Open Biology最新文献_第2页

The roles of symmetric and asymmetric parental histone recycling in cell fate, development, and disease. 对称和不对称亲本组蛋白循环在细胞命运、发育和疾病中的作用。

IF 3.1 3区生物学

Open Biology Pub Date : 2026-09-02 DOI: 10.1098/rsob.260102

Brendon E M Davis, Alex C Pan, Xin Chen

{"title":"The roles of symmetric and asymmetric parental histone recycling in cell fate, development, and disease.","authors":"Brendon E M Davis, Alex C Pan, Xin Chen","doi":"10.1098/rsob.260102","DOIUrl":"https://doi.org/10.1098/rsob.260102","url":null,"abstract":"Replication of the epigenome occurs concurrently with DNA replication. A major component of epigenetic memory is contained in histones, and this memory is preserved via recycling of parental histones onto the leading and lagging strands of the replication fork. The histones of one parental strand must be incorporated into two nascent strands, a process governed by the replisome's histone chaperones. These chaperones determine which strand each histone is incorporated into and the frequency with which each strand receives parental histones, a determination that is essential for preserving epigenetic landscapes and ensuring proper gene expression following DNA replication. Here, we describe recent developments in our understanding of how parental histone recycling occurs and the effects it has on cells in developmental contexts. Although histones are generally recycled symmetrically to the leading and lagging strands, asymmetric histone recycling can occur naturally in some asymmetrically dividing cells or be induced by manipulating replisome components. Asymmetric histone recycling generates distinct epigenetic states at a given genomic locus, which can result in differential gene expression and ultimately different cell fates following cell division in multicellular organisms. This is important for future studies examining the role of epigenetics in both development and disease contexts.","PeriodicalId":19629,"journal":{"name":"Open Biology","volume":"16 9","pages":""},"PeriodicalIF":3.1,"publicationDate":"2026-09-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148875612","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}

引用次数: 0

Challenges and opportunities in type III secretion system effector prediction. III型分泌系统效应物预测的挑战与机遇。

IF 3.1 3区生物学

Open Biology Pub Date : 2026-08-26 DOI: 10.1098/rsob.250485

Iva Rosić, Ivan Nikolić

{"title":"Challenges and opportunities in type III secretion system effector prediction.","authors":"Iva Rosić, Ivan Nikolić","doi":"10.1098/rsob.250485","DOIUrl":"https://doi.org/10.1098/rsob.250485","url":null,"abstract":"Type III secretion system effectors (T3SEs) are small bacterial proteins with big biological roles. They act as central molecular mediators of interactions between Gram-negative bacteria and eukaryotic hosts, spanning pathogenic, symbiotic and environmental contexts. Over the past three decades, T3SE discovery has progressed from genome-independent experimental assays to an expanding landscape of computational prediction methods. Early in silico approaches formalized empirically defined protein N-terminal properties into feature-engineered machine-learning models, followed by deep-learning methods that learn sequence patterns directly from amino acid sequences. More recent pipelines integrate multiple layers of information, including homology, regulatory elements, genomic context, pan-genomic context and protein language model embeddings, primarily to prioritize candidate novel effectors. Despite these advances, several challenges remain. Training data and available databases remain biased towards a limited set of well-known plant and animal pathogens; many tools are no longer maintained, and the extent to which current predictors generalize to non-pathogenic, symbiotic, environmental and host-unknown bacteria remains unclear. Here, we review the conceptual evolution of T3SE prediction, highlight persistent limitations and sources of bias, and outline open questions that must be addressed to enable robust, interpretable and ecologically inclusive prediction of T3SEs, pointing towards the need for centralized, user-friendly platforms that integrate diverse biological signals into transparent, ranked outputs suitable for experimental validation.","PeriodicalId":19629,"journal":{"name":"Open Biology","volume":"16 8","pages":""},"PeriodicalIF":3.1,"publicationDate":"2026-08-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148818831","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}

引用次数: 0

Contribution of mechanical forces in multiciliated cell differentiation. 机械力在多毛细胞分化中的作用。

IF 3.1 3区生物学

Open Biology Pub Date : 2026-08-26 DOI: 10.1098/rsob.260101

Nathalie Spassky, Nathalie Delgehyr

引用次数: 0

A modern toolbox to elucidate the role of the human microbiome in modulating mycobacterial gut infections. 一个现代工具箱来阐明人类微生物组在调节分枝杆菌肠道感染中的作用。

IF 3.1 3区生物学

Open Biology Pub Date : 2026-08-19 DOI: 10.1098/rsob.250258

Chiara Foini, Ariane Briegel, Herman P Spaink

{"title":"A modern toolbox to elucidate the role of the human microbiome in modulating mycobacterial gut infections.","authors":"Chiara Foini, Ariane Briegel, Herman P Spaink","doi":"10.1098/rsob.250258","DOIUrl":"https://doi.org/10.1098/rsob.250258","url":null,"abstract":"Inflammatory bowel diseases (IBDs) are a major public and veterinary health concern, but the causes are poorly understood. In this review, we discuss the potential of mycobacteria as causative factors for such diseases. We focus on similarities between the most common human IBD, Crohn's disease, and a common IBD in cattle, Johne's disease. Both are multifactorial diseases, leading to a chronic hyperinflammatory immune response of the intestines. However, the underlying genetic and environmental factors, such as variations in the intestinal microbiome, are still poorly understood. While Johne's disease has been shown to be caused by Mycobacterium avium subsp. paratuberculosis, the likeliness of mycobacteria as a causative factor of Crohn's disease is still heavily debated. In this review, we summarize the advances in research that could be used to further investigate the role of mycobacteria in intestinal diseases and to give better estimations about which mycobacterial species are most probably hazards for health. New advances in molecular, genetic and imaging methods give hope for better diagnostics, disease prevention, and development of new therapeutics. In addition, these techniques offer researchers a toolbox and general model systems for better understanding the mechanisms of intestinal diseases caused by mycobacteria and the role of the microbiome in the control of disease progression.","PeriodicalId":19629,"journal":{"name":"Open Biology","volume":"16 8","pages":""},"PeriodicalIF":3.1,"publicationDate":"2026-08-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148796371","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}

引用次数: 0

Structural insights into the polytopic Escherichia coli phosphoglycosyl transferase WbaP. 多聚大肠杆菌磷酸糖基转移酶WbaP的结构研究。

IF 3.1 3区生物学

Open Biology Pub Date : 2026-08-19 DOI: 10.1098/rsob.250369

Miriam Weckener, Audrey Le Bas, Philip N Ward, Bradley R Clarke, Peter J Harrison, Stephen A McMahon, Huanting Liu, Alice Eddershaw, Andrew M Giltrap, Els Pardon, Abirami Lakshminarayanan, Jan Steyaert, Benjamin G Davis, Chris Whitfield, James H Naismith

{"title":"Structural insights into the polytopic Escherichia coli phosphoglycosyl transferase WbaP.","authors":"Miriam Weckener, Audrey Le Bas, Philip N Ward, Bradley R Clarke, Peter J Harrison, Stephen A McMahon, Huanting Liu, Alice Eddershaw, Andrew M Giltrap, Els Pardon, Abirami Lakshminarayanan, Jan Steyaert, Benjamin G Davis, Chris Whitfield, James H Naismith","doi":"10.1098/rsob.250369","DOIUrl":"https://doi.org/10.1098/rsob.250369","url":null,"abstract":"Host-pathogen interactions frequently depend on key components of the bacterial cell surface, such as capsules and lipopolysaccharides in Gram-negative bacteria. The first step in the synthesis of lipid-linked polysaccharides is the substitution of a uridine diphosphate (UDP)-sugar by a lipid monophosphate catalysed by a phosphoglycosyl transferase (PGT). We report the 3.0 Å cryo-electron microscopy apo-structure of the PGT enzyme WbaP from Escherichia coli, a UDP-galactose:undecaprenolphosphate galactose-1-phosphoryl transferase. The structure is a dimer with each monomer formed of four N-terminal transmembrane helices, a small α/β domain with a distinctive β-hairpin that inserts into the other monomer, and a catalytic domain, which sits perpendicular to the transmembrane domain. A complex of WbaP with the UDP-galactose substrate shows binding of the UDP moiety by R319 and R377. Mutations of R319 and R377, along with K331 and R401, highlighted the essential nature of these residues for the catalytic activity of the protein, as confirmed by an in vivo functional assay. Our results provide new insights into the PGT family of enzymes.","PeriodicalId":19629,"journal":{"name":"Open Biology","volume":"16 8","pages":""},"PeriodicalIF":3.1,"publicationDate":"2026-08-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148796409","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}

引用次数: 0

CDK1-Cyclin B mediated phosphorylation of PP2A-B56 on B56Par1.T73T75 controls mitotic entry timing and Schizosaccharomyces pombe cell size. CDK1-Cyclin B介导PP2A-B56在B56Par1上的磷酸化。T73T75控制有丝分裂进入时间和裂糖菌pombe细胞大小。

IF 3.1 3区生物学

Open Biology Pub Date : 2026-08-19 DOI: 10.1098/rsob.260089

Lenka Halova, Yvonne Connolly, Duncan Smith, Janni Petersen, Iain Hagan

引用次数: 0

The p97 adaptor p47/NSFL1C is necessary for stress granule dissolution after heat stress. p97适配器p47/NSFL1C是热应力后应力颗粒溶解所必需的。

IF 3.1 3区生物学

Open Biology Pub Date : 2026-08-12 DOI: 10.1098/rsob.260021

Michelle A Johnson, Richa Khanna, Sirisha Mukkavalli, Ly Nguyen, Malavika Raman

{"title":"The p97 adaptor p47/NSFL1C is necessary for stress granule dissolution after heat stress.","authors":"Michelle A Johnson, Richa Khanna, Sirisha Mukkavalli, Ly Nguyen, Malavika Raman","doi":"10.1098/rsob.260021","DOIUrl":"10.1098/rsob.260021","url":null,"abstract":"Stress granules form in response to diverse cellular perturbations to sequester translation components until the stress is resolved. Stress granules are composed of RNA-protein assemblies in membrane-delimited structures and must be rapidly disassembled to release components to allow translation to resume. Disassembly of stress granules formed in response to heat stress is dependent on ubiquitylation of stress granule components such as G3BP1. Ubiquitylation of stress granule proteins recruits the AAA-ATPase p97 (also known as VCP) to enable ubiquitin-dependent disassembly of these structures. Loss of p97 activity leads to the persistence of stress granules and is implicated in several age-related neurodegenerative diseases. Here, we show that p97 recruitment to stress granules is dependent on its ubiquitin-binding co-factor p47. p47 translocates to stress granules in response to a variety of cellular stressors and is required for the recruitment of p97 to stress granules. Loss of p47 leads to an inhibition in stress granule disassembly. We further show that p47 associates with G3BP1 in response to heat stress in a ubiquitin-dependent manner. Taken together, our data add to the growing list of p97 adaptors that are implicated in the recruitment of p97 for the dissolution of stress granules.","PeriodicalId":19629,"journal":{"name":"Open Biology","volume":"16 8","pages":""},"PeriodicalIF":3.1,"publicationDate":"2026-08-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148713274","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}

引用次数: 0

Regulation of actin polarization by Edwardsiella piscicida during invasion of Sebastes schlegeli intestinal mucosa and cellular immune responses. 鱼腥味爱德华菌对施莱格氏杆菌侵袭肠黏膜及细胞免疫应答过程中肌动蛋白极化的调控。

IF 3.1 3区生物学

Open Biology Pub Date : 2026-08-05 DOI: 10.1098/rsob.250346

Ting Xue, Yanmin Wang, Baofeng Su, Min Cao, Yuping Liu, Yiping Liu, Chao Li

{"title":"Regulation of actin polarization by Edwardsiella piscicida during invasion of Sebastes schlegeli intestinal mucosa and cellular immune responses.","authors":"Ting Xue, Yanmin Wang, Baofeng Su, Min Cao, Yuping Liu, Yiping Liu, Chao Li","doi":"10.1098/rsob.250346","DOIUrl":"https://doi.org/10.1098/rsob.250346","url":null,"abstract":"Intestinal epithelial cells play a crucial role in teleost defence against complex aquatic environments. However, the study of intestinal mucosal immunity in teleosts has been hindered by the lack of reliable and specific marker genes to distinguish between different cell types. In this study, single-cell RNA-seq analysis of the intestinal epithelial cells from healthy and infected Sebastes schlegeli was performed to investigate the heterogeneity of teleost intestinal epithelial cells. Immune cells, including T cells, B cells, non-specific cytotoxic cells (NCCs) and myeloid cells, and non-immune cells including enterocyte, erythrocyte, BEST4+ cell, goblet cell and enteroendocrine cell, were identified. Several notable cell populations, including early myeloid cells, lysosome-rich enterocytes, enterocyte progenitors and BEST4+ cells, were characterized in detail. Additionally, significant changes in the expression of actin polymerization-related genes were observed in various intestinal mucosal cell types following Edwardsiella piscicida infection, suggesting a mechanism of invasion with E. piscicida. These findings enhance our understanding of teleost intestinal cellular composition and provide valuable insights for the development of therapeutic strategies against E. piscicida.","PeriodicalId":19629,"journal":{"name":"Open Biology","volume":"16 8","pages":""},"PeriodicalIF":3.1,"publicationDate":"2026-08-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148673853","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}

引用次数: 0

Reviewers in 2025. 2025年的评论者。

IF 3.1 3区生物学

Open Biology Pub Date : 2026-08-05 DOI: 10.1098/rsob.260110

Jonathon Pines

引用次数: 0

Cooperation, privatization and cheating in microbial exoenzyme synthesis: theoretical analysis in view of biotechnological applications. 微生物外酶合成中的合作、私有化和欺骗：从生物技术应用角度的理论分析。

IF 3.1 3区生物学

Open Biology Pub Date : 2026-07-29 DOI: 10.1098/rsob.250484

Tanvir Hassan, Shalu Dwivedi, Stefan Schuster, Anna Matuszyńska

{"title":"Cooperation, privatization and cheating in microbial exoenzyme synthesis: theoretical analysis in view of biotechnological applications.","authors":"Tanvir Hassan, Shalu Dwivedi, Stefan Schuster, Anna Matuszyńska","doi":"10.1098/rsob.250484","DOIUrl":"10.1098/rsob.250484","url":null,"abstract":"This study presents a mathematical framework for investigating the dynamics of coexistence and competition among heterotrophic microbes across different time scales. Focusing on metabolic interactions, we examine how three strategies, public metabolizing, private metabolizing and cheating, shape population behaviour. The framework integrates generalized Lotka-Volterra dynamics with evolutionary game theory to capture the effects of resource exchange, particularly glucose made available by public metabolizers and sucrose as a shared substrate driving population growth. Game-theoretic pay-offs encode ecological costs and benefits, enabling analysis of frequency-dependent interactions among strategies. To capture evolutionary realism, we implement laboratory-inspired simulations in which strategies can switch between generations, mimicking mutation or phenotypic plasticity in microbial populations. These eco-evolutionary dynamics reveal conditions under which all three strategies coexist at interior equilibria and show how variation in growth advantages and, illustratively, phenotype-switching perturbations produce evolutionary shifts. Numerical analysis identifies ecological thresholds and fitness asymmetries that determine system robustness, long-term coexistence, and the persistence of a synthetic, cross-kingdom system linked by nutrient exchange. Together, these insights provide general principles for microbial coexistence and offer design guidelines for ecosystem engineering, biotechnological applications and the construction of stable synthetic communities under ecological and evolutionary constraints.","PeriodicalId":19629,"journal":{"name":"Open Biology","volume":"16 7","pages":""},"PeriodicalIF":3.1,"publicationDate":"2026-07-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148606011","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}

引用次数: 0