PLoS ONE最新文献

{"title":"Prevalence and diagnostic reliability of BRAF, RAS mutations, and RET/PTC rearrangements in a Latin American public health service population with thyroid nodular disease.","authors":"Freddy David Moposita Molina, Grasiela Agnes, Marília Remuzzi Zandoná, Rogério Izquierdo, Fábio Alves Bilhar, Laura Berton Eidt, Virgílio Gonzales Zanella, Luiz Felipe Osowski, Sofia de Oliveira Belardinelli, Amanda Cometti de Andrade, Erika Laurini de Souza Meyer, Lenara Golbert, Vanessa Suñé Mattevi","doi":"10.1371/journal.pone.0329407","DOIUrl":"https://doi.org/10.1371/journal.pone.0329407","url":null,"abstract":"<p><p>Despite their high prevalence and generally benign nature in most cases, the investigation of thyroid nodules still presents potential diagnostic pitfalls, especially in cases with indeterminate cytology results. The performance of molecular markers of thyroid cancer may vary across centers and populations. This study aimed to verify the prevalence of mutations in the BRAF, and RAS genes, and RET/PTC rearrangements in patients undergoing fine-needle aspiration biopsy (FNAB) for thyroid nodule evaluation in a real-world public health service population. Point mutations and rearrangements were detected by Sanger DNA sequencing. A total of 231 thyroid nodules in 220 patients were evaluated, being 86.8% females and a mean age of 55.6 ± 13.9 years. For molecular analysis, high-quality DNA and RNA were obtained from 200 samples. Mutations or rearrangements in target genes were identified in 14% of the 200 samples evaluated. The frequency of the BRAF-like mutations was 5.5%, detected in 9 out of 17 malignant nodules (52.9%) and one in a benign nodule (0.7%). Fourteen RAS-like mutations were identified in benign nodules (57.1% HRAS, 21.5% NRAS and 21.5% KRAS) and only one was present in a malignant nodule (5.9%). Considering only nodules with indeterminate cytology (Bethesda III and IV, n = 53), 9 mutations were detected, 6 in benign histology (all RAS-like), 1 in malignant histology (BRAF-like), and 2 still unoperated, therefore without a histopathological diagnosis. This research concludes that the presence of the BRAF V600E mutation could be useful in supporting the diagnosis of thyroid cancer, due to its high positive predictive value, since 89% of nodules with BRAF V600E mutation were malignant. Additionally, clinical criteria should be established to determine which nodules with RAS-like mutations require closer follow-up, particularly those with indeterminate cytology.</p>","PeriodicalId":20189,"journal":{"name":"PLoS ONE","volume":"20 8","pages":"e0329407"},"PeriodicalIF":2.6,"publicationDate":"2025-08-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144765259","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"综合性期刊","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Loss of Ufsp1 does not cause major changes at the neuromuscular junction.","authors":"Cristofer Calvo, Coalesco Smith, Taejeong Song, Fabian Montecino-Morales, Sakthivel Sadayappan, Douglas P Millay, Minchul Kim","doi":"10.1371/journal.pone.0328690","DOIUrl":"https://doi.org/10.1371/journal.pone.0328690","url":null,"abstract":"<p><p>UFMylation is a Ubiquitin-like post-translational modification involved in myriad of cellular processes. Enzymes involved in this pathway, including ligases and UFM1-specific proteases, are essential for development and homeostasis. Our previous transcriptomic analyses identified an enrichment of Ufsp1 at the neuromuscular junction of skeletal muscle cells. Ufsp1, one of the two UFM1 proteases, had been considered a pseudogene due to truncation of its catalytic domain in several species, including humans. However, recent findings revealed that Ufsp1 is translated from a non-canonical start codon in humans, yielding a catalytically active enzyme. This discovery has revived interest in studying Ufsp1's role in vivo. We generated two mutant mouse models, one with a point mutation abolishing catalytic activity and another with complete knockout of the gene. Unlike other UFMylation pathway enzymes, both Ufsp1 mutants were born in normal ratios and did not exhibit gross phenotypic abnormalities. Despite the enrichment of Ufsp1 at neuromuscular junctions, only mild structural alterations of this synapse were detected, which did not impact overall muscle function. Our findings indicate that Ufsp1 is dispensable for normal development and homeostasis in mice, but further exploration of its function is needed in pathological conditions.</p>","PeriodicalId":20189,"journal":{"name":"PLoS ONE","volume":"20 8","pages":"e0328690"},"PeriodicalIF":2.6,"publicationDate":"2025-08-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144765270","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"综合性期刊","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Mental and physical health of US rural/urban caregivers of persons with dementia.","authors":"Phoebe Tran, Fei Wang, E-Shien Chang","doi":"10.1371/journal.pone.0329260","DOIUrl":"https://doi.org/10.1371/journal.pone.0329260","url":null,"abstract":"<p><strong>Purpose: </strong>Increased dependence on caregiving and limited access to healthcare services in rural US communities may contribute to worse mental and physical health in rural caregivers of persons with dementia (PWD) relative to their urban counterparts. We assessed the association between rural/urban residence and mental and physical health among US caregivers of PWD.</p><p><strong>Methods: </strong>Using 2020-2022 Behavioral Risk Factor Surveillance System data, we identified caregivers of PWD from rural (n = 2311) and urban (n = 15094) areas. Mental health outcome was operationalized as poor mental health days (PMHD); categorized as 0, 1-13, and ≥14 PMHD in previous month. Poor physical health (PPHD) was operationalized in the same manner. Covariates included socio-demographic and caregiving factors. Four sets of unadjusted and adjusted survey-weighted multinomial logistic models (reference: 0 days) were created for PMHD and PPHD.</p><p><strong>Results: </strong>Approximately, 25.7% of rural and 20.8% of urban caregivers reported ≥14 PMHD while 25% of rural and 10% of urban caregivers reported ≥14 PPHD. Prior to adjustment, rural caregivers had lower odds (0.59, 95% CI: 0.34-1.05) of 1-13 vs. 0 PMHD but higher odds (1.13, 95% CI: 0.55-2.30) of 14 + vs 0 PMHD compared to urban caregivers with neither association being statistically significant. In adjusted models, the association for 1-13 vs 0 PMHD became significant, while rural residence became associated with lower, non-significant odds of 14 + vs. 0 PMHD. For physical health, rural caregivers had lower odds (0.86, 95% CI: 0.53-1.41) of 1-13 vs 0 PPHD but higher odds (2.57, 95% CI: 1.00-6.63) of 14 + vs 0 PPHD in unadjusted models with neither result being significant. After adjustment, the associations for 1-13 vs. 0 PPHD were attenuated and remained non-significant, while rural caregivers had significantly higher odds of 14 + vs 0 PPHD, consistent with unadjusted results.</p><p><strong>Conclusions: </strong>Rural caregivers of PWD are less likely to experience short-term mental health problems compared to their urban counterparts. However, they face similar levels of experiencing PMHD. Additionally, rural caregivers of PWD are more likely to endure more PPHD than urban caregivers. Considering the extensive day-to-day responsibilities that caregivers of PWD carry and the ongoing need for their support, it is crucial to enhance long-term mental health resources for both rural and urban caregivers. Furthermore, targeted initiatives to support the long-term physical health of rural caregivers are equally essential.</p>","PeriodicalId":20189,"journal":{"name":"PLoS ONE","volume":"20 8","pages":"e0329260"},"PeriodicalIF":2.6,"publicationDate":"2025-08-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144765277","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"综合性期刊","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Protocol for a scoping review investigating success in research capacity building for nurses, midwives and allied health professionals.","authors":"Colin Hamilton, Alexandra Malyon, Natalie Pike, Lok Yiu Wong, Kieran Lock, Emma Jones, Gabrielle Deora, Graham Martin, Joanne McPeake","doi":"10.1371/journal.pone.0329264","DOIUrl":"https://doi.org/10.1371/journal.pone.0329264","url":null,"abstract":"<p><strong>Objective: </strong>To identify and describe how success is currently conceptualised in research capacity building in nurses, midwives and allied health professionals in the UK.</p><p><strong>Introduction: </strong>Having a research active healthcare workforce is associated with improved patient outcomes as well as staff retention. It is therefore seen as a key target for many healthcare organisations. Nurses, Midwives and Allied Health Professionals form the largest group of healthcare professionals but are traditionally less involved in research than medically trained staff. A variety of schemes have aimed to address this through so called \"research capacity building\" activities but an understanding of what constitutes success is needed to aid development of future interventions.</p><p><strong>Inclusion criteria: </strong>Participants - Any or all of Nurses, Midwives or Allied Health Professionals. Concept- Definition of success or description of aims of activities aimed at research capacity building. Context- Within in the UK.</p><p><strong>Methods: </strong>Content from peer reviewed journals will be searched for in: Embase, CINAHL, MEDLINE, AMED, BNI and EMCARE Web of Science Core Collection. Grey Literature will be searched for in Google and Overton as well as key websites of organisations that work in developing research capacity. Website searches will include National Institute for Health and Care Research, all charities that form the Association of Medical Research Charities as of search date and the websites for the recognised professional bodies for Nurses, Midwives and Allied Health Professionals. Screening of titles and abstracts then full text will be undertaken by one person with 20% cross checked by a second reviewer. Data extraction will use a bespoke data extraction tool and will be undertaken by one person, with 20% cross checked with a second reviewer. A narrative synthesis and qualitative content analysis will be used to synthesise the data.</p><p><strong>Registered: </strong>OSF Registries: https://doi.org/10.17605/OSF.IO/QVCDX.</p>","PeriodicalId":20189,"journal":{"name":"PLoS ONE","volume":"20 8","pages":"e0329264"},"PeriodicalIF":2.6,"publicationDate":"2025-08-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144765287","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"综合性期刊","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Public education during epidemics of infectious diseases: A national mixed-method study with parallel convergent design in a low and middle-income country.","authors":"Saber Azami-Aghdash, Salar Mohammaddokht, Maryam Kashani, Nima Pourgholam, Mohsen Nouri, Elaheh Nasiri","doi":"10.1371/journal.pone.0328451","DOIUrl":"https://doi.org/10.1371/journal.pone.0328451","url":null,"abstract":"<p><strong>Introduction: </strong>Proper and effective public education during epidemics of infectious diseases can have a key effect in controlling epidemics and reducing their complications. Therefore, the present study aims to assess public education methods during infectious disease epidemics from the perspectives of both the public and experts in Iran.</p><p><strong>Method: </strong>The present study is a mixed-methods (quantitative-qualitative) with a parallel convergent design conducted in 2024 in Iran. The public's views on the effectiveness, strengths, and weaknesses of each method used for educating people during epidemics, with a focus on the COVID-19 epidemic, were collected through a self-development valid and reliable questionnaire (with closed and open-ended questions). Quantitative data was analyzed using SPSS:16 software. In the qualitative section, data were collected by semi-structured interviews and manually analyzed using content analysis methods.</p><p><strong>Results: </strong>Television (79.9%), social networks (78.8%), and websites (78.5%) were introduced as sources that have performed best, provided various information and education, had a high impact on the audience, and successfully gained people's trust during epidemics of infectious diseases. In the qualitative section, the majority of participants identified in-person training as the most effective method of educating people. Utilizing the capacities of mass media and providing accurate information to the public were strengths, while dissemination of false and unscientific information and lack of trust in relevant institutions were identified as weaknesses in educating people during epidemics of infectious diseases.</p><p><strong>Conclusion: </strong>In this study, an attempt was made to provide comprehensive and sufficient information for decision-making and effective planning for public education in the next epidemics of infectious diseases.</p>","PeriodicalId":20189,"journal":{"name":"PLoS ONE","volume":"20 8","pages":"e0328451"},"PeriodicalIF":2.6,"publicationDate":"2025-08-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144765288","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"综合性期刊","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Spike substitutions E484D, P812R and Q954H mediate ACE2-independent entry of SARS-CoV-2 across different cell lines.","authors":"Greta Vizgirda, Alexander P Underwood, Ulrik Fahnøe, Nina Weis, Santseharay Ramirez, Jens Bukh","doi":"10.1371/journal.pone.0326419","DOIUrl":"https://doi.org/10.1371/journal.pone.0326419","url":null,"abstract":"<p><p>Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), which causes coronavirus disease 2019 (COVID-19), has evolved into variants with multiple spike protein coding mutations that affect its transmissibility, infectivity, and immune evasion, in particular from neutralizing antibodies. Several of these amino acid changes have been associated with reduced dependency on the principal angiotensin converting enzyme-2 (ACE2) receptor for cell entry. The present study investigates the role of spike protein changes observed in a cell-culture adapted SARS-CoV-2 isolate (DK-AHH1) in modulating entry, ACE2 dependency, and neutralization across different cells, including human liver and lung cell lines. Using a pseudoparticle system, spike proteins with substitutions E484D, P812R, Q954H, and deletion Δ68-76 were evaluated in Vero E6 and Huh7.5, as well as in A549 cells with and without ACE2 overexpression. Pseudoparticles carrying E484D or P812R individually permitted entry in Huh7.5 cells, and their combination further enhanced this capacity. ACE2 blocking experiments revealed the differential roles of these mutations in mediating entry across cell lines. In Vero E6 cells, P812R was the primary driver for ACE2-independent entry, while E484D facilitated ACE2-independent entry in Huh7.5 cells. In A549 cells, all three substitutions (E484D+P812R + Q954H) were required for ACE2-independent entry. Addition of the Δ68-76 deletion did not increase infectivity in any cell line. Notably, pseudoparticles carrying these mutations, maintained susceptibility to neutralization by convalescent plasma from subjects with COVID-19, regardless of the cell line used. These findings highlight the adaptability of SARS-CoV-2 in utilizing alternative entry mechanisms across various cell types, with E484D and P812R playing critical roles in ACE2-independent entry in cell culture. Overall, this study provides valuable insights into how SARS-CoV-2 can alter its receptor usage to ensure robust infectivity of human cell lines while preserving neutralization sensitivity, contributing to our understanding of viral evolution, and informing potential therapeutic strategies targeting viral entry.</p>","PeriodicalId":20189,"journal":{"name":"PLoS ONE","volume":"20 8","pages":"e0326419"},"PeriodicalIF":2.6,"publicationDate":"2025-08-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144765295","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"综合性期刊","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"The porphyran degradation system is complete, phylogenetically and geographically diverse across the gut microbiota of East Asian populations.","authors":"Laure Ségurel, Thirumalai Selvi Ulaganathan, Sophie Mathieu, Mélanie Loiodice, Laurent Poulet, Sophie Drouillard, Miroslaw Cygler, William Helbert","doi":"10.1371/journal.pone.0329457","DOIUrl":"https://doi.org/10.1371/journal.pone.0329457","url":null,"abstract":"<p><p>The human gut microbiota can acquire new catabolic functions by integrating genetic material coming from the environment, for example from food-associated bacteria. An illustrative example of that is the acquisition by the human gut microbiota of Asian populations of genes coming from marine bacteria living on the surface of red algae that are incorporated into their diet when eating maki-sushi. To better understand the function and evolution of this set of algal genes corresponding to a polysaccharide utilization locus (PUL) dedicated to the degradation of porphyran, the main polysaccharide of the red algae Porphyra sp., we characterized it biochemically, assessed its genetic diversity and investigated its geographical distribution in large public worldwide datasets. We first demonstrated that both methylated and unmethylated fractions are catabolized without the help of external enzymes. By scanning the genomic data of more than 10,000 cultivated isolates as well as metagenomic data from more than 14,000 worldwide individuals, we found that the porphyran PUL is present in 17 different Phocaeicola/Bacteroides species (including 12 species that were not known to carry it), as well as in two Parabacteroides species and two genera from the Bacillota phylum, highlighting multiple lateral transfers within the gut microbiota. We then analyzed the prevalence of this porphyran PUL across 32 countries and showed that it exists in appreciable frequencies (>1%) only in East Asia (Japan, China, Korea). Finally, we identified three major PUL haplotypes which frequencies significantly differ between these East Asian countries. This geographic structure likely reflects the rate of bacterial horizontal transmission between individuals.</p>","PeriodicalId":20189,"journal":{"name":"PLoS ONE","volume":"20 8","pages":"e0329457"},"PeriodicalIF":2.6,"publicationDate":"2025-08-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144765304","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"综合性期刊","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"The role of music in ADHD: A multi-dimensional computational and theoretical analysis.","authors":"Krishnashree Achuthan, Sugandh Khobragade","doi":"10.1371/journal.pone.0324369","DOIUrl":"https://doi.org/10.1371/journal.pone.0324369","url":null,"abstract":"<p><p>Attention-Deficit Hyperactivity Disorder (ADHD), a neurodevelopmental disorder affecting children and adults worldwide, has seen a significant rise in diagnoses and medication prescriptions in recent decades. This trend has emphasized the need for non-pharmacological interventions such as music to aid ADHD management. This study explores the musical experiences of individuals with ADHD through a comprehensive analysis of user-generated content from the Reddit r/ADHD community between 2014-2024. Advanced computational techniques, including large language models such as Gemini 1.5 Pro and LLAMA 3.1 were employed for data extraction and categorization. Additionally, APIs from digital streaming platforms were utilized to analyze musical characteristics and lyrical content of 9,215 tracks across three distinct categories: focus music, stuck songs, and general purpose. Insights from selective attention, emotion arousal and mood congruence theories were used to interpret the findings. Statistical analysis revealed significant variations in musical characteristics, with instrumentalness showing the largest effect size across contexts, suggesting unique musical preferences among individuals with ADHD. Correlation analyses uncovered complex interrelationships between musical attributes, particularly in focus music, where energy, speechiness, and instrumental characteristics displayed distinctive patterns. The sentiment and popularity analysis of lyrics further illuminated the emotional landscape of music in ADHD experiences, revealing a strategic approach to musical selection as a potential cognitive and emotional self-regulation mechanism.</p>","PeriodicalId":20189,"journal":{"name":"PLoS ONE","volume":"20 8","pages":"e0324369"},"PeriodicalIF":2.6,"publicationDate":"2025-08-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144765306","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"综合性期刊","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Adopting Soft Logic to enhance an Adizes tool: A comprehensive approach to represent the evaluation of management styles.","authors":"Sigal Kordova, Ron S Hirschprung","doi":"10.1371/journal.pone.0327672","DOIUrl":"https://doi.org/10.1371/journal.pone.0327672","url":null,"abstract":"<p><p>Management skills assessment has become increasingly complex in today's digital age, as these skills are multi-dimensional and require a nuanced approach. Beyond evaluating each dimension independently, it is crucial to consider the tension and balance between them, as they often exist in inverse proportions. To address this complexity, this study introduces a methodology based on Soft Logic, a mathematical theory designed to represent realities that are not clear-cut, such as conflicting traits. This approach is particularly suited to the assessment of managerial skills. The research focuses on the Adizes Management Style Questionnaire, a widely recognized tool that evaluates four distinct managerial styles: Producer, Administrator, Entrepreneur, and Integrator. Unlike traditional assessments that focus on isolated behaviors, the proposed method highlights the dynamic interplay between these styles. By incorporating Soft Logic, the framework provides a more flexible and comprehensive evaluation, capturing both dominant traits and the tensions between them. This methodology was tested in an empirical study with 40 participants and offers organizations deeper insights into leadership dynamics, aiding in recruitment, leadership development, and team composition. Although developed with the Adizes tool, the methodology can be adapted to other managerial assessment tools and potentially extended to other multi-dimensional domains.</p>","PeriodicalId":20189,"journal":{"name":"PLoS ONE","volume":"20 8","pages":"e0327672"},"PeriodicalIF":2.6,"publicationDate":"2025-08-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144765204","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"综合性期刊","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Analysis and comparison of the bacterial σ54 regulon: Evidence of phylogenetic trends in gene regulation.","authors":"Maricela Carrera-Reyna, Edna Cruz-Flores, Enrique Merino","doi":"10.1371/journal.pone.0327805","DOIUrl":"https://doi.org/10.1371/journal.pone.0327805","url":null,"abstract":"<p><p>While the role of σ54 in regulating genes involved in nitrogen metabolism, flagellar biosynthesis, and stress responses in Pseudomonadota is well established, its involvement in regulating alternative metabolic pathways and cellular processes in other phyla has been less explored. By employing position-specific scoring matrices (PSSMs) to identify promoter sequences regulated by the σ54 factor, we successfully predicted genes under its control across 33 taxonomic classes spanning 16 distinct phyla. For the first time, we conducted a comprehensive statistical assessment of σ54 regulation across major bacterial phylogenetic groups. Our findings provide an extensive perspective on the regulatory role of σ54 beyond nitrogen metabolism and reveal the different trends in which metabolic and biological processes can be regulated by this sigma factor depending on the phylogenetic group. The main findings of our study are available on the aRpoNDB webpage (https://biocomputo.ibt.unam.mx/arpondb/).</p>","PeriodicalId":20189,"journal":{"name":"PLoS ONE","volume":"20 8","pages":"e0327805"},"PeriodicalIF":2.6,"publicationDate":"2025-08-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144765208","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"综合性期刊","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}