BMC Biology最新文献

{"title":"Proteasome regulation of petite-negativity in fission yeast.","authors":"Katie Lin Amberg, Lyrica Hao, Susanne Cranz-Mileva, Mikel Zaratiegui","doi":"10.1186/s12915-025-02409-2","DOIUrl":"https://doi.org/10.1186/s12915-025-02409-2","url":null,"abstract":"<p><strong>Background: </strong>Mitochondria carry out essential functions in eukaryotic cells. The mitochondrial genome encodes factors critical to support oxidative phosphorylation and mitochondrial protein import necessary for these functions. However, organisms like budding yeast can readily lose their mitochondrial genome, yielding respiration-deficient petite mutants. The fission yeast Schizosaccharomyces pombe is petite-negative, but some nuclear mutations enable the loss of its mitochondrial genome.</p><p><strong>Results: </strong>Here, we characterize the classical petite-positive mutation ptp1-1 as a loss of function allele of the proteasome 19S regulatory subunit component mts4/rpn1, involved in the ubiquitin-dependent degradation pathway. By comparison with another petite-enabling mutation in the g-subunit of the F₁-ATPase, we show that ptp1-1 does not rescue mitochondrial membrane potential. Instead, the mutation results in increased levels of mitochondrial and cytoplasmic chaperones and an altered oxidative stress response.</p><p><strong>Conclusions: </strong>ptp1-1 is a partial loss of function mutation of the proteasome that enables growth of cells devoid of mitochondrial DNA through a mechanism that is independent of mitochondrial membrane potential rescue and associated with proteasome-dependent regulation of mitochondrial protein import precursors and the oxidative stress response.</p>","PeriodicalId":9339,"journal":{"name":"BMC Biology","volume":"23 1","pages":"302"},"PeriodicalIF":4.5,"publicationDate":"2025-10-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145257492","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Exploring fern pathosystems and immune receptors to bridge gaps in plant immunity.","authors":"Baptiste Castel, Madeleine Baker, Jean Keller, Yves Martinez, Maxime Bonhomme, Pierre-Marc Delaux, Christophe Jacquet","doi":"10.1186/s12915-025-02413-6","DOIUrl":"https://doi.org/10.1186/s12915-025-02413-6","url":null,"abstract":"<p><p>Land plants include angiosperms, gymnosperms, bryophytes, lycophytes, and ferns, each of which may deploy distinct strategies to resist pathogens. Here, we investigate fern-pathogen interactions by characterizing novel pathosystems and analyzing the diversity of fern immune receptors. A collection of fern species was inoculated with a diverse set of filamentous microbes, and disease symptoms were assessed. We further leveraged published genome mining tools to analyse the diversity of RECEPTOR-LIKE KINASES, RECEPTOR-LIKE PROTEINS (RLKs/RLPs) and NUCLEOTIDE-BINDING AND LEUCINE-RICH REPEATS (NLRs), along with key immune signalling components, in ferns. Our results reveal that ferns exhibit a range of responses to pathogens, including putative non-host resistance and more specific resistance mechanisms. Among ten ferns tested, Pteris vittata displays the broadest spectrum of pathogen compatibility. Genome mining indicates that ferns encode a diverse repertoire of putative immune receptors, antimicrobial peptides, and mediators of systemic acquired resistance. Ferns possess numerous RLKs/RLPs, resembling those required for cell-surface immunity in angiosperms. They also encode diverse NLRs, including sub-families lost in flowering plants. These findings provide insights into disease resistance evolution and open promising perspectives for crop protection strategies.</p>","PeriodicalId":9339,"journal":{"name":"BMC Biology","volume":"23 1","pages":"301"},"PeriodicalIF":4.5,"publicationDate":"2025-10-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145257547","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Requirements for designing cluster randomised control trials to detect suppression of malaria vector population densities.","authors":"Penelope A Hancock, Tin-Yu J Hui, Patric S Epopa, Azize Milogo, Andrew R McKemey, Franck A Yao, Abdoulaye Diabaté, Austin Burt","doi":"10.1186/s12915-025-02414-5","DOIUrl":"https://doi.org/10.1186/s12915-025-02414-5","url":null,"abstract":"<p><strong>Background: </strong>Novel interventions for mosquito-borne disease control which release modified mosquitoes that are sterilised or genetically modified to cause offspring inviability are progressing towards field applications. Cluster randomised control trials (CRCTs) could provide robust assessment of intervention efficacy in suppressing mosquito populations in field environments, but guidance on designing CRCTs to detect mosquito suppression impacts is limited.</p><p><strong>Results: </strong>We developed statistical models to simulate CRCTs, informed by a 5-year time series measuring densities of malaria vector species from the Anopheles gambiae complex in four villages in western Burkina Faso. We estimated requirements for parallel and step wedge designs, varying the targeted vector species, the suppression effect and the monitoring regime. For a suppression effect of 50%, 21-22 clusters were required to detect suppression with 90% power when all An. gambiae complex species were targeted, while 24-26 clusters were required when only An. coluzzii was targeted and 60-66 clusters were required when only An. gambiae was targeted. For stronger suppression effects, required trial sizes depended less on target species, with 9-10 clusters being sufficient to detect a 90% suppression effect. We investigated how reducing sampling effort, by sampling fewer houses and restricting sampling to rainy season months, affected statistical power.</p><p><strong>Conclusions: </strong>Our results provide empirically based guidance for designing CRCTs to evaluate interventions aiming to suppress malaria vector populations.</p>","PeriodicalId":9339,"journal":{"name":"BMC Biology","volume":"23 1","pages":"303"},"PeriodicalIF":4.5,"publicationDate":"2025-10-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145257532","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Chromosome-level genome assembly and Oligo-FISH confirmation of chromosome models for the Tasmanian snow skink Carinascincus ocellatus (Scincidae, Eugongylinae).","authors":"Paul A Saunders, Francisco M C Sassi, Marcelo B Cioffi, Oleg Simakov, Christopher P Burridge, Tariq Ezaz, Erik Wapstra","doi":"10.1186/s12915-025-02402-9","DOIUrl":"https://doi.org/10.1186/s12915-025-02402-9","url":null,"abstract":"<p><strong>Background: </strong>Skinks (Scincidae) are one of the most diverse and ecologically versatile lizard families, making them key models for studying major evolutionary transitions including viviparity, limb reduction, and shifts between modes of sex determination. Despite their diversity and research potential, skinks remain underrepresented in genome databases, limiting comparative studies and our ability to investigate the genetic foundations of their evolutionary diversity.</p><p><strong>Results: </strong>We generated a high-quality chromosome-level genome assembly for the Tasmanian snow skink, Carinascincus ocellatus, using PacBio long-read sequencing and Hi-C scaffolding. We validated the accuracy of chromosome models in this genome using an innovative application of Oligo-FISH, designing thousands of short probes directly from the genome assembly and hybridizing them to a single C. ocellatus metaphase slide. This single-step approach provides direct and independent cytogenetic validation of all 15 chromosomes in the assembly, including microchromosomes, which are broadly recognized as more susceptible to misassembly. We further demonstrate the approach's cross-species utility through comparative cytogenomics and in silico probe alignment to multiple other skink genomes, highlighting its potential for multi-genome validation and comparative analyses.</p><p><strong>Conclusions: </strong>Our study establishes C. ocellatus as a genomic model for skinks and positions Oligo-FISH as a scalable, cost-effective, and broadly applicable approach for chromosome-level genome validation. By applying it across species, we demonstrate the method's potential to support more reliable genome reconstruction and comparative genomic analyses.</p>","PeriodicalId":9339,"journal":{"name":"BMC Biology","volume":"23 1","pages":"300"},"PeriodicalIF":4.5,"publicationDate":"2025-10-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145249861","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"GhAOS integrates circadian rhythm and jasmonic acid signaling to regulate high temperature stress responses in cotton and Arabidopsis.","authors":"Aamir Hamid Khan, Qingyuan Li, Anyu Luo, Huanhuan Ma, Marcin Kiedrzyński, Abdullah Shalmani, Adnan Akbar, Adnan Iqbal, Jing Cao, Longfu Zhu, Xianlong Zhang, Ling Min","doi":"10.1186/s12915-025-02406-5","DOIUrl":"10.1186/s12915-025-02406-5","url":null,"abstract":"<p><strong>Background: </strong>Cotton (Gossypium spp.) cultivation is significantly challenged by high temperatures (HT), especially during reproductive stages, leading to male abortion and yield losses.</p><p><strong>Results: </strong>This study investigated the complex interplay between circadian rhythm (CR), HT, and jasmonic acid (JA) signaling in cotton and Arabidopsis. Disruption of CR led to reduced JA content, triggering bud yellowing and abscission at the tetrad stage (TS) in the HT-sensitive cotton line H05 and longer stigma in Arabidopsis. To elucidate the role of JA under continuous light (CL), targeting the JA biosynthesis gene GhAOS in cotton and using Arabidopsis mutants aos and aoc2 revealed accelerated drying, decreased JA content, and male sterility, alongside altered expression patterns of pivotal bioclock-associated genes (PRR1 and LHY). Additionally, mutant anthers manifested elevated ion leakage and H₂O₂ levels, coupled with reduced activities of antioxidant enzymes SOD and POD during CL + HT stress.</p><p><strong>Conclusions: </strong>Current study investigated the complex interplay between CR, HT, and JA signaling pathways in cotton and Arabidopsis, focusing on their impact on male fertility under HT stress. These findings highlight the importance of JA and CR in plant fitness, crucial for future crop improvement and sustainable agriculture.</p>","PeriodicalId":9339,"journal":{"name":"BMC Biology","volume":"23 1","pages":"297"},"PeriodicalIF":4.5,"publicationDate":"2025-10-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12506428/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145243759","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Review of wing morphology in fossil and modern species of humpbacked flies (Diptera: Phoridae).","authors":"Mélanie C M Herbert, André Nel, Brian V Brown, Antonio Arillo, Brendon E Boudinot, Mónica M Solórzano-Kraemer","doi":"10.1186/s12915-025-02376-8","DOIUrl":"10.1186/s12915-025-02376-8","url":null,"abstract":"<p><strong>Background: </strong>The wing veins of known fossil and living phorids are reduced, making them difficult to homologise. Consequently, different interpretations have led to much confusion over the years. However, veins are crucial for phylogenetic and taxonomy studies, especially for fossils. We addressed these challenges by studying Cretaceous specimens, which exhibit fewer reductions in wing veins compared to modern fauna, along with post-Cretaceous specimens that display recent wing patterns. Furthermore, we examined related families such as Ironomyiidae, Platypezidae, Opetiidae, and Lonchopteridae to show wing similarities to the Phoridae.</p><p><strong>Results: </strong>We propose two wing models that include the majority of veins found in each taxon. The early model (Phoridae sensu lato, including Sciadocerinae + \"†Prioriphorinae\") consists of most Cretaceous species, except †Metopina goeleti from New Jersey amber, which displays a recent pattern. The recent model (Phoridae sensu stricto, i.e. Euphorida) is present in the majority of recent phorids. Based on this new interpretation, we re-evaluate three holotypes of Phoridae: †Euliphora grimaldii, †Prioriphora schroederhohenwarthi, and †Ulrichophora lobata. Additionally, we described a Phoridae specimen belonging to †Prioriphora in the Fouras-Bois Vert amber (France) and a new genus within the Ironomyiidae family in the San Just amber (Spain).</p><p><strong>Conclusion: </strong>The newly proposed wing models facilitate rapid identification of Phoridae wing veins based on their degree of reduction. The two newly described specimens are the first records of these taxa in their respective localities.</p>","PeriodicalId":9339,"journal":{"name":"BMC Biology","volume":"23 1","pages":"298"},"PeriodicalIF":4.5,"publicationDate":"2025-10-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12505603/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145243836","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Signatures in domesticated beet genomes pointing at genes under selection in a sucrose-storing root crop.","authors":"Amar Singh Dhiman, Demetris Taliadoros, Eva H Stukenbrock, J Mitchell McGrath, Nazgol Emrani, Christian Jung","doi":"10.1186/s12915-025-02422-5","DOIUrl":"10.1186/s12915-025-02422-5","url":null,"abstract":"<p><strong>Background: </strong>The genus Beta encompasses important crops such as sugar, table, fodder, and leaf beets. All cultivated beets are believed to have originated from the wild sea beet, B. vulgaris subsp. maritima. Sugar beet, a recent crop dating back nearly 200 years, was selectively bred for enhanced root yield in combination with high sucrose content.</p><p><strong>Results: </strong>We assembled a Beta diversity panel comprising wild and cultivated beet accessions. Whole-genome sequencing identified 10.3 million SNP markers. Four distinct genetic clusters were identified: table beet, sugar beet, Mediterranean sea beet, and Atlantic sea beet. A phylogenetic analysis revealed that cultivated beet accessions were genetically closer to Mediterranean than to Atlantic sea beet and that cultivated beets producing storage roots share a common ancestor. Cultivated beets exhibited genome regions with reduced nucleotide diversity compared to Mediterranean sea beets, indicating selection signatures. These regions contained putative candidate genes with potential roles in root development, suppression of lateral root formation, flowering time, and sucrose metabolism.</p><p><strong>Conclusions: </strong>A yet unknown sucrose transporter on chromosome 6 showed reduced nucleotide diversity exclusively in sugar beet accessions compared to other Beta types with low sucrose content, suggesting its role in sucrose storage. Within a region of high nucleotide diversity between accessions with contrasting root phenotypes, we found two genes encoding auxin response factors, which play a crucial role in root development. We reason these genes to be significant root thickening regulators in root crops.</p>","PeriodicalId":9339,"journal":{"name":"BMC Biology","volume":"23 1","pages":"299"},"PeriodicalIF":4.5,"publicationDate":"2025-10-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12505646/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145243842","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Bending the rules: curvature's impact on cell biology.","authors":"Carole Arnold, Ismail Tahmaz, Marie-Ly Chapon, Hasna Maayouf, Valeriy Luchnikov, Jean-Louis Milan, Fabricio Borghi, Laurent Pieuchot","doi":"10.1186/s12915-025-02416-3","DOIUrl":"10.1186/s12915-025-02416-3","url":null,"abstract":"<p><p>Curvature is a ubiquitous feature in biology, shaping structures at every scale and playing diverse roles in processes ranging from membrane dynamics to tissue organization. In this review, we first introduce briefly the fundamental concepts and mathematical principles of curvature. The second section explores how membrane curvature is perceived by molecular sensors and integrated into cellular responses. The third section examines the effects of curvature on cellular processes and behaviors at the cell-scale, providing a detailed discussion of the underlying mechanisms. Finally, we offer insights into emerging perspectives and highlight the future challenges in unraveling the multifaceted roles of curvature in biology.</p>","PeriodicalId":9339,"journal":{"name":"BMC Biology","volume":"23 1","pages":"296"},"PeriodicalIF":4.5,"publicationDate":"2025-10-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12502368/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145238001","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Species' urbanization time but not present urban tolerance predicts avian fear responses towards human.","authors":"Peter Mikula, Jan Grünwald, Jiří Reif","doi":"10.1186/s12915-025-02427-0","DOIUrl":"10.1186/s12915-025-02427-0","url":null,"abstract":"<p><strong>Background: </strong>Urban environments exert strong pressures on animal behavior, leading to altered fear responses to humans. Species with a longer history of urban presence and greater tolerance to urban environments are expected to show reduced fear responses towards humans. Here, we examined whether avian flight initiation distance (a proxy of fear)-the distance at which a bird flees from an approaching human-is associated with a species' timing of urban colonization (i.e., when it has started to breed in urban areas) and with present-day urban tolerance (i.e., how common it is in the city). Unlike previous studies which paired avian fear responses and urbanization timing from different regions, we collected both in the same city (Prague, Czechia), minimizing regional differences in urban history and providing a more rigorous test of the link between urbanization timing and avian fear responses.</p><p><strong>Results: </strong>Using standardized data from 4420 flight initiation distance observations across 68 species, we applied Bayesian phylogenetic mixed models while controlling for ecological and contextual variables. We found that species with a longer urban history (i.e., earlier timing of urban colonization) showed significantly shorter flight initiation distances, suggesting reduced fear responses. In contrast, present-day urban tolerance based on breeding commonness was not related to flight initiation distance variation.</p><p><strong>Conclusions: </strong>We found that the timing of urban colonization better predicts reduced fear of humans in birds than present-day urban tolerance, emphasizing the role of long-term behavioral filtering and/or selection in shaping urban wildlife behavior. By explicitly separating urbanization time from contemporary urban commonness within a single city and analyzing individual-level fear responses, our study shows that earlier urban colonizers exhibit consistently shorter escape distances, reflecting cumulative long-term processes rather than short-term plasticity alone. These findings highlight the importance of incorporating urban colonization history into behavioral ecology and urban wildlife management frameworks.</p>","PeriodicalId":9339,"journal":{"name":"BMC Biology","volume":"23 1","pages":"295"},"PeriodicalIF":4.5,"publicationDate":"2025-10-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12492597/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145211614","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Temperature variability and other climatic attributes linked to genomic features in the lichen-forming fungal genus Umbilicaria.","authors":"Edgar L Y Wong, Anjuli Calchera, Jürgen Otte, Imke Schmitt","doi":"10.1186/s12915-025-02373-x","DOIUrl":"10.1186/s12915-025-02373-x","url":null,"abstract":"<p><strong>Background: </strong>Many species of lichen-forming fungi exhibit large geographical ranges and broad thermal niches, making them excellent models for investigating the genomics of climate adaptation. In this study, we examined the impacts of climatic variables on genomic features in 11 Umbilicaria species. We compared PacBio genomes of individuals from the same species collected in different climate zones: alpine, cold temperate, or Mediterranean.</p><p><strong>Results: </strong>Our findings revealed several links between climatic and genomic features: (1) Selection pressure: in each climate zone, specific genes are under strong selection. (2) Genomic feature correlations: certain temperature variables (BIO2: mean diurnal range, BIO4: seasonality, BIO6: minimum in coldest month, BIO7: annual range) are correlated with GC content and the usage of the amino acids arginine and valine, suggesting these variables may drive convergent evolution of these genomic features. (3) Temperature variability: bioclimatic variables representing temperature variability, e.g. BIO2,4,7 are more influential in shaping genomic features than temperature means or extrema, with BIO6 also playing a significant role. (4) Epigenetic modifications: the rate of 5-methylcytosine (5mc) methylation within species is generally higher in samples from the colder habitat, suggesting that epigenetic modifications may contribute to climate adaptation.</p><p><strong>Conclusions: </strong>Overall, our study shows that genome evolution is partially shaped by climate and, particularly, temperature variability. This aligns with numerous ecological and climate modelling studies, which show that climate variability has a stronger impact on species behaviour and evolution than climate means and extrema. Further genomics studies are required to provide additional evidence on this topic.</p>","PeriodicalId":9339,"journal":{"name":"BMC Biology","volume":"23 1","pages":"293"},"PeriodicalIF":4.5,"publicationDate":"2025-10-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12492740/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145211710","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}