生物学最新文献

{"title":"High-throughput measurement of adipocyte size with open-source software using whole-slide adipose tissue images.","authors":"Alan Ramalho, Marie-Frédérique Gauthier, Ina Maltais-Payette, Giada Ostinelli, Frédéric Hould, Laurent Biertho, André Tchernof","doi":"10.1080/21623945.2025.2528437","DOIUrl":"10.1080/21623945.2025.2528437","url":null,"abstract":"<p><p>The aim of this study was to create and validate a high-throughput method based on open-source software for the measurement of adipocyte diameters in white adipose tissue histological sections. Human omental and subcutaneous adipose tissue samples collected during bariatric surgery were used to prepare haematoxylin and eosin-stained histological slides. Adipocyte diameters were measured both manually and with an automated procedure created using ImageJ. Comparative analysis of our automated method with the manual measurement and associations of the mean adipocyte diameters with cardiometabolic markers were used to validate our method. A total of 377 adipose samples (190 participants) were included in the analysis. Pearson correlation of mean adipocyte diameters showed a strong linear relationship between methods (<i>r</i> = 0.87, <i>p</i> < 0.0001). Omental adipocyte diameters of both methods were significantly associated with the same markers of cardiometabolic risk (fasting concentrations of TG, HDL-Chol, homoeostasis model assessment of insulin resistance, and visceral adiposity index values) with no significant differences between methods. There were also no significant differences between the manual and automated method regarding the correlations between mean subcutaneous adipocyte diameters and anthropometric or metabolic markers. In conclusion, we have created and validated a rapid automated method to measure adipocyte diameters from whole-slide adipose tissue images.</p>","PeriodicalId":7226,"journal":{"name":"Adipocyte","volume":"14 1","pages":"2528437"},"PeriodicalIF":3.1,"publicationDate":"2025-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12309532/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144726360","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":"Predicting the evolutionary and epidemiological dynamics of SARS-CoV-2 in South Africa.","authors":"Chaojing Ma, Yantao Yang, Jian Zu","doi":"10.1080/21505594.2025.2520335","DOIUrl":"10.1080/21505594.2025.2520335","url":null,"abstract":"<p><p>Since the outbreak of coronavirus disease 2019 (COVID-19), the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has continuously mutated and evolved, causing several waves of infection. Predicting the evolutionary and epidemiological dynamics of SARS-CoV-2 remains a challenge. This study combines the epidemic data of different variants of SARS-CoV-2 in South Africa to predict their evolutionary and epidemiological dynamics. Based on the susceptible-infectious-recovered-susceptible (SIRS) transmission dynamics, we consider the transmission rate as an evolutionary trait and the disease-deduced mortality and recovery rates as trade-off functions of the trait. Using the adaptive dynamics method, combined with the epidemic data of the five most recent variants in South Africa, we find that South Africa will be continuously invaded and infected by the new mutant strain with a higher transmission rate. In addition, we find that changing the recovery rate by enhancing treatment, for example, will alter the trade-off function and thereby affect the evolutionary dynamics of SARS-CoV-2, which may evolve into a continuously stable strategy. This study is the first to use evolutionary dynamics theory to predict the future evolutionary and epidemiological dynamics of SARS-CoV-2, which is helpful for the government to predict the epidemic dynamics of COVID-19 and to take effective measures in advance, and it is proposed that advancing treatment time and improving treatment efficiency will contribute to disease control.</p>","PeriodicalId":23747,"journal":{"name":"Virulence","volume":" ","pages":"2520335"},"PeriodicalIF":5.4,"publicationDate":"2025-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12323434/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144302989","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Extracellular vesicle-derived MicroRNAs as potential therapies for spinal cord and peripheral nerve injuries.","authors":"Young-Ju Lim, Min-Soo Seo, Wook-Tae Park, Sangbum Park, Gun Woo Lee","doi":"10.1080/15476286.2025.2512618","DOIUrl":"10.1080/15476286.2025.2512618","url":null,"abstract":"<p><p>Complete nerve regeneration is limited in current therapeutic approaches for spinal cord injuries (SCIs) and peripheral nerve injuries (PNIs). Extracellular vesicles (EVs) and microRNAs (miRNAs) play a pivotal role in intercellular communication by transporting various biomolecules, including miRNAs, to the recipient cells. Thus, they are promising targets for novel neural regeneration drugs. This comprehensive study examined the roles of EV-derived miRNAs in facilitating neural rejuvenation after SCI and PNI. It also explored the mechanisms by which they augment neuroprotection and promote cell viability. It also discusses their translational potential for treating nerve injury and evaluates their potential impact on advancements in nerve resurrection and prospective research in regenerative medicine. The findings may provide effective treatments and improve outcomes, as well as contribute to addressing the direction for the next studies, for the pathologies of SCI and PNI.</p>","PeriodicalId":21351,"journal":{"name":"RNA Biology","volume":"22 1","pages":"1-9"},"PeriodicalIF":3.6,"publicationDate":"2025-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12128652/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144192160","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":"Differential methylation patterns in cord blood associated with prenatal exposure to neighborhood crime: an epigenome-wide association study and regional analysis.","authors":"Chantel L Martin, Jiawen Chen, Alena S D'Alessio, Cavin K Ward-Caviness, Ai Ye, Evans K Lodge, Lea Ghastine, Radhika Dhingra, Dereje D Jima, Susan K Murphy, Cathrine Hoyo","doi":"10.1080/15592294.2025.2511553","DOIUrl":"10.1080/15592294.2025.2511553","url":null,"abstract":"<p><p>Exposure to prenatal social stressors during pregnancy is associated with adverse birth outcomes and has been linked to epigenetic changes in DNA methylation (DNAm); however, less understood is the effect of neighborhood-level stressors like crime during pregnancy on offspring DNAm. Using data from the Newborn Epigenetic Study, we conducted epigenome-wide and regional analyses of the association between exposure to neighborhood crime and DNAm in offspring cord blood using Illumina's HumanMethylation450k BeadChip among 185 mother-offspring pairs. Prenatal exposure to neighborhood crime at the census block group level was mapped to participants' residential addresses during the gestational window from the date of last menstrual period to delivery. Models for the epigenome-wide and regional analyses were adjusted for maternal age, race/ethnicity, education, smoking, cell-type composition, and offspring sex. Genetic influence and gene expression enrichment were assessed using methylation quantitative trait loci (mQTLs) and expression quantitative trait methylation (eQTMs) analyses. Functional enrichment was determined using Gene Ontology and KEGG databases. We did not find evidence of epigenome-wide associations between prenatal neighborhood crime exposure and DNAm; however, we identified nine differentially methylated regions (DMRs) comprising 51 CpG sites associated with neighborhood crime. CpG sites within significant differentially methylated regions were associated with mQTLs at birth and eQTMs upon further examination. KEGG analysis identified a significant Th1 and Th2 cell differentiation pathway. Our results suggest potential links between prenatal neighborhood crime exposure and offspring DNAm; however, additional research is needed in larger cohorts across wider geographic areas to confirm our results.</p>","PeriodicalId":11767,"journal":{"name":"Epigenetics","volume":"20 1","pages":"2511553"},"PeriodicalIF":2.9,"publicationDate":"2025-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12153387/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144265735","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":"The hidden power of antisense long non-coding RNAs: a dive into a novel regulatory layer mediated by double-stranded RNA formation.","authors":"Jan-Philipp Lamping, Heike Krebber","doi":"10.1080/15476286.2025.2530797","DOIUrl":"10.1080/15476286.2025.2530797","url":null,"abstract":"<p><p>Over the past decade, non-coding RNAs (ncRNAs) have gained prominence in research due to their widespread presence in cells, yet their functions remain increasingly complex and less understood. Despite being initially deemed 'junk', many lncRNAs are now recognized as key regulators in cells and are often affected in disease contexts. Notably, numerous mRNAs have annotated antisense RNAs (asRNAs). Because asRNAs resemble the largest group of lncRNAs and were identified to serve a general function in <i>Saccharomyces cerevisiae</i>, they are the focus of this review. In <i>S. cerevisiae</i>, the absence of RNA interference (RNAi) enables unbiased study and allowed researchers to investigate their roles in gene regulation more directly with intriguing results, summarized here. Expression of asRNA leads to the formation of double-stranded RNAs (dsRNAs) with the regarding sense counterpart, resulting in enhanced gene expression through preferential nuclear export. Thus, these hidden leaders can boost gene expression and require future attention pivotal for elucidating their influence on biological processes and revealing disease mechanisms.</p>","PeriodicalId":21351,"journal":{"name":"RNA Biology","volume":" ","pages":"1-16"},"PeriodicalIF":3.6,"publicationDate":"2025-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12247107/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144592109","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":"Pathogenic mechanisms and molecular features of a novel UL2 gene-deficient duck enteritis virus endemic to China.","authors":"Dan Yin, Yuehua Gao, Mingqing Xu, Jianhua Wang, Xiaofei Song, Zhen Li, Jianyun Peng, Min Kang, Bai Wei, Chengdong Yu, Yingjuan Qian, Yong-Sam Jung, Feng Hu, Junfeng Lv, Zhuoming Qin, Yufeng Li","doi":"10.1080/21505594.2025.2547325","DOIUrl":"10.1080/21505594.2025.2547325","url":null,"abstract":"<p><p>Duck enteritis virus (DEV) was identified as the etiological agent responsible for an outbreak of morbidity and mortality in adult ducks on a farm in Jiangsu, China. Diagnostic approaches confirmed that the outbreak was caused by the highly pathogenic DEV-JS2024 isolate. The clinical progression of the disease, characterized by lethargy, anorexia, ocular discharge, and high mortality, was accompanied by extensive hemorrhagic lesions in critical organs such as the liver, spleen, lungs, and bursa of Fabricius, consistent with known signs of DEV infection. Genomic analysis of DEV-JS2024 revealed a 45% G+C content and 76 open reading frames. BLASTn analysis revealed that the genome of DEV-JS2024 shares the highest sequence similarity with the Chinese virulent strain CV and the DEV attenuated vaccine strain C-KCE in the database. These results indicate a close genetic relationship between DEV-JS2024 and both the virulent and attenuated strains, suggesting potential similarities in their genomic architecture. Comparative genomic analysis identified 28 nucleotide mutations, including 15 non-synonymous mutations potentially related to virulence factors. The study also highlighted the first reported 528 base pairs deletion in the <i>UL2</i> gene of a virulent strain, challenging its utility as a marker for distinguishing virulent from attenuated strains. Phylogenetic analysis suggested that DEV-JS2024 may result from recombination between the vaccine and virulent strains, further complicating our understanding of DEV pathogenicity. This study provides new insights into the molecular evolution of DEV and stresses the importance of continued genomic surveillance to enhance vaccine development and control measures for duck plague.</p>","PeriodicalId":23747,"journal":{"name":"Virulence","volume":" ","pages":"2547325"},"PeriodicalIF":5.4,"publicationDate":"2025-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12372499/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144838002","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Emergence and molecular evolution of carbapenem-resistant hypervirulent ST23 <i>Klebsiella pneumoniae</i>: The superbug phenomenon in China.","authors":"Tao Chen, Xueting Wang, Luying Xiong, Ping Shen, Yonghong Xiao","doi":"10.1080/21505594.2025.2545556","DOIUrl":"10.1080/21505594.2025.2545556","url":null,"abstract":"<p><p>This study aimed to investigate the molecular epidemiology of carbapenem-resistant hypervirulent <i>Klebsiella pneumoniae</i> (CR-hvKP) ST23 in China. We conducted comprehensive searches across five databases (PubMed, Web of Science, MEDLINE, CNKI, and Wanfang) spanning 1980-2024, identifying 30 eligible studies through rigorous screening. Our synthesis documents 120 ST23 CR-hvKP clinical isolates, including the earliest known case from Zhejiang in 2013 which harbored <i>bla</i>_KPC-2 alongside hallmark virulence loci (<i>rmpA</i>, <i>rmpA2</i>, <i>iroN</i>, <i>iucA</i>, and <i>pagO</i>). Epidemiological analysis of 119 isolates reveals geographic disparities: Hebei (25.2%) and Jiangxi (22.7%) are hotspots, while carbapenemase distribution exhibits a north-south divide (<i>bla</i>_NDM predominating in northern China versus <i>bla</i>_KPC in the south). Phylogenetic analysis of 584 global ST23 genomes suggests independent plasmid-mediated acquisition of carbapenemase genes, with evidence of clonal transmission both among humans and between humans and environmental niches. This review highlights the urgent need for surveillance to track CR-hvKP's evolving epidemiology, alongside interventions targeting plasmid-driven resistance spread.</p>","PeriodicalId":23747,"journal":{"name":"Virulence","volume":"16 1","pages":"2545556"},"PeriodicalIF":5.4,"publicationDate":"2025-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12351723/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144849240","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Global dynamics of respiratory process in a class of bacterial culture.","authors":"Jiazhou Wu, Fabao Gao","doi":"10.1080/17513758.2025.2528680","DOIUrl":"https://doi.org/10.1080/17513758.2025.2528680","url":null,"abstract":"<p><p>The global dynamic behavior of the respiration process in bacterial culture at different concentrations was comprehensively described using the qualitative theory of differential equations and symbolic calculation software.</p>","PeriodicalId":48809,"journal":{"name":"Journal of Biological Dynamics","volume":"19 1","pages":"2528680"},"PeriodicalIF":1.8,"publicationDate":"2025-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144568021","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":"<i>PIK3R1</i> and <i>G0S2</i> are human placenta-specific imprinted genes associated with germline-inherited maternal DNA methylation.","authors":"Dagne Daskeviciute, Becky Sainty, Louise Chappell-Maor, Caitlin Bone, Sarah Russell, Isabel Iglesias-Platas, Philippe Arnaud, Ana Monteagudo-Sánchez, Maxim V C Greenberg, Keran Chen, Africa Manerao-Azua, Guiomar Perez de Nanclares, Jon Lartey, David Monk","doi":"10.1080/15592294.2025.2523191","DOIUrl":"10.1080/15592294.2025.2523191","url":null,"abstract":"<p><p>Genomic imprinting is the parent-of-origin specific monoallelic expression of genes that result from complex epigenetic interactions. It is often achieved by monoallelic 5-methylcytosine, resulting in the formation of differentially methylated regions (DMRs). These show a bias towards oocyte-derived methylation and survive reprogramming in the pre-implantation embryo. Imprinting is widespread in the human placenta. We have recently performed whole-genome screens for novel imprinted placenta-specific germline DMRs (gDMRs) by comparing methylomes of gametes, blastocysts and various somatic tissues, including placenta. We observe that, unlike conventional imprinting, for which methylation at gDMRs is observed in all tissues, placenta-specific imprinting is associated with transient gDMRs, present only in the pre-implantation embryo and extra-embryonic lineages. To expand the list of <i>bona fide</i> imprinted genes subject to placenta-specific imprinting, we reinvestigated our list of candidate loci and characterized two novel imprinted genes, <i>PIK3R1</i> and <i>G0S2</i>, both of which display polymorphic imprinting. Interrogation of placenta single-cell RNA-seq datasets, as well as cell-type methylation profiles, revealed complex cell-type specificity. We further interrogated their methylation and expression in placental samples from complicated pregnancies, but failed to identify differences between intrauterine growth restricted or pre-eclamptic samples and controls, suggesting they are not involved in these conditions.</p>","PeriodicalId":11767,"journal":{"name":"Epigenetics","volume":"20 1","pages":"2523191"},"PeriodicalIF":2.9,"publicationDate":"2025-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12203861/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144495310","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":"<i>Staphylococcus aureus</i> β-hemolysin impairs oxygen transport without causing hemolysis.","authors":"Qi Li, Nan Chen, Chenghua Liu, Zhen Zhao, Minjun Huang, Jingjing Li, Guang Yang","doi":"10.1080/21505594.2025.2490208","DOIUrl":"10.1080/21505594.2025.2490208","url":null,"abstract":"<p><p><i>Staphylococcus aureus</i> (<i>S. aureus</i>) infection can lead to the occurrence of hypoxia, however, the underlying mechanisms have not been fully elucidated. β-hemolysin (Hlb) induced hemolysis of red blood cells (RBCs) requires a temperature transition from \"hot\" to \"cold,\" a phenomenon not observed under physiological conditions. In this study, we discovered that RBCs treated with Hlb exhibited a high level of intracellular Ca²⁺ and underwent a shape transformation from biconcave discoid to spherical, which was contingent upon the degradation of sphingomyelin of the cell membrane and led to impaired oxygen transport. The increase in intracellular Ca²⁺ levels induced by Hlb was dependent on the activation of the ion channel N-methyl-D-aspartate receptor. Furthermore, we found that Hlb-induced Ca²⁺ influx increased the cytoplasmic pH and subsequently attenuated the oxygen release from RBCs, which were also observed in both <i>hlb</i> transgenic mice and a murine model with <i>S. aureus</i> challenge. Our findings reveal a novel role for Hlb as sphingomyelinase in impairing RBC function under non-lytic conditions, shedding light on the mechanism behind hypoxia associated with <i>S. aureus</i> infection.</p>","PeriodicalId":23747,"journal":{"name":"Virulence","volume":"16 1","pages":"2490208"},"PeriodicalIF":5.4,"publicationDate":"2025-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11988224/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143999183","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}