PeerJ
type: channel
link: https://peerj.com/articles/
description: Articles published in PeerJ
publisher: PeerJ Inc.
publication name: PeerJ
issn: 2167-8359
items: Prevalence of oral submucous fibrosis across diverse populations: a systematic review and meta-analysis
items: Long-term changes in soil biological activity and other properties of raised beds in Longan orchards
items: https://peerj.com/articles/18409
items: Identification of Meloidogyne panyuensis (Nematoda: Meloidogynidae) infecting Orah (Citrus reticulata Blanco) and its impact on rhizosphere microbial dynamics: Guangxi, China
items: MiR-301b-3p promotes breast cancer development through inhibiting the expression of transforming growth factor-beta receptor 2
items: Optimizing chlorine dioxide treatment for enhanced post-harvest storage quality of Toona Sinensis
items: Long-term alfalfa planting mediates the coupling of soil water and organic carbon storage in a semi-arid area of the Loess Plateau, China
items: Citizen science enhances understanding of sea turtle distribution in the Gulf of California
items: Effect of habitual physical activity on motor performance and prefrontal cortex activity during implicit motor learning
items: Genomic complexity and clinical significance of the RCCX locus

Prevalence of oral submucous fibrosis across diverse populations: a systematic review and meta-analysis
type: item
type: AcademicArticle
description: Purpose The aim is to offer a comprehensive overview of oral submucous fibrosis (OSF) prevalence and explore its epidemiological characteristics across various demographic groups and geographical locations, thereby helping the formulation of public health management policies. Methods Studies reporting OSF prevalence were identified from electronic databases including the Cochrane Central Register of Controlled Trials (CENTRAL), MEDLINE via PubMed, EMBASE via OVID, and Web of Science. Pooled prevalence and quality assessment using the New-Ottawa Scale were conducted. Two reviewers screened and selected records, assessed quality, and independently extracted data. This systematic review and meta-analysis followed the PRISMA guidelines and was registered on PROSPERO (CRD42024532975). Results Sixty-three studies, encompassing 11,434 cases in a total population of 769,860, reported OSF prevalence. The majority of studies (forty-one) were from India. The pooled prevalence of OSF across all populations was 3.0% (95% CI [2.8–3.2]%). In non-risk populations, risk populations, and consecutive dental patients, the pooled prevalence stood at 2.4% (95% CI [2.1–2.6]%), 4.5% (95% CI 3.5-5.6%), and 5.6% (95% CI [3.8–7.5]%), respectively. Subgroup analysis by age, sex, and geographical region revealed higher prevalence rates among those aged 50 and above (4.2%, 95% CI [3.0–5.4]%), males (3.3%, 95% CI [2.9–3.7]%), and in India (4.0%, 95% CI [3.7–4.3]%). As the exposure to risk factors exceeded 50% in the surveyed population, the prevalence of OSF notably increased. Most studies met satisfactory quality standards. Conclusions Our research findings reveal a comprehensive prevalence of OSF across all populations at 3.0% (95% CI [2.8–3.2]%). And, existing evidence indicates a relatively low prevalence of OSF associated with tobacco, alcohol, and Areca (betel) nut use. However, further large-scale studies are recommended to validate these findings. Understanding the prevalence and distribu…
format: application/pdf
format: text/html
creator: Mengqi Wang
creator: Chengchen Duan
creator: Yuzi Wei
creator: Xiaoping Xu
subject: Dentistry
subject: Epidemiology
subject: Evidence Based Medicine
description: doi:10.7717/peerj.18385
publisher: PeerJ Inc.
rights: © 2024 Wang et al.
abstract: Purpose The aim is to offer a comprehensive overview of oral submucous fibrosis (OSF) prevalence and explore its epidemiological characteristics across various demographic groups and geographical locations, thereby helping the formulation of public health management policies. Methods Studies reporting OSF prevalence were identified from electronic databases including the Cochrane Central Register of Controlled Trials (CENTRAL), MEDLINE via PubMed, EMBASE via OVID, and Web of Science. Pooled prevalence and quality assessment using the New-Ottawa Scale were conducted. Two reviewers screened and selected records, assessed quality, and independently extracted data. This systematic review and meta-analysis followed the PRISMA guidelines and was registered on PROSPERO (CRD42024532975). Results Sixty-three studies, encompassing 11,434 cases in a total population of 769,860, reported OSF prevalence. The majority of studies (forty-one) were from India. The pooled prevalence of OSF across all populations was 3.0% (95% CI [2.8–3.2]%). In non-risk populations, risk populations, and consecutive dental patients, the pooled prevalence stood at 2.4% (95% CI [2.1–2.6]%), 4.5% (95% CI 3.5-5.6%), and 5.6% (95% CI [3.8–7.5]%), respectively. Subgroup analysis by age, sex, and geographical region revealed higher prevalence rates among those aged 50 and above (4.2%, 95% CI [3.0–5.4]%), males (3.3%, 95% CI [2.9–3.7]%), and in India (4.0%, 95% CI [3.7–4.3]%). As the exposure to risk factors exceeded 50% in the surveyed population, the prevalence of OSF notably increased. Most studies met satisfactory quality standards. Conclusions Our research findings reveal a comprehensive prevalence of OSF across all populations at 3.0% (95% CI [2.8–3.2]%). And, existing evidence indicates a relatively low prevalence of OSF associated with tobacco, alcohol, and Areca (betel) nut use. However, further large-scale studies are recommended to validate these findings. Understanding the prevalence and distribu…
bibliographic citation: Wang et al. (2024) Prevalence of oral submucous fibrosis across diverse populations: a systematic review and meta-analysis. PeerJ 12:e18385 https://doi.org/10.7717/peerj.18385
date submitted: 2024-05-27
date accepted: 2024-10-01
issued: 2024-11-06
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Wang
  given name: Mengqi
author list: Agent
  family name: Duan
  given name: Chengchen
author list: Agent
  family name: Wei
  given name: Yuzi
author list: Agent
  family name: Xu
  given name: Xiaoping
doi: 10.7717/peerj.18385
volume: 12
issn: 2167-8359
publication name: PeerJ
publication date: 2024-11-06
copyright: ©2024 Wang et al.
attribution name: Wang et al.

Long-term changes in soil biological activity and other properties of raised beds in Longan orchards
type: item
type: AcademicArticle
description: Introduction The Longan fruit tree of the Vietnam Mekong Delta is grown in raised beds to improve water drainage during the rainy season and can live as long as 100 years. Objective This research explores the extent to which the soil microorganisms as well as soil physical and chemical properties of these raised beds degrade over a period of 60 years under traditional management practices. Materials and Methods Raised bed topsoil samples at depths of 0–20 cm were obtained from four different Longan orchards raised bed age groups: group 1) 15–25 years (L1–L5); group 2) 26–37 years (L6–L10); group 3) 38–45 years (L11–L15); and group 4) 46–60 years. Soil biological properties were tested for nitrogen-fixing bacteria, phosphorus solubilizing bacteria, potassium solubilizing bacteria, calcium solubilizing bacteria and silicate solubilizing bacteria, β-glucosidase, urease, phosphomonoesterase, and phytase. Soil samples were also tested for moisture content, soil texture, soil porosity, and bulk density as well as soil chemical properties including pH, electrical conductivity (EC), soil organic matter (SOM), total nitrogen (TN), total phosphorus (TP), total potassium (TK), available nitrogen (NH4+, NO3−), available phosphorus (AP), exchangeable potassium (K+), exchangeable calcium (Ca2 +), available silicate (SiO2), available copper (Cu), zinc (Zn), boron (B) and manganese (Mn). Key findings: The results showed that soil moisture, soil porosity, sand content, SOM, TP, TK, available P, exchangeable Ca2 +, available Si, nitrogen fixing bacteria number, β-glucosidase, urease, phosphomonoesterase, and phytase gradually and significantly decreased in the raised bed soil as the Longan orchard increased in age. Pearson correlation analysis between the ages of Longan orchards and soil properties revealed that raised bed ages were positively correlated with soil bulk density, but negatively correlated with soil moisture content, soil porosity, SOM, TN, β-glucosidase, urease, phosph…
format: application/pdf
format: text/html
creator: Nghia Khoi Nguyen
creator: Phuong Minh Nguyen
creator: Anh Thy Thi Chau
creator: Luan Thanh Do
creator: Thu Ha Thi Nguyen
creator: Duong Hai Vo Tran
creator: Xa Thi Le
creator: Javad Robatjazi
creator: Hendra Gonsalve W. Lasar
creator: Lois Wright Morton
creator: M. Scott Demyan
creator: Huu-Tuan Tran
creator: Hüseyin Barış Tecimen
subject: Agricultural Science
subject: Plant Science
subject: Soil Science
description: doi:10.7717/peerj.18396
publisher: PeerJ Inc.
rights: © 2024 Nguyen et al.
abstract: Introduction The Longan fruit tree of the Vietnam Mekong Delta is grown in raised beds to improve water drainage during the rainy season and can live as long as 100 years. Objective This research explores the extent to which the soil microorganisms as well as soil physical and chemical properties of these raised beds degrade over a period of 60 years under traditional management practices. Materials and Methods Raised bed topsoil samples at depths of 0–20 cm were obtained from four different Longan orchards raised bed age groups: group 1) 15–25 years (L1–L5); group 2) 26–37 years (L6–L10); group 3) 38–45 years (L11–L15); and group 4) 46–60 years. Soil biological properties were tested for nitrogen-fixing bacteria, phosphorus solubilizing bacteria, potassium solubilizing bacteria, calcium solubilizing bacteria and silicate solubilizing bacteria, β-glucosidase, urease, phosphomonoesterase, and phytase. Soil samples were also tested for moisture content, soil texture, soil porosity, and bulk density as well as soil chemical properties including pH, electrical conductivity (EC), soil organic matter (SOM), total nitrogen (TN), total phosphorus (TP), total potassium (TK), available nitrogen (NH4+, NO3−), available phosphorus (AP), exchangeable potassium (K+), exchangeable calcium (Ca2 +), available silicate (SiO2), available copper (Cu), zinc (Zn), boron (B) and manganese (Mn). Key findings: The results showed that soil moisture, soil porosity, sand content, SOM, TP, TK, available P, exchangeable Ca2 +, available Si, nitrogen fixing bacteria number, β-glucosidase, urease, phosphomonoesterase, and phytase gradually and significantly decreased in the raised bed soil as the Longan orchard increased in age. Pearson correlation analysis between the ages of Longan orchards and soil properties revealed that raised bed ages were positively correlated with soil bulk density, but negatively correlated with soil moisture content, soil porosity, SOM, TN, β-glucosidase, urease, phosph…
bibliographic citation: Nguyen et al. (2024) Long-term changes in soil biological activity and other properties of raised beds in Longan orchards. PeerJ 12:e18396 https://doi.org/10.7717/peerj.18396
date submitted: 2024-07-08
date accepted: 2024-10-03
issued: 2024-11-06
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Nguyen
  given name: Nghia Khoi
author list: Agent
  family name: Nguyen
  given name: Phuong Minh
author list: Agent
  family name: Chau
  given name: Anh Thy Thi
author list: Agent
  family name: Do
  given name: Luan Thanh
author list: Agent
  family name: Nguyen
  given name: Thu Ha Thi
author list: Agent
  family name: Tran
  given name: Duong Hai Vo
author list: Agent
  family name: Le
  given name: Xa Thi
author list: Agent
  family name: Robatjazi
  given name: Javad
author list: Agent
  family name: Lasar
  given name: Hendra Gonsalve W.
author list: Agent
  family name: Morton
  given name: Lois Wright
author list: Agent
  family name: Demyan
  given name: M. Scott
author list: Agent
  family name: Tran
  given name: Huu-Tuan
author list: Agent
  family name: Tecimen
  given name: Hüseyin Barış
doi: 10.7717/peerj.18396
volume: 12
issn: 2167-8359
publication name: PeerJ
publication date: 2024-11-06
copyright: ©2024 Nguyen et al.
attribution name: Nguyen et al.

https://peerj.com/articles/18409
type: item
type: AcademicArticle
title: Construction of a high-density genetic map using specific-locus amplified fragment sequencing and quantitative trait loci analysis for tillering related traits in Psathyrostachys juncea perennial grass
description: Background Russian wildrye (RWR, Psathyrostachys juncea) is an outcrossing perennial grass that plays a crucial role in foragaing and rangeland restoration due to its tiller producing capabilities, nevertheless, a genetic map has yet to be constructed due to a shortage of efficient and reliable molecular markers. This also limits the identification, localization, and cloning of economically important traits related to tiller density during breeding. Methods Therefore, this study aimed to create a F1 mapping population with 147 individual lines and their two parents, which were selected based on varying tiller densities. We then used this mapping population to conduct specific-locus amplified fragment sequencing (SLAF-seq) to generate SLAF markers and discover single nucleotide polymorphisms (SNPs). Results Initially, we generated a total of 1,438.38 million pair-end reads with an average sequencing depth of 84.92 in the maternal line, 79.34 in the parental line, and 27.05 in each F1 individual line, respectively. Following the filtering of low-depth SLAF tags, a total of 558,344 high-quality SLAFs were identified. A total of 1,519,903 SNP markers were obtained, and 62,424 polymorphic SNPs were discovered. From these, 4,644 polymorphic SNPs were selected and used for the construction of a genetic map encompassing seven linkage groups. The genetic map spanned 1,416.60 cM with an average distance of 0.31 cM between adjacent markers. Comparative analysis between the seven linkage groups of RWR SLAF tag and the whole-genome sequences in barley (Hordeum vulgare L.) revealed homology values ranging from 17.5% to 34.6%, and the collinearity between the RWR linkage groups and the barley homology groups ranged from 0.6787 to 0.9234, with an average value of 0.8158. Additionally, 143 significant quantitative trait locus (QTLs) with Logarithm of Odds (LOD) value greater than 2.5 for five tiller related traits were detected using three consecutive years of phenotypic trait data …
format: application/pdf
format: text/html
creator: Yingmei Ma
creator: Yudong Chang
creator: Zhen Li
creator: Zhiqi Gao
creator: Feng Han
creator: Yong Wang
creator: Lan Yun
subject: Agricultural Science
subject: Genomics
subject: Plant Science
description: doi:10.7717/peerj.18409
publisher: PeerJ Inc.
rights: © 2024 Ma et al.
abstract: Background Russian wildrye (RWR, Psathyrostachys juncea) is an outcrossing perennial grass that plays a crucial role in foragaing and rangeland restoration due to its tiller producing capabilities, nevertheless, a genetic map has yet to be constructed due to a shortage of efficient and reliable molecular markers. This also limits the identification, localization, and cloning of economically important traits related to tiller density during breeding. Methods Therefore, this study aimed to create a F1 mapping population with 147 individual lines and their two parents, which were selected based on varying tiller densities. We then used this mapping population to conduct specific-locus amplified fragment sequencing (SLAF-seq) to generate SLAF markers and discover single nucleotide polymorphisms (SNPs). Results Initially, we generated a total of 1,438.38 million pair-end reads with an average sequencing depth of 84.92 in the maternal line, 79.34 in the parental line, and 27.05 in each F1 individual line, respectively. Following the filtering of low-depth SLAF tags, a total of 558,344 high-quality SLAFs were identified. A total of 1,519,903 SNP markers were obtained, and 62,424 polymorphic SNPs were discovered. From these, 4,644 polymorphic SNPs were selected and used for the construction of a genetic map encompassing seven linkage groups. The genetic map spanned 1,416.60 cM with an average distance of 0.31 cM between adjacent markers. Comparative analysis between the seven linkage groups of RWR SLAF tag and the whole-genome sequences in barley (Hordeum vulgare L.) revealed homology values ranging from 17.5% to 34.6%, and the collinearity between the RWR linkage groups and the barley homology groups ranged from 0.6787 to 0.9234, with an average value of 0.8158. Additionally, 143 significant quantitative trait locus (QTLs) with Logarithm of Odds (LOD) value greater than 2.5 for five tiller related traits were detected using three consecutive years of phenotypic trait data …
bibliographic citation: Ma et al. (2024) Construction of a high-density genetic map using specific-locus amplified fragment sequencing and quantitative trait loci analysis for tillering related traits in Psathyrostachys juncea perennial grass. PeerJ 12:e18409 https://doi.org/10.7717/peerj.18409
date submitted: 2024-08-19
date accepted: 2024-10-06
issued: 2024-11-06
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Ma
  given name: Yingmei
author list: Agent
  family name: Chang
  given name: Yudong
author list: Agent
  family name: Li
  given name: Zhen
author list: Agent
  family name: Gao
  given name: Zhiqi
author list: Agent
  family name: Han
  given name: Feng
author list: Agent
  family name: Wang
  given name: Yong
author list: Agent
  family name: Yun
  given name: Lan
doi: 10.7717/peerj.18409
volume: 12
issn: 2167-8359
publication name: PeerJ
publication date: 2024-11-06
copyright: © 2024 Ma et al.
attribution name: Ma et al.

Identification of Meloidogyne panyuensis (Nematoda: Meloidogynidae) infecting Orah (Citrus reticulata Blanco) and its impact on rhizosphere microbial dynamics: Guangxi, China
type: item
type: AcademicArticle
description: Root-knot nematode disease severely affects the yield and quality of the mandarin variety Citrus reticulata Blanco “Orah” in Guangxi, China. Nevertheless, the pathogen and the effects of this disease on microbial communities remain inadequately understood. This study identified the root-knot nematode Meloidogyne panyuensis in the rhizosphere of infected Orah using morphological and molecular biological methods. Soil chemical properties indicated that organic matter, total nitrogen (TN), total phosphorus (TP), available phosphorus (AP), total potassium (TK), and available potassium (AK) were significantly higher in the rhizosphere soil of M. panyuensis-infected Orah than in that of healthy plants. The relative abundance of the bacteria Bacillus, Sphingomonas, and Burkholderia-Caballeronia-Paraburkholderia, as well as the fungi Lycoperdon, Fusarium, Neocosmospora, Talaromyces, and Tetragoniomyces, was elevated in the rhizosphere soil of M. panyuensis-infected plants. Furthermore, organic matter, TN, available nitrogen (AN), TP, AP, TK, and AK exhibited positive correlationswith these bacteria and fungi in the rhizosphere soil of M. panyuensis-infected Orah. Potential biocontrol strains, such as Burkholderia spp., were identified by comparing the differences in rhizosphere microbial composition between healthy Orah and M. panyuensis-infected Orah. Our findings provide a foundation for the early warning and prevention of root-knot nematode disease in Orah.
format: application/pdf
format: text/html
creator: Xiaoxiao Zhang
creator: Wei Zhao
creator: Yuming Lin
creator: Bin Shan
creator: Shanshan Yang
subject: Agricultural Science
subject: Microbiology
subject: Plant Science
subject: Soil Science
description: doi:10.7717/peerj.18495
publisher: PeerJ Inc.
rights: © 2024 Zhang et al.
abstract: Root-knot nematode disease severely affects the yield and quality of the mandarin variety Citrus reticulata Blanco “Orah” in Guangxi, China. Nevertheless, the pathogen and the effects of this disease on microbial communities remain inadequately understood. This study identified the root-knot nematode Meloidogyne panyuensis in the rhizosphere of infected Orah using morphological and molecular biological methods. Soil chemical properties indicated that organic matter, total nitrogen (TN), total phosphorus (TP), available phosphorus (AP), total potassium (TK), and available potassium (AK) were significantly higher in the rhizosphere soil of M. panyuensis-infected Orah than in that of healthy plants. The relative abundance of the bacteria Bacillus, Sphingomonas, and Burkholderia-Caballeronia-Paraburkholderia, as well as the fungi Lycoperdon, Fusarium, Neocosmospora, Talaromyces, and Tetragoniomyces, was elevated in the rhizosphere soil of M. panyuensis-infected plants. Furthermore, organic matter, TN, available nitrogen (AN), TP, AP, TK, and AK exhibited positive correlationswith these bacteria and fungi in the rhizosphere soil of M. panyuensis-infected Orah. Potential biocontrol strains, such as Burkholderia spp., were identified by comparing the differences in rhizosphere microbial composition between healthy Orah and M. panyuensis-infected Orah. Our findings provide a foundation for the early warning and prevention of root-knot nematode disease in Orah.
bibliographic citation: Zhang et al. (2024) Identification of Meloidogyne panyuensis (Nematoda: Meloidogynidae) infecting Orah (Citrus reticulata Blanco) and its impact on rhizosphere microbial dynamics: Guangxi, China. PeerJ 12:e18495 https://doi.org/10.7717/peerj.18495
date submitted: 2023-09-15
date accepted: 2024-10-17
issued: 2024-11-06
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Zhang
  given name: Xiaoxiao
author list: Agent
  family name: Zhao
  given name: Wei
author list: Agent
  family name: Lin
  given name: Yuming
author list: Agent
  family name: Shan
  given name: Bin
author list: Agent
  family name: Yang
  given name: Shanshan
doi: 10.7717/peerj.18495
volume: 12
issn: 2167-8359
publication name: PeerJ
publication date: 2024-11-06
copyright: © 2024 Zhang et al.
attribution name: Zhang et al.

MiR-301b-3p promotes breast cancer development through inhibiting the expression of transforming growth factor-beta receptor 2
type: item
type: AcademicArticle
description: Background Breast cancer (BC) is a serious health threat to the patients. The present work explored the mechanism of miR-301b-3p and transforming growth factor-beta receptor 2 (TGFBR2 ) in affecting BC progression. Methods The miR-301b-3p-inhibitor and si-TGFBR2 solution were added to the DEME/F12 medium to culture the BC and normal breast epithelial cell lines to prepare negative control, miR-301b-3p-IN and miR-301b-3p-IN+si-TGFBR2 in the two types of cell lines. The relative expression of target genes and the interference effect were analyzed by quantitative real-time PCR (qRT- PCR). Cell viability was detected applying cell counting kit-8 (CCK-8) assay. Transwell and wound healing assay were conducted to evaluate the invasion and migration of BC cells after miR-301b-3p inhibition. Additionally, cell apoptosis and the expression STAT protein were measured by flow cytometry and Western blot, respectively Results The qRT-PCR results showed that miR-301b-3p were high-expressed but the level of TGFBR2 was significantly inhibited in BC cells. The miR-301b-3p-inhibitor significantly downregulated the expression of miR-301b-3p and upregulated that of TGFBR2. Meanwhile, inhibition of miR-301b-3p suppressed the cell viability, invasion, and migration of BC cells, which, however, were restored by the inhibition of TGFBR2. MiR-301b-3p conferred anti-apoptosis ability to BC cells, while TGFBR2 promoted apoptosis of BC cells through producing an antagonistic effect with miR-301b-3p. We found that miR-301b-3p played a crucial role in the phosphorylation of STAT1 and STAT3 to promote BC progression. Conclusion The present findings demonstrated that miR-301b-3p played a crucial role in promoting BC cell growth, invasion and migration and anti-apoptosis, and that targeting TGFBR2 could inhibit the tumor-promoting effect of miR-301b-3p.
format: application/pdf
format: text/html
creator: Jian Lou
creator: Xueni Liu
creator: Yanru Xie
creator: Minhua Wu
creator: Weibo Mao
creator: Xiaozhen Ying
subject: Bioinformatics
subject: Cell Biology
subject: Gynecology and Obstetrics
subject: Immunology
description: doi:10.7717/peerj.18324
publisher: PeerJ Inc.
rights: © 2024 Lou et al.
abstract: Background Breast cancer (BC) is a serious health threat to the patients. The present work explored the mechanism of miR-301b-3p and transforming growth factor-beta receptor 2 (TGFBR2 ) in affecting BC progression. Methods The miR-301b-3p-inhibitor and si-TGFBR2 solution were added to the DEME/F12 medium to culture the BC and normal breast epithelial cell lines to prepare negative control, miR-301b-3p-IN and miR-301b-3p-IN+si-TGFBR2 in the two types of cell lines. The relative expression of target genes and the interference effect were analyzed by quantitative real-time PCR (qRT- PCR). Cell viability was detected applying cell counting kit-8 (CCK-8) assay. Transwell and wound healing assay were conducted to evaluate the invasion and migration of BC cells after miR-301b-3p inhibition. Additionally, cell apoptosis and the expression STAT protein were measured by flow cytometry and Western blot, respectively Results The qRT-PCR results showed that miR-301b-3p were high-expressed but the level of TGFBR2 was significantly inhibited in BC cells. The miR-301b-3p-inhibitor significantly downregulated the expression of miR-301b-3p and upregulated that of TGFBR2. Meanwhile, inhibition of miR-301b-3p suppressed the cell viability, invasion, and migration of BC cells, which, however, were restored by the inhibition of TGFBR2. MiR-301b-3p conferred anti-apoptosis ability to BC cells, while TGFBR2 promoted apoptosis of BC cells through producing an antagonistic effect with miR-301b-3p. We found that miR-301b-3p played a crucial role in the phosphorylation of STAT1 and STAT3 to promote BC progression. Conclusion The present findings demonstrated that miR-301b-3p played a crucial role in promoting BC cell growth, invasion and migration and anti-apoptosis, and that targeting TGFBR2 could inhibit the tumor-promoting effect of miR-301b-3p.
bibliographic citation: Lou et al. (2024) MiR-301b-3p promotes breast cancer development through inhibiting the expression of transforming growth factor-beta receptor 2. PeerJ 12:e18324 https://doi.org/10.7717/peerj.18324
date submitted: 2024-06-17
date accepted: 2024-09-25
issued: 2024-11-05
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Lou
  given name: Jian
author list: Agent
  family name: Liu
  given name: Xueni
author list: Agent
  family name: Xie
  given name: Yanru
author list: Agent
  family name: Wu
  given name: Minhua
author list: Agent
  family name: Mao
  given name: Weibo
author list: Agent
  family name: Ying
  given name: Xiaozhen
doi: 10.7717/peerj.18324
volume: 12
issn: 2167-8359
publication name: PeerJ
publication date: 2024-11-05
copyright: ©2024 Lou et al.
attribution name: Lou et al.

Optimizing chlorine dioxide treatment for enhanced post-harvest storage quality of Toona Sinensis
type: item
type: AcademicArticle
description: This study investigated the impact of chlorine dioxide (ClO2) treatment on the storage quality of Toona sinensis after harvesting. Toona sinensis samples treated with different concentrations (0.2, 0.4, 0.8, 1.6 mg/L) of chlorine dioxide and stored at (4 ± 1) °C, with sampling test every 2nd day. The changes in sensory, nutritional, and chlorine dioxide residues of T. sinensis were checked regularly. Results revealed that moderate (0.4~0.8 mg/L) chlorine dioxide concentrations maintained sensory quality, inhibited T. sinensis weight loss, slowed flavonoid and vitamin C content depletion, reduced nitrite content, and enhanced superoxide dismutase activity. The chlorine dioxide resides in T. sinensis were below the national standards (<2.0 mg/kg; GB 5009.244-2016). Overall, 0.4~0.8 mg/L chlorine dioxide treatment showed optimal effects on T. sinensis, providing a scientific basis for extended storage and preservation of T. sinensis.
format: application/pdf
format: text/html
creator: Rui Zeng
creator: Yunhong Gao
creator: Mingmin Zheng
creator: Min Lai
creator: Yishi JiGu
creator: Jiayu Chen
creator: Yun Pei
creator: Muhammad Umer Farooq
creator: Khalid Mashay Al-Anazi
creator: Mohammad Abul Farah
subject: Agricultural Science
subject: Food Science and Technology
subject: Plant Science
description: doi:10.7717/peerj.18346
publisher: PeerJ Inc.
rights: © 2024 Zeng et al.
abstract: This study investigated the impact of chlorine dioxide (ClO2) treatment on the storage quality of Toona sinensis after harvesting. Toona sinensis samples treated with different concentrations (0.2, 0.4, 0.8, 1.6 mg/L) of chlorine dioxide and stored at (4 ± 1) °C, with sampling test every 2nd day. The changes in sensory, nutritional, and chlorine dioxide residues of T. sinensis were checked regularly. Results revealed that moderate (0.4~0.8 mg/L) chlorine dioxide concentrations maintained sensory quality, inhibited T. sinensis weight loss, slowed flavonoid and vitamin C content depletion, reduced nitrite content, and enhanced superoxide dismutase activity. The chlorine dioxide resides in T. sinensis were below the national standards (<2.0 mg/kg; GB 5009.244-2016). Overall, 0.4~0.8 mg/L chlorine dioxide treatment showed optimal effects on T. sinensis, providing a scientific basis for extended storage and preservation of T. sinensis.
bibliographic citation: Zeng et al. (2024) Optimizing chlorine dioxide treatment for enhanced post-harvest storage quality of Toona Sinensis. PeerJ 12:e18346 https://doi.org/10.7717/peerj.18346
date submitted: 2024-06-21
date accepted: 2024-09-27
issued: 2024-11-05
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Zeng
  given name: Rui
author list: Agent
  family name: Gao
  given name: Yunhong
author list: Agent
  family name: Zheng
  given name: Mingmin
author list: Agent
  family name: Lai
  given name: Min
author list: Agent
  family name: JiGu
  given name: Yishi
author list: Agent
  family name: Chen
  given name: Jiayu
author list: Agent
  family name: Pei
  given name: Yun
author list: Agent
  family name: Farooq
  given name: Muhammad Umer
author list: Agent
  family name: Al-Anazi
  given name: Khalid Mashay
author list: Agent
  family name: Farah
  given name: Mohammad Abul
doi: 10.7717/peerj.18346
volume: 12
issn: 2167-8359
publication name: PeerJ
publication date: 2024-11-05
copyright: © 2024 Zeng et al.
attribution name: Zeng et al.

Long-term alfalfa planting mediates the coupling of soil water and organic carbon storage in a semi-arid area of the Loess Plateau, China
type: item
type: AcademicArticle
description: The key to restoring arid and semi-arid ecosystems is maintaining soil water and organic carbon contents. Alfalfa (Medicago sativa L.) is a high-yield perennial forage crop and performs ecological functions as a drought-resistance leguminous herb. It has been widely planted for reconstruction of degraded soils in the Loess Plateau in northwestern China, but long-term planting may affect soil carbon–water coupling and lead to crop yield reduction. To maximize the benefits of reconstructed grassland, this study explored the couplings of soil water, organic carbon, and alfalfa productivity along a reconstruction chronosequence in a semi-arid area of the Loess Plateau. Space-for-time substitution approach was used to select different-aged stands of reconstructed grassland (1, 5, 7, 10, 15, 20, 30 years old). Alfalfa above-ground biomass (AGB), soil water storage (SWS), organic carbon storage (SOCS), and carbon–water coupling coordination degree (D) were measured in the 0–100 cm soil profile. Alfalfa AGB reached a peak in the 7th year, and the degradation began in the 10th year. Both SWS and SOCS varied nonlinearly with stand age. The greatest loss of SWS occurred in the 15th year (80–100 cm depth), whereas the largest increase of SOCS occurred in the 30th year (0–20 cm depth). There was a negative feedback relationship between AGB and SWS over the 30-year study period (Pearson r = −0.835, P = 0.098). AGB and SOCS initially showed a trade-off within the first 10 years (Pearson r = −0.7431, P = 0.2569), in contrast to their positive feedback in the 20–30th years (Pearson r = 0.9978, P = 0.0421). A decoupling between SWS and SOCS (D < 0.6) was observed after 12 years of alfalfa planting. For agricultural production, a greater supply of water and organic fertilizer is required from the 7th year of alfalfa planting, and reseeding may be needed around the 10th year to prolong the life of alfalfa community. Alfalfa should be planted for no more than 12 consecutive years in the…
format: application/pdf
format: text/html
creator: Yuanyuan Ma
creator: Xiaoping Zhou
creator: Yan Shen
creator: Hongbin Ma
creator: Bingzhe Fu
creator: Jian Lan
subject: Agricultural Science
subject: Ecology
subject: Plant Science
subject: Soil Science
description: doi:10.7717/peerj.18373
publisher: PeerJ Inc.
rights: © 2024 Ma et al.
abstract: The key to restoring arid and semi-arid ecosystems is maintaining soil water and organic carbon contents. Alfalfa (Medicago sativa L.) is a high-yield perennial forage crop and performs ecological functions as a drought-resistance leguminous herb. It has been widely planted for reconstruction of degraded soils in the Loess Plateau in northwestern China, but long-term planting may affect soil carbon–water coupling and lead to crop yield reduction. To maximize the benefits of reconstructed grassland, this study explored the couplings of soil water, organic carbon, and alfalfa productivity along a reconstruction chronosequence in a semi-arid area of the Loess Plateau. Space-for-time substitution approach was used to select different-aged stands of reconstructed grassland (1, 5, 7, 10, 15, 20, 30 years old). Alfalfa above-ground biomass (AGB), soil water storage (SWS), organic carbon storage (SOCS), and carbon–water coupling coordination degree (D) were measured in the 0–100 cm soil profile. Alfalfa AGB reached a peak in the 7th year, and the degradation began in the 10th year. Both SWS and SOCS varied nonlinearly with stand age. The greatest loss of SWS occurred in the 15th year (80–100 cm depth), whereas the largest increase of SOCS occurred in the 30th year (0–20 cm depth). There was a negative feedback relationship between AGB and SWS over the 30-year study period (Pearson r = −0.835, P = 0.098). AGB and SOCS initially showed a trade-off within the first 10 years (Pearson r = −0.7431, P = 0.2569), in contrast to their positive feedback in the 20–30th years (Pearson r = 0.9978, P = 0.0421). A decoupling between SWS and SOCS (D < 0.6) was observed after 12 years of alfalfa planting. For agricultural production, a greater supply of water and organic fertilizer is required from the 7th year of alfalfa planting, and reseeding may be needed around the 10th year to prolong the life of alfalfa community. Alfalfa should be planted for no more than 12 consecutive years in the…
bibliographic citation: Ma et al. (2024) Long-term alfalfa planting mediates the coupling of soil water and organic carbon storage in a semi-arid area of the Loess Plateau, China. PeerJ 12:e18373 https://doi.org/10.7717/peerj.18373
date submitted: 2024-08-20
date accepted: 2024-09-30
issued: 2024-11-05
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Ma
  given name: Yuanyuan
author list: Agent
  family name: Zhou
  given name: Xiaoping
author list: Agent
  family name: Shen
  given name: Yan
author list: Agent
  family name: Ma
  given name: Hongbin
author list: Agent
  family name: Fu
  given name: Bingzhe
author list: Agent
  family name: Lan
  given name: Jian
doi: 10.7717/peerj.18373
volume: 12
issn: 2167-8359
publication name: PeerJ
publication date: 2024-11-05
copyright: ©2024 Ma et al.
attribution name: Ma et al.

Citizen science enhances understanding of sea turtle distribution in the Gulf of California
type: item
type: AcademicArticle
description: Citizen science is a valuable tool for addressing spatial distribution gaps in endangered species, especially in data-limited regions. Given the logistical and financial challenges of studying migratory species, this cost-effective approach contributes to strategic conservation planning. The Bay of La Paz, located in Baja California Sur, México, is considered an ecologically important region within the larger Gulf of California. Due to its rich biodiversity and abundant natural resources, the region serves as a hub for ecotourism and fishing, affording diverse opportunities for community-based scientific initiatives. This paper examines the value of citizen science contributions from three diverse community groups (i.e., coastal residents, SCUBA divers, and artisanal fishers) to help scientists obtain information on sea turtle distribution in the Bay of La Paz. Our findings represent the first records of loggerhead turtles (Caretta caretta) in the bay based on ten citizen science reports that include live and dead turtles (either observed swimming, as bycatch, or stranded), providing new information on an endangered pelagic species identified in a coastal bay. Although the sample size is small, our diversity of sources and sighting types highlight the value of collaborative citizen science initiatives in complementing traditional research methods.
format: application/pdf
format: text/html
creator: Stephanie J. Rousso
creator: María Dinorah Herrero Perezrul
creator: Agnese Mancini
creator: Alan A. Zavala-Norzagaray
creator: Jesse F. Senko
subject: Biodiversity
subject: Conservation Biology
subject: Marine Biology
subject: Natural Resource Management
subject: Environmental Impacts
description: doi:10.7717/peerj.18203
publisher: PeerJ Inc.
rights: © 2024 Rousso et al.
abstract: Citizen science is a valuable tool for addressing spatial distribution gaps in endangered species, especially in data-limited regions. Given the logistical and financial challenges of studying migratory species, this cost-effective approach contributes to strategic conservation planning. The Bay of La Paz, located in Baja California Sur, México, is considered an ecologically important region within the larger Gulf of California. Due to its rich biodiversity and abundant natural resources, the region serves as a hub for ecotourism and fishing, affording diverse opportunities for community-based scientific initiatives. This paper examines the value of citizen science contributions from three diverse community groups (i.e., coastal residents, SCUBA divers, and artisanal fishers) to help scientists obtain information on sea turtle distribution in the Bay of La Paz. Our findings represent the first records of loggerhead turtles (Caretta caretta) in the bay based on ten citizen science reports that include live and dead turtles (either observed swimming, as bycatch, or stranded), providing new information on an endangered pelagic species identified in a coastal bay. Although the sample size is small, our diversity of sources and sighting types highlight the value of collaborative citizen science initiatives in complementing traditional research methods.
bibliographic citation: Rousso et al. (2024) Citizen science enhances understanding of sea turtle distribution in the Gulf of California. PeerJ 12:e18203 https://doi.org/10.7717/peerj.18203
date submitted: 2024-06-13
date accepted: 2024-09-09
issued: 2024-11-04
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Rousso
  given name: Stephanie J.
author list: Agent
  family name: Herrero Perezrul
  given name: María Dinorah
author list: Agent
  family name: Mancini
  given name: Agnese
author list: Agent
  family name: Zavala-Norzagaray
  given name: Alan A.
author list: Agent
  family name: Senko
  given name: Jesse F.
doi: 10.7717/peerj.18203
volume: 12
issn: 2167-8359
publication name: PeerJ
publication date: 2024-11-04
copyright: ©2024 Rousso et al.
attribution name: Rousso et al.

Effect of habitual physical activity on motor performance and prefrontal cortex activity during implicit motor learning
type: item
type: AcademicArticle
description: Background Acute bouts of exercise have been shown to improve motor learning. However, whether these benefits can be observed from habitual physical activity (PA) levels remains unclear and has important implications around PA guidelines to promote motor learning across the lifespan. This study investigated the effect of habitual PA levels on brain activity within the dorsolateral prefrontal cortex (DLPFC) during procedural motor skill acquisition. Methods Twenty-six right-handed healthy young adults had physical activity levels quantified by calculating the metabolic equivalent of task (METs) in minutes per week, derived from the International Physical Activity Questionnaire (IPAQ). Functional near-infrared spectroscopy (fNIRS) over the DLPFC was recorded to measure neural activation during a serial reaction time task (SRTT). Behavioural indicators of procedural motor skill acquisition were quantified as reaction time and accuracy of correct trials during the SRTT. DLPFC activation was characterised as task-related changes in oxyhaemoglobin (∆[HbO2]). Results Findings showed that higher PA levels were associated with improvements in reaction time during procedural motor skill acquisition (p = 0.03). However, no significant effects of PA levels on accuracy or ∆[HbO2] during procedural motor skill acquisition were observed. These findings show that while habitual PA may promote motor performance in young adults, this is not reflected by changes in the DLPFC area of the brain.
format: application/pdf
format: text/html
creator: Fu-Miao Tan
creator: Wei-Peng Teo
creator: Jessie Siew-Pin Leuk
creator: Alicia M. Goodwill
subject: Neuroscience
subject: Kinesiology
subject: Psychiatry and Psychology
description: doi:10.7717/peerj.18217
publisher: PeerJ Inc.
rights: © 2024 Tan et al.
abstract: Background Acute bouts of exercise have been shown to improve motor learning. However, whether these benefits can be observed from habitual physical activity (PA) levels remains unclear and has important implications around PA guidelines to promote motor learning across the lifespan. This study investigated the effect of habitual PA levels on brain activity within the dorsolateral prefrontal cortex (DLPFC) during procedural motor skill acquisition. Methods Twenty-six right-handed healthy young adults had physical activity levels quantified by calculating the metabolic equivalent of task (METs) in minutes per week, derived from the International Physical Activity Questionnaire (IPAQ). Functional near-infrared spectroscopy (fNIRS) over the DLPFC was recorded to measure neural activation during a serial reaction time task (SRTT). Behavioural indicators of procedural motor skill acquisition were quantified as reaction time and accuracy of correct trials during the SRTT. DLPFC activation was characterised as task-related changes in oxyhaemoglobin (∆[HbO2]). Results Findings showed that higher PA levels were associated with improvements in reaction time during procedural motor skill acquisition (p = 0.03). However, no significant effects of PA levels on accuracy or ∆[HbO2] during procedural motor skill acquisition were observed. These findings show that while habitual PA may promote motor performance in young adults, this is not reflected by changes in the DLPFC area of the brain.
bibliographic citation: Tan et al. (2024) Effect of habitual physical activity on motor performance and prefrontal cortex activity during implicit motor learning. PeerJ 12:e18217 https://doi.org/10.7717/peerj.18217
date submitted: 2024-05-23
date accepted: 2024-09-11
issued: 2024-11-04
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Tan
  given name: Fu-Miao
author list: Agent
  family name: Teo
  given name: Wei-Peng
author list: Agent
  family name: Leuk
  given name: Jessie Siew-Pin
author list: Agent
  family name: Goodwill
  given name: Alicia M.
doi: 10.7717/peerj.18217
volume: 12
issn: 2167-8359
publication name: PeerJ
publication date: 2024-11-04
copyright: © 2024 Tan et al.
attribution name: Tan et al.

Genomic complexity and clinical significance of the RCCX locus
type: item
type: AcademicArticle
description: Nearly identical, repetitive elements in the genome contribute to the variability in genetic inheritance patterns, particularly in regions like the RCCX locus, where such repeats can lead to structural variations. In addition, during the formation of gametes as a result of meiosis, variants of loci with repetitive elements that do not code for the required proteins may occur. As a result, an individual with certain genetic rearrangements in this region may have an increased risk of developing a congenital disorder, particularly in cases where the non-functional allele is inherited dominantly. At the same time, there is still no routine or generally recognized diagnostic method to determine the sequence of the repetitive fragments. The functionally important RCCX locus consists of such repetitive fragments. The available knowledge about the genomic variants of the RCCX locus is fragmented, as there is no standardized method to determine its structure. It should be noted that in some structural variants of the RCCX locus, the sequence of protein-coding genes is disrupted, leading to the development of diseases such as congenital adrenal hyperplasia (CAH). Although genetic testing is generally accepted as a gold standard for CAH diagnosis, there are a myriad of strategies on which exact methods to use and in which order. The reason for this inconsistency lies in the complexity of the RCCX locus and the fact that each patient or carrier may have a highly individualized mutation or combination thereof. In this review, we have discussed all known methods that can be used to study the structure of the RCCX locus. As a result, optimal approaches are proposed for the diagnosis of the most common disease caused by lesions in the RCCX–CAH due to CYP21A2 deficiency.
format: application/pdf
format: text/html
creator: Vladimir V. Shiryagin
creator: Andrey A. Devyatkin
creator: Oleg D. Fateev
creator: Ekaterina S. Petriaikina
creator: Viktor P. Bogdanov
creator: Zoia G. Antysheva
creator: Pavel Yu Volchkov
creator: Sergey M. Yudin
creator: Mary Woroncow
creator: Veronika I. Skvortsova
subject: Genetics
subject: Genomics
subject: Medical Genetics
description: doi:10.7717/peerj.18243
publisher: PeerJ Inc.
rights: © 2024 Shiryagin et al.
abstract: Nearly identical, repetitive elements in the genome contribute to the variability in genetic inheritance patterns, particularly in regions like the RCCX locus, where such repeats can lead to structural variations. In addition, during the formation of gametes as a result of meiosis, variants of loci with repetitive elements that do not code for the required proteins may occur. As a result, an individual with certain genetic rearrangements in this region may have an increased risk of developing a congenital disorder, particularly in cases where the non-functional allele is inherited dominantly. At the same time, there is still no routine or generally recognized diagnostic method to determine the sequence of the repetitive fragments. The functionally important RCCX locus consists of such repetitive fragments. The available knowledge about the genomic variants of the RCCX locus is fragmented, as there is no standardized method to determine its structure. It should be noted that in some structural variants of the RCCX locus, the sequence of protein-coding genes is disrupted, leading to the development of diseases such as congenital adrenal hyperplasia (CAH). Although genetic testing is generally accepted as a gold standard for CAH diagnosis, there are a myriad of strategies on which exact methods to use and in which order. The reason for this inconsistency lies in the complexity of the RCCX locus and the fact that each patient or carrier may have a highly individualized mutation or combination thereof. In this review, we have discussed all known methods that can be used to study the structure of the RCCX locus. As a result, optimal approaches are proposed for the diagnosis of the most common disease caused by lesions in the RCCX–CAH due to CYP21A2 deficiency.
bibliographic citation: Shiryagin et al. (2024) Genomic complexity and clinical significance of the RCCX locus. PeerJ 12:e18243 https://doi.org/10.7717/peerj.18243
date submitted: 2024-05-28
date accepted: 2024-09-15
issued: 2024-11-04
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Shiryagin
  given name: Vladimir V.
author list: Agent
  family name: Devyatkin
  given name: Andrey A.
author list: Agent
  family name: Fateev
  given name: Oleg D.
author list: Agent
  family name: Petriaikina
  given name: Ekaterina S.
author list: Agent
  family name: Bogdanov
  given name: Viktor P.
author list: Agent
  family name: Antysheva
  given name: Zoia G.
author list: Agent
  family name: Volchkov
  given name: Pavel Yu
author list: Agent
  family name: Yudin
  given name: Sergey M.
author list: Agent
  family name: Woroncow
  given name: Mary
author list: Agent
  family name: Skvortsova
  given name: Veronika I.
doi: 10.7717/peerj.18243
volume: 12
issn: 2167-8359
publication name: PeerJ
publication date: 2024-11-04
copyright: ©2024 Shiryagin et al.
attribution name: Shiryagin et al.

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