title: PeerJ description: Articles published in PeerJ link: https://peerj.com/articles/index.rss3?journal=peerj&page=264 creator: info@peerj.com PeerJ errorsTo: info@peerj.com PeerJ language: en title: Realistic nitrate concentrations diminish reproductive indicators in Skiffia lermae, an endemic species in critical endangered status link: https://peerj.com/articles/17876 last-modified: 2024-09-09 description: Goodeinae is a subfamily of critically endangered fish native to central Mexico. Populations of Skiffia lermae, a species belonging to this subfamily, have significantly decreased in the past two decades. A previous study showed that S. lermae is sensitive to acute nitrate-nitrogen (NO3-N) exposure, leading to noticeable changes in both behavioral and histopathological bioindicators. The aim herein was to determine the vulnerability of S. lermae to NO3-N exposure at realistic concentrations registered in freshwater ecosystems in central Mexico where the species was historically reported. Offspring of S. lermae were chronically exposed during 60 days to concentrations of 5, 10 and 20 mg NO3-N/L, with 2 mg NO3-N/L used as the reference value (control). Survival rate, feeding behavior, aquatic surface respiration, body growth, scaled mass index, immature red blood cells, as well as histopathological changes in branchial, hepatic and gonadal tissues were evaluated. Additionally, this study analyzed water quality in freshwater ecosystems where S. lermae presently persists. The results showed decreased survival as NO3-N concentration increased, as well as increased feeding latency, aquatic surface respiration and histological damage in the gills and liver. These organs showed differential sex-dependent responses to NO3-N exposure; females were more sensitive than males. In the ovaries, a decreased density of stage III oocytes was associated with increased NO3-N concentrations. No changes were observed in body growth and number of immature red blood cells. Concentrations recorded in the three freshwater ecosystems that S. lermae inhabit were below 2 mg NO3-N/L. Together, the results could explain why the species has disappeared from more contaminated freshwater ecosystems where NO3-N levels exceed 5 mg/L. Moreover, the study warns about the risks of increasing NO3-N concentrations in the current sites where the species lives. creator: Ivette Marai Villa-Villaseñor creator: Ma. Antonia Herrera-Vargas creator: Beatriz Yáñez-Rivera creator: Mari Carmen Uribe creator: Rebeca Aneli Rueda-Jasso creator: Bryan V. Phillips-Farfán creator: Valentin Mar-Silva creator: Esperanza Meléndez-Herrera creator: Omar Domínguez-Domínguez uri: https://doi.org/10.7717/peerj.17876 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2024 Villa-Villaseñor et al. title: Transcriptome analysis of Citrus Aurantium L. to study synephrine biosynthesis during developmental stages link: https://peerj.com/articles/17965 last-modified: 2024-09-09 description: Citrus aurantium L., sometimes known as “sour orange,” is an important Chinese herb with young, immature fruits, or “zhishi,” that are high in synephrine. Synephrine is a commonly utilized natural chemical with promising applications in effectively increasing metabolism, heat expenditure, energy level, oxidative fat, and weight loss. However, little is known about the genes and pathways involved in synephrine production during the critical developmental stages of C. aurantium L., which limits the development of the industry. According to this study, the concentration of synephrine gradually decreased as the fruit developed. Transcriptome sequencing was used to examine the DEGs associated with synephrine connections and served as the foundation for creating synephrine-rich C. aurantium L. Comparisons conducted between different developmental stages to obtain DEGs, and the number of DEGs varied from 690 to 3,019. Tyrosine and tryptophan biosynthesis, glycolysis/gluconeogenesis, pentose phosphate pathway, phenylalanine, and tyrosine metabolism were the main KEGG pathways that were substantially enriched. The results showed that 25 genes among these KEGG pathways may be related to synephrine synthesis. The WGCNA and one-way ANOVA analysis adoption variance across the groups suggested that 11 genes might play a crucial role in synephrine synthesis and should therefore be further analyzed. We also selected six DEGs at random and analyzed their expression levels by RT-qPCR, and high repeatability and reliability were demonstrated by our finished RNA-seq study results. These results may be useful in selecting or modifying genes to increase the quantity of synephrine in sour oranges. creator: Can Zhong creator: Xitao Yang creator: Juan Niu creator: Xin Zhou creator: Jiahao Zhou creator: Gen Pan creator: Zhimin Sun creator: Jianhua Chen creator: Ke Cao creator: Mingbao Luan uri: https://doi.org/10.7717/peerj.17965 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2024 Zhong et al. title: Burnout experience among healthcare workers post third COVID-19 wave in India; findings of a cross-sectional study link: https://peerj.com/articles/18039 last-modified: 2024-09-09 description: BackgroundThe pandemic exacerbated burnout experienced by healthcare personnel, whose mental health had long been a public health concern before COVID-19. This study used the Copenhagen burnout inventory (CBI) tool to assess burnout and identify predictors among Indian healthcare workers managing COVID-19.MethodsA cross-sectional study was conducted from June to December 2022, after the third pandemic wave. A web-based, fillable Google form was used to recruit COVID-19 management professionals from multiple Jaipur district hospitals. Healthcare professionals provided socio-demographic, work-related, and CBI scores. Multiple linear regression was used to control for model covariant independent variables.ResultsWe evaluated the responses of a total of 578 participants with a mean age of 36.59 ± 9.1 years. Based on the CBI cut-off score of 50, 68.1% reported burnout. A total of 67.5%, 56.4%, and 48.6% of healthcare workers reported work-related, personal, and patient-related burnout, respectively. High burnout scores were significantly associated with the nursing profession (β = 7.89, 95% CI; 3.66, 12.11, p < 0.0001). The p-value indicates the probability of observing the data if the null hypothesis is true, and the confidence interval shows the range within which we can be 95% confident that the true effect lies. An independent relationship exists between male gender and higher personal-related burnout scores (β = 4.45, 95% CI 1.9–6.9).ConclusionThis study identified key indicators that need further emphasis and the need for organizational and individual-level burnout monitoring in healthcare delivery sectors. Health workers continue to experience burnout due to a combination of personal, professional, and patient-related factors. This underscores the need for targeted organizational and individual interventions. The findings also suggest that the CBI tool could identify healthcare worker burnout risk groups. creator: Mohammad Sidiq creator: Sai Jaya Prakash Ch creator: Balamurugan Janakiraman creator: Aksh Chahal creator: Imran Khan creator: Surbhi Kaura creator: Faizan Kashoo creator: Farha Khan creator: Shabnam Khan creator: Chhavi Arora Sehgal creator: Shashank Baranwal creator: Sheenam Popli creator: Mshari Alghadier uri: https://doi.org/10.7717/peerj.18039 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2024 Sidiq et al. title: Burden changes in notifiable infectious diseases in Taiwan during the COVID-19 pandemic link: https://peerj.com/articles/18048 last-modified: 2024-09-09 description: BackgroundThis study aimed to assess the impact of the COVID-19 pandemic on the disease burden of Taiwan’s notifiable infectious diseases (NIDs). We compared disease burdens between the pandemic and pre-pandemic year of 2020 (with non-pharmaceutical interventions (NPIs)) and 2010 (without NPIs), respectively, to understand the overall pandemic impact on NIDs in Taiwan.MethodsForty-three national NIDs were analyzed using the Statistics of Communicable Diseases and Surveillance Report by estimating the premature death and disability via different transmission categories, sex, and age groups. The study evaluated the impact of diseases by assessing the years lost due to death (YLLs), the duration of living with disability (YLDs), and the overall disability-adjusted life years (DALYs) by measuring both the severity of the illness and its duration.ResultsTaiwan recorded 1,577 (2010) and 1,260 (2020) DALYs per million population and lost 43 NIDs, decreasing 317 DALYs per million population. Tuberculosis, HIV/AIDS and acute hepatitis B/D were the leading causes of DALYs, accounting for 89% (2010) and 77% (2020).ConclusionOverall, this study provided the first insight of changes in disease burdens in NIDs between pre- and post-COVID-19 based on a nationwide viewpoint for further preventive measures and interventions to be focused on specific diseases by associated health administrations and policies. creator: Ying-Fei Yang creator: Yu-Miao Chen creator: Si-Yu Chen creator: Po-Hao Chiu creator: Szu-Chieh Chen uri: https://doi.org/10.7717/peerj.18048 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Yang et al. title: Polycystic ovarian syndrome (PCOS) and recurrent spontaneous abortion (RSA) are associated with the PI3K-AKT pathway activation link: https://peerj.com/articles/17950 last-modified: 2024-09-06 description: AimsWe aimed to elucidate the mechanism leading to polycystic ovarian syndrome (PCOS) and recurrent spontaneous abortion (RSA).BackgroundPCOS is an endocrine disorder. Patients with RSA also have a high incidence rate of PCOS, implying that PCOS and RSA may share the same pathological mechanism.ObjectiveThe single-cell RNA-seq datasets of PCOS (GSE168404 and GSE193123) and RSA GSE113790 and GSE178535) were downloaded from the Gene Expression Omnibus (GEO) database.MethodsDatasets of PSCO and RSA patients were retrieved from the Gene Expression Omnibus (GEO) database. The “WGCNA” package was used to determine the module eigengenes associated with the PCOS and RSA phenotypes and the gene functions were analyzed using the “DAVID” database. The GSEA analysis was performed in “clusterProfiler” package, and key genes in the activated pathways were identified using the Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis. Real-time quantitative PCR (RT-qPCR) was conducted to determine the mRNA level. Cell viability and apoptosis were measured by cell counting kit-8 (CCK-8) and flow cytometry, respectively.ResultsThe modules related to PCOS and RSA were sectioned by weighted gene co-expression network analysis (WGCNA) and positive correlation modules of PCOS and RSA were all enriched in angiogenesis and Wnt pathways. The GSEA further revealed that these biological processes of angiogenesis, Wnt and regulation of cell cycle were significantly positively correlated with the PCOS and RSA phenotypes. The intersection of the positive correlation modules of PCOS and RSA contained 80 key genes, which were mainly enriched in kinase-related signal pathways and were significant high-expressed in the disease samples. Subsequently, visualization of these genes including PDGFC, GHR, PRLR and ITGA3 showed that these genes were associated with the PI3K-AKT signal pathway. Moreover, the experimental results showed that PRLR had a higher expression in KGN cells, and that knocking PRLR down suppressed cell viability and promoted apoptosis of KGN cells.ConclusionThis study revealed the common pathological mechanisms between PCOS and RSA and explored the role of the PI3K-AKT signaling pathway in the two diseases, providing a new direction for the clinical treatment of PCOS and RSA. creator: Wenjing Lin creator: Yuting Wang creator: Lei Zheng uri: https://doi.org/10.7717/peerj.17950 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Lin et al. title: CDMPred: a tool for predicting cancer driver missense mutations with high-quality passenger mutations link: https://peerj.com/articles/17991 last-modified: 2024-09-06 description: Most computational methods for predicting driver mutations have been trained using positive samples, while negative samples are typically derived from statistical methods or putative samples. The representativeness of these negative samples in capturing the diversity of passenger mutations remains to be determined. To tackle these issues, we curated a balanced dataset comprising driver mutations sourced from the COSMIC database and high-quality passenger mutations obtained from the Cancer Passenger Mutation database. Subsequently, we encoded the distinctive features of these mutations. Utilizing feature correlation analysis, we developed a cancer driver missense mutation predictor called CDMPred employing feature selection through the ensemble learning technique XGBoost. The proposed CDMPred method, utilizing the top 10 features and XGBoost, achieved an area under the receiver operating characteristic curve (AUC) value of 0.83 and 0.80 on the training and independent test sets, respectively. Furthermore, CDMPred demonstrated superior performance compared to existing state-of-the-art methods for cancer-specific and general diseases, as measured by AUC and area under the precision-recall curve. Including high-quality passenger mutations in the training data proves advantageous for CDMPred’s prediction performance. We anticipate that CDMPred will be a valuable tool for predicting cancer driver mutations, furthering our understanding of personalized therapy. creator: Lihua Wang creator: Haiyang Sun creator: Zhenyu Yue creator: Junfeng Xia creator: Xiaoyan Li uri: https://doi.org/10.7717/peerj.17991 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2024 Wang et al. title: A lipidomic study on the lens epithelial cells of patients with age related cataracts link: https://peerj.com/articles/17998 last-modified: 2024-09-06 description: Age related cataracts (ARC) represent the main reason for blindness globally. The lens epithelial cells (LECs) participate not only in the metabolism of many substances in the lens but also in maintaining lens transparency. This study used lipidomics to investigate the metabolic differences in LECs of ARC patients with different severity, aiming at identifying potential metabolic biomarkers of ARC. Patients diagnosed with ARC and underwent cataract surgery at Shanghai Tongren Hospital were selected to participate in this study, which were classified as mild ARC group and severe ARC group. During their cataract surgery, anterior lens capsules(LCs) containing LECs were obtained. The lipidomics of LECs were analyzed using the liquid chromatography‑mass spectrometry (LC-MS). Potential pathways of lipids were searched for using databases such as the Kyoto Encyclopedia of Genes and Genomes (KEGG) and MetaboAnalyst platform. In LEC lipids, 26 lipids have been identified as potential biomarkers between mild ARC and severe ARC, with AUC values of 0.67–0.94. The pathway analysis results revealed that the Glycerophospholipid (GPL) metabolism was significantly influenced, indicating that these metabolic markers contribute significantly to regulating this pathway. The LEC metabolic spectrum demonstrates a proficient ability to differentiate between patients with varying levels of cataracts. Herein, we have successfully identified potential metabolic biomarkers and pathways that have proven to be valuable in enhancing our understanding of ARC pathogenesis. The finding has translational value for developing new cataract treatment methods in the future. creator: Yingying Gong creator: Qingquan Wei creator: Liying Luo creator: Wei Qiu creator: Yanyun Jiang uri: https://doi.org/10.7717/peerj.17998 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Gong et al. title: Asiatic acid reduces lipopolysaccharides-induced pulp inflammation through activation of nuclear factor erythroid 2-related factor 2 in rats link: https://peerj.com/articles/18004 last-modified: 2024-09-06 description: BackgroundDental pulp inflammation, often initiated by Gram-negative microorganisms and lipopolysaccharides (LPS), can lead to pulpitis and, subsequently, dental pulp necrosis, compromising tooth structure and increasing susceptibility to fracture. Asiatic acid, derived from Centella asiatica, has demonstrated pharmacological properties, including anti-inflammatory and antioxidant effects, making it a potential candidate for mitigating LPS-induced pulp inflammation. This in vivo study aims to investigate the impact of Asiatic acid on the nuclear factor erythroid 2-related factor 2 (Nrf2) pathway in Rattus norvegicus with LPS-induced pulp inflammation.MethodsThis quasi-laboratory experimental in vivo study employed a post-test-only control group design to investigate the effects of Asiatic acid on LPS-induced pulp inflammation in Wistar rats. Thirty rats were randomly divided into six groups subjected to various interventions. LPS was administered to all groups for 6 h except the standard control group (CG, n = 5). The negative control group (NCG, n = 5) received only glass ionomer cement. The positive control group (PCG, n = 5) received Eugenol with glass ionomer cement. Intervention groups 1, 2, and 3 (IG1, IG2, IG3; n = 5 each) received Asiatic acid at concentrations of 0.5%, 1%, and 2%, respectively, with glass ionomer cement. Dental pulp inflammation was confirmed through immunological (tumor necrosis factor alpha (TNF-α) levels), histopathological (inflammatory parameters), and physiological (pain assessment using the rat grimace scale) analyses. Additionally, Nrf2 levels were examined using enzyme-linked immunosorbent assay (ELISA).ResultsAsiatic acid administration significantly influenced Nrf2 levels in rats with LPS-induced pulp inflammation. Nrf2 levels were significantly higher in groups treated with 0.5% (IG1) (8.810 ± 1.092 ng/mL; p = 0.047), 1.0% (IG2) (9.132 ± 1.285 ng/mL; p = 0.020), and 2.0% (IG3) (11.972 ± 1.888 ng/mL; p = 0.000) Asiatic acid compared to NCG (7.146 ± 0.706). Notably, Nrf2 levels were also significantly higher in the 2.0% Asiatic acid group (IG3) compared to the PCG treated with Eugenol (8.846 ± 0.888 ng/mL; p = 0.001), as well as IG1 (p = 0.001) and IG2 (p = 0.002). However, no significant difference was observed between administering 0.5% Asiatic acid (IG1), 1.0% Asiatic acid (IG2), and Eugenol (PCG).ConclusionThis research showed that Asiatic acid significantly impacted the Nrf2 levels in rats with LPS-induced pulp inflammation. This suggests that it has the potential to be used as a therapeutic agent for reducing dental pulp inflammation. These findings support the need to further explore Asiatic acid as a promising intervention for maintaining dental pulp health. creator: Risya Cilmiaty creator: Arlina Nurhapsari creator: Adi Prayitno creator: Annisa Aghnia Rahma creator: Muhana Fawwazy Ilyas uri: https://doi.org/10.7717/peerj.18004 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Cilmiaty et al. title: Widespread occurrence of fecal indicator bacteria in oligotrophic tropical streams. Are common culture-based coliform tests appropriate? link: https://peerj.com/articles/18007 last-modified: 2024-09-06 description: Monitoring of stream water quality is a key element of water resource management worldwide, but methods that are commonly used in temperate habitats may not be appropriate in humid tropical systems. We assessed the influence of four land uses on microbial water quality in 21 streams in the Panama Canal Watershed over a one-year period, using a common culture-based fecal indicator test and 16S rDNA metabarcoding. Each stream was located within one of four land uses: mature forest, secondary forest, silvopasture, and traditional cattle pasture. Culturing detected total coliforms and Escherichia coli across all sites but found no significant differences in concentrations between land uses. However, 16S rDNA metabarcoding revealed variability in the abundance of coliforms across land uses and several genera that can cause false positives in culture-based tests. Our results indicate that culture-based fecal indicator bacteria tests targeting coliforms may be poor indicators of fecal contamination in Neotropical oligotrophic streams and suggest that tests targeting members of the Bacteroidales would provide a more reliable indication of fecal contamination. creator: Karina Chavarria creator: Jorge Batista creator: Kristin Saltonstall uri: https://doi.org/10.7717/peerj.18007 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2024 Chavarria et al. title: Omics approaches to unravel insecticide resistance mechanism in Bemisia tabaci (Gennadius) (Hemiptera: Aleyrodidae) link: https://peerj.com/articles/17843 last-modified: 2024-09-05 description: Bemisia tabaci (Gennadius) whitefly (BtWf) is an invasive pest that has already spread worldwide and caused major crop losses. Numerous strategies have been implemented to control their infestation, including the use of insecticides. However, prolonged insecticide exposures have evolved BtWf to resist these chemicals. Such resistance mechanism is known to be regulated at the molecular level and systems biology omics approaches could shed some light on understanding this regulation wholistically. In this review, we discuss the use of various omics techniques (genomics, transcriptomics, proteomics, and metabolomics) to unravel the mechanism of insecticide resistance in BtWf. We summarize key genes, enzymes, and metabolic regulation that are associated with the resistance mechanism and review their impact on BtWf resistance. Evidently, key enzymes involved in the detoxification system such as cytochrome P450 (CYP), glutathione S-transferases (GST), carboxylesterases (COE), UDP-glucuronosyltransferases (UGT), and ATP binding cassette transporters (ABC) family played key roles in the resistance. These genes/proteins can then serve as the foundation for other targeted techniques, such as gene silencing techniques using RNA interference and CRISPR. In the future, such techniques will be useful to knock down detoxifying genes and crucial neutralizing enzymes involved in the resistance mechanism, which could lead to solutions for coping against BtWf infestation. creator: Muhammad Aqil Fitri Rosli creator: Sharifah Nabihah Syed Jaafar creator: Kamalrul Azlan Azizan creator: Salmah Yaakop creator: Wan Mohd Aizat uri: https://doi.org/10.7717/peerj.17843 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Rosli et al.