PeerJ
type: channel
link: https://peerj.com/articles/
description: Articles published in PeerJ
publisher: PeerJ Inc.
publication name: PeerJ
issn: 2167-8359
items: Tomato yellow leaf curl virus manipulates Bemisia tabaci, MEAM1 both directly and indirectly through changes in visual and volatile cues
items: An investigation of the pigments, antioxidants and free radical scavenging potential of twenty medicinal weeds found in the southern part of Bangladesh
items: Worse than nothing at all: the inequality of fusions joining autosomes to the PAR and non-PAR portions of sex chromosomes
items: Machine learning and bioinformatics analysis of diagnostic biomarkers associated with the occurrence and development of lung adenocarcinoma
items: Patterns of molecular evolution in a parthenogenic terrestrial isopod (Trichoniscus pusillus)
items: Vernicia fordii leaf extract inhibited anthracnose growth by downregulating reactive oxygen species (ROS) levels in vitro and in vivo
items: Identifying highly connected sites for risk-based surveillance and control of cucurbit downy mildew in the eastern United States
items: Co-administration of either curcumin or resveratrol with cisplatin treatment decreases hepatotoxicity in rats via anti-inflammatory and oxidative stress-apoptotic pathways
items: Population-specific equations of age-related maximum handgrip force: a comprehensive review
items: Clinical characteristics, anti-SARS-CoV-2 IgG titers, and inflammatory markers in individuals with post-COVID-19 condition in Kenya: a cross-sectional study

Tomato yellow leaf curl virus manipulates Bemisia tabaci, MEAM1 both directly and indirectly through changes in visual and volatile cues
type: item
type: AcademicArticle
description: The sweetpotato whitefly, Bemisia tabaci MEAM1, is one of the most devastating pests of row-crop vegetables worldwide, damaging crops directly through feeding and indirectly through the transmission of many different viruses, including the geminivirus Tomato yellow leaf curl virus (TYLCV). Y-tube olfactometer tests were conducted at different stages of TYLCV infection in tomatoes to understand how TYLCV affects B. tabaci behavior. We also recorded changes in tomato hosts’ color and volatile profiles using color spectrophotometry and gas chromatography-mass spectrometry (GC-MS). We found that the infection status of B. tabaci and the infection stage of TYLCV influenced host selection, with uninfected whiteflies showing a preference for TYLCV-infected hosts, especially during the late stages of infection. Viruliferous B. tabaci attraction to visual targets significantly differed from non-viruliferous B. tabaci. Late-stage infected hosts had larger surface areas reflecting yellow-green wavelengths and higher emissions of methyl salicylate in their volatile profiles. These findings shed new light on several critical mechanisms involved in the viral manipulation of an insect vector and its economically important host.
format: application/pdf
format: text/html
creator: Thomson M. Paris
creator: Nicholas Johnston
creator: Iris Strzyzewski
creator: Jessica L. Griesheimer
creator: Benjamin Reimer
creator: Kathi Malfa
creator: Sandra A. Allan
creator: Xavier Martini
subject: Agricultural Science
subject: Entomology
subject: Plant Science
description: doi:10.7717/peerj.17665
publisher: PeerJ Inc.
rights: © 2024 Paris et al.
abstract: The sweetpotato whitefly, Bemisia tabaci MEAM1, is one of the most devastating pests of row-crop vegetables worldwide, damaging crops directly through feeding and indirectly through the transmission of many different viruses, including the geminivirus Tomato yellow leaf curl virus (TYLCV). Y-tube olfactometer tests were conducted at different stages of TYLCV infection in tomatoes to understand how TYLCV affects B. tabaci behavior. We also recorded changes in tomato hosts’ color and volatile profiles using color spectrophotometry and gas chromatography-mass spectrometry (GC-MS). We found that the infection status of B. tabaci and the infection stage of TYLCV influenced host selection, with uninfected whiteflies showing a preference for TYLCV-infected hosts, especially during the late stages of infection. Viruliferous B. tabaci attraction to visual targets significantly differed from non-viruliferous B. tabaci. Late-stage infected hosts had larger surface areas reflecting yellow-green wavelengths and higher emissions of methyl salicylate in their volatile profiles. These findings shed new light on several critical mechanisms involved in the viral manipulation of an insect vector and its economically important host.
bibliographic citation: Paris et al. (2024) Tomato yellow leaf curl virus manipulates Bemisia tabaci, MEAM1 both directly and indirectly through changes in visual and volatile cues. PeerJ 12:e17665 https://doi.org/10.7717/peerj.17665
date submitted: 2024-03-15
date accepted: 2024-06-11
issued: 2024-07-23
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Paris
  given name: Thomson M.
author list: Agent
  family name: Johnston
  given name: Nicholas
author list: Agent
  family name: Strzyzewski
  given name: Iris
author list: Agent
  family name: Griesheimer
  given name: Jessica L.
author list: Agent
  family name: Reimer
  given name: Benjamin
author list: Agent
  family name: Malfa
  given name: Kathi
author list: Agent
  family name: Allan
  given name: Sandra A.
author list: Agent
  family name: Martini
  given name: Xavier
doi: 10.7717/peerj.17665
volume: 12
issn: 2167-8359
publication name: PeerJ
publication date: 2024-07-23
copyright: ©2024 Paris et al.
attribution name: Paris et al.

An investigation of the pigments, antioxidants and free radical scavenging potential of twenty medicinal weeds found in the southern part of Bangladesh
type: item
type: AcademicArticle
description: Despite their overlooked status, weeds are increasingly recognized for their therapeutic value, aligning with historical reliance on plants for medicine and nutrition. This study investigates the medicinal potential of native weed species in Bangladesh, specifically pigments, antioxidants, and free radical scavenging abilities. Twenty different medicinal weed species were collected from the vicinity of Khulna Agricultural University and processed in the Crop Botany Department Laboratory. Pigment levels were determined using spectrophotometer analysis, and phenolics, flavonoids, and DPPH were quantified accordingly. Chlorophyll levels in leaves ranged from 216.70 ± 9.41 to 371.14 ± 28.67 µg g−1 FW, and in stems from 51.98 ± 3.21 to 315.89 ± 17.19 µg g−1 FW. Flavonoid content also varied widely, from 1,624.62 ± 102.03 to 410.00 ± 115.58 mg CE 100 g−1 FW in leaves, and from 653.08 ± 32.42 to 80.00 ± 18.86 mg CE 100 g−1 FW in stems. In case of phenolics content Euphorbia hirta L. displaying the highest total phenolic content in leaves (1,722.33 ± 417.89 mg GAE 100 g−1 FW) and Ruellia tuberosa L. in stems (977.70 ± 145.58 mg GAE 100 g−1 FW). The lowest DPPH 2.505 ± 1.028 mg mL−1was found in Heliotropium indicum L. leaves. Hierarchical clustering links species with pigment, phenolic/flavonoid content, and antioxidant activity. PCA, involving 20 species and seven traits, explained 70.07% variability, with significant PC1 (14.82%) and PC2 (55.25%). Leaves were shown to be superior, and high-performing plants such as E. hirta and H. indicum stood out for their chemical composition and antioxidant activity. Thus, this research emphasizes the value of efficient selection while concentrating on the therapeutic potential of native weed species.
format: application/pdf
format: text/html
creator: Mousumi Jahan Sumi
creator: Samia Binta Zaman
creator: Shahin Imran
creator: Prosenjit Sarker
creator: Mohammad Saidur Rhaman
creator: Ahmed Gaber
creator: Milan Skalicky
creator: Debojyoti Moulick
creator: Akbar Hossain
subject: Agricultural Science
subject: Biochemistry
subject: Plant Science
description: doi:10.7717/peerj.17698
publisher: PeerJ Inc.
rights: © 2024 Sumi et al.
abstract: Despite their overlooked status, weeds are increasingly recognized for their therapeutic value, aligning with historical reliance on plants for medicine and nutrition. This study investigates the medicinal potential of native weed species in Bangladesh, specifically pigments, antioxidants, and free radical scavenging abilities. Twenty different medicinal weed species were collected from the vicinity of Khulna Agricultural University and processed in the Crop Botany Department Laboratory. Pigment levels were determined using spectrophotometer analysis, and phenolics, flavonoids, and DPPH were quantified accordingly. Chlorophyll levels in leaves ranged from 216.70 ± 9.41 to 371.14 ± 28.67 µg g−1 FW, and in stems from 51.98 ± 3.21 to 315.89 ± 17.19 µg g−1 FW. Flavonoid content also varied widely, from 1,624.62 ± 102.03 to 410.00 ± 115.58 mg CE 100 g−1 FW in leaves, and from 653.08 ± 32.42 to 80.00 ± 18.86 mg CE 100 g−1 FW in stems. In case of phenolics content Euphorbia hirta L. displaying the highest total phenolic content in leaves (1,722.33 ± 417.89 mg GAE 100 g−1 FW) and Ruellia tuberosa L. in stems (977.70 ± 145.58 mg GAE 100 g−1 FW). The lowest DPPH 2.505 ± 1.028 mg mL−1was found in Heliotropium indicum L. leaves. Hierarchical clustering links species with pigment, phenolic/flavonoid content, and antioxidant activity. PCA, involving 20 species and seven traits, explained 70.07% variability, with significant PC1 (14.82%) and PC2 (55.25%). Leaves were shown to be superior, and high-performing plants such as E. hirta and H. indicum stood out for their chemical composition and antioxidant activity. Thus, this research emphasizes the value of efficient selection while concentrating on the therapeutic potential of native weed species.
bibliographic citation: Sumi et al. (2024) An investigation of the pigments, antioxidants and free radical scavenging potential of twenty medicinal weeds found in the southern part of Bangladesh. PeerJ 12:e17698 https://doi.org/10.7717/peerj.17698
date submitted: 2024-02-28
date accepted: 2024-06-17
issued: 2024-07-23
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Sumi
  given name: Mousumi Jahan
author list: Agent
  family name: Zaman
  given name: Samia Binta
author list: Agent
  family name: Imran
  given name: Shahin
author list: Agent
  family name: Sarker
  given name: Prosenjit
author list: Agent
  family name: Rhaman
  given name: Mohammad Saidur
author list: Agent
  family name: Gaber
  given name: Ahmed
author list: Agent
  family name: Skalicky
  given name: Milan
author list: Agent
  family name: Moulick
  given name: Debojyoti
author list: Agent
  family name: Hossain
  given name: Akbar
doi: 10.7717/peerj.17698
volume: 12
issn: 2167-8359
publication name: PeerJ
publication date: 2024-07-23
copyright: ©2024 Sumi et al.
attribution name: Sumi et al.

Worse than nothing at all: the inequality of fusions joining autosomes to the PAR and non-PAR portions of sex chromosomes
type: item
type: AcademicArticle
description: Chromosomal fusions play an integral role in genome remodeling and karyotype evolution. Fusions that join a sex chromosome to an autosome are particularly abundant across the tree of life. However, previous models on the establishment of such fusions have not accounted for the physical structure of the chromosomes. We predict a fusion joining an autosome to the pseudoautosomal region (PAR) of a sex chromosome will not remain stable, and the fusion will switch from the X to the Y chromosome each generation due to recombination. We have produced a forward-time population genetic simulation to explore the outcomes of fusions to both the PAR and non-PAR of sex chromosomes. The model can simulate the fusion of an autosome containing a sexually antagonistic locus to either the PAR or non-PAR end of a sex chromosome. Our model is diploid, two-locus, and biallelic. Our results show a clear pattern where fusions to the non-PAR are favored in the presence of sexual antagonism, whereas fusions to the PAR are disfavored in the presence of sexual antagonism.
format: application/pdf
format: text/html
creator: Kayla T. Wilhoit
creator: Emmarie P. Alexander
creator: Heath Blackmon
subject: Evolutionary Studies
subject: Genetics
description: doi:10.7717/peerj.17740
publisher: PeerJ Inc.
rights: © 2024 Wilhoit et al.
abstract: Chromosomal fusions play an integral role in genome remodeling and karyotype evolution. Fusions that join a sex chromosome to an autosome are particularly abundant across the tree of life. However, previous models on the establishment of such fusions have not accounted for the physical structure of the chromosomes. We predict a fusion joining an autosome to the pseudoautosomal region (PAR) of a sex chromosome will not remain stable, and the fusion will switch from the X to the Y chromosome each generation due to recombination. We have produced a forward-time population genetic simulation to explore the outcomes of fusions to both the PAR and non-PAR of sex chromosomes. The model can simulate the fusion of an autosome containing a sexually antagonistic locus to either the PAR or non-PAR end of a sex chromosome. Our model is diploid, two-locus, and biallelic. Our results show a clear pattern where fusions to the non-PAR are favored in the presence of sexual antagonism, whereas fusions to the PAR are disfavored in the presence of sexual antagonism.
bibliographic citation: Wilhoit et al. (2024) Worse than nothing at all: the inequality of fusions joining autosomes to the PAR and non-PAR portions of sex chromosomes. PeerJ 12:e17740 https://doi.org/10.7717/peerj.17740
date submitted: 2023-07-25
date accepted: 2024-06-24
issued: 2024-07-23
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Wilhoit
  given name: Kayla T.
author list: Agent
  family name: Alexander
  given name: Emmarie P.
author list: Agent
  family name: Blackmon
  given name: Heath
doi: 10.7717/peerj.17740
volume: 12
issn: 2167-8359
publication name: PeerJ
publication date: 2024-07-23
copyright: ©2024 Wilhoit et al.
attribution name: Wilhoit et al.

Machine learning and bioinformatics analysis of diagnostic biomarkers associated with the occurrence and development of lung adenocarcinoma
type: item
type: AcademicArticle
description: Objective Lung adenocarcinoma poses a major global health challenge and is a leading cause of cancer-related deaths worldwide. This study is a review of three molecular biomarkers screened by machine learning that are not only important in the occurrence and progression of lung adenocarcinoma but also have the potential to serve as biomarkers for clinical diagnosis, prognosis evaluation and treatment guidance. Methods Differentially expressed genes (DEGs) were identified using comprehensive GSE1987 and GSE18842 gene expression databases. A comprehensive bioinformatics analysis of these DEGs was conducted to explore enriched functions and pathways, relative expression levels, and interaction networks. Random Forest and LASSO regression analysis techniques were used to identify the three most significant target genes. The TCGA database and quantitative polymerase chain reaction (qPCR) experiments were used to verify the expression levels and receiver operating characteristic (ROC) curves of these three target genes. Furthermore, immune invasiveness, pan-cancer, and mRNA-miRNA interaction network analyses were performed. Results Eighty-nine genes showed increased expression and 190 genes showed decreased expression. Notably, the upregulated DEGs were predominantly associated with organelle fission and nuclear division, whereas the downregulated DEGs were mainly associated with genitourinary system development and cell-substrate adhesion. The construction of the DEG protein-protein interaction network revealed 32 and 19 hub genes with the highest moderate values among the upregulated and downregulated genes, respectively. Using random forest and LASSO regression analyses, the hub genes were employed to identify three most significant target genes.TCGA database and qPCR experiments were used to verify the expression levels and ROC curves of these three target genes, and immunoinvasive analysis, pan-cancer analysis and mRNA-miRNA interaction network analysis were performe…
format: application/pdf
format: text/html
creator: Yong Li
creator: Yunxiang Cai
creator: Longfei Ji
creator: Binyu Wang
creator: Danfei Shi
creator: Xinmin Li
subject: Bioinformatics
subject: Molecular Biology
subject: Oncology
subject: Respiratory Medicine
subject: Data Mining and Machine Learning
description: doi:10.7717/peerj.17746
publisher: PeerJ Inc.
rights: © 2024 Li et al.
abstract: Objective Lung adenocarcinoma poses a major global health challenge and is a leading cause of cancer-related deaths worldwide. This study is a review of three molecular biomarkers screened by machine learning that are not only important in the occurrence and progression of lung adenocarcinoma but also have the potential to serve as biomarkers for clinical diagnosis, prognosis evaluation and treatment guidance. Methods Differentially expressed genes (DEGs) were identified using comprehensive GSE1987 and GSE18842 gene expression databases. A comprehensive bioinformatics analysis of these DEGs was conducted to explore enriched functions and pathways, relative expression levels, and interaction networks. Random Forest and LASSO regression analysis techniques were used to identify the three most significant target genes. The TCGA database and quantitative polymerase chain reaction (qPCR) experiments were used to verify the expression levels and receiver operating characteristic (ROC) curves of these three target genes. Furthermore, immune invasiveness, pan-cancer, and mRNA-miRNA interaction network analyses were performed. Results Eighty-nine genes showed increased expression and 190 genes showed decreased expression. Notably, the upregulated DEGs were predominantly associated with organelle fission and nuclear division, whereas the downregulated DEGs were mainly associated with genitourinary system development and cell-substrate adhesion. The construction of the DEG protein-protein interaction network revealed 32 and 19 hub genes with the highest moderate values among the upregulated and downregulated genes, respectively. Using random forest and LASSO regression analyses, the hub genes were employed to identify three most significant target genes.TCGA database and qPCR experiments were used to verify the expression levels and ROC curves of these three target genes, and immunoinvasive analysis, pan-cancer analysis and mRNA-miRNA interaction network analysis were performe…
bibliographic citation: Li et al. (2024) Machine learning and bioinformatics analysis of diagnostic biomarkers associated with the occurrence and development of lung adenocarcinoma. PeerJ 12:e17746 https://doi.org/10.7717/peerj.17746
date submitted: 2024-03-28
date accepted: 2024-06-24
issued: 2024-07-23
is part of: PeerJ
license: https://creativecommons.org/licenses/by-nc/4.0
author list: Agent
  family name: Li
  given name: Yong
author list: Agent
  family name: Cai
  given name: Yunxiang
author list: Agent
  family name: Ji
  given name: Longfei
author list: Agent
  family name: Wang
  given name: Binyu
author list: Agent
  family name: Shi
  given name: Danfei
author list: Agent
  family name: Li
  given name: Xinmin
doi: 10.7717/peerj.17746
volume: 12
issn: 2167-8359
publication name: PeerJ
publication date: 2024-07-23
copyright: ©2024 Li et al.
attribution name: Li et al.

Patterns of molecular evolution in a parthenogenic terrestrial isopod (Trichoniscus pusillus)
type: item
type: AcademicArticle
description: The “paradox of sex” refers to the question of why sexual reproduction is maintained in the wild, despite how costly it is compared to asexual reproduction. Because of these costs, one might expect nature to select for asexual reproduction, yet sex seems to be continually selected for. Multiple hypotheses have been proposed to explain this incongruence, including the niche differentiation hypothesis, the Red Queen hypothesis, and accumulation of harmful mutations in asexual species due to inefficient purifying selection. This study focuses on the accumulation of mutations in two terrestrial isopods, Trichoniscus pusillus, which has sexual diploid and parthenogenic triploid forms, and Hyloniscus riparius, an obligately sexual relative. We surveyed sex ratios of both species in an upstate New York population and obtained RNA-seq data from wild-caught individuals of both species to examine within- and between-species patterns of molecular evolution in protein-coding genes. The sex ratio and RNA-seq data together provide strong evidence that this T. pusillus population is entirely asexual and triploid, while the H. riparius population is sexual and diploid. Although all the wild T. pusillus individuals used for sequencing shared identical genotypes at nearly all SNPs, supporting a clonal origin, heterozygosity and SNP density were much higher in T. pusillus than in the sexually reproducing H. riparius. This observation suggests this parthenogenic lineage may have arisen via mating between two divergent diploid lineages. Between-species sequence comparisons showed no evidence of ineffective purifying selection in the asexual T. pusillus lineage, as measured by the ratio of nonsynonymous to synonymous substitutions (dN/dS ratios). Likewise, there was no difference between T. pusillus and H. riparius in the ratios of nonsynonymous to synonymous SNPs overall (pN/pS). However, pN/pS ratios in T. pusillus were significantly higher when considering only SNPs that may have aris…
format: application/pdf
format: text/html
creator: Emily Yarbrough
creator: Christopher Chandler
subject: Evolutionary Studies
subject: Genetics
subject: Genomics
subject: Zoology
description: doi:10.7717/peerj.17780
publisher: PeerJ Inc.
rights: © 2024 Yarbrough and Chandler
abstract: The “paradox of sex” refers to the question of why sexual reproduction is maintained in the wild, despite how costly it is compared to asexual reproduction. Because of these costs, one might expect nature to select for asexual reproduction, yet sex seems to be continually selected for. Multiple hypotheses have been proposed to explain this incongruence, including the niche differentiation hypothesis, the Red Queen hypothesis, and accumulation of harmful mutations in asexual species due to inefficient purifying selection. This study focuses on the accumulation of mutations in two terrestrial isopods, Trichoniscus pusillus, which has sexual diploid and parthenogenic triploid forms, and Hyloniscus riparius, an obligately sexual relative. We surveyed sex ratios of both species in an upstate New York population and obtained RNA-seq data from wild-caught individuals of both species to examine within- and between-species patterns of molecular evolution in protein-coding genes. The sex ratio and RNA-seq data together provide strong evidence that this T. pusillus population is entirely asexual and triploid, while the H. riparius population is sexual and diploid. Although all the wild T. pusillus individuals used for sequencing shared identical genotypes at nearly all SNPs, supporting a clonal origin, heterozygosity and SNP density were much higher in T. pusillus than in the sexually reproducing H. riparius. This observation suggests this parthenogenic lineage may have arisen via mating between two divergent diploid lineages. Between-species sequence comparisons showed no evidence of ineffective purifying selection in the asexual T. pusillus lineage, as measured by the ratio of nonsynonymous to synonymous substitutions (dN/dS ratios). Likewise, there was no difference between T. pusillus and H. riparius in the ratios of nonsynonymous to synonymous SNPs overall (pN/pS). However, pN/pS ratios in T. pusillus were significantly higher when considering only SNPs that may have aris…
bibliographic citation: Yarbrough et al. (2024) Patterns of molecular evolution in a parthenogenic terrestrial isopod (Trichoniscus pusillus). PeerJ 12:e17780 https://doi.org/10.7717/peerj.17780
date submitted: 2024-01-18
date accepted: 2024-06-30
issued: 2024-07-23
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Yarbrough
  given name: Emily
author list: Agent
  family name: Chandler
  given name: Christopher
doi: 10.7717/peerj.17780
volume: 12
issn: 2167-8359
publication name: PeerJ
publication date: 2024-07-23
copyright: ©2024 Yarbrough and Chandler
attribution name: Yarbrough and Chandler

Vernicia fordii leaf extract inhibited anthracnose growth by downregulating reactive oxygen species (ROS) levels in vitro and in vivo
type: item
type: AcademicArticle
description: Background Colletotrichum fructicola is a predominant anthracnose species in Camellia oleifera, causing various adverse effects. Traditional intercropping Vernicia fordii with C. oleifera may enhance anthracnose resistance, but the mechanism remains elusive. Methods We utilized UPLC-MS/MS and acid-base detection to identify the major antimicrobial alkaloid components in the V. fordii leaf extract. Subsequently, by adding different concentrations of V. fordii leaf extract for cultivating C. fructicola, with untreated C. fructicola as a control, we investigated the impact of the V. fordii leaf extract, cell wall integrity, cell membrane permeability, MDA, and ROS content changes. Additionally, analysis of key pathogenic genes of C. fructicola confirmed that the V. fordii leaf extract inhibits the growth of the fungus through gene regulation. Results This study discovered the alkaloid composition of V. fordii leaf extract by UPLC-MS/MS and acid-base detection, such as trigonelline, stachydrine, betaine, and O-Phosphocholine. V. fordii leaf extract successfully penetrated C. fructicola mycelia, damaged cellular integrity, and increased ROS and MDA levels by 1.75 and 2.05 times respectively, thereby inhibiting C. fructicola proliferation. By analyzing the key pathogenic genes of C. fructicola, it was demonstrated that the antifungal function of V. fordii leaf extract depends mainly on the regulation of RAB7 and HAC1 gene expression. Therefore, this study elucidates the mechanism of V. fordii -C. oleifera intercropping in strengthening anthracnose resistance in C. oleifera, contributing to efficient C. oleifera cultivation.
format: application/pdf
format: text/html
creator: Luyao Ge
creator: Yanling Zeng
creator: Xinyun Liu
creator: Xinhai Pan
creator: Guliang Yang
creator: Qinhui Du
creator: Wenlin He
subject: Biochemistry
subject: Conservation Biology
subject: Mycology
subject: Toxicology
description: doi:10.7717/peerj.17607
publisher: PeerJ Inc.
rights: © 2024 Ge et al.
abstract: Background Colletotrichum fructicola is a predominant anthracnose species in Camellia oleifera, causing various adverse effects. Traditional intercropping Vernicia fordii with C. oleifera may enhance anthracnose resistance, but the mechanism remains elusive. Methods We utilized UPLC-MS/MS and acid-base detection to identify the major antimicrobial alkaloid components in the V. fordii leaf extract. Subsequently, by adding different concentrations of V. fordii leaf extract for cultivating C. fructicola, with untreated C. fructicola as a control, we investigated the impact of the V. fordii leaf extract, cell wall integrity, cell membrane permeability, MDA, and ROS content changes. Additionally, analysis of key pathogenic genes of C. fructicola confirmed that the V. fordii leaf extract inhibits the growth of the fungus through gene regulation. Results This study discovered the alkaloid composition of V. fordii leaf extract by UPLC-MS/MS and acid-base detection, such as trigonelline, stachydrine, betaine, and O-Phosphocholine. V. fordii leaf extract successfully penetrated C. fructicola mycelia, damaged cellular integrity, and increased ROS and MDA levels by 1.75 and 2.05 times respectively, thereby inhibiting C. fructicola proliferation. By analyzing the key pathogenic genes of C. fructicola, it was demonstrated that the antifungal function of V. fordii leaf extract depends mainly on the regulation of RAB7 and HAC1 gene expression. Therefore, this study elucidates the mechanism of V. fordii -C. oleifera intercropping in strengthening anthracnose resistance in C. oleifera, contributing to efficient C. oleifera cultivation.
bibliographic citation: Ge et al. (2024) Vernicia fordii leaf extract inhibited anthracnose growth by downregulating reactive oxygen species (ROS) levels in vitro and in vivo. PeerJ 12:e17607 https://doi.org/10.7717/peerj.17607
date submitted: 2024-02-23
date accepted: 2024-05-30
issued: 2024-07-22
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Ge
  given name: Luyao
author list: Agent
  family name: Zeng
  given name: Yanling
author list: Agent
  family name: Liu
  given name: Xinyun
author list: Agent
  family name: Pan
  given name: Xinhai
author list: Agent
  family name: Yang
  given name: Guliang
author list: Agent
  family name: Du
  given name: Qinhui
author list: Agent
  family name: He
  given name: Wenlin
doi: 10.7717/peerj.17607
volume: 12
issn: 2167-8359
publication name: PeerJ
publication date: 2024-07-22
copyright: ©2024 Ge et al.
attribution name: Ge et al.

Identifying highly connected sites for risk-based surveillance and control of cucurbit downy mildew in the eastern United States
type: item
type: AcademicArticle
description: Objective Surveillance is critical for the rapid implementation of control measures for diseases caused by aerially dispersed plant pathogens, but such programs can be resource-intensive, especially for epidemics caused by long-distance dispersed pathogens. The current cucurbit downy mildew platform for monitoring, predicting and communicating the risk of disease spread in the United States is expensive to maintain. In this study, we focused on identifying sites critical for surveillance and treatment in an attempt to reduce disease monitoring costs and determine where control may be applied to mitigate the risk of disease spread. Methods Static networks were constructed based on the distance between fields, while dynamic networks were constructed based on the distance between fields and wind speed and direction, using disease data collected from 2008 to 2016. Three strategies were used to identify highly connected field sites. First, the probability of pathogen transmission between nodes and the probability of node infection were modeled over a discrete weekly time step within an epidemic year. Second, nodes identified as important were selectively removed from networks and the probability of node infection was recalculated in each epidemic year. Third, the recurring patterns of node infection were analyzed across epidemic years. Results Static networks exhibited scale-free properties where the node degree followed a power-law distribution. Betweenness centrality was the most useful metric for identifying important nodes within the networks that were associated with disease transmission and prediction. Based on betweenness centrality, field sites in Maryland, North Carolina, Ohio, South Carolina and Virginia were the most central in the disease network across epidemic years. Removing field sites identified as important limited the predicted risk of disease spread based on the dynamic network model. Conclusions Combining the dynamic network model and centrality metr…
format: application/pdf
format: text/html
creator: Awino M. E. Ojwang’
creator: Alun L. Lloyd
creator: Sharmodeep Bhattacharyya
creator: Shirshendu Chatterjee
creator: David H. Gent
creator: Peter S. Ojiambo
subject: Computational Biology
subject: Ecology
subject: Parasitology
subject: Plant Science
description: doi:10.7717/peerj.17649
publisher: PeerJ Inc.
rights: © 2024 Ojwang’ et al.
abstract: Objective Surveillance is critical for the rapid implementation of control measures for diseases caused by aerially dispersed plant pathogens, but such programs can be resource-intensive, especially for epidemics caused by long-distance dispersed pathogens. The current cucurbit downy mildew platform for monitoring, predicting and communicating the risk of disease spread in the United States is expensive to maintain. In this study, we focused on identifying sites critical for surveillance and treatment in an attempt to reduce disease monitoring costs and determine where control may be applied to mitigate the risk of disease spread. Methods Static networks were constructed based on the distance between fields, while dynamic networks were constructed based on the distance between fields and wind speed and direction, using disease data collected from 2008 to 2016. Three strategies were used to identify highly connected field sites. First, the probability of pathogen transmission between nodes and the probability of node infection were modeled over a discrete weekly time step within an epidemic year. Second, nodes identified as important were selectively removed from networks and the probability of node infection was recalculated in each epidemic year. Third, the recurring patterns of node infection were analyzed across epidemic years. Results Static networks exhibited scale-free properties where the node degree followed a power-law distribution. Betweenness centrality was the most useful metric for identifying important nodes within the networks that were associated with disease transmission and prediction. Based on betweenness centrality, field sites in Maryland, North Carolina, Ohio, South Carolina and Virginia were the most central in the disease network across epidemic years. Removing field sites identified as important limited the predicted risk of disease spread based on the dynamic network model. Conclusions Combining the dynamic network model and centrality metr…
bibliographic citation: Ojwang’ et al. (2024) Identifying highly connected sites for risk-based surveillance and control of cucurbit downy mildew in the eastern United States. PeerJ 12:e17649 https://doi.org/10.7717/peerj.17649
date submitted: 2023-12-12
date accepted: 2024-06-06
issued: 2024-07-22
is part of: PeerJ
license: https://creativecommons.org/licenses/by-nc/4.0
author list: Agent
  family name: Ojwang’
  given name: Awino M. E.
author list: Agent
  family name: Lloyd
  given name: Alun L.
author list: Agent
  family name: Bhattacharyya
  given name: Sharmodeep
author list: Agent
  family name: Chatterjee
  given name: Shirshendu
author list: Agent
  family name: Gent
  given name: David H.
author list: Agent
  family name: Ojiambo
  given name: Peter S.
doi: 10.7717/peerj.17649
volume: 12
issn: 2167-8359
publication name: PeerJ
publication date: 2024-07-22
copyright: © 2024 Ojwang’ et al.
attribution name: Ojwang’ et al.

Co-administration of either curcumin or resveratrol with cisplatin treatment decreases hepatotoxicity in rats via anti-inflammatory and oxidative stress-apoptotic pathways
type: item
type: AcademicArticle
description: Background Cisplatin (CIS) is a broad-spectrum anticancer drug, with cytotoxic effects on either malignant or normal cells. We aimed to evaluate the hepatotoxicity in rats caused by CIS and its amelioration by the co-administration of either curcumin or resveratrol. Materials and Methods Forty adult male rats divided into four equal groups: (control group): rats were given a saline solution (0.9%) once intraperitoneally, daily for the next 28 days; (cisplatin group): rats were given a daily oral dose of saline solution (0.9%) for 28 days after receiving a single dose of cisplatin (3.3 mg/kg) intraperitoneally for three successive days; (CIS plus curcumin/resveratrol groups): rats received the same previous dose of cisplatin (3.3 mg/kg) daily for three successive days followed by oral administration of either curcumin/resveratrol solution at a dose of (20 mg/kg) or (10 mg/kg) consequently daily for 28 days. Different laboratory tests (ALT, AST, ALP, bilirubin, oxidative stress markers) and light microscopic investigations were done. Results Administration of CIS resulted in hepatotoxicity in the form of increased liver enzymes, oxidative stress markers; degenerative and apoptotic changes, the co-administration of CIS with either curcumin or resveratrol improved hepatotoxicity through improved microscopic structural changes, reduction in liver enzymes activity, decreased oxidative stress markers, improved degenerative, and apoptotic changes in liver tissues. Conclusion Co-administration of either curcumin or resveratrol with cisplatin treatment could ameliorate hepatotoxicity caused by cisplatin in rats via anti-inflammatory and oxidative stress-apoptotic pathways.
format: application/pdf
format: text/html
creator: Osama I. Ramadan
creator: Lashin S. Ali
creator: Fatma M. Abd-Allah
creator: Rafik E. A. Ereba
creator: Humeda S. Humeda
creator: Ahmed A. Damanhory
creator: Ahmed E. Moustafa
creator: Amr M. Younes
creator: Moaaz M. Y. Awad
creator: Nassar A. A. Omar
subject: Biochemistry
subject: Toxicology
subject: Histology
description: doi:10.7717/peerj.17687
publisher: PeerJ Inc.
rights: © 2024 Ramadan et al.
abstract: Background Cisplatin (CIS) is a broad-spectrum anticancer drug, with cytotoxic effects on either malignant or normal cells. We aimed to evaluate the hepatotoxicity in rats caused by CIS and its amelioration by the co-administration of either curcumin or resveratrol. Materials and Methods Forty adult male rats divided into four equal groups: (control group): rats were given a saline solution (0.9%) once intraperitoneally, daily for the next 28 days; (cisplatin group): rats were given a daily oral dose of saline solution (0.9%) for 28 days after receiving a single dose of cisplatin (3.3 mg/kg) intraperitoneally for three successive days; (CIS plus curcumin/resveratrol groups): rats received the same previous dose of cisplatin (3.3 mg/kg) daily for three successive days followed by oral administration of either curcumin/resveratrol solution at a dose of (20 mg/kg) or (10 mg/kg) consequently daily for 28 days. Different laboratory tests (ALT, AST, ALP, bilirubin, oxidative stress markers) and light microscopic investigations were done. Results Administration of CIS resulted in hepatotoxicity in the form of increased liver enzymes, oxidative stress markers; degenerative and apoptotic changes, the co-administration of CIS with either curcumin or resveratrol improved hepatotoxicity through improved microscopic structural changes, reduction in liver enzymes activity, decreased oxidative stress markers, improved degenerative, and apoptotic changes in liver tissues. Conclusion Co-administration of either curcumin or resveratrol with cisplatin treatment could ameliorate hepatotoxicity caused by cisplatin in rats via anti-inflammatory and oxidative stress-apoptotic pathways.
bibliographic citation: Ramadan et al. (2024) Co-administration of either curcumin or resveratrol with cisplatin treatment decreases hepatotoxicity in rats via anti-inflammatory and oxidative stress-apoptotic pathways. PeerJ 12:e17687 https://doi.org/10.7717/peerj.17687
date submitted: 2024-01-18
date accepted: 2024-06-14
issued: 2024-07-22
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Ramadan
  given name: Osama I.
author list: Agent
  family name: S. Ali
  given name: Lashin
author list: Agent
  family name: M. Abd-Allah
  given name: Fatma
author list: Agent
  family name: E. A. Ereba
  given name: Rafik
author list: Agent
  family name: S. Humeda
  given name: Humeda
author list: Agent
  family name: A. Damanhory
  given name: Ahmed
author list: Agent
  family name: E. Moustafa
  given name: Ahmed
author list: Agent
  family name: M. Younes
  given name: Amr
author list: Agent
  family name: M. Y. Awad
  given name: Moaaz
author list: Agent
  family name: A. A. Omar
  given name: Nassar
doi: 10.7717/peerj.17687
volume: 12
issn: 2167-8359
publication name: PeerJ
publication date: 2024-07-22
copyright: © 2024 Ramadan et al.
attribution name: Ramadan et al.

Population-specific equations of age-related maximum handgrip force: a comprehensive review
type: item
type: AcademicArticle
description: Background The measurement of handgrip force responses is important in many aspects, for example: to complement neurological assessments, to investigate the contribution of muscle mass in predicting functional outcomes, in setting realistic treatment goals, evaluating rehabilitation strategies. Normative data about handgrip force can assist the therapist in interpreting a patient’s results compared with healthy individuals of the same age and gender and can serve as key decision criteria. In this context, establishing normative values of handgrip strength is crucial. Hence, the aim of the this study is to develop a tool that could be used both in rehabilitation and in the prevention of work-related musculoskeletal disorders. This tool takes the form of population-specific predictive equations, which express maximum handgrip force as a function of age. Methodology In order to collect data from studies measuring maximum handgrip force, three databases were searched. The search yielded 5,058 articles. Upon the removal of duplicates, the screening of abstracts and the full-text review of potentially relevant articles, 143 publications which focussed on experimental studies on various age groups were considered as fulfilling the eligibility criteria. A comprehensive literature review produced 1,276 mean values of maximum handgrip force. Results A meta-analysis resulted in gender- and world region-specific (general population, USA, Europe and Asia) equations expressing maximum force as a function of age. The equations showed quantitative differences and trends in maximum handgrip force among age, gender and national groups. They also showed that values of maximum handgrip force are about 40% higher for males than for females and that age-induced decrease in force differs between males and females, with a proved 35% difference between the ages of 35 and 75. The difference was lowest for the 60–64 year olds and highest for the 18–25 year-olds. The equations also showed that…
format: application/pdf
format: text/html
creator: Danuta Roman-Liu
creator: Joanna Kamińska
creator: Tomasz Macjej Tokarski
subject: Biomechanics
subject: Rehabilitation
subject: Sports Medicine
description: doi:10.7717/peerj.17703
publisher: PeerJ Inc.
rights: © 2024 Roman-Liu et al.
abstract: Background The measurement of handgrip force responses is important in many aspects, for example: to complement neurological assessments, to investigate the contribution of muscle mass in predicting functional outcomes, in setting realistic treatment goals, evaluating rehabilitation strategies. Normative data about handgrip force can assist the therapist in interpreting a patient’s results compared with healthy individuals of the same age and gender and can serve as key decision criteria. In this context, establishing normative values of handgrip strength is crucial. Hence, the aim of the this study is to develop a tool that could be used both in rehabilitation and in the prevention of work-related musculoskeletal disorders. This tool takes the form of population-specific predictive equations, which express maximum handgrip force as a function of age. Methodology In order to collect data from studies measuring maximum handgrip force, three databases were searched. The search yielded 5,058 articles. Upon the removal of duplicates, the screening of abstracts and the full-text review of potentially relevant articles, 143 publications which focussed on experimental studies on various age groups were considered as fulfilling the eligibility criteria. A comprehensive literature review produced 1,276 mean values of maximum handgrip force. Results A meta-analysis resulted in gender- and world region-specific (general population, USA, Europe and Asia) equations expressing maximum force as a function of age. The equations showed quantitative differences and trends in maximum handgrip force among age, gender and national groups. They also showed that values of maximum handgrip force are about 40% higher for males than for females and that age-induced decrease in force differs between males and females, with a proved 35% difference between the ages of 35 and 75. The difference was lowest for the 60–64 year olds and highest for the 18–25 year-olds. The equations also showed that…
bibliographic citation: Roman-Liu et al. (2024) Population-specific equations of age-related maximum handgrip force: a comprehensive review. PeerJ 12:e17703 https://doi.org/10.7717/peerj.17703
date submitted: 2024-02-13
date accepted: 2024-06-18
issued: 2024-07-22
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Roman-Liu
  given name: Danuta
author list: Agent
  family name: Kamińska
  given name: Joanna
author list: Agent
  family name: Tokarski
  given name: Tomasz Macjej
doi: 10.7717/peerj.17703
volume: 12
issn: 2167-8359
publication name: PeerJ
publication date: 2024-07-22
copyright: ©2024 Roman-Liu et al.
attribution name: Roman-Liu et al.

Clinical characteristics, anti-SARS-CoV-2 IgG titers, and inflammatory markers in individuals with post-COVID-19 condition in Kenya: a cross-sectional study
type: item
type: AcademicArticle
description: Background Post-coronavirus disease 2019 (post-COVID-19) is associated with considerable morbidity and reduced quality of life. However, studies characterizing the post-COVID-19 condition in Kenya are limited. This study aimed to determine the prevalence of post-COVID-19 condition and determine the clinical characteristics, anti-SARS-CoV-2 IgG titers, and concentrations of inflammatory markers of individuals with post-COVID-19 condition in Kenya. Methods This descriptive cross-sectional study was conducted at the Kenyatta University Health Unit, Kenya. Demographic and clinical data were collected using a questionnaire. The serum levels of anti-SARS-CoV-2 antibodies, interleukin 6 (IL-6), and C-reactive protein (CRP) were quantified by enzyme-linked immunosorbent assays. Independent samples t-test was used to compare the anti-SARS-CoV-2 IgG, IL-6, and CRP levels between the participants with and without post-COVID-19 symptoms. The case definition for post-COVID-19 condition was persistence of acute COVID-19 symptoms or emergence of new symptoms 3 months after COVID-19 diagnosis, symptoms lasting for ≥2 months, and absence of any other etiological basis to explain the symptoms. Results A total of 189 volunteers were recruited in this study (median age: 21 years, range: 18–71 years; male, 49.2%). Forty participants reported having had at least one COVID-19 positive diagnosis in the past, of which 12 (30%) complained of post-COVID-19 symptoms. Significant differences in the number and duration of symptoms were observed between the individuals with and without post-COVID-19 symptoms (t-statistic = 2.87, p = 0.01; t-statistic = 2.39, p = 0.02, respectively). However, no significant differences in serum levels of anti-SARS-CoV-2 IgG, IL-6, and CRP were observed between the two groups (P = 0.08, 0.9, and 0.28, respectively). Conclusion These findings suggest that post-COVID-19 condition is a health concern even for a relatively young population in Kenya and globally. This c…
format: application/pdf
format: text/html
creator: Martin Theuri
creator: Eric M. Ndombi
creator: Peris Thamaini
creator: James Opiyo Ogutu
creator: Lister Onsongo
creator: June K. Madete
creator: Victor Ofula
creator: Samuel Gitau
creator: Gladys Mwangi
creator: Paul Okemo
subject: Epidemiology
subject: Infectious Diseases
subject: Pathology
subject: Public Health
subject: COVID-19
description: doi:10.7717/peerj.17723
publisher: PeerJ Inc.
rights: © 2024 Theuri et al.
abstract: Background Post-coronavirus disease 2019 (post-COVID-19) is associated with considerable morbidity and reduced quality of life. However, studies characterizing the post-COVID-19 condition in Kenya are limited. This study aimed to determine the prevalence of post-COVID-19 condition and determine the clinical characteristics, anti-SARS-CoV-2 IgG titers, and concentrations of inflammatory markers of individuals with post-COVID-19 condition in Kenya. Methods This descriptive cross-sectional study was conducted at the Kenyatta University Health Unit, Kenya. Demographic and clinical data were collected using a questionnaire. The serum levels of anti-SARS-CoV-2 antibodies, interleukin 6 (IL-6), and C-reactive protein (CRP) were quantified by enzyme-linked immunosorbent assays. Independent samples t-test was used to compare the anti-SARS-CoV-2 IgG, IL-6, and CRP levels between the participants with and without post-COVID-19 symptoms. The case definition for post-COVID-19 condition was persistence of acute COVID-19 symptoms or emergence of new symptoms 3 months after COVID-19 diagnosis, symptoms lasting for ≥2 months, and absence of any other etiological basis to explain the symptoms. Results A total of 189 volunteers were recruited in this study (median age: 21 years, range: 18–71 years; male, 49.2%). Forty participants reported having had at least one COVID-19 positive diagnosis in the past, of which 12 (30%) complained of post-COVID-19 symptoms. Significant differences in the number and duration of symptoms were observed between the individuals with and without post-COVID-19 symptoms (t-statistic = 2.87, p = 0.01; t-statistic = 2.39, p = 0.02, respectively). However, no significant differences in serum levels of anti-SARS-CoV-2 IgG, IL-6, and CRP were observed between the two groups (P = 0.08, 0.9, and 0.28, respectively). Conclusion These findings suggest that post-COVID-19 condition is a health concern even for a relatively young population in Kenya and globally. This c…
bibliographic citation: Theuri et al. (2024) Clinical characteristics, anti-SARS-CoV-2 IgG titers, and inflammatory markers in individuals with post-COVID-19 condition in Kenya: a cross-sectional study. PeerJ 12:e17723 https://doi.org/10.7717/peerj.17723
date submitted: 2024-04-16
date accepted: 2024-06-20
issued: 2024-07-22
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Theuri
  given name: Martin
author list: Agent
  family name: Ndombi
  given name: Eric M.
author list: Agent
  family name: Thamaini
  given name: Peris
author list: Agent
  family name: Ogutu
  given name: James Opiyo
author list: Agent
  family name: Onsongo
  given name: Lister
author list: Agent
  family name: Madete
  given name: June K.
author list: Agent
  family name: Ofula
  given name: Victor
author list: Agent
  family name: Gitau
  given name: Samuel
author list: Agent
  family name: Mwangi
  given name: Gladys
author list: Agent
  family name: Okemo
  given name: Paul
doi: 10.7717/peerj.17723
volume: 12
issn: 2167-8359
publication name: PeerJ
publication date: 2024-07-22
copyright: © 2024 Theuri et al.
attribution name: Theuri et al.

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