Open Biology最新文献

{"title":"<i>Glissandra oviformis</i> n. sp.: a novel predatory flagellate illuminates the character evolution within the eukaryotic clade CRuMs.","authors":"Euki Yazaki, Ryo Harada, Ryu Isogai, Kohei Bamba, Ken-Ichiro Ishida, Yuji Inagaki, Takashi Shiratori","doi":"10.1098/rsob.250057","DOIUrl":"10.1098/rsob.250057","url":null,"abstract":"<p><p>Culturing protists offers a powerful approach to exploring eukaryotic diversity, especially for deep-branching lineages. In this study, we cultured and described a novel protist species, named <i>Glissandra oviformis</i> n sp. within the poorly studied and unclassified genus <i>Glissandra</i>. While an SSU rDNA gene phylogeny failed to resolve its phylogenetic placement in the eukaryotic tree, a phylogenomic analysis of 340 proteins indicated <i>G. oviformis</i> as a member of the CRuMs clade. Prior to this study, this clade consisted of diverse heterotrophic amoeba and flagellates, and lacked clear synapomorphies. Ultrastructural observations revealed that <i>G. oviformis</i> shares the characteristics with some CRuMs members, including the pellicle underlying the plasma membrane and an internal sleeve surrounding the central pair of the axoneme at the flagellar transitional region. Our findings suggest potential shared characteristics and synapomorphies for CRuMs and contribute to a deeper understanding of the character evolution within this clade.</p>","PeriodicalId":19629,"journal":{"name":"Open Biology","volume":"15 6","pages":"250057"},"PeriodicalIF":4.5,"publicationDate":"2025-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12133344/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144216503","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":"Functional characterization of the store-operated calcium entry pathway in naked mole-rat cells.","authors":"Polina Drugachenok, Paulina Urriola-Muñoz, Lanhui Qiu, Zhuang Zhuang Han, Ewan St John Smith, Taufiq Rahman","doi":"10.1098/rsob.250052","DOIUrl":"10.1098/rsob.250052","url":null,"abstract":"<p><p>Naked mole-rats (NMRs, <i>Heterocephalus glaber</i>) are highly unusual rodents exhibiting remarkable adaptations to their subterranean habitat and resistance to developing various age-related diseases such as those related to abnormal cell proliferation or cancer, neurodegeneration and inflammation. In other rodents, as well as humans, a ubiquitous Ca²⁺ influx pathway, namely the store-operated Ca²⁺ entry (SOCE), has been implicated in all these diseases. SOCE is triggered by intracellular Ca²⁺ store depletion resulting in interaction of Stim proteins with Orai proteins, the putative homologues of which appear to be present in the NMR genome, but no functional characterization of SOCE in NMRs has yet been conducted. In this study, we provide the first functional and pharmacological characterization of SOCE in NMR using both excitable and non-excitable cells.</p>","PeriodicalId":19629,"journal":{"name":"Open Biology","volume":"15 6","pages":"250052"},"PeriodicalIF":4.5,"publicationDate":"2025-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12133337/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144216504","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":"Unravelling axonal transcriptional landscapes: insights from induced pluripotent stem cell-derived cortical neurons and implications for motor neuron degeneration.","authors":"Jishu Xu, Michaela Hörner, Maike Nagel, Perwin Perhat, Milena Korneck, Marvin Noß, Stefan Hauser, Ludger Schoels, Jakob Admard, Nicolas Casadei, Rebecca Schuele","doi":"10.1098/rsob.250101","DOIUrl":"10.1098/rsob.250101","url":null,"abstract":"<p><p>Neuronal function and pathology are deeply influenced by the distinct molecular profiles of the axon and soma. Traditional studies have often overlooked these differences due to the technical challenges of compartment-specific analysis. In this study, we employ a robust RNA-sequencing approach, using microfluidic devices, to generate high-quality axonal transcriptomes from induced pluripotent stem cells-derived cortical neurons (CNs). We achieve high specificity of axonal fractions, ensuring sample purity without contamination. Comparative analysis revealed a unique and specific transcriptional landscape in axonal compartments, characterized by diverse transcript types, including protein-coding mRNAs, RNAs encoding ribosomal proteins, mitochondrial-encoded RNAs and long non-coding RNAs. Previous works have reported the existence of transcription factors (TFs) in the axon. Here, we detect a set of TFs specific to the axon and indicative of their active participation in transcriptional regulation. To investigate transcripts and pathways essential for central motor neuron (MN) degeneration and maintenance we analysed kinesin family member 1C (<i>KIF1C</i>)<i>-</i>knockout <i>(KO</i>) CNs, modelling hereditary spastic paraplegia, a disorder associated with prominent length-dependent degeneration of central MN axons. We found that several key factors crucial for survival and health were absent in <i>KIF1C-KO</i> axons, highlighting a possible role of these also in other neurodegenerative diseases. Taken together, this study underscores the utility of microfluidic devices in studying compartment-specific transcriptomics in human neuronal models and reveals complex molecular dynamics of axonal biology. The impact of <i>KIF1C</i> on the axonal transcriptome not only deepens our understanding of MN diseases but also presents a promising avenue for exploration of compartment-specific disease mechanisms.</p>","PeriodicalId":19629,"journal":{"name":"Open Biology","volume":"15 6","pages":"250101"},"PeriodicalIF":4.5,"publicationDate":"2025-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12152748/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144266890","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":"Cell fate acquisition and reprogramming by the proneural transcription factor ASCL1.","authors":"Jethro Lundie-Brown, Francesca Puletti, Anna Philpott, Roberta Azzarelli","doi":"10.1098/rsob.250018","DOIUrl":"10.1098/rsob.250018","url":null,"abstract":"<p><p>ASCL1 is a key member of the proneural basic helix-loop-helix (bHLH) transcription factor (TF) family and it plays diverse roles in nervous system development and maintenance. ASCL1 is also one of the most studied bHLH TFs in the field of somatic cell reprogramming, as it can reconfigure the chromatin of the cell of origin to impose a neuronal identity. However, the ability of ASCL1 to drive neuronal fate does not come without exceptions, as there are cell types that are refractory to ASCL1-mediated reprogramming, and there are developmental contexts where ASCL1 does not drive neurogenesis but supports the generation of other lineages. ASCL1 has also emerged as an important player in cancers like neuroblastoma and glioblastoma, underscoring the clinical need for a robust understanding of how ASCL1 controls cell identity. In this review, we revisit the foundational studies that established ASCL1 as a critical regulator of neuronal differentiation and incorporate recent advances in our understanding of ASCL1 post-translational regulation and transcriptional control. By integrating these perspectives, this review provides a comprehensive overview of the diverse roles of ASCL1 in development, reprogramming and cancer, offering insights into its molecular functions and therapeutic potential.</p>","PeriodicalId":19629,"journal":{"name":"Open Biology","volume":"15 6","pages":"250018"},"PeriodicalIF":4.5,"publicationDate":"2025-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12173495/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144317564","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":"Kaiso mediates transcription and RNA splicing in colorectal carcinoma: role of BRCA1 in the Kaiso enhanceosome.","authors":"Weifeng Luo, Manish K Tripathi, Qi Liu, Lei Chen, Robert W Cowan, Juliet M Daniel, Chi Yan, Ann Richmond, Albert B Reynolds","doi":"10.1098/rsob.240329","DOIUrl":"10.1098/rsob.240329","url":null,"abstract":"<p><p>Kaiso (ZBTB33) is a transcription factor involved in mitotic clonal expansion and tumorigenesis in association with Adenomatous Polyposis Coli (APC) loss of heterozygosity. ENCODE data show strong overlap of the Kaiso promoter-binding site-encode-derived Kaiso-binding site (eKBS) and many other transcription factors, including BRCA1. Here we sought to determine whether BRCA1 is a component of the Kaiso enhanceosome that regulates gene transcription. Using proximal ligation assays, immunoprecipitation followed by mass spectrometry, luciferase assays and ChIP-seq experiments, we evaluated the association between BRCA1 and Kaiso. Kaiso nuclear extract immunoprecipitation experiments revealed that Kaiso associates strongly with genes involved in RNA splicing and processing. When Kaiso was not crosslinked to DNA, BRCA1 was not detected among Kaiso-binding proteins. However, overexpression of BRCA1 increased Kaiso-mediated gene transcription in luciferase assays in a Kaiso-dependent manner. Comparison of BRCA1 ChIP-seq and Kaiso ChIP-seq data from HCT116 cells revealed both BRCA1 and Kaiso commonly bind to the promoters of 379 genes. The most enriched term associated with these genes where BRCA1 and Kaiso bind their promoters is metabolism of RNA. Disease processes associated with these BRCA1/Kaiso gene promoters indicate that BRCA1 is functionally linked to a Kaiso-directed programme of RNAP2-mediated gene transcription and likely associated with colorectal cancer development and maintenance.</p>","PeriodicalId":19629,"journal":{"name":"Open Biology","volume":"15 6","pages":"240329"},"PeriodicalIF":4.5,"publicationDate":"2025-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12133338/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144216505","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 role of endothelial-derived factors in neural tube development: implications for organoid models.","authors":"Amy van der Hoven, Mubeen Goolam","doi":"10.1098/rsob.240341","DOIUrl":"10.1098/rsob.240341","url":null,"abstract":"<p><p>The study of the neural tube (NT), the antecedent structure of the central nervous system, is challenging due to the inaccessibility of the embryo. Thus, our understanding of this crucial timepoint in development is limited. The use of organoid models in recent years has proven immensely beneficial in the field of embryology, allowing the direct study of <i>in vitro</i> models of early neural development. As organoids advance in complexity, the vascularization of brain organoids has become a point of interest due to its significant role in neural development. This raises the question of whether the vascularization of NT organoids is necessary to improve their accuracy. This review summarizes the role of vascularization both during and before NT formation and explores the effects of endothelial-derived factors on this process. While the data indicate that vascularization is essential for proper NT formation, this review also highlights a significant gap in our knowledge and the need to clarify these interactions in order to generate more accurate organoid models.</p>","PeriodicalId":19629,"journal":{"name":"Open Biology","volume":"15 6","pages":"240341"},"PeriodicalIF":4.5,"publicationDate":"2025-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12152747/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144266889","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":"Enterohaemorrhagic <i>Escherichia coli</i> AdhE spirosome length correlates with enzymatic directionality and is perturbed by salicylidene acylhydrazides.","authors":"Ester Serrano, Tianxiao Zhao, David R Mark, Mostafa Soroor, Iris Floria, Nicholas J Terrill, Nikil Kapur, Arwen I I Tyler, Mathew H Horrocks, Andrew J Roe, Olwyn Byron","doi":"10.1098/rsob.250041","DOIUrl":"10.1098/rsob.250041","url":null,"abstract":"<p><p>Enterohaemorrhagic <i>Escherichia coli</i> causes sporadic, and sometimes large-scale, food poisoning outbreaks, for which antibiotic treatment in humans is contraindicated. As an alternative form of therapy, previous studies developed the family of salicylidene acylhydrazide (SA) anti-virulence compounds. One target of the SA compounds is AdhE, an enzyme that converts acetyl-CoA to ethanol and vice versa. AdhE oligomerizes, forming helicoidal filaments, heterogeneous in length, called spirosomes. We show it is possible to only partially fractionate AdhE spirosomes because <i>in vitro</i> they oligomerize in the absence of stimuli, and that spirosome formation is necessary to regulate the direction of AdhE enzymatic reactions. We also show that the SA compound ME0054 binds and perturbs AdhE spirosomes, enhancing the conversion of ethanol to acetyl-CoA. This mechanistic understanding of how ME0054 impacts AdhE function will help in the development of SA compounds as novel anti-virulence inhibitors.</p>","PeriodicalId":19629,"journal":{"name":"Open Biology","volume":"15 6","pages":"250041"},"PeriodicalIF":4.5,"publicationDate":"2025-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12173503/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144317565","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":"Sex-specific loss of mitochondrial membrane integrity in the auditory brainstem of a mouse model of Fragile X Syndrome.","authors":"Claire Caron, Elizabeth Anne McCullagh, Giulia Bertolin","doi":"10.1098/rsob.240384","DOIUrl":"10.1098/rsob.240384","url":null,"abstract":"<p><p>Sound sensitivity is a common sensory complaint for people with autism spectrum disorder (ASD). How and why sounds are perceived as overwhelming by affected people is unknown. To process sound information properly, the brain requires high activity and fast processing, as seen in areas like the medial nucleus of the trapezoid body (MNTB) of the auditory brainstem. Recent work has shown dysfunction in mitochondria in a genetic model of ASD, Fragile X Syndrome (FXS). Whether mitochondrial functions are also altered in sound-processing neurons has not been characterized yet. To address this question, we imaged MNTB in a mouse model of FXS. We stained MNTB brain slices from wild-type and FXS mice with two mitochondrial markers, TOMM20 and PMPCB, located on the outer mitochondrial membrane and in the matrix, respectively. Our imaging reveals significant sex-specific differences between genotypes. Colocalization analyses between TOMM20 and PMPCB show that the integrity of mitochondrial subcompartments is most disrupted in female FXS mice compared with female wild-type mice. We highlight a quantitative fluorescence microscopy pipeline to monitor mitochondrial functions in the MNTB from control or FXS mice and provide four complementary readouts, paving the way to understanding how cellular mechanisms important to sound encoding are altered in ASD.</p>","PeriodicalId":19629,"journal":{"name":"Open Biology","volume":"15 5","pages":"240384"},"PeriodicalIF":4.5,"publicationDate":"2025-05-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12082877/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143974224","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":"Exploration of gene presence/absence variations in <i>Oncorhynchus mykiss</i> and their differentiation between wild and selection populations.","authors":"Hancheng Bao, Na Xue, Boyuan Wang, Han Yu, Ming Huang, Jinghong He, Shuanglin Dong, Yangen Zhou, Qinfeng Gao, Yuan Tian","doi":"10.1098/rsob.240382","DOIUrl":"10.1098/rsob.240382","url":null,"abstract":"<p><p>Gene presence/absence variations (PAVs) have been considered as the important determinants of genome evolution and phenotypic diversity. However, studies on gene PAVs have been poorly documented, especially in fishes. In the present study, the pan-genome of rainbow trout was constructed based on 268 whole-genome re-sequencing accessions (4.38 Tb data). It recovered an additional 62 Mb sequences and 1288 protein-coding genes. Then, 9831 (22.77%) gene PAVs were genotyped across the 268 individuals. PAV-based PCA analysis, together with phylogenetic topology and STRUCTURE, revealed the clear separation among the different wild and selection populations. Additionally, a PAV-based genome-wide association study (GWAS) identified three candidate PAVs significantly associated with artificial selection. Meanwhile, fixation index analysis revealed 35 PAVs with significant frequency differences between wild and selection populations in Canada, while 15 candidate PAVs were detected between the populations in America. Their biological functions have been reported to participate in the regulation of growth performance and stress response. The present study deepens our understanding of widespread gene PAVs and facilitates the identification of key candidates that contribute to important traits.</p>","PeriodicalId":19629,"journal":{"name":"Open Biology","volume":"15 5","pages":"240382"},"PeriodicalIF":4.5,"publicationDate":"2025-05-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12092107/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144111658","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":"Beyond pathogenicity: the immunomodulatory role of the type III secretion system in beneficial plant-microbe interactions.","authors":"Iva Atanasković, Marija Nedeljković, Jelena Lozo","doi":"10.1098/rsob.240318","DOIUrl":"10.1098/rsob.240318","url":null,"abstract":"<p><p>The type III secretion system (T3SS) has traditionally been studied for its role in bacterial virulence. However, recent research emphasizes its dual role in beneficial interactions between bacteria and plants. This review examines the immunomodulatory functions of T3SS beyond pathogenicity and focuses on how T3SS effectors manipulate plant immune responses to promote symbioses. By comparing T3SS mechanisms in pathogenic and non-pathogenic bacteria, we aim to understand how this system enables beneficial microbes to colonize plants and improve plant growth and stress resilience. We also investigate the potential of T3SS to trigger induced systemic resistance in plants, a mechanism that could be utilized in agriculture to improve crop resistance to pathogens. The review concludes with an outlook on future research and emphasizes the need for comprehensive studies on T3SS effectors in non-pathogenic bacteria and their interactions with plant hosts.</p>","PeriodicalId":19629,"journal":{"name":"Open Biology","volume":"15 5","pages":"240318"},"PeriodicalIF":4.5,"publicationDate":"2025-05-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12115841/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144160761","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}