Open BiologyPub Date : 2025-10-01DOI: 10.1098/rsob.250103
Yuta Nakai, Wanida Ono, Noriaki Ono
{"title":"Bone marrow endosteum in homeostasis and metastasis.","authors":"Yuta Nakai, Wanida Ono, Noriaki Ono","doi":"10.1098/rsob.250103","DOIUrl":"10.1098/rsob.250103","url":null,"abstract":"<p><p>The endosteum is a thin layer of connective tissue lining the inner surfaces of bones adjoining the medullary cavity. The endosteum houses a variety of cells crucial for bone growth, repair and remodelling, including bone-forming osteoblasts, bone-resorbing osteoclasts and their precursor cells. Historically, the endosteum has been extensively studied as a key site for haematopoiesis by which blood cells are incessantly produced. However, recent studies have defined the endosteum as a niche for skeletal stem cells, underscoring the importance of the harmony between the inner endosteum and the outer periosteum in maintaining bone homeostasis. The endosteum also plays a significant role in pathological conditions, as it is recognized as a preferential site for bone metastasis of several common carcinomas, including breast and prostate cancers. The uniquely complex microenvironment of the endosteum favours the survival of cancer cells, contributing to dormancy, resistance to therapies and eventually, reemergence and progression. In this review, we discuss the multifaceted functions of the bone marrow endosteum, focusing on its dual roles in normal bone haematopoiesis and tumour metastasis.</p>","PeriodicalId":19629,"journal":{"name":"Open Biology","volume":"15 10","pages":"250103"},"PeriodicalIF":3.6,"publicationDate":"2025-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12483635/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145200538","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":"Transcriptomic and metabolomic insights into light-mediated unicellular-to-multicellular transition in <i>Dictyostelium discoideum</i>.","authors":"Yuehui Tian, Huiru Liu, Shanshan Xu, Zihe Wang, Zhili He, Ruiqi Liu, Longfei Shu","doi":"10.1098/rsob.250125","DOIUrl":"https://doi.org/10.1098/rsob.250125","url":null,"abstract":"<p><p><i>Dictyostelium discoideum</i> is a social amoeba that transitions from unicellular to multicellular forms in response to environmental signals, making it an intriguing model for studying cell aggregation and differentiation. Although previous studies have demonstrated that <i>Dictyostelium</i> slugs exhibit phototaxis, the mechanisms behind light-induced developmental changes remain unclear. In this study, we investigated how light triggers the transition to multicellularity and its associated metabolites and genes. Our findings revealed that spore yield depends on light exposure, with slower multicellular development under dark incubation. Transcriptomics analysis on QS9 amoebae identified upregulation of small GTPases such as <i>rasD</i> and <i>racL</i> in response to light, which likely promote cell movement, phagocytosis and actin protrusions. Light also enhanced cAMP production, driving the aggregation, post-aggregation and development of single cells. Additionally, c-di-GMP was essential for cell differentiation during multicellular growth and was upregulated by light. Metabolomic analysis on QS9 amoebae revealed that the downregulation of LPC (lysophosphatidylcholine) was detected under both unicellular and multicellular phases. Moreover, reduced levels of GSH (glutathione) in dark may impede multicellular structures of <i>D. discoideum</i>. These findings provide insights into light-triggered cell differentiation and pattern formation, offering a better understanding of molecular mechanisms underlying the transition to multicellularity in <i>Dictyostelium</i> cells.</p>","PeriodicalId":19629,"journal":{"name":"Open Biology","volume":"15 10","pages":"250125"},"PeriodicalIF":3.6,"publicationDate":"2025-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145244772","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}
Open BiologyPub Date : 2025-10-01Epub Date: 2025-10-08DOI: 10.1098/rsob.250194
Louna Fruchard, Claudia Salinas, Andre Carvalho, Zeynep Baharoglu
{"title":"tRNA-modifying enzymes in bacterial stress adaptation.","authors":"Louna Fruchard, Claudia Salinas, Andre Carvalho, Zeynep Baharoglu","doi":"10.1098/rsob.250194","DOIUrl":"https://doi.org/10.1098/rsob.250194","url":null,"abstract":"<p><p>Transfer RNAs (tRNAs) and their modifications are central to bacterial translation and physiology, yet their roles in stress adaptation remain underexplored. While extensively studied in eukaryotes, and linked to diseases, bacterial tRNA modifications are only recently gaining attention. This review highlights emerging insights into how tRNA modifications and associated enzymes contribute to bacterial survival under oxidative and antibiotic stresses, both disrupting proteostasis. We examine the environmental and physiological stresses bacteria encounter, focussing on reactive oxygen species and sub-lethal antibiotic exposure. These stresses challenge proteome integrity and trigger adaptive responses involving key stress regulators. We explore the expanding field of bacterial epitranscriptomics, detailing the diversity, dynamics and structural impact of tRNA modifications, and how they influence selective translation. Central to this is the concept of modification tunable transcripts, linking specific codon usage patterns to stress-responsive translation reprogramming. Beyond their catalytic roles, tRNA-modifying enzymes also have additional functions. We discuss this dual functionality and its broader implications for bacterial adaptability. By integrating recent technological advances and conceptual models, this review underscores the potential of targeting tRNA modifications as a novel strategy to combat bacterial pathogenicity and antibiotic resistance. With many aspects still unresolved, the study of bacterial tRNA modifications promises rich opportunities for discovery and therapeutic innovation.</p>","PeriodicalId":19629,"journal":{"name":"Open Biology","volume":"15 10","pages":"250194"},"PeriodicalIF":3.6,"publicationDate":"2025-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145244767","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}
Open BiologyPub Date : 2025-10-01Epub Date: 2025-10-08DOI: 10.1098/rsob.250135
Nadine Randel
{"title":"Effects of food availability on larval development during ontogenetic niche shift in a marine annelid.","authors":"Nadine Randel","doi":"10.1098/rsob.250135","DOIUrl":"https://doi.org/10.1098/rsob.250135","url":null,"abstract":"<p><p>Many marine invertebrates have a biphasic life cycle with a free-swimming larva and a bottom-dwelling adult. The transition from a planktonic to a benthic lifestyle is a significant step in the animal's life history, highly regulated and influenced by external and internal factors. Since the readiness to settle and the presence of a suitable seafloor habitat do not always coincide, larvae sometimes need to extend their planktonic phase. Little is currently known regarding how larvae partition their energy for coordinating development and growth according to food type and availability in their settlement habitat. Here, I investigate the effect of food availability and type on development in <i>Platynereis dumerilii</i> larvae. I assessed cell proliferation, growth and feeding onset over six days using two different food sources. The results indicate that food availability and type affect larval growth, with starved larvae slowing development and conserving resources, whereas fed larvae allocate resources to brain development and posterior growth. Overall, this work contributes to our understanding of how competent marine larvae regulate the duration of their planktonic phase and how nutritional status affects development.</p>","PeriodicalId":19629,"journal":{"name":"Open Biology","volume":"15 10","pages":"250135"},"PeriodicalIF":3.6,"publicationDate":"2025-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145244780","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}
Open BiologyPub Date : 2025-09-01Epub Date: 2025-09-24DOI: 10.1098/rsob.250133
Peng Wu, Li Wang, Ting Wen, Qiao Yi Chen
{"title":"Implications of canonical histone H3.1 and histone variant H3.3 in cancer.","authors":"Peng Wu, Li Wang, Ting Wen, Qiao Yi Chen","doi":"10.1098/rsob.250133","DOIUrl":"10.1098/rsob.250133","url":null,"abstract":"<p><p>Histones are the fundamental building blocks of chromatin and serve as pivotal regulators of gene expression. Differential expression and mutations of H3.1 and H3.3 genes have been implicated in the pathogenesis of various cancer types. Mutations in H3.3, especially lysine to methionine substitutions (K27M/K36M), are particularly prevalent. Moreover, genetic alterations such as G34R/W/V/L, as well as variations in <i>H3F3A</i> and <i>H3F3B</i> genes, have also been identified. Despite high similarity in amino acid sequences, H3.1 and H3.3 have discrete functions in cancer. In this review, we delve into the recent advances in elucidating the implications of canonical histone H3.1 and its variant H3.3 on chromatin structure and function. Additionally, we explore how potential enhancing factors such as PTEN, MLL5, GPR87 and histone chaperones influence H3.1/H3.3 function.</p>","PeriodicalId":19629,"journal":{"name":"Open Biology","volume":"15 9","pages":"250133"},"PeriodicalIF":3.6,"publicationDate":"2025-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12457037/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145131363","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}
Open BiologyPub Date : 2025-09-01Epub Date: 2025-09-17DOI: 10.1098/rsob.250073
Pranav Prabhu, Puli Chandramouli Reddy
{"title":"An <i>in silico</i> pipeline identifies new neuropeptides and reveals a non-amidated regulator of muscle contraction in the freshwater cnidarian <i>Hydra</i>.","authors":"Pranav Prabhu, Puli Chandramouli Reddy","doi":"10.1098/rsob.250073","DOIUrl":"10.1098/rsob.250073","url":null,"abstract":"<p><p>Neuropeptides play a critical role in neurotransmission and organismal development. Members of the phylum Cnidaria, with a diffused nervous system, are one of the earliest divergent animals and might provide insights into the fundamentals of the emergence of neuronal communications. The neuropeptide diversity in <i>Hydra</i> (a cnidarian model) has been extensively studied using various strategies, each with certain limitations. Here, we have developed an <i>in silico</i> pipeline which identified both reported peptides and many new potential candidates. A comparative analysis within Cnidaria suggests a rapid divergence of neuropeptides which might be involved in complex behaviours. We identified new <i>Hydra</i> neuropeptides that belong to the RFamide and PRXamide families and a novel class of peptides lacking amidation (LW-peptides). A detailed expression and functional analysis of a new LW-peptide indicates its role in the longitudinal contraction of <i>Hydra</i> polyps. This study provides compelling evidence for the existence of intricate peptidergic communication in early neuronal circuits. The extensive diversity of neuropeptides within this phylum underscores their rapid evolutionary adaptability. This current pipeline also proves to be simple and adaptable to perform neuropeptide identification in other multicellular organisms.</p>","PeriodicalId":19629,"journal":{"name":"Open Biology","volume":"15 9","pages":"250073"},"PeriodicalIF":3.6,"publicationDate":"2025-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12440616/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145075836","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}
Open BiologyPub Date : 2025-09-01Epub Date: 2025-09-24DOI: 10.1098/rsob.250062
Emily K Belcher, Travis K Johnson, Christen Mirth, Keyne Monro
{"title":"Temperature and the progression of developmental milestones in embryogenesis of a marine ectotherm.","authors":"Emily K Belcher, Travis K Johnson, Christen Mirth, Keyne Monro","doi":"10.1098/rsob.250062","DOIUrl":"10.1098/rsob.250062","url":null,"abstract":"<p><p>Embryos are among the most temperature-sensitive life stages. To survive and produce juvenile stages, embryos must be robust to changes in temperature that also change development time profoundly. Yet, how robustness is achieved during embryogenesis, and which developmental events are most prone to perturbation by temperature, is only known for a handful of species. Such insights are especially lacking for marine ectotherms, which often develop in direct contact with the external environment. We address these gaps using the tubeworm, <i>Galeolaria caespitosa</i>, a typical marine ectotherm with external development. We fluorescently labelled F-actin and nuclear DNA in embryos sampled hourly throughout embryogenesis at the minimum temperature of the coldest month (11°C), annual mean temperature (17°C) and maximum temperature of the warmest month (22°C) in nature. Based on confocal imaging, we identified key developmental stages (milestones) in embryogenesis and compared their progression across temperatures. We found that developmental progression is similar across temperatures when normalized to development time, but earlier milestones are less robust to warming than later ones. Our results suggest that embryos achieve robustness by tightly coordinating the relative timing of embryonic events, offering clues to how embryos may withstand contemporary climate change in marine systems.</p>","PeriodicalId":19629,"journal":{"name":"Open Biology","volume":"15 9","pages":"250062"},"PeriodicalIF":3.6,"publicationDate":"2025-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12457034/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145131339","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 E3 ligase MEX3B forms a tripartite complex with <i>Rest</i> and <i>Hotair</i> to determine the proliferative capacity of neural progenitor cells.","authors":"Kamakshi Garg, Gourav Sharma, Sarbani Samaddar, Sourav Banerjee","doi":"10.1098/rsob.250164","DOIUrl":"10.1098/rsob.250164","url":null,"abstract":"<p><p>E3 ubiquitin ligases regulate the cellular proteome <i>via</i> proteasome-dependent protein degradation; however, there exist limited studies outlining their non-canonical functions. RNA-binding ubiquitin ligases (RBULs) represent a subset of E3 ligases that harbour RNA-binding domains, making them uniquely positioned to function as both RNA-binding proteins and E3 ligases. Our initial microarray screen for E3 ligases from mouse cortical neural progenitor cells identified MEX3B, a known RNA-binding ubiquitin ligase, to be differentially expressed. Here, we characterize the non-canonical role of MEX3B in the context of neural proliferation. We find that MEX3B is significantly reduced following the differentiation of neural progenitor cells (NPCs). The knockdown of MEX3B blocks the proliferative state of NPCs and leads to the enhancement of neurite length and dendrite branching. We observed that MEX3B regulates the stability of <i>Rest</i> mRNA in proliferative NPCs. Mechanistically, MEX3B interacts with <i>Rest</i> mRNA and the lncRNA <i>Hotair</i> to form a tripartite complex in the presence of basic fibroblast growth factor (bFGF). Loss of <i>Hotair</i> disrupts this complex; conversely, MEX3B RNAi significantly reduces <i>Hotair</i> abundance. <i>Rest</i> mRNA levels remain unaffected by <i>Hotair</i> knockdown, suggesting that the latter acts as a scaffold to facilitate bFGF-dependent MEX3B<i>-Rest</i> interaction in the MEX3B<i>-Rest-Hotair</i> tripartite axis. Our study demonstrates an RNA-driven post-transcriptional mechanism underlying NPC proliferation.</p>","PeriodicalId":19629,"journal":{"name":"Open Biology","volume":"15 9","pages":"250164"},"PeriodicalIF":3.6,"publicationDate":"2025-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12419896/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145030258","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}
Open BiologyPub Date : 2025-09-01Epub Date: 2025-09-17DOI: 10.1098/rsob.250199
Samir G Chethan, Jessie M Rogers, Drisya Vijayakumari, Wendi Williams, Vojislav Gligorovski, Sahand Jamal Rahi, Silke Hauf
{"title":"A distinct phase of cyclin B (Cdc13) nuclear export at mitotic entry in <i>Schizosaccharomyces pombe</i>.","authors":"Samir G Chethan, Jessie M Rogers, Drisya Vijayakumari, Wendi Williams, Vojislav Gligorovski, Sahand Jamal Rahi, Silke Hauf","doi":"10.1098/rsob.250199","DOIUrl":"10.1098/rsob.250199","url":null,"abstract":"<p><p>In eukaryotes, cell division requires coordination between the nucleus and cytoplasm. Entry into cell division is driven by cyclin-dependent kinases (CDKs), which need a cyclin binding partner for their activity. In <i>Schizosaccharomyces pombe</i> (fission yeast), the B-type cyclin Cdc13 is essential and sufficient for cell cycle progression and is strongly enriched in the nucleus. Here, we show that a fraction of Cdc13 is exported from the nucleus to the cytoplasm just prior to mitosis. This export could be critical to propagate CDK activity throughout the cell. Mutating three Cdc13 nuclear localization signals (NLSs) led to precocious enrichment of Cdc13 in the cytoplasm but did not accelerate mitotic entry, indicating that the export is not sufficient to trigger entry into mitosis. The export coincides with spindle pole body integration into the nuclear envelope and may be required to coordinate nuclear and cytoplasmic signalling required for this integration. The onset and stop of Cdc13 nuclear export are remarkably abrupt, underscoring that <i>S. pombe</i> mitotic entry consists of several switch-like transitions over the course of minutes. Our findings add another instance to the various cyclin nuclear transport events known to occur at critical cell cycle transitions throughout eukaryotes.</p>","PeriodicalId":19629,"journal":{"name":"Open Biology","volume":"15 9","pages":"250199"},"PeriodicalIF":3.6,"publicationDate":"2025-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12440626/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145075797","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}
Open BiologyPub Date : 2025-09-01Epub Date: 2025-09-03DOI: 10.1098/rsob.250159
Khalida Bainour, Nabilah Zulkifli, Ka-Kei Sam, Juan C Navarro, Luis Filipe C Castro, Christopher J Glasby, Alexander C Shu-Chien, Óscar Monroig
{"title":"Freshwater-adapted polychaetes exhibit a complete enzymatic machinery for synthesizing long-chain polyunsaturated fatty acids.","authors":"Khalida Bainour, Nabilah Zulkifli, Ka-Kei Sam, Juan C Navarro, Luis Filipe C Castro, Christopher J Glasby, Alexander C Shu-Chien, Óscar Monroig","doi":"10.1098/rsob.250159","DOIUrl":"10.1098/rsob.250159","url":null,"abstract":"<p><p>The sustainability of aquaculture is challenged by limited fishmeal and fish oil supplies, key sources of long-chain polyunsaturated fatty acids (LC-PUFA) such as eicosapentaenoic acid (EPA, 20:5 n-3), docosahexaenoic acid (DHA, 22:6 n-3) and arachidonic acid (ARA, 20:4 n-6), essential for fish health and product quality. Polychaetes represent a promising alternative. While marine polychaetes show complete LC-PUFA biosynthetic pathways involving elongases (Elovl), front-end desaturases (Fed), and methyl-end desaturases (ω des), freshwater species remain poorly studied. We hypothesize that freshwater-adapted polychaetes exhibit enhanced LC-PUFA biosynthesis to compensate for limited dietary sources in freshwater environments. This study focuses on <i>Namalycastis rhodochorde</i>, a freshwater nereid polychaete found in Southeast Asia. We isolated and characterized elongase and desaturase genes from <i>N. rhodochorde</i> using a yeast-based heterologous expression system. Our results revealed three Elovl (Elovl2/5, Elovl4, Elovl1/7) that elongate PUFA substrates from C<sub>18</sub> to C<sub>22</sub>, two Fed (Fed1 with Δ5 and Fed2 with dual Δ6/Δ8 activities), and two ω des: a Δ12 desaturase enabling linoleic acid (18:2 n-6) synthesis, and an ω3 desaturase converting n-6 into n-3 PUFA. These findings indicate that <i>N. rhodochorde</i> has the enzymatic capacity to synthesize LC-PUFA like ARA and EPA, supporting its potential for sustainable biomass production using low-nutrient substrates.</p>","PeriodicalId":19629,"journal":{"name":"Open Biology","volume":"15 9","pages":"250159"},"PeriodicalIF":3.6,"publicationDate":"2025-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12405942/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144963431","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}