生物学最新文献

{"title":"Balancing harm and harmony: Evolutionary dynamics between gut microbiota-derived flagellin and TLR5-mediated host immunity and metabolism.","authors":"Boram Seo, Mi Young Lim","doi":"10.1080/21505594.2025.2512035","DOIUrl":"10.1080/21505594.2025.2512035","url":null,"abstract":"<p><p>The gut microbiota maintains host health and shapes immune responses through intricate host-microbe interactions. Bacterial flagellin, a key microbe-associated molecular pattern, is recognized by Toll-like receptor 5 (TLR5) and NOD-like receptor family caspase activation and recruitment domain-containing 4 inflammasome. This dual recognition maintains the delicate balance between immune tolerance and activation, thereby influencing health and disease outcomes. Therefore, we explored the structural and functional evolution of bacterial flagellin to elucidate its role in innate and adaptive immune responses, along with its impact on metabolic processes, particularly via TLR5. In this review, we highlight the diagnostic and therapeutic potential of flagellin, including its application in vaccine development, cancer immunotherapy, and microbiome-based therapies. We integrated perspectives from structural biology, immunology, and microbiome research to elucidate the co-evolutionary dynamics between gut microbiota-derived flagellin and host immunity. Our interpretations provide a basis for the development of innovative strategies to improve health and disease management.</p>","PeriodicalId":23747,"journal":{"name":"Virulence","volume":"16 1","pages":"2512035"},"PeriodicalIF":5.5,"publicationDate":"2025-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12128667/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144188139","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":"A dual fluorescence channel RAA-based CRISPR-Cas12a/Cas13a system for highly sensitive detection of <i>Gyrovirus galga1</i> and <i>Gyrovirus homsa1</i>.","authors":"Dan Yu, Zhixun Xie, Yanfang Zhang, Zhiqin Xie, Qing Fan, Sisi Luo, Liji Xie, Meng Li, Tingting Zeng, Minxiu Zhang, Xiaofeng Li, You Wei, Aiqiong Wu, Lijun Wan","doi":"10.1080/21505594.2025.2521012","DOIUrl":"10.1080/21505594.2025.2521012","url":null,"abstract":"<p><p><i>Gyrovirus galga1</i> (GyG1) and <i>Gyrovirus homsa1</i> (GyH1) are the second and third most common gyroviruses identified, respectively, after chicken anaemia virus. They were first reported in 2011 and are currently prevalent worldwide. However, limited research on these pathogens and a lack of prevention and control strategies have necessitated the establishment of a rapid diagnostic technique to address new challenges in infectious diseases. Recombinase acid amplification (RAA) combined with CRISPR - Cas12a or CRISPR - Cas13a technology has major advantages for highly sensitive and rapid diagnosis. Specific targets can activate CRISPR-Cas trans-cleavage activity, resulting in non-specific cleavage of single-stranded DNA by the CRISPR - Cas12a complex and RNA cleavage by the CRISPR - Cas13a complex. In this study, for the first time, we combined RAA-based CRISPR - Cas12a and CRISPR - Cas13a systems for simultaneous differential diagnosis of GyG1 and GyH1 infection. The results showed that dual fluorescence channel RAA-based CRISPR - Cas12a/Cas13a technology could detect GyG1 and GyH1 within one hour, with a minimum detection limit of 1.5 copies of the target DNA standard/µL and no cross-reactivity with other avian pathogens. In addition, this method could be used for clinical detection, with the results exhibiting high consistency with those obtained by qPCR. These findings demonstrate that our RAA-based CRISPR - Cas12a/Cas13a dual-channel detection system can detect two different subtypes of gyrovirus in a sample with good specificity and high sensitivity, improving the detection efficiency and providing a new technique for the study of viral infection dynamics.</p>","PeriodicalId":23747,"journal":{"name":"Virulence","volume":"16 1","pages":"2521012"},"PeriodicalIF":5.5,"publicationDate":"2025-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144369303","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Plasmids of two novel incompatibility groups IncFII_pPROV114-NR and Inc_pCHS4.1-3 from <i>Providencia</i>.","authors":"Xiuhui Lu, Jiaqi He, Yali Zheng, Fangzhou Chen, Jing Luo, Kejiao Ma, Fan Yang, Peng Wang, Dongsheng Zhou, Bo Gao, Zhe Yin","doi":"10.1080/21505594.2025.2512034","DOIUrl":"10.1080/21505594.2025.2512034","url":null,"abstract":"<p><p>This study presents the genetic structure of two incompatibility (Inc) groups found in <i>Providencia</i>: the newly discovered IncFII_pPROV114-NR and the newly designated Inc_pCHS4.1-3. An extensive genomic comparison was performed on all 14 plasmids (three IncFII_pPROV114-NR plasmids and 11 Inc_pCHS4.1-3 plasmids) from <i>Providencia</i>, including 12 newly sequenced in this study and two from GenBank. Three IncFII_pPROV114-NR plasmids had similar conserved backbones but differed in accessory modules. The 11 Inc_pCHS4.1-3 plasmids fell into two groups according to differences in the conserved genes of the plasmid backbone. The accessory modules of 11 Inc_pCHS4.1-3 plasmids showed significant diversity, indicating numerous gene gains and losses, including in the Tn<i>1696-</i>related region, in Tn<i>7504</i>, in a 17.3-kb <i>sul2</i> region, and a 63.6-kb <i>bla</i>_NDM-1 region. A minimum of 45 obtained antimicrobial resistance genes (ARGs) were identified in 13 of the 14 plasmids, covering resistance to 14 classes of antimicrobials and heavy metals. Five new mobile genetic elements (MGEs) were identified, including In2168, In1790, Tn<i>7500</i>, Tn<i>7501</i>, and Tn<i>7502</i>. Additionally, three MGEs, Tn<i>7499</i>, Tn<i>7503</i>, and Tn<i>7504</i> were newly designated. These two Inc group plasmids integrate abundant accessory modules that allow them to accumulate and distribute ARGs and improve the survivability of <i>Providencia</i> under the pressure of drug selection.</p>","PeriodicalId":23747,"journal":{"name":"Virulence","volume":"16 1","pages":"2512034"},"PeriodicalIF":5.5,"publicationDate":"2025-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12184191/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144326998","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":"Melioidosis molecular diagnostics: An update.","authors":"Prachi Gangil, Manash K Paul, Prathyoosha B, Debadrita Mondal, Sneha Kumari, P R Prasad, Vandana K E, Bharti Bisht, Chiranjay Mukhopadhyay","doi":"10.1080/21505594.2025.2505698","DOIUrl":"10.1080/21505594.2025.2505698","url":null,"abstract":"<p><p>Melioidosis, a fatal tropical disease, presents a wide array of clinical manifestations, including abscesses, pneumonia, septic shock, bacteraemia, osteomyelitis, septic arthritis, and skin infection. The Centers for Disease Control and Prevention (CDC) has classified <i>Burkholderia pseudomallei</i> (<i>B. pseudomallei</i>), a gram-negative bacterium found in soil, as a Tier 1 select agent. Referred to as the \"great mimicker,\" this organism can infect several organs imitating the symptoms of different illnesses. According to worldwide data, there are around 165,000 cases and 89,000 deaths annually. Current diagnostic procedures rely primarily on culturing <i>B. pseudomallei</i>, are slow and have low sensitivity, resulting in delayed treatment and higher fatality rates. This review examines the substantial difficulties related to diagnosing melioidosis in response to the urgent need for precise and prompt diagnosis. We have summarized the results of diagnostic kits that are currently sold in the market and assessed the market for melioidosis diagnostic kits.</p>","PeriodicalId":23747,"journal":{"name":"Virulence","volume":"16 1","pages":"2505698"},"PeriodicalIF":5.5,"publicationDate":"2025-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12169043/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144295039","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":"<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":"Advancements in genetic engineering for enhanced Polyhydroxyalkanoates (PHA) production: a comprehensive review of metabolic pathway manipulation and gene deletion strategies.","authors":"Raghavendra Paduvari, Divyashree Mysore Somashekara","doi":"10.1080/21655979.2025.2458363","DOIUrl":"10.1080/21655979.2025.2458363","url":null,"abstract":"<p><p>Polyhydroxyalkanoates (PHA) are bioplastics produced by few bacteria as intracellular lipid inclusions under excess carbon source and nutrient-deprived conditions. These polymers are biodegradable and resemble petroleum-based plastics. The rising environmental concerns have increased the demand for PHA, but the low yield in wild-type bacterial strains limits large-scale production. An improvement in the PHA production can be achieved by genetically engineering the wild-type bacterial strains by removing competitive pathways that divert the metabolites away from PHA biosynthesis, cloning strong promotors to overexpress the genes involved in PHA biosynthesis and constructing non-native metabolic pathways that feed the metabolites for PHA production. The desired monomers in the PHA polymers were obtained by elimination of genes involved in PHA biosynthetic pathway. The chain length degradation specific-gene deletion of β-oxidation pathway resulted in the accumulation of PHA monomers having high carbon chain length. A controlled accumulation of monomers in the PHA polymer was achieved by constructing novel pathways in the bacteria and deleting native genes of competitive pathways from the genome of non-PHA producers. The present review attempts to showcase the novel genetic modification approaches conducted so far to enhance the PHA production with a special focus on metabolic pathway gene deletion in various bacteria.</p>","PeriodicalId":8919,"journal":{"name":"Bioengineered","volume":"16 1","pages":"2458363"},"PeriodicalIF":4.2,"publicationDate":"2025-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11784650/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143063475","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":"Correlation analysis of key genes and immune infiltration in visceral adipose tissue and subcutaneous adipose tissue of patients with type 2 diabetes in women.","authors":"Qian Shi, Yongxin Li, Chunyan Liu, Mengjie Liang, Hefei Zha, Xin Zhang, Fuchun Zhang","doi":"10.1080/21623945.2024.2442419","DOIUrl":"https://doi.org/10.1080/21623945.2024.2442419","url":null,"abstract":"<p><p>Immune cell infiltration into adipose tissue (AT) is a key factor in type 2 diabetes (T2DM). However, research on the impact of fat distribution on immune cells and immune responses in women is still lacking. This study used enrichment, protein-protein interaction network, immune cell infiltration, and correlation analysis to compare the similarities and differences between the transcriptome data of visceral AT (VAT) and subcutprotein-proteinaneous AT (SAT) obtained from the omprehensive database of gene expression in women with non-T2DM and T2DM. DEGs with the same biological function in two types of ATs often exhibited different expression trends. SharedVAT-specific and SAT-specific hub genes were mainly associated with transcription factors, monocyte-macrophage markers, and chemokines, respectively. Immune cells affected by both AT types included monocytes, granulocytes, T and B lymphocytes, and NK cells. VAT affected more immune cells, mainly myeloid cells. Shared hub genes in VAT correlated positively with M1 macrophages, suggesting pro-inflammatory effects, while those in SAT correlated negatively with M1 macrophages and lymphocytes, suggesting anti-inflammatory effects. This study provides a theoretical basis for further understanding the correlation between AT and T2DM in women.</p>","PeriodicalId":7226,"journal":{"name":"Adipocyte","volume":"14 1","pages":"2442419"},"PeriodicalIF":3.5,"publicationDate":"2025-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142881051","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"tRNA modifications: greasing the wheels of translation and beyond.","authors":"Minjie Zhang, Zhipeng Lu","doi":"10.1080/15476286.2024.2442856","DOIUrl":"https://doi.org/10.1080/15476286.2024.2442856","url":null,"abstract":"<p><p>Transfer RNA (tRNA) is one of the most abundant RNA types in cells, acting as an adaptor to bridge the genetic information in mRNAs with the amino acid sequence in proteins. Both tRNAs and small fragments processed from them play many nonconventional roles in addition to translation. tRNA molecules undergo various types of chemical modifications to ensure the accuracy and efficiency of translation and regulate their diverse functions beyond translation. In this review, we discuss the biogenesis and molecular mechanisms of tRNA modifications, including major tRNA modifications, writer enzymes, and their dynamic regulation. We also summarize the state-of-the-art technologies for measuring tRNA modification, with a particular focus on 2'-O-methylation (Nm), and discuss their limitations and remaining challenges. Finally, we highlight recent discoveries linking dysregulation of tRNA modifications with genetic diseases.</p>","PeriodicalId":21351,"journal":{"name":"RNA Biology","volume":"22 1","pages":"1-25"},"PeriodicalIF":3.6,"publicationDate":"2025-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142897124","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}