsan
  given name: Abbas
author list: Agent
  family name: AlMahmoud
  given name: Sana
author list: Agent
  family name: Alhumaid
  given name: Saad
doi: 10.7717/peerj.11469
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-05-17
copyright: © 2021 Al Mutair et al.
attribution name: Al Mutair et al.

Longer leisure walking time is associated with positive self-rated health among adults and older adults: a Brazilian nationwide study
type: item
type: AcademicArticle
description: Background To verify the association between weekly leisure walking time and positive self-rated health in the Brazilian adult and elderly population. Methods This cross-sectional study used information collected in 2019 across all regions of Brazil. This study included 25,785 people aged ≥ 18 years (mean = 51.6; standard deviation = 18.0) from all capitals of the Brazilian states who reported practicing walking as physical activity during leisure time. Self-rated health was the dependent variable (positive or negative). The leisure walking time/week was the main exposure and it was categorized in “150 minutes/week”, “150–299 minutes/week” and “≥ 300 minutes/week”. We used binary logistic regression to estimate odds ratio (OR) and 95% confidence intervals (95% CI) that was adjusted for relevant covariates. Results We found that individuals who reported leisure walking for a period from 150 to 299 minutes/week and those who reported walking for a period ≥ 300 minutes/week were respectively 28% (OR = 1.28. 95% CI [1.10–1.48]) and 52% (OR = 1.52. 95% CI [1.27–1.82]) more likely of perceiving their health positively compared to those who reported walking for a period < 150 minutes/week. Individuals who reported leisure walking time <150 minutes/week had 72.3% (95% CI [70.4–74.1]) probability of perceiving their health positively. Individuals who reported leisure walking time from 150 to 299 minutes/week had 76.6% (95% CI [75.0 –78.3) probability of perceiving their health positively. On the other hand, individuals who reported leisure walking time ≥ 300 minutes/week had 79.2% probability (95% CI [77.1–81.4]) of perceiving their health positively. Conclusion Longer leisure walking time was associated with positive self-rated health among adults and older adults in Brazil.
format: application/pdf
format: text/html
creator: Diego Augusto Santos Silva
subject: Epidemiology
subject: Kinesiology
subject: Psychiatry and Psychology
subject: Public Health
description: doi:10.7717/peerj.11471
publisher: PeerJ Inc.
rights: © 2021 Silva
abstract: Background To verify the association between weekly leisure walking time and positive self-rated health in the Brazilian adult and elderly population. Methods This cross-sectional study used information collected in 2019 across all regions of Brazil. This study included 25,785 people aged ≥ 18 years (mean = 51.6; standard deviation = 18.0) from all capitals of the Brazilian states who reported practicing walking as physical activity during leisure time. Self-rated health was the dependent variable (positive or negative). The leisure walking time/week was the main exposure and it was categorized in “150 minutes/week”, “150–299 minutes/week” and “≥ 300 minutes/week”. We used binary logistic regression to estimate odds ratio (OR) and 95% confidence intervals (95% CI) that was adjusted for relevant covariates. Results We found that individuals who reported leisure walking for a period from 150 to 299 minutes/week and those who reported walking for a period ≥ 300 minutes/week were respectively 28% (OR = 1.28. 95% CI [1.10–1.48]) and 52% (OR = 1.52. 95% CI [1.27–1.82]) more likely of perceiving their health positively compared to those who reported walking for a period < 150 minutes/week. Individuals who reported leisure walking time <150 minutes/week had 72.3% (95% CI [70.4–74.1]) probability of perceiving their health positively. Individuals who reported leisure walking time from 150 to 299 minutes/week had 76.6% (95% CI [75.0 –78.3) probability of perceiving their health positively. On the other hand, individuals who reported leisure walking time ≥ 300 minutes/week had 79.2% probability (95% CI [77.1–81.4]) of perceiving their health positively. Conclusion Longer leisure walking time was associated with positive self-rated health among adults and older adults in Brazil.
bibliographic citation: Silva (2021) Longer leisure walking time is associated with positive self-rated health among adults and older adults: a Brazilian nationwide study. PeerJ 9:e11471 https://doi.org/10.7717/peerj.11471
date submitted: 2020-12-17
date accepted: 2021-04-26
issued: 2021-05-17
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Silva
  given name: Diego Augusto Santos
doi: 10.7717/peerj.11471
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-05-17
copyright: ©2021 Silva
attribution name: Silva

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.
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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…
format: application/pdf
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.
format: application/pdf
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.
format: application/pdf
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.

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