生物学最新文献

{"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":"Nhe1 is required for directional sensing in vegetative <i>Dictyostelium</i> cell migration.","authors":"Uri Han, Nara Han, Taeck Joong Jeon","doi":"10.1080/19336918.2025.2514374","DOIUrl":"10.1080/19336918.2025.2514374","url":null,"abstract":"<p><p>Na+/H+ exchanger 1 (Nhe1) is a crucial regulator of pH homeostasis and the present study demonstrates that Nhe1 is required for directional sensing in vegetative <i>Dictyostelium</i> cell migration. <i>nhe1</i> null cells exhibited severe defects in directional sensing and migration in response to folate gradients and applied electric fields.Specifically, <i>nhe1</i> null cells failed to exhibit proper translocation of phosphatidylinositol (3,4,5)-trisphosphate (PIP3) to the cell cortex and showed abnormal intracellular calcium signaling upon folate stimulation. Additionally, cells lacking Nhe1 exhibited a reduced capacity to engulf bacteria and latex beads. In contrast, <i>nhe1</i> null cells in the developed stage displayed a defect in cAMP-directed chemotaxis, but normal translocation kinetics of PIP3 to the cell cortex upon cAMP stimulation.</p>","PeriodicalId":9680,"journal":{"name":"Cell Adhesion & Migration","volume":"19 1","pages":"2514374"},"PeriodicalIF":3.3,"publicationDate":"2025-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12143694/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144215029","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":"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}

{"title":"Computational Systems Biology Approaches to Cellular Aging - Integrating Network Maps and Dynamical Models.","authors":"Hetian Su, Nan Hao","doi":"10.1002/qub2.70007","DOIUrl":"10.1002/qub2.70007","url":null,"abstract":"<p><p>Cellular aging is a multifaceted, complex process. Many genes and factors have been identified that regulate cellular aging. However, how these genes and factors interact with one another and how these interactions drive the aging processes in single cells remain largely unclear. Recently, computational systems biology has demonstrated its potential to empower aging research by providing quantitative descriptions and explanations of complex aging phenotypes, mechanistic insights into the emergent dynamic properties of regulatory networks, and testable predictions that can guide the design of new experiments and interventional strategies. In general, current complex systems approaches can be categorized into two types: (1) network maps that depict the topologies of large-scale molecular networks without detailed characterization of the dynamics of individual components and (2) dynamical models that describe the temporal behavior in a particular set of interacting factors. In this review, we discuss examples that showcase the application of these approaches to cellular aging, with a specific focus on the progress in quantifying and modeling the replicative aging of budding yeast <i>Saccharomyces cerevisiae</i>. We further propose potential strategies for integrating network maps and dynamical models toward a more comprehensive, mechanistic, and predictive understanding of cellular aging. Finally, we outline directions and questions in aging research where systems-level approaches may be especially powerful.</p>","PeriodicalId":45660,"journal":{"name":"Quantitative Biology","volume":"13 4","pages":""},"PeriodicalIF":0.6,"publicationDate":"2025-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12277577/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144691910","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":"ACSF2-PGK1 interaction promotes ferroptosis in renal tubular epithelial cells of diabetic nephropathy by regulating Keap1/Nrf2 signaling.","authors":"Xinran Liu, Chaoyi Chen, Sai Zhu, Xiaomei Luo, Li Gao, Ziyun Hu, Yu Ma, Ling Jiang, Yonggui Wu","doi":"10.1080/13510002.2025.2529618","DOIUrl":"10.1080/13510002.2025.2529618","url":null,"abstract":"<p><strong>Objectives: </strong>Recent studies have highlighted the strong association between kidney disease and ferroptosis. However, the role of ferroptosis in diabetic nephropathy (DN) remains unclear. This study aimed to determine the role of ACSF2 in renal tubule injury in DN and its underlying mechanisms.</p><p><strong>Methods: </strong>We established diabetic kidney disease models both in vivo, using db/db mice, and in vitro, using high glucose induced HK-2 cells.</p><p><strong>Results: </strong>A significant upregulation of ACSF2 was observed in the renal tubules of patients with DN and db/db mice. ACSF2 expression correlated with renal tubule injury and renal function, indicating its potential as an independent biomarker in patients with DN. Silencing ACSF2 alleviated high glucose-induced renal tubular epithelial cell injury by reducing oxidative stress-induced ferroptosis in vivo and in vitro. Mechanistically, liquid chromatography-tandem mass spectrometry and co-immunoprecipitation demonstrated that ACSF2 specifically binds to PGK1. ACSF2 affected Keap1 dimerization by regulating PGK1 phosphorylation at serine 203, which subsequently affects the levels of NRF2. Moreover, PGK1 stabilizes ACSF2 via deubiquitination, establishing a positive feedback loop. The results provide evidence that the interaction between ACSF2 and PGK1 promotes DN progression by regulating oxidative stress-induced ferroptosis.</p><p><strong>Discussion: </strong>ACSF2 participates in crosstalk between oxidative stress and ferroptosis. This could be a potential therapeutic target for DN.</p>","PeriodicalId":21096,"journal":{"name":"Redox Report","volume":"30 1","pages":"2529618"},"PeriodicalIF":5.2,"publicationDate":"2025-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12269058/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144650221","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":"CpG island demethylation and recruitment of SP1 to the promoter region regulates human thymic stromal lymphopoietin expression.","authors":"Krishna Priya Ganti, Milan Surjit","doi":"10.1080/15592294.2025.2529358","DOIUrl":"10.1080/15592294.2025.2529358","url":null,"abstract":"<p><p>Thymic Stromal Lymphopoietin (TSLP), an immunomodulatory cytokine, plays a pivotal role in the development and progression of atopic and allergic diseases. Atopy follows familial inheritance, and genome-wide studies have shown association of atopy with TSLP polymorphisms. Here, we analysed the conserved transcriptional regulatory elements in the human TSLP promoter, which revealed the presence of three CpG islands. Demethylation of the CpG island using 5-azacytidine or siRNA-mediated knockdown of DNA methyl transferases significantly upregulated TSLP expression. Sequence analysis revealed the presence of two overlapping SP1 transcription factor DNA-binding sites (DBSs), between -1494 and -1510 nucleotides on the human TSLP promoter. Further experiments showed that demethylation of the CpG island enables the binding of SP1 to its cognate DBS present on the TSLP promoter, resulting in its transcriptional activation. Moreover, retinoic acid-induced transcription of human TSLP was associated with CpG island demethylation and SP1 binding to the TSLP promoter. These findings unravel a distinct mechanism of transcriptional regulation of the human TSLP gene and suggest possible epigenetic regulation of TSLP expression in modulating atopic and allergic disease severity in different individuals.</p>","PeriodicalId":11767,"journal":{"name":"Epigenetics","volume":"20 1","pages":"2529358"},"PeriodicalIF":2.9,"publicationDate":"2025-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12269656/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144625618","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}