生物学最新文献

{"title":"Prp16 enables efficient splicing of introns with diverse exonic consensus elements in the short-intron rich <i>Cryptococcus neoformans</i> transcriptome.","authors":"Manendra Singh Negi, Vishnu Priya Krishnan, Niharika Saraf, Usha Vijayraghavan","doi":"10.1080/15476286.2025.2477844","DOIUrl":"10.1080/15476286.2025.2477844","url":null,"abstract":"<p><p>DEAH box splicing helicase Prp16 in budding yeast governs spliceosomal remodelling from the branching conformation (C complex) to the exon ligation conformation (C* complex). In this study, we examined the genome-wide functions of Prp16 in the short intron-rich genome of the basidiomycete yeast <i>Cryptococcus neoformans</i>. The presence of multiple introns per transcript with intronic features that are more similar to those of higher eukaryotes makes it a promising model for studying spliceosomal splicing. Using a promoter-shutdown conditional Prp16 knockdown strain, we uncovered genome-wide but substrate-specific roles in <i>C. neoformans</i> splicing. The splicing functions of Prp16 are dependent on helicase motifs I and II, which are conserved motifs for helicase activity. A small subset of introns spliced independent of Prp16 activity was investigated to discover that exonic sequences at the 5' splice site (5'SS) and 3' splice site (3'SS) with stronger affinity for U5 loop 1 are a common feature in these introns. Furthermore, short (60-100nts) and ultrashort introns (<60nts) prevalent in the <i>C. neoformans</i> transcriptome were more sensitive to Prp16 knockdown than longer introns, indicating that Prp16 is required for the efficient splicing of short and ultrashort introns. We propose that stronger U5 snRNA-pre-mRNA interactions enable efficient transition of the spliceosome from the first to the second catalytic confirmation in Prp16 knockdown, particularly for short introns and introns with suboptimal features. This study provides insights into fine-tuning spliceosomal helicase function with variations in <i>cis-</i>element features.</p>","PeriodicalId":21351,"journal":{"name":"RNA Biology","volume":" ","pages":"1-14"},"PeriodicalIF":3.6,"publicationDate":"2025-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11913375/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143597670","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Involvement of oxidative stress in post-acute sequelae of COVID-19: clinical implications.","authors":"Paola Mayara Valente Coronel, Denise Caroline Luiz Soares Basilio, Isabelly Teixeira Espinoça, Kamylla Fernanda Souza de Souza, Nathalia Miranda Campos, Rafael Seiji Nakano Ota, Edgar Julian Paredes-Gamero, Danilo Wilhelm Filho, Ana Rita Coimbra Motta-Castro, Renata Trentin Perdomo, Eduardo Benedetti Parisotto","doi":"10.1080/13510002.2025.2471738","DOIUrl":"10.1080/13510002.2025.2471738","url":null,"abstract":"<p><p>Oxidative stress (OS) plays a key role in the pathophysiology of COVID-19 and may be associated with sequelae after severe SARS-CoV-2 infection. This study evaluated OS and inflammation biomarkers in blood from individuals with post-acute sequelae of COVID-19 (PASC). 64 male and female participants were distributed into three groups: healthy individuals (<i>n</i> = 20), acute COVID-19 patients (symptoms for <3 weeks, <i>n</i> = 15), and PASC patients (symptoms for >12 weeks, <i>n</i> = 29). Analyses included inflammatory cytokines, myeloperoxidase (MPO) activity, and OS markers, such as superoxide dismutase (SOD), catalase (CAT), glutathione <i>S</i>-transferase (GST), gamma-glutamyl transferase (GGT), reduced glutathione (GSH), uric acid (UA), thiobarbituric acid reactive substances (TBARS), and protein carbonyls (PC). Individuals with PASC showed increased IL-6 and IL-8. Both COVID-19 groups exhibited decreased SOD and CAT. GST decreased only in the acute group. Elevated GGT and GSH were found in the PASC group. High UA levels were observed in PASC individuals. There were no changes in TBARS values ⁣⁣in the PASC group. However, PC concentrations were elevated only in this group. Correlations were identified between inflammatory markers and OS parameters. These findings suggest that individuals with PASC pronounced OS, which potentially exacerbates disease complications. Monitoring OS biomarkers could aid in patient prognosis and management.</p>","PeriodicalId":21096,"journal":{"name":"Redox Report","volume":"30 1","pages":"2471738"},"PeriodicalIF":5.2,"publicationDate":"2025-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11878172/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143543369","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Statement of Retraction: Extracellular vesicles derived from HBMSCs improved myocardial infarction through inhibiting zinc finger antisense 1 and activating Akt/Nrf2/HO-1 pathway.","authors":"","doi":"10.1080/21655979.2025.2491942","DOIUrl":"https://doi.org/10.1080/21655979.2025.2491942","url":null,"abstract":"","PeriodicalId":8919,"journal":{"name":"Bioengineered","volume":"16 1","pages":"2491942"},"PeriodicalIF":4.2,"publicationDate":"2025-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12026251/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143966608","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Modelling and analysis of an epidemic model with awareness caused by deaths due to fear.","authors":"Ling Xue, Junqi Huo, Yuxin Zhang","doi":"10.1080/17513758.2025.2458890","DOIUrl":"10.1080/17513758.2025.2458890","url":null,"abstract":"<p><p>In this paper, we establish a compartmental model in which the transmission rate is associated with the fear of being infected by COVID-19. We provide a detailed analysis of the epidemic model and established results for the existence of a positively invariant set. The expression of the basic reproduction number <math><msub><mi>R</mi><mn>0</mn></msub></math> is characterized. It is shown that the disease-free equilibrium (DFE) is globally asymptotically stable if <math><msub><mi>R</mi><mn>0</mn></msub><mo><</mo><mn>1</mn></math>, and the system exhibits a forward bifurcation if <math><msub><mi>R</mi><mn>0</mn></msub><mo>=</mo><mn>1</mn></math>. When <math><msub><mi>R</mi><mn>0</mn></msub><mo>></mo><mn>1</mn></math>, the system is uniformly persistent, the DFE is unstable and there exists a unique and globally asymptotic stable endemic equilibrium (EE). We fit unknown parameters using the reported data in Canada from September 1 to October 10, 2021, and carry out sensitivity analysis. The quantitative analysis of the model with awareness demonstrates the significance of reducing the transmission rate and enhancing public protective awareness.</p>","PeriodicalId":48809,"journal":{"name":"Journal of Biological Dynamics","volume":"19 1","pages":"2458890"},"PeriodicalIF":1.8,"publicationDate":"2025-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143069004","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"数学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Dynamical analysis of a stochastic prey-predator model with fear effect and feedback control.","authors":"Yan Zhang, Feng Lai, Shujing Gao, Yang Liu, Shuixian Yan","doi":"10.1080/17513758.2025.2479461","DOIUrl":"10.1080/17513758.2025.2479461","url":null,"abstract":"<p><p>In this work, the intricacies and complexities of dynamical properties are extensively studied for the proposed deterministic and stochastic prey-predator models. The influence of fear effects, prey refuge and feedback control are considered and thorough theoretical research is conducted on the systems. It commences by establishing the global stability and uniqueness of the positive equilibrium of the deterministic model. Then for the stochastic system, the existence, uniqueness and boundedness of a global positive solution are analysed by constructing appropriate Lyapunov functions. Sufficient conditions are established for the extinction and persistence of the stochastic model. It can be observed that both the fear effect and prey refuge have a greatly impact on the dynamics of system. Intermediate values of feedback control intensity may be the most beneficial to species coexistence. It provides new insights into the sustainability of ecosystems.</p>","PeriodicalId":48809,"journal":{"name":"Journal of Biological Dynamics","volume":"19 1","pages":"2479461"},"PeriodicalIF":1.8,"publicationDate":"2025-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143651600","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"数学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"The oncogenic microRNA miR-222 promotes human LINE-1 retrotransposition.","authors":"Tomer Friehmann, Yamama Abu Mohsen, Yehuda Schlesinger, Lucy Ghantous, Lika Gamaev, Chavah Landau Zenilman, Avi Harazi, Eithan Galun, Daniel S Goldenberg","doi":"10.1080/15476286.2025.2511318","DOIUrl":"10.1080/15476286.2025.2511318","url":null,"abstract":"<p><p>The Long Interspersed Element-1 (LINE-1) contributes significantly to carcinogenesis and to tumour heterogeneity in many cancer types, including hepatocellular carcinoma (HCC), by its autonomous retrotransposition (RTP) and by its ability to retrotranspose some non-autonomous transposable elements. Previously, multiple proteins and a few microRNAs (miRs) were described as regulators of LINE-1 RTP. Here, we demonstrate that miR-222, which is oncogenic in HCC, promotes LINE-1 RTP in human HCC and some other cell lines <i>in vitro</i>, and that both miR-222-3p and miR-222-5p activate LINE-1 RTP in a cell-type specific manner. We generated miR-222-knockout mutants of the Huh7 and FLC4 hCC cell lines, and performed RNA-seq analysis of Huh7/miR-222-knockout cells and global proteomics analysis of both Huh7 and FLC4 miR-222-knockout mutants. We demonstrate that miR-222 decreases let-7c expression in both Huh7 and FLC4 cells, and that this decrease contributes to promotion of LINE-1 RTP by miR-222 in Huh7 cells.</p>","PeriodicalId":21351,"journal":{"name":"RNA Biology","volume":" ","pages":"1-15"},"PeriodicalIF":3.6,"publicationDate":"2025-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12143727/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144151352","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Deciphering the multifaceted role of double-stranded RNA sensor protein kinase R: pathophysiological function beyond the antiviral response.","authors":"Jiyoon Chung, Yerim Lee, Jimin Yoon, Yoosik Kim","doi":"10.1080/15476286.2025.2512610","DOIUrl":"10.1080/15476286.2025.2512610","url":null,"abstract":"<p><p>Protein kinase R (PKR) is a serine/threonine kinase that recognizes double-stranded RNAs (dsRNAs) to initiate innate immune signalling during viral infection. PKR dimerizes on long dsRNAs and undergoes autophosphorylation. Phosphorylated/Activated PKR then catalyses the phosphorylation of numerous substrates to control global translation, inflammatory response, and cell signalling pathways. While primarily known for its antiviral role, emerging evidence suggests that PKR can play multifaceted roles in uninfected cells by interacting with cellular dsRNAs and protein regulators. The misactivation of PKR in uninfected cells is associated with many degenerative and inflammatory diseases. Even in healthy cells, PKR can affect gene expression by controlling mRNA splicing and gene-specific translation under stress. In addition, PKR can modulate cell cycle progression and promote cellular differentiation in several tissue types. This review explores PKR function in various pathological and physiological contexts in the absence of viral stimuli. By elucidating these diverse functions, we aim to highlight the perspectives in cellular dsRNA research and the therapeutic implications of targeting PKR, stimulating further research into this versatile and essential RNA-dependent kinase.</p>","PeriodicalId":21351,"journal":{"name":"RNA Biology","volume":"22 1","pages":"1-14"},"PeriodicalIF":3.6,"publicationDate":"2025-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12128661/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144187811","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Mathematical modelling and optimal control of malaria transmission with antimalarial drug and insecticide resistance.","authors":"Gasper G Mwanga","doi":"10.1080/17513758.2025.2522345","DOIUrl":"https://doi.org/10.1080/17513758.2025.2522345","url":null,"abstract":"<p><p>This study presents a mathematical model to explore malaria transmission dynamics in the presence of antimalarial drug-resistant parasites and insecticide-resistant mosquitoes. The analytical findings demonstrate a stable disease-free equilibrium when the effective reproduction number is below one. For single-strain malaria infections, the endemic equilibrium may exhibit one, two or no solutions. The model is extended to incorporate three time-dependent controls: long-lasting insecticidal nets, antimalarial treatment and mosquito adulticides. Simulation results indicate that interventions excluding drug-resistant parasites and insecticide-resistant mosquitoes are ineffective. The most effective strategies combine insecticides targeting all vectors with treatments for all malaria cases, regardless of resistance. Efficiency analysis suggests implementing all three controls at <math><mo>≥</mo><mn>80</mn><mi>%</mi></math> efficacy for the maximum impact, while assessments of cost-effectiveness highlight the combination of long-lasting insecticidal nets and antimalarial treatment as a practical option in resource-constrained settings. Nonetheless, integrating all three measures is recommended for substantial malaria transmission reduction.</p>","PeriodicalId":48809,"journal":{"name":"Journal of Biological Dynamics","volume":"19 1","pages":"2522345"},"PeriodicalIF":1.8,"publicationDate":"2025-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144486737","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"数学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Fractionation of waste-derived volatile fatty acids by multi-stage adsorption using activated charcoal and Diaion HP-20 resin.","authors":"Negar Basereh, Steven Wainaina, Amir Mahboubi, Mohammad J Taherzadeh","doi":"10.1080/21655979.2025.2458366","DOIUrl":"10.1080/21655979.2025.2458366","url":null,"abstract":"<p><p>Substituting waste-derived Volatile Fatty Acids (VFAs) with their conventionally applied fossil-derived counterparts in a spectrum of industrial applications necessitates its proper fractionation into individual acids. This study explored a multi-stage batch adsorption approach for fractionating acidogenic fermentation VFAs effluents from food waste (FW) and chicken manure (CKM) using Diaion HP-20 and activated charcoal. Initial screening at different washing conditions and pH (3.5 and 6.5) revealed the unwashed granular-activated charcoal (GAC-Unwashed) and milli-Q water-washed Diaion (DI-MQ Washed) as the most promising candidates for VFA fractionation of a synthetic VFA mixture at 4 gL^-1. At pH 3.5 (<math><mo><</mo><mi>p</mi><mrow><msub><mi>K</mi><mi>a</mi></msub></mrow></math>), GAC-Unwashed adsorbed 2-6 carbon atom VFAs completely, while DI-MQ Washed exhibited minimal adsorption of acetic acid (AA) (8%), favoring caproic (CA) and valeric acids (VA) (<math><mo>></mo></math>97%). While at pH 6.5 <math><mo>(</mo><mo>></mo><mi>p</mi><mrow><msub><mi>K</mi><mi>a</mi></msub></mrow></math>), GAC-Unwashed selectively targeted VA (79%) and CA (100%). Fractionating VFAs from FW and CKM were conducted in a two-stage adsorption process with optimal results being achieved using GAC-Unwashed at FW initial pH (5.3) and DI-MQ Washed at pH below CKM <math><mi>p</mi><mrow><msub><mi>K</mi><mi>a</mi></msub></mrow></math> (3.5), respectively. The first adsorption stage primarily adsorbed higher molecular weight (MW) VFAs (FW:99.1% CA, CKM:72.9% butyric acid (BA)) with a minor quantity of lower ones (FW:56.5% BA, CKM:29.3% propionic acid (PA)), leaving AA intact. Subsequent stages aimed to isolate AA by adsorbing the remaining low MW VFA (FW:58.9% BA, CKM:27.8% PA, 70% BA) other than AA, indicating effluent fractionation while preserving and purifying AA. Applied selective multi-stage adsorption approach offers a promising method to broaden waste-derived VFA applications.</p>","PeriodicalId":8919,"journal":{"name":"Bioengineered","volume":"16 1","pages":"2458366"},"PeriodicalIF":4.2,"publicationDate":"2025-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11801348/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143188005","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Anti-obese potentiality of marine Topse (<i>Polynemus paradiseus</i>) fish oil by inhibiting the expression of SREBP-1c & promoting β-oxidation of fat through upregulating PPAR-α.","authors":"Riya Kar, Pipika Das, Titli Panchali, Ananya Dutta, Manisha Phoujdar, Kuntal Ghosh, Shrabani Pradhan","doi":"10.1080/21623945.2025.2524640","DOIUrl":"10.1080/21623945.2025.2524640","url":null,"abstract":"<p><p>Considering the adverse effects of marketed drugs, we isolated and analysed topse fish oil (FO) in this study for the first time and examined its effect on obesity. Topse, scientifically known as <i>Polynemus paradiseus</i>, is a common fish species found in the maritime environment of the West Bengal region. To explore the role of marine P. paradiseus FO in alleviating obesity-related metabolic disorders in vivo model. Twenty-four male BALB/c mice with a standard body weight of 18.2 ± 2.1 g were taken and randomly divided into four groups: control group (C), normal chow feeding; obese control (OC), high fat diet (HFD) feeding; Treatment I (T-I) and Treatment II (T-II) group received 200 mg and 400 mg crude oil/kg body weight/day by gavage along with HFD. Here, we examined the effects of P. paradiseus oil on white adipose tissue (WAT) weight, lipid profiles, blood glucose, and adipokine expression levels in the OC group compared to the treated groups to evaluate the anti-obesity effects of FO. Compared to the HFD-induced OC group, the treated obese mice group (T-I and T-II) showed a significant reduction in body weight, Body Mass Index (BMI), and serum lipid profiles following the application of FO. The FO-treated HFD-induced obese mice group showed a moderate reduction in obesity and inflammatory-related adipocytokines compared to the OC group. Topse FO was enhanced with a large amount of essential fatty acids (FAs) and it might be administered as a dietary supplement to prevent obesity.</p>","PeriodicalId":7226,"journal":{"name":"Adipocyte","volume":"14 1","pages":"2524640"},"PeriodicalIF":3.5,"publicationDate":"2025-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12218541/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144525975","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}