PeerJ
type: channel
link: https://peerj.com/articles/
description: Articles published in PeerJ
publisher: PeerJ Inc.
publication name: PeerJ
issn: 2167-8359
items: SERBP1 affects the apoptotic level by regulating the expression and alternative splicing of cellular and metabolic process genes in HeLa cells
items: Genome-wide identification, phylogenetic and expression pattern analysis of Dof transcription factors in blueberry (Vaccinium corymbosum L.)
items: Effects of artificially-simulated acidification on potential soil nitrification activity and ammonia oxidizing microbial communities in greenhouse conditions
items: Uncovering the mechanism of anthocyanin accumulation in a purple-leaved variety of foxtail millet (Setaria italica) by transcriptome analysis
items: Effect of chronic unpredicted mild stress-induced depression on clopidogrel pharmacokinetics in rats
items: The fungal pathogen Batrachochytrium salamandrivorans is not detected in wild and captive amphibians from Mexico
items: Effects of quarantine on Physical Activity prevalence in Italian Adults: a pilot study
items: Soil microbial diversity and functional capacity associated with the production of edible mushroom Stropharia rugosoannulata in croplands
items: Identification of neoplasm-specific signatures of miRNA interactions by employing a systems biology approach
items: Association between clinical oral health status and perceived oral health in different age groups

SERBP1 affects the apoptotic level by regulating the expression and alternative splicing of cellular and metabolic process genes in HeLa cells
type: item
type: AcademicArticle
description: Background RNA-binding proteins (RBPs) have important roles in orchestrating posttranscriptional regulation and modulating many tumorigenesis events. SERBP1 has been recognized as an important regulator in multiple cancers, while it remains unclear whether SERBP1-regulated gene expression at the transcriptome-wide level is significantly correlated with tumorigenesis. Methods We overexpressed SERBP1 in HeLa cells and explored whether SERBP1 overexpression (SERBP1-OE) affects the proliferation and apoptosis of HeLa cells. We analyzed the transcriptome-wide gene expression changes and alternative splicing changes mediated by SERBP1-OE using the transcriptome sequencing method (RNA-seq). RT-qPCR was conducted to assay SERBP1-regulated alternative splicing. Results SERBP1-OE induced the apoptosis of HeLa cells. The downregulated genes were strongly enriched in the cell proliferation and apoptosis pathways according to the GO analysis, including FOS, FOSB, PAK6 and RAB26. The genes undergoing at least one SERBP1-regulated alternative splicing event were enriched in transcriptional regulation, suggesting a mechanism of the regulation of gene expression, and in pyruvate and fatty acid metabolic processes critical for tumorigenesis events. The SERBP1-regulated alternative splicing of ME3, LPIN3, CROT, PDP1, SLC27A1 and ALKBH7 was validated by RT-qPCR analysis. Conclusions We for the first time demonstrated the cellular function and molecular targets of SERBP1 in HeLa cells at transcriptional and post-transcriptional levels. The SERBP1-regulated gene expression and alternative splicing networks revealed by this study provide important information for exploring the functional roles and regulatory mechanisms of SERBP1 in cancer development and progression.
format: application/pdf
format: text/html
creator: Junjie Zhou
creator: Wenhao Chen
creator: Qianwen He
creator: Dong Chen
creator: Chunguang Li
creator: Congqing Jiang
creator: Zhao Ding
creator: Qun Qian
subject: Bioinformatics
subject: Genomics
subject: Molecular Biology
description: doi:10.7717/peerj.14084
publisher: PeerJ Inc.
rights: © 2022 Zhou et al.
abstract: Background RNA-binding proteins (RBPs) have important roles in orchestrating posttranscriptional regulation and modulating many tumorigenesis events. SERBP1 has been recognized as an important regulator in multiple cancers, while it remains unclear whether SERBP1-regulated gene expression at the transcriptome-wide level is significantly correlated with tumorigenesis. Methods We overexpressed SERBP1 in HeLa cells and explored whether SERBP1 overexpression (SERBP1-OE) affects the proliferation and apoptosis of HeLa cells. We analyzed the transcriptome-wide gene expression changes and alternative splicing changes mediated by SERBP1-OE using the transcriptome sequencing method (RNA-seq). RT-qPCR was conducted to assay SERBP1-regulated alternative splicing. Results SERBP1-OE induced the apoptosis of HeLa cells. The downregulated genes were strongly enriched in the cell proliferation and apoptosis pathways according to the GO analysis, including FOS, FOSB, PAK6 and RAB26. The genes undergoing at least one SERBP1-regulated alternative splicing event were enriched in transcriptional regulation, suggesting a mechanism of the regulation of gene expression, and in pyruvate and fatty acid metabolic processes critical for tumorigenesis events. The SERBP1-regulated alternative splicing of ME3, LPIN3, CROT, PDP1, SLC27A1 and ALKBH7 was validated by RT-qPCR analysis. Conclusions We for the first time demonstrated the cellular function and molecular targets of SERBP1 in HeLa cells at transcriptional and post-transcriptional levels. The SERBP1-regulated gene expression and alternative splicing networks revealed by this study provide important information for exploring the functional roles and regulatory mechanisms of SERBP1 in cancer development and progression.
bibliographic citation: Zhou et al. (2022) SERBP1 affects the apoptotic level by regulating the expression and alternative splicing of cellular and metabolic process genes in HeLa cells. PeerJ 10:e14084 https://doi.org/10.7717/peerj.14084
date submitted: 2022-05-13
date accepted: 2022-08-29
issued: 2022-10-03
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Zhou
  given name: Junjie
author list: Agent
  family name: Chen
  given name: Wenhao
author list: Agent
  family name: He
  given name: Qianwen
author list: Agent
  family name: Chen
  given name: Dong
author list: Agent
  family name: Li
  given name: Chunguang
author list: Agent
  family name: Jiang
  given name: Congqing
author list: Agent
  family name: Ding
  given name: Zhao
author list: Agent
  family name: Qian
  given name: Qun
doi: 10.7717/peerj.14084
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-10-03
copyright: © 2022 Zhou et al.
attribution name: Zhou et al.

Genome-wide identification, phylogenetic and expression pattern analysis of Dof transcription factors in blueberry (Vaccinium corymbosum L.)
type: item
type: AcademicArticle
description: Background DNA binding with one finger (Dof) proteins are plant-specific transcription factor (TF) that plays a significant role in various biological processes such as plant growth and development, hormone regulation, and resistance to abiotic stress. The Dof genes have been identified and reported in multiple plants, but so far, the whole genome identification and analysis of Dof transcription factors in blueberry (Vaccinium corymbosum L.) have not been reported yet. Methods Using the Vaccinium genome, we have identified 51 VcDof genes in blueberry. We have further analyzed their physicochemical properties, phylogenetic relationships, gene structure, collinear analysis, selective evolutionary pressure, cis-acting promoter elements, and tissue and abiotic stress expression patterns. Results Fifty-one VcDof genes were divided into eight subfamilies, and the genes in each subfamily contained similar gene structure and motif ordering. A total of 24 pairs of colinear genes were screened; VcDof genes expanded mainly due to whole-genome duplication, which was subjected to strong purifying selection pressure during the evolution. The promoter of VcDof genes contains three types of cis-acting elements for plant growth and development, phytohormone and stress defense responsiveness. Expression profiles of VcDof genes in different tissues and fruit developmental stages of blueberry indicated that VcDof2 and VcDof45 might play a specific role in anthesis and fruit growth and development. Expression profiles of VcDof genes in different stress indicated that VcDof1, VcDof11, and VcDof15 were highly sensitive to abiotic stress. This study provides a theoretical basis for further clarifying the biological function of Dof genes in blueberry.
format: application/pdf
format: text/html
creator: Tianjie Li
creator: Xiaoyu Wang
creator: Dinakaran Elango
creator: Weihua Zhang
creator: Min Li
creator: Fan Zhang
creator: Qi Pan
creator: Ying Wu
subject: Agricultural Science
subject: Bioinformatics
subject: Genetics
subject: Molecular Biology
subject: Plant Science
description: doi:10.7717/peerj.14087
publisher: PeerJ Inc.
rights: © 2022 Li et al.
abstract: Background DNA binding with one finger (Dof) proteins are plant-specific transcription factor (TF) that plays a significant role in various biological processes such as plant growth and development, hormone regulation, and resistance to abiotic stress. The Dof genes have been identified and reported in multiple plants, but so far, the whole genome identification and analysis of Dof transcription factors in blueberry (Vaccinium corymbosum L.) have not been reported yet. Methods Using the Vaccinium genome, we have identified 51 VcDof genes in blueberry. We have further analyzed their physicochemical properties, phylogenetic relationships, gene structure, collinear analysis, selective evolutionary pressure, cis-acting promoter elements, and tissue and abiotic stress expression patterns. Results Fifty-one VcDof genes were divided into eight subfamilies, and the genes in each subfamily contained similar gene structure and motif ordering. A total of 24 pairs of colinear genes were screened; VcDof genes expanded mainly due to whole-genome duplication, which was subjected to strong purifying selection pressure during the evolution. The promoter of VcDof genes contains three types of cis-acting elements for plant growth and development, phytohormone and stress defense responsiveness. Expression profiles of VcDof genes in different tissues and fruit developmental stages of blueberry indicated that VcDof2 and VcDof45 might play a specific role in anthesis and fruit growth and development. Expression profiles of VcDof genes in different stress indicated that VcDof1, VcDof11, and VcDof15 were highly sensitive to abiotic stress. This study provides a theoretical basis for further clarifying the biological function of Dof genes in blueberry.
bibliographic citation: Li et al. (2022) Genome-wide identification, phylogenetic and expression pattern analysis of Dof transcription factors in blueberry (Vaccinium corymbosum L.). PeerJ 10:e14087 https://doi.org/10.7717/peerj.14087
date submitted: 2022-07-06
date accepted: 2022-08-29
issued: 2022-10-03
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Li
  given name: Tianjie
author list: Agent
  family name: Wang
  given name: Xiaoyu
author list: Agent
  family name: Elango
  given name: Dinakaran
author list: Agent
  family name: Zhang
  given name: Weihua
author list: Agent
  family name: Li
  given name: Min
author list: Agent
  family name: Zhang
  given name: Fan
author list: Agent
  family name: Pan
  given name: Qi
author list: Agent
  family name: Wu
  given name: Ying
doi: 10.7717/peerj.14087
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-10-03
copyright: ©2022 Li et al.
attribution name: Li et al.

Effects of artificially-simulated acidification on potential soil nitrification activity and ammonia oxidizing microbial communities in greenhouse conditions
type: item
type: AcademicArticle
description: Background Nitrification can lead to large quantities of nitrate leaching into the soil during vegetable production, which may result in soil acidification in a greenhouse system. A better understanding is needed of the nitrification process and its microbial mechanisms in soil acidification. Materials and Methods A simulated acidification experiment with an artificially manipulated pH environment (T1: pH 7.0; T2: pH 6.5; T3: pH 6.0; T4: pH 5.5; T5: pH 4.5) was conducted in potted tomatoes grown in greenhouse conditions. The abundance and community structures of ammonia oxidizers under different pH environment were analyzed using q-PCR and high-throughput sequencing methods, respectively. Results and discussions Soil acidification was accompanied by a reduction of soil organic matter (SOM), total nitrogen (TN), NH3 concentration, and enzyme activities. The abundance of ammonia-oxidizing archaea (AOA) in the soil was higher than that of ammonia-oxidizing bacteria (AOB) in soils with a pH of 6.93 to 5.33. The opposite trend was observed when soil pH was 4.21. In acidified soils, the dominant strain of AOB was Nitrosospira, while the dominant strain of AOA was Nitrososphaera. The abundance and community structure of ammonia oxidizers were mainly affected by soil pH, NH4+ content, and microbial biomass. Soil nitrification activity (PNA) has a relationship with both AOA and AOB, in which the abundance of AOA was the crucial factor affecting PNA. Conclusions PNA was co-dominated by AOA and AOB in soils with simulated acidification. Changes of soil pH, NH4+, and microbial biomass caused by acidification were the main factors for the differences in the ammonia-oxidizing microbial community in greenhouse soils. Under acidic conditions (pH < 5), the pH significantly inhibited nitrification and had a strong negative effect on the production of tomatoes in greenhouse conditions.
format: application/pdf
format: text/html
creator: Xiaolan Zhang
creator: Xuan Shan
creator: Hongdan Fu
creator: Zhouping Sun
subject: Agricultural Science
subject: Microbiology
subject: Molecular Biology
subject: Plant Science
subject: Soil Science
description: doi:10.7717/peerj.14088
publisher: PeerJ Inc.
rights: © 2022 Zhang et al.
abstract: Background Nitrification can lead to large quantities of nitrate leaching into the soil during vegetable production, which may result in soil acidification in a greenhouse system. A better understanding is needed of the nitrification process and its microbial mechanisms in soil acidification. Materials and Methods A simulated acidification experiment with an artificially manipulated pH environment (T1: pH 7.0; T2: pH 6.5; T3: pH 6.0; T4: pH 5.5; T5: pH 4.5) was conducted in potted tomatoes grown in greenhouse conditions. The abundance and community structures of ammonia oxidizers under different pH environment were analyzed using q-PCR and high-throughput sequencing methods, respectively. Results and discussions Soil acidification was accompanied by a reduction of soil organic matter (SOM), total nitrogen (TN), NH3 concentration, and enzyme activities. The abundance of ammonia-oxidizing archaea (AOA) in the soil was higher than that of ammonia-oxidizing bacteria (AOB) in soils with a pH of 6.93 to 5.33. The opposite trend was observed when soil pH was 4.21. In acidified soils, the dominant strain of AOB was Nitrosospira, while the dominant strain of AOA was Nitrososphaera. The abundance and community structure of ammonia oxidizers were mainly affected by soil pH, NH4+ content, and microbial biomass. Soil nitrification activity (PNA) has a relationship with both AOA and AOB, in which the abundance of AOA was the crucial factor affecting PNA. Conclusions PNA was co-dominated by AOA and AOB in soils with simulated acidification. Changes of soil pH, NH4+, and microbial biomass caused by acidification were the main factors for the differences in the ammonia-oxidizing microbial community in greenhouse soils. Under acidic conditions (pH < 5), the pH significantly inhibited nitrification and had a strong negative effect on the production of tomatoes in greenhouse conditions.
bibliographic citation: Zhang et al. (2022) Effects of artificially-simulated acidification on potential soil nitrification activity and ammonia oxidizing microbial communities in greenhouse conditions. PeerJ 10:e14088 https://doi.org/10.7717/peerj.14088
date submitted: 2022-05-20
date accepted: 2022-08-29
issued: 2022-10-03
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Zhang
  given name: Xiaolan
author list: Agent
  family name: Shan
  given name: Xuan
author list: Agent
  family name: Fu
  given name: Hongdan
author list: Agent
  family name: Sun
  given name: Zhouping
doi: 10.7717/peerj.14088
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-10-03
copyright: © 2022 Zhang et al.
attribution name: Zhang et al.

Uncovering the mechanism of anthocyanin accumulation in a purple-leaved variety of foxtail millet (Setaria italica) by transcriptome analysis
type: item
type: AcademicArticle
description: Anthocyanin is a natural pigment that has a functional role in plants to attract pollinating insects and is important in stress response. Foxtail millet (Setaria italica) is known as a nutritional crop with high resistance to drought and barren. However, the molecular mechanism regulating anthocyanin accumulation and the relationship between anthocyanin and the stress resistance of foxtail millet remains obscure. In this study, we screened hundreds of germplasm resources and obtained several varieties with purple plants in foxtail millet. By studying the purple-leaved B100 variety and the control variety, Yugu1 with green leaves, we found that B100 could accumulate a large amount of anthocyanin in the leaf epiderma, and B100 had stronger stress tolerance. Further transcriptome analysis revealed the differences in gene expression patterns between the two varieties. We identified nine genes encoding enzymes related to anthocyanin biosynthesis using quantitative PCR validation that showed significantly higher expression levels in B100 than Yugu1. The results of this study lay the foundation for the analysis of the molecular mechanism of anthocyanin accumulation in foxtail millet, and provided genetic resources for the molecular breeding of crops with high anthocyanin content.
format: application/pdf
format: text/html
creator: Yaofei Zhao
creator: Yaqiong Li
creator: Xiaoxi Zhen
creator: Jinli Zhang
creator: Qianxiang Zhang
creator: Zhaowen Liu
creator: Shupei Hou
creator: Yuanhuai Han
creator: Bin Zhang
subject: Agricultural Science
subject: Genomics
subject: Plant Science
description: doi:10.7717/peerj.14099
publisher: PeerJ Inc.
rights: © 2022 Zhao et al.
abstract: Anthocyanin is a natural pigment that has a functional role in plants to attract pollinating insects and is important in stress response. Foxtail millet (Setaria italica) is known as a nutritional crop with high resistance to drought and barren. However, the molecular mechanism regulating anthocyanin accumulation and the relationship between anthocyanin and the stress resistance of foxtail millet remains obscure. In this study, we screened hundreds of germplasm resources and obtained several varieties with purple plants in foxtail millet. By studying the purple-leaved B100 variety and the control variety, Yugu1 with green leaves, we found that B100 could accumulate a large amount of anthocyanin in the leaf epiderma, and B100 had stronger stress tolerance. Further transcriptome analysis revealed the differences in gene expression patterns between the two varieties. We identified nine genes encoding enzymes related to anthocyanin biosynthesis using quantitative PCR validation that showed significantly higher expression levels in B100 than Yugu1. The results of this study lay the foundation for the analysis of the molecular mechanism of anthocyanin accumulation in foxtail millet, and provided genetic resources for the molecular breeding of crops with high anthocyanin content.
bibliographic citation: Zhao et al. (2022) Uncovering the mechanism of anthocyanin accumulation in a purple-leaved variety of foxtail millet (Setaria italica) by transcriptome analysis. PeerJ 10:e14099 https://doi.org/10.7717/peerj.14099
date submitted: 2022-02-25
date accepted: 2022-08-31
issued: 2022-10-03
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Zhao
  given name: Yaofei
author list: Agent
  family name: Li
  given name: Yaqiong
author list: Agent
  family name: Zhen
  given name: Xiaoxi
author list: Agent
  family name: Zhang
  given name: Jinli
author list: Agent
  family name: Zhang
  given name: Qianxiang
author list: Agent
  family name: Liu
  given name: Zhaowen
author list: Agent
  family name: Hou
  given name: Shupei
author list: Agent
  family name: Han
  given name: Yuanhuai
author list: Agent
  family name: Zhang
  given name: Bin
doi: 10.7717/peerj.14099
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-10-03
copyright: ©2022 Zhao et al.
attribution name: Zhao et al.

Effect of chronic unpredicted mild stress-induced depression on clopidogrel pharmacokinetics in rats
type: item
type: AcademicArticle
description: Background Clopidogrel is widely used to prevent and treat cardiovascular atherosclerosis and thrombosis. However, disturbance in the expression and activity of liver cytochrome metabolic enzymes significantly changes clopidogrel efficacy. Therefore, the effect of chronic unpredictable mild stress (CUMS)-induced depression on the expression of liver cytochrome metabolic enzymes and clopidogrel pharmacokinetics in rats were explored. Methods Nine different CUMSs were selected to establish a rat model of depression. Open field experiment and sucrose preference test were applied to explore the depressive behaviors. The concentration of serotonin in the cortex of depressed rats was determined using enzyme linked immunosorbent assay (ELISA). All rats were given 10 mg/kg clopidogrel orally after 12 weeks, and blood samples were collected at different time points. The clopidogrel concentration and CYP2C19/ CYP2C9 activity in rat liver microsomes were assayed by high performance liquid chromatography-tandem mass spectrometry (HPLC-MS/MS). The rat liver drug enzymes expression was determined by Real-Time Quantitative Reverse Transcription PCR (RT-qPCR). Results Open field experiment and sucrose preference test indicated the successful construction of the CUMS-induced depression model. The concentration of serotonin in the cortex of depressed rats decreased by 42.56% (∗∗p < 0.01). The area under the curve of clopidogrel pharmacokinetics decreased by 33.13% (∗p < 0.05) in the depression rats, while distribution volume and clearance increased significantly (∗∗p < 0.01). The half-time and distribution volume did not significantly differ. The CYP2C19 and CYP2C9 activity of liver microsomes in the CUMS-induced depression group were significantly higher than that in the control group (∗∗p < 0.01). CYP2C11 and CYP1A2 mRNA expression up-regulated approximately 1.3 - fold in the depressed rat livers compared with that in the control, whereas that of CYP2C13 was down-regulated by 27.43…
format: application/pdf
format: text/html
creator: Xueyao Jiang
creator: Jing Wu
creator: Boyu Tan
creator: Sulan Yan
creator: Nan Deng
creator: Hongyan Wei
subject: Biochemistry
subject: Molecular Biology
subject: Neuroscience
description: doi:10.7717/peerj.14111
publisher: PeerJ Inc.
rights: © 2022 Jiang et al.
abstract: Background Clopidogrel is widely used to prevent and treat cardiovascular atherosclerosis and thrombosis. However, disturbance in the expression and activity of liver cytochrome metabolic enzymes significantly changes clopidogrel efficacy. Therefore, the effect of chronic unpredictable mild stress (CUMS)-induced depression on the expression of liver cytochrome metabolic enzymes and clopidogrel pharmacokinetics in rats were explored. Methods Nine different CUMSs were selected to establish a rat model of depression. Open field experiment and sucrose preference test were applied to explore the depressive behaviors. The concentration of serotonin in the cortex of depressed rats was determined using enzyme linked immunosorbent assay (ELISA). All rats were given 10 mg/kg clopidogrel orally after 12 weeks, and blood samples were collected at different time points. The clopidogrel concentration and CYP2C19/ CYP2C9 activity in rat liver microsomes were assayed by high performance liquid chromatography-tandem mass spectrometry (HPLC-MS/MS). The rat liver drug enzymes expression was determined by Real-Time Quantitative Reverse Transcription PCR (RT-qPCR). Results Open field experiment and sucrose preference test indicated the successful construction of the CUMS-induced depression model. The concentration of serotonin in the cortex of depressed rats decreased by 42.56% (∗∗p < 0.01). The area under the curve of clopidogrel pharmacokinetics decreased by 33.13% (∗p < 0.05) in the depression rats, while distribution volume and clearance increased significantly (∗∗p < 0.01). The half-time and distribution volume did not significantly differ. The CYP2C19 and CYP2C9 activity of liver microsomes in the CUMS-induced depression group were significantly higher than that in the control group (∗∗p < 0.01). CYP2C11 and CYP1A2 mRNA expression up-regulated approximately 1.3 - fold in the depressed rat livers compared with that in the control, whereas that of CYP2C13 was down-regulated by 27.43…
bibliographic citation: Jiang et al. (2022) Effect of chronic unpredicted mild stress-induced depression on clopidogrel pharmacokinetics in rats. PeerJ 10:e14111 https://doi.org/10.7717/peerj.14111
date submitted: 2022-04-19
date accepted: 2022-09-02
issued: 2022-10-03
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Jiang
  given name: Xueyao
author list: Agent
  family name: Wu
  given name: Jing
author list: Agent
  family name: Tan
  given name: Boyu
author list: Agent
  family name: Yan
  given name: Sulan
author list: Agent
  family name: Deng
  given name: Nan
author list: Agent
  family name: Wei
  given name: Hongyan
doi: 10.7717/peerj.14111
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-10-03
copyright: ©2022 Jiang et al.
attribution name: Jiang et al.

The fungal pathogen Batrachochytrium salamandrivorans is not detected in wild and captive amphibians from Mexico
type: item
type: AcademicArticle
description: The recent emergence of the pathogen Batrachochytrium salamandrivorans (Bsal) is associated with rapid population declines of salamanders in Europe and its arrival to new areas could cause dramatic negative effects on other amphibian populations and species. Amphibian species, present in areas with high amphibian diversity such as Mexico, could be highly threatened due to the arrival of Bsal, particularly salamander species which are more vulnerable to chytridiomycosis caused by this pathogen. Thus, immediate surveillance is needed as a strategy to efficiently contend with this emerging infectious disease. In this study, we analyzed 490 wild and captive amphibians from 48 species across 76 sites in the North, Central, and South of Mexico to evaluate the presence of Bsal. Amphibians were sampled in sites with variable degrees of amphibian richness and suitability for Bsal according to previous studies. From the 76 sampling sites, 10 of them were located in areas with high amphibian richness and potential moderate to high Bsal habitat suitability. We did not detect Bsal in any of the samples, and no signs of the disease were observed in any individual at the time of sampling. Our results suggest that Bsal has not yet arrived at the sampled sites or could be at low prevalence within populations with low occurrence probability. This is the first study that evaluates the presence of Bsal in different regions and amphibian species in Mexico, which is the second most diverse country in salamander species in the world. We highlight the risk and the importance of continuing surveillance of Bsal in Mexico and discuss control strategies to avoid the introduction and spread of Bsal in the country.
format: application/pdf
format: text/html
creator: M. Delia Basanta
creator: Victor Avila-Akerberg
creator: Allison Q. Byrne
creator: Gabriela Castellanos-Morales
creator: Tanya M. González Martínez
creator: Yurixhi Maldonado-López
creator: Erica Bree Rosenblum
creator: Ireri Suazo-Ortuño
creator: Gabriela Parra Olea
creator: Eria A. Rebollar
subject: Conservation Biology
subject: Mycology
subject: Zoology
subject: Freshwater Biology
description: doi:10.7717/peerj.14117
publisher: PeerJ Inc.
rights: © 2022 Basanta et al.
abstract: The recent emergence of the pathogen Batrachochytrium salamandrivorans (Bsal) is associated with rapid population declines of salamanders in Europe and its arrival to new areas could cause dramatic negative effects on other amphibian populations and species. Amphibian species, present in areas with high amphibian diversity such as Mexico, could be highly threatened due to the arrival of Bsal, particularly salamander species which are more vulnerable to chytridiomycosis caused by this pathogen. Thus, immediate surveillance is needed as a strategy to efficiently contend with this emerging infectious disease. In this study, we analyzed 490 wild and captive amphibians from 48 species across 76 sites in the North, Central, and South of Mexico to evaluate the presence of Bsal. Amphibians were sampled in sites with variable degrees of amphibian richness and suitability for Bsal according to previous studies. From the 76 sampling sites, 10 of them were located in areas with high amphibian richness and potential moderate to high Bsal habitat suitability. We did not detect Bsal in any of the samples, and no signs of the disease were observed in any individual at the time of sampling. Our results suggest that Bsal has not yet arrived at the sampled sites or could be at low prevalence within populations with low occurrence probability. This is the first study that evaluates the presence of Bsal in different regions and amphibian species in Mexico, which is the second most diverse country in salamander species in the world. We highlight the risk and the importance of continuing surveillance of Bsal in Mexico and discuss control strategies to avoid the introduction and spread of Bsal in the country.
bibliographic citation: Basanta et al. (2022) The fungal pathogen Batrachochytrium salamandrivorans is not detected in wild and captive amphibians from Mexico. PeerJ 10:e14117 https://doi.org/10.7717/peerj.14117
date submitted: 2022-07-13
date accepted: 2022-09-04
issued: 2022-10-03
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Basanta
  given name: M. Delia
author list: Agent
  family name: Avila-Akerberg
  given name: Victor
author list: Agent
  family name: Byrne
  given name: Allison Q.
author list: Agent
  family name: Castellanos-Morales
  given name: Gabriela
author list: Agent
  family name: González Martínez
  given name: Tanya M.
author list: Agent
  family name: Maldonado-López
  given name: Yurixhi
author list: Agent
  family name: Rosenblum
  given name: Erica Bree
author list: Agent
  family name: Suazo-Ortuño
  given name: Ireri
author list: Agent
  family name: Parra Olea
  given name: Gabriela
author list: Agent
  family name: Rebollar
  given name: Eria A.
doi: 10.7717/peerj.14117
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-10-03
copyright: ©2022 Basanta et al.
attribution name: Basanta et al.

Effects of quarantine on Physical Activity prevalence in Italian Adults: a pilot study
type: item
type: AcademicArticle
description: Background COVID-19 is a respiratory disease that caused a global pandemic status in March 2020. Due to its fast diffusion, many governments adopted forced solutions including social restrictions, which could negatively affect citizens’ habits as physical activity. Our study aimed to investigate how and why the physical activity prevalence varied from the period before the quarantine up to the period after it, and understand what citizens thought of physical inactivity COVID-19 related to and whether they were satisfied with physical activity promotion during the lockdown. Methods A new questionnaire was created and administered online. A sample of 749 interviews (female = 552 (73.7%), male = 197 (26.3%)) was collected and analysed. Results The prevalence of people who were older than 50 years reduced both during and after the lockdown (P < 0.05) and the most common reason for which they have quitted physical activity practice was related to psychological problems (lockdown = 64.57%; post-lockdown = 62.17%). In addition, youngers seemed to be more sensitive than elders to unhealthy consequences generated by forced isolation (P < 0.05), and they believed that children/adolescents and older adults practised an insufficient amount of physical activity and/or sport, which could negatively impact public health. Conclusions Although many strategies were implemented during the lockdown to promote regular physical activity practice, several results suggested that quarantine negatively affected citizens’ habits. The future government should focus on adequate measures to improve health behaviours.
format: application/pdf
format: text/html
creator: Mario Mauro
creator: Stefania Toselli
creator: Silvia Bonazzi
creator: Alessia Grigoletto
creator: Stefania Cataldi
creator: Gianpiero Greco
creator: Pasqualino Maietta Latessa
subject: Global Health
subject: Health Policy
subject: Kinesiology
subject: Public Health
subject: COVID-19
description: doi:10.7717/peerj.14123
publisher: PeerJ Inc.
rights: © 2022 Mauro et al.
abstract: Background COVID-19 is a respiratory disease that caused a global pandemic status in March 2020. Due to its fast diffusion, many governments adopted forced solutions including social restrictions, which could negatively affect citizens’ habits as physical activity. Our study aimed to investigate how and why the physical activity prevalence varied from the period before the quarantine up to the period after it, and understand what citizens thought of physical inactivity COVID-19 related to and whether they were satisfied with physical activity promotion during the lockdown. Methods A new questionnaire was created and administered online. A sample of 749 interviews (female = 552 (73.7%), male = 197 (26.3%)) was collected and analysed. Results The prevalence of people who were older than 50 years reduced both during and after the lockdown (P < 0.05) and the most common reason for which they have quitted physical activity practice was related to psychological problems (lockdown = 64.57%; post-lockdown = 62.17%). In addition, youngers seemed to be more sensitive than elders to unhealthy consequences generated by forced isolation (P < 0.05), and they believed that children/adolescents and older adults practised an insufficient amount of physical activity and/or sport, which could negatively impact public health. Conclusions Although many strategies were implemented during the lockdown to promote regular physical activity practice, several results suggested that quarantine negatively affected citizens’ habits. The future government should focus on adequate measures to improve health behaviours.
bibliographic citation: Mauro et al. (2022) Effects of quarantine on Physical Activity prevalence in Italian Adults: a pilot study. PeerJ 10:e14123 https://doi.org/10.7717/peerj.14123
date submitted: 2022-07-28
date accepted: 2022-09-06
issued: 2022-10-03
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Mauro
  given name: Mario
author list: Agent
  family name: Toselli
  given name: Stefania
author list: Agent
  family name: Bonazzi
  given name: Silvia
author list: Agent
  family name: Grigoletto
  given name: Alessia
author list: Agent
  family name: Cataldi
  given name: Stefania
author list: Agent
  family name: Greco
  given name: Gianpiero
author list: Agent
  family name: Maietta Latessa
  given name: Pasqualino
doi: 10.7717/peerj.14123
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-10-03
copyright: © 2022 Mauro et al.
attribution name: Mauro et al.

Soil microbial diversity and functional capacity associated with the production of edible mushroom Stropharia rugosoannulata in croplands
type: item
type: AcademicArticle
description: In recent years, a rare edible mushroom Stropharia rugosoannulata has become popular. S. rugosoannulata has the characteristics of easy cultivation, low cost, high output value, and low labor requirement, making its economic benefits significantly superior to those of other planting industries. Accumulating research demonstrates that cultivating edible fungus is advantageous for farming soil. The present experiment used idle croplands in winter for S. rugosoannulata cultivation. We explored the effects of S. rugosoannulata cultivation on soil properties and soil microbial community structure in paddy and dry fields, respectively. We cultivated S. rugosoannulata in the fields after planting chili and rice, respectively. The results showed that Chili-S. rugosoannulata and Rice-S. rugosoannulata planting patterns increased the yield, quality and amino acid content of S. rugosoannulata. By analyzing the soil properties, we found that the Chili-S. rugosoannulata and Rice-S. rugosoannulata cropping patterns increased the total nitrogen, available phosphorus, soil organic carbon, and available potassium content of the soil. We used 16s amplicons for bacteria and internal transcribed spacer (ITS) region for fungi to analyze the microbial communities in rhizosphere soils. Notably, S. rugosoannulata cultivation significantly increased the abundance of beneficial microorganisms such as Chloroflexi, Cladosporium and Mortierella and reduce the abundance of Botryotrichumin and Archaeorhizomyces. We consider S. rugosoannulata cultivation in cropland can improve soil properties, regulate the community structure of soil microorganisms, increase the expression abundance of beneficial organisms and ultimately improve the S. rugosoannulata yield and lay a good foundation for a new round of crops after this edible mushroom cultivation.
format: application/pdf
format: text/html
creator: Shaojun Tang
creator: Tingting Fan
creator: Lei Jin
creator: Pin Lei
creator: Chenxia Shao
creator: Shenlian Wu
creator: Yi Yang
creator: Yuelin He
creator: Rui Ren
creator: Jun Xu
subject: Agricultural Science
subject: Genomics
subject: Molecular Biology
subject: Mycology
subject: Soil Science
description: doi:10.7717/peerj.14130
publisher: PeerJ Inc.
rights: © 2022 Tang et al.
abstract: In recent years, a rare edible mushroom Stropharia rugosoannulata has become popular. S. rugosoannulata has the characteristics of easy cultivation, low cost, high output value, and low labor requirement, making its economic benefits significantly superior to those of other planting industries. Accumulating research demonstrates that cultivating edible fungus is advantageous for farming soil. The present experiment used idle croplands in winter for S. rugosoannulata cultivation. We explored the effects of S. rugosoannulata cultivation on soil properties and soil microbial community structure in paddy and dry fields, respectively. We cultivated S. rugosoannulata in the fields after planting chili and rice, respectively. The results showed that Chili-S. rugosoannulata and Rice-S. rugosoannulata planting patterns increased the yield, quality and amino acid content of S. rugosoannulata. By analyzing the soil properties, we found that the Chili-S. rugosoannulata and Rice-S. rugosoannulata cropping patterns increased the total nitrogen, available phosphorus, soil organic carbon, and available potassium content of the soil. We used 16s amplicons for bacteria and internal transcribed spacer (ITS) region for fungi to analyze the microbial communities in rhizosphere soils. Notably, S. rugosoannulata cultivation significantly increased the abundance of beneficial microorganisms such as Chloroflexi, Cladosporium and Mortierella and reduce the abundance of Botryotrichumin and Archaeorhizomyces. We consider S. rugosoannulata cultivation in cropland can improve soil properties, regulate the community structure of soil microorganisms, increase the expression abundance of beneficial organisms and ultimately improve the S. rugosoannulata yield and lay a good foundation for a new round of crops after this edible mushroom cultivation.
bibliographic citation: Tang et al. (2022) Soil microbial diversity and functional capacity associated with the production of edible mushroom Stropharia rugosoannulata in croplands. PeerJ 10:e14130 https://doi.org/10.7717/peerj.14130
date submitted: 2022-08-15
date accepted: 2022-09-06
issued: 2022-10-03
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Tang
  given name: Shaojun
author list: Agent
  family name: Fan
  given name: Tingting
author list: Agent
  family name: Jin
  given name: Lei
author list: Agent
  family name: Lei
  given name: Pin
author list: Agent
  family name: Shao
  given name: Chenxia
author list: Agent
  family name: Wu
  given name: Shenlian
author list: Agent
  family name: Yang
  given name: Yi
author list: Agent
  family name: He
  given name: Yuelin
author list: Agent
  family name: Ren
  given name: Rui
author list: Agent
  family name: Xu
  given name: Jun
doi: 10.7717/peerj.14130
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-10-03
copyright: ©2022 Tang et al.
attribution name: Tang et al.

Identification of neoplasm-specific signatures of miRNA interactions by employing a systems biology approach
type: item
type: AcademicArticle
description: MicroRNAs represent major regulatory components of the disease epigenome and they constitute powerful biomarkers for the accurate diagnosis and prognosis of various diseases, including cancers. The advent of high-throughput technologies facilitated the generation of a vast amount of miRNA-cancer association data. Computational approaches have been utilized widely to effectively analyze and interpret these data towards the identification of miRNA signatures for diverse types of cancers. Herein, a novel computational workflow was applied to discover core sets of miRNA interactions for the major groups of neoplastic diseases by employing network-based methods. To this end, miRNA-cancer association data from four comprehensive publicly available resources were utilized for constructing miRNA-centered networks for each major group of neoplasms. The corresponding miRNA-miRNA interactions were inferred based on shared functionally related target genes. The topological attributes of the generated networks were investigated in order to detect clusters of highly interconnected miRNAs that form core modules in each network. Those modules that exhibited the highest degree of mutual exclusivity were selected from each graph. In this way, neoplasm-specific miRNA modules were identified that could represent potential signatures for the corresponding diseases.
format: application/pdf
format: text/html
creator: Reza Arshinchi Bonab
creator: Seyedehsadaf Asfa
creator: Panagiota Kontou
creator: Gökhan Karakülah
creator: Athanasia Pavlopoulou
subject: Bioinformatics
subject: Genomics
description: doi:10.7717/peerj.14149
publisher: PeerJ Inc.
rights: © 2022 Arshinchi Bonab et al.
abstract: MicroRNAs represent major regulatory components of the disease epigenome and they constitute powerful biomarkers for the accurate diagnosis and prognosis of various diseases, including cancers. The advent of high-throughput technologies facilitated the generation of a vast amount of miRNA-cancer association data. Computational approaches have been utilized widely to effectively analyze and interpret these data towards the identification of miRNA signatures for diverse types of cancers. Herein, a novel computational workflow was applied to discover core sets of miRNA interactions for the major groups of neoplastic diseases by employing network-based methods. To this end, miRNA-cancer association data from four comprehensive publicly available resources were utilized for constructing miRNA-centered networks for each major group of neoplasms. The corresponding miRNA-miRNA interactions were inferred based on shared functionally related target genes. The topological attributes of the generated networks were investigated in order to detect clusters of highly interconnected miRNAs that form core modules in each network. Those modules that exhibited the highest degree of mutual exclusivity were selected from each graph. In this way, neoplasm-specific miRNA modules were identified that could represent potential signatures for the corresponding diseases.
bibliographic citation: Arshinchi Bonab et al. (2022) Identification of neoplasm-specific signatures of miRNA interactions by employing a systems biology approach. PeerJ 10:e14149 https://doi.org/10.7717/peerj.14149
date submitted: 2022-04-28
date accepted: 2022-09-07
issued: 2022-10-03
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Arshinchi Bonab
  given name: Reza
author list: Agent
  family name: Asfa
  given name: Seyedehsadaf
author list: Agent
  family name: Kontou
  given name: Panagiota
author list: Agent
  family name: Karakülah
  given name: Gökhan
author list: Agent
  family name: Pavlopoulou
  given name: Athanasia
doi: 10.7717/peerj.14149
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-10-03
copyright: ©2022 Arshinchi Bonab et al.
attribution name: Arshinchi Bonab et al.

Association between clinical oral health status and perceived oral health in different age groups
type: item
type: AcademicArticle
description: Objective The perceived oral health refers to the very own perception of a person’s oral health (OH). This study aims to explore the association of perceived oral health status (PSR-OHS) with clinically determined OHS in three age groups: young adults, adults and older adults. This study also aims to identify demographic, socio-economic and/or clinical factors that influence PSR-OHS. Methods A cross-sectional study was conducted in ten different dental hospitals of Pakistan. The one-way ANOVA test was used to analyze patient’s demographic distribution with PSR-OHS and oral functions. The complex sample general linear model was used to determine association between clinical OH and PSR-OHS. Analyses of each age group were conducted separately. Results A total of 1,804 outdoor patients participated in the study, out of which 660 were young adults, 685 adults and 459 were older adults. Overall self-perception of all age groups about their oral health was ‘good’ (mean = 3.71). Female gender and education status were a significant factor in young adults and adults. Family income affected PSR-OHS of only the adult age group. Frequent visit to dental clinic and preventive reason of dental attendance were associated with good PSR-OHS. DMFT score, prosthesis score and periodontal score also affected the PSR-OHS of individuals. Association between PSR-OHS and clinical examination was confirmed by complex general linear model. Conclusion There are differences in the perceived oral health status of young adults, adults and older adults. The variables, age, education, family income, DMFT score, prosthesis score and periodontal score directly influence the self-perception of individuals.
format: application/pdf
format: text/html
creator: Ayesha Fahim
creator: Rizwan Mahmood
creator: Irsam Haider
creator: Mamoona Luqman
creator: Ifra Ikhlaq
creator: Tariq Mahmood
creator: Mohammad Khursheed Alam
subject: Dentistry
subject: Public Health
description: doi:10.7717/peerj.14152
publisher: PeerJ Inc.
rights: © 2022 Fahim et al.
abstract: Objective The perceived oral health refers to the very own perception of a person’s oral health (OH). This study aims to explore the association of perceived oral health status (PSR-OHS) with clinically determined OHS in three age groups: young adults, adults and older adults. This study also aims to identify demographic, socio-economic and/or clinical factors that influence PSR-OHS. Methods A cross-sectional study was conducted in ten different dental hospitals of Pakistan. The one-way ANOVA test was used to analyze patient’s demographic distribution with PSR-OHS and oral functions. The complex sample general linear model was used to determine association between clinical OH and PSR-OHS. Analyses of each age group were conducted separately. Results A total of 1,804 outdoor patients participated in the study, out of which 660 were young adults, 685 adults and 459 were older adults. Overall self-perception of all age groups about their oral health was ‘good’ (mean = 3.71). Female gender and education status were a significant factor in young adults and adults. Family income affected PSR-OHS of only the adult age group. Frequent visit to dental clinic and preventive reason of dental attendance were associated with good PSR-OHS. DMFT score, prosthesis score and periodontal score also affected the PSR-OHS of individuals. Association between PSR-OHS and clinical examination was confirmed by complex general linear model. Conclusion There are differences in the perceived oral health status of young adults, adults and older adults. The variables, age, education, family income, DMFT score, prosthesis score and periodontal score directly influence the self-perception of individuals.
bibliographic citation: Fahim et al. (2022) Association between clinical oral health status and perceived oral health in different age groups. PeerJ 10:e14152 https://doi.org/10.7717/peerj.14152
date submitted: 2022-01-11
date accepted: 2022-09-07
issued: 2022-10-03
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Fahim
  given name: Ayesha
author list: Agent
  family name: Mahmood
  given name: Rizwan
author list: Agent
  family name: Haider
  given name: Irsam
author list: Agent
  family name: Luqman
  given name: Mamoona
author list: Agent
  family name: Ikhlaq
  given name: Ifra
author list: Agent
  family name: Mahmood
  given name: Tariq
author list: Agent
  family name: Alam
  given name: Mohammad Khursheed
doi: 10.7717/peerj.14152
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-10-03
copyright: © 2022 Fahim et al.
attribution name: Fahim et al.

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