title: PeerJ description: Articles published in PeerJ link: https://peerj.com/articles/index.rss3?journal=peerj&page=279 creator: info@peerj.com PeerJ errorsTo: info@peerj.com PeerJ language: en title: Worse than nothing at all: the inequality of fusions joining autosomes to the PAR and non-PAR portions of sex chromosomes link: https://peerj.com/articles/17740 last-modified: 2024-07-23 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. creator: Kayla T. Wilhoit creator: Emmarie P. Alexander creator: Heath Blackmon uri: https://doi.org/10.7717/peerj.17740 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2024 Wilhoit et al. title: Machine learning and bioinformatics analysis of diagnostic biomarkers associated with the occurrence and development of lung adenocarcinoma link: https://peerj.com/articles/17746 last-modified: 2024-07-23 description: ObjectiveLung 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.MethodsDifferentially 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.ResultsEighty-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 performed.ConclusionThree target genes identified by machine learning: BUB1B, CENPF, and PLK1 play key roles in LUAD development of lung adenocarcinoma. creator: Yong Li creator: Yunxiang Cai creator: Longfei Ji creator: Binyu Wang creator: Danfei Shi creator: Xinmin Li uri: https://doi.org/10.7717/peerj.17746 license: https://creativecommons.org/licenses/by-nc/4.0 rights: ©2024 Li et al. title: Patterns of molecular evolution in a parthenogenic terrestrial isopod (Trichoniscus pusillus) link: https://peerj.com/articles/17780 last-modified: 2024-07-23 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 arisen via recent mutation after the transition to parthenogenesis. Thus, these recent SNPs are consistent with the hypothesis that purifying selection is less effective against new mutations in asexual lineages, but only over long time scales. This system provides a useful model for future studies on the evolutionary tradeoffs between sexual and asexual reproduction in nature. creator: Emily Yarbrough creator: Christopher Chandler uri: https://doi.org/10.7717/peerj.17780 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2024 Yarbrough and Chandler title: Vernicia fordii leaf extract inhibited anthracnose growth by downregulating reactive oxygen species (ROS) levels in vitro and in vivo link: https://peerj.com/articles/17607 last-modified: 2024-07-22 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.MethodsWe 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.ResultsThis 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. creator: Luyao Ge creator: Yanling Zeng creator: Xinyun Liu creator: Xinhai Pan creator: Guliang Yang creator: Qinhui Du creator: Wenlin He uri: https://doi.org/10.7717/peerj.17607 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2024 Ge et al. title: Identifying highly connected sites for risk-based surveillance and control of cucurbit downy mildew in the eastern United States link: https://peerj.com/articles/17649 last-modified: 2024-07-22 description: ObjectiveSurveillance 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.MethodsStatic 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.ResultsStatic 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.ConclusionsCombining the dynamic network model and centrality metrics facilitated the identification of highly connected fields in the southeastern United States and the mid-Atlantic region. These highly connected sites may be used to inform surveillance and strategies for controlling cucurbit downy mildew in the eastern United States. creator: Awino M. E. Ojwang’ creator: Alun L. Lloyd creator: Sharmodeep Bhattacharyya creator: Shirshendu Chatterjee creator: David H. Gent creator: Peter S. Ojiambo uri: https://doi.org/10.7717/peerj.17649 license: https://creativecommons.org/licenses/by-nc/4.0 rights: © 2024 Ojwang’ et al. title: Co-administration of either curcumin or resveratrol with cisplatin treatment decreases hepatotoxicity in rats via anti-inflammatory and oxidative stress-apoptotic pathways link: https://peerj.com/articles/17687 last-modified: 2024-07-22 description: BackgroundCisplatin (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 MethodsForty 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.ResultsAdministration 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.ConclusionCo-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. 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 uri: https://doi.org/10.7717/peerj.17687 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Ramadan et al. title: Population-specific equations of age-related maximum handgrip force: a comprehensive review link: https://peerj.com/articles/17703 last-modified: 2024-07-22 description: BackgroundThe 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.MethodologyIn 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.ResultsA 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 differences due to region are smaller than those due to age or gender.ConclusionsThe equations that were developed for this study can be beneficial in setting population-specific thresholds for rehabilitation programmes and workstation exposure. They can also contribute to the modification of commonly used methods for assessing musculoskeletal load and work-related risk of developing musculoskeletal disorders by scaling their limit values. creator: Danuta Roman-Liu creator: Joanna Kamińska creator: Tomasz Macjej Tokarski uri: https://doi.org/10.7717/peerj.17703 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2024 Roman-Liu et al. title: Clinical characteristics, anti-SARS-CoV-2 IgG titers, and inflammatory markers in individuals with post-COVID-19 condition in Kenya: a cross-sectional study link: https://peerj.com/articles/17723 last-modified: 2024-07-22 description: BackgroundPost-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.MethodsThis 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.ResultsA 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).ConclusionThese findings suggest that post-COVID-19 condition is a health concern even for a relatively young population in Kenya and globally. This condition requires more attention and well-designed studies to better define it and identify clinical chemistry markers that can be used for its diagnosis. 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 uri: https://doi.org/10.7717/peerj.17723 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Theuri et al. title: Methodology for the assessment of poor-data water resources link: https://peerj.com/articles/17755 last-modified: 2024-07-22 description: Surface hydrologic modeling becomes a problem when insufficient spatial and temporal information is available. It is common to have useful modeling periods of less than 15 years. The purpose of this work is to develop a methodology that allows the selection of meteorological and hydrometric stations that are suitable for modeling when information is scarce in the area. Based on the scarcity of data, a series of statistical tests are proposed to eliminate stations according to a decision-making process. Although the number of stations decreases drastically, the information used is reliable and of adequate quality, ensuring less uncertainty in the surface simulation models. Individual basin modeling can be carried out considering the poor data. The transfer of parameters can be applied through the nesting of basins to have information distributed over an extensive area. Therefore, temporally and spatially extended modeling can be achieved with information that preserves statistical parameters over time. If data management and validation is performed, the modeled watersheds are well represented; if this is not done, only 26% to 50% of the runoff is represented. creator: María del Mar Navarro-Farfán creator: Liliana García-Romero creator: Marco A. Martínez-Cinco creator: Constantino Domínguez-Sánchez creator: Sonia Tatiana Sánchez-Quispe uri: https://doi.org/10.7717/peerj.17755 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Navarro-Farfán et al. title: Green manure combined with reduced nitrogen reduce NH3 emissions, improves yield and nitrogen use efficiencies of rice link: https://peerj.com/articles/17761 last-modified: 2024-07-22 description: BackgroundGreen manure is an important source of organic fertilizer. Exploring green fertilizer and nitrogen fertilizer reduction is important for agricultural production. However, few studies have been conducted, especially on the effects of different green fertilizers along with reduced nitrogen fertilizer application on soil ammonia volatilization emissions, rice yield, and nitrogen fertilizer uptake and utilization.MethodsIn this study, the effects of different types of green manure and reduced nitrogen fertilizer application on soil ammonia volatilization emissions, aboveground population characteristics of rice, and nitrogen fertilizer uptake and utilization were explored. This study was based on a field-positioning experiment conducted between 2020 and 2022. Six treatments were established: no nitrogen fertilizer application (CK), conventional fertilization in wheat-rice (WR), villous villosa-rice (VvR), vetch sativa-rice (VsR), rapeseed seed-rice (RR), and milk vetch-rice (GR), with a 20% reduction in nitrogen fertilizer application. The amounts of phosphorus and potassium fertilizers remained unchanged. The characteristics of ammonia volatilization loss in rice fields, agronomic traits of rice, yield traits, and nitrogen uptake and utilization were investigated.ResultsThe results indicated a significant difference (P < 0.05) in the impact of different treatments on ammonia volatilization emissions from rice in the two-year experiment. Compared with WR treatment, VvR, VsR, RR, and GR treatments reduced the total ammonia volatilization loss by 23.58 to 39.21 kg ha−1, respectively. Compared with the conventional WR treatment, other treatments increased rice yield by 0.09 to 0.83 t ha−1. GR treatment was significantly higher than other green fertilizer treatments, except for VsR (P < 0.05). It increased the nitrogen uptake of rice by an average of 4.24%–22.24% and 13.08%–33.21% over the two years, respectively. The impact of different types of green manure on the nitrogen uptake and utilization of rice varied greatly, indicating that the combination of green manure and fertilizer is a sustainable fertilization model for crops to achieve high yields. In particular, the Chinese milk vetch as green manure was more beneficial for ammonia volatilization reduction in paddy field and stable grain production of rice. creator: Zhongze Hu creator: Daliu Yang creator: Yaming Feng creator: Shuanglin Zhang creator: An Wang creator: Qiaozhen Wang creator: Yayun Yang creator: Chunying Chen creator: Yuefang Zhang creator: Xian Wang uri: https://doi.org/10.7717/peerj.17761 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2024 Hu et al.