BMC Biology最新文献

{"title":"Cardiac cycle shapes spinal cord excitability.","authors":"Nikolay Syrov, Polina Morozova, Anna Popova, Elizaveta Melashenko, Renat Takhirov, Alfia Mustafina, Asma Benachour, Lev Yakovlev, Mikhail Knyshenko, Alexander Kaplan","doi":"10.1186/s12915-026-02752-y","DOIUrl":"10.1186/s12915-026-02752-y","url":null,"abstract":"<p><strong>Background: </strong>The heart exerts a rhythmic influence on the nervous system, modulating neural excitability throughout the cardiac cycle. Although cardiac-phase effects on cortical excitability have been extensively studied, the temporal profile and mechanisms of cardiac-cycle modulation of spinal excitability remain largely unknown. Addressing this gap is important both for a more complete understanding of heart-brain interactions and for development of neurostimulation-based rehabilitation strategies.</p><p><strong>Results: </strong>We investigated cardiac-phase-dependent modulation of cervical spinal excitability in 20 healthy volunteers using real-time, heart-rate-adapted trans-spinal magnetic stimulation (TSMS). Single-pulse TSMS was delivered at five cardiac phases (0%, 15%, 30%, 60%, and 85% of the RR interval), spanning systole and diastole. Motor-evoked potential (MEP) amplitude served as an index of spinal excitability. Linear mixed-effects models (LMMs) were used to assess cardiac-phase effects while controlling for RR-intervals duration and respiratory phase. MEP amplitudes varied significantly across the cardiac cycle, with maximal facilitation during mid-diastole (60% of the RR interval). This temporal profile contrasts with the systolic facilitation previously reported for cortical excitability. Additionally, LMM showed that preceding RR-interval duration was significantly associated with spinal excitability, whereas respiratory phase was not.</p><p><strong>Conclusions: </strong>We discuss our findings in the context of two non-exclusive mechanisms: (1) physiological modulation via baroreflex-related pathways and (2) mechanical displacement of the spinal cord within the cardiac cycle. Our findings highlight the importance for future studies of heart-nervous system interactions to account for both mechanisms, as each has implications for understanding of how neurostimulation-based treatments work and for developing advanced clinical protocols.</p>","PeriodicalId":9339,"journal":{"name":"BMC Biology","volume":"24 1","pages":""},"PeriodicalIF":5.4,"publicationDate":"2026-10-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13663046/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149179506","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":"Odorant receptor structures predict the major female sex pheromone component in a moth.","authors":"Arthur Comte, Zhiqiang Wei, Hui Li, Wen-Zhe Xing, Riccardo Moracci, Jin Zhang, Sébastien Fiorucci, Emmanuelle Jacquin-Joly","doi":"10.1186/s12915-026-02717-1","DOIUrl":"10.1186/s12915-026-02717-1","url":null,"abstract":"<p><strong>Background: </strong>Species isolation in insects can be ensured by prezygotic barriers, such as species-specific sex pheromone blends that mediate sexual attraction and mate recognition. Yet, sex pheromone compositions of many species remain poorly characterized outside important agricultural pests, because of the necessity to access live insects for pheromone extraction, the difficulties in identifying the production period, and the precise identification of behaviorally relevant compounds in extracts.</p><p><strong>Results: </strong>Here, we use an odorant receptor (OR)-guided approach to identify the major female sex pheromone component of the previously unexplored lily moth, Spodoptera picta. Genome analysis identified S. picta orthologs of the pheromone receptors OR5 and OR75, previously characterized in S. litura and S. littoralis. Structural modeling of OR5 and OR75 combined with molecular docking predicted conserved ligand binding to (Z,E)-9,11-14:OAc, which was confirmed by functional assays on the ORs. Gas chromatography-mass spectrometry analyses of female pheromone gland extracts identified this compound as the major pheromone component, and electrophysiological and behavioral assays further demonstrated that it elicits antennal responses and is sufficient to attract males.</p><p><strong>Conclusions: </strong>Together, these results establish an innovative receptor structure-based strategy for pheromone identification in non-model species, provide insights into the sexual chemical ecology of S. picta, and clarify the evolutionary pathway by which a unique class of pheromone receptors emerged by gene duplication and gained specificity.</p>","PeriodicalId":9339,"journal":{"name":"BMC Biology","volume":"24 1","pages":""},"PeriodicalIF":5.4,"publicationDate":"2026-09-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13591803/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149011933","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":"Foxn1 regulates epidermal structure, redox balance, and age related changes.","authors":"Sylwia Machcinska-Zielinska, Marta Kopcewicz, Joanna Wisniewska, Karla Valdivieso, Mikolaj Ogrodnik, Katarzyna Walendzik, Barbara Gawronska-Kozak","doi":"10.1186/s12915-026-02737-x","DOIUrl":"10.1186/s12915-026-02737-x","url":null,"abstract":"<p><strong>Background: </strong>Skin aging is a complex process, marked by structural decline, functional impairment, and diminished regenerative capacity. In this study, we shine a spotlight on the transcription factor Foxn1 and its pivotal role in modulating age-related changes in skin architecture and redox homeostasis. Using a murine model across three life stages (young - 20-days-old, middle-age - 1-year-old, old - 2-year-old), we compared wild-type (Foxn1^+/+) and Foxn1 heterozygotic knock out (Foxn1^+/-) mice to unravel the interplay between genetic regulation and skin aging.</p><p><strong>Results: </strong>Our findings reveal a striking impact of Foxn1 on skin morphology: Foxn1^+/- mice displayed thinner epidermis, thicker dermis, and disrupted keratinocyte differentiation, favoring large spinous layer of epidermal cells. Notably, the skin of Foxn1^+/+ mice was associated with increased collagen I and a shift toward repair-oriented fibers, whereas Foxn1^+/- skin maintained elevated collagen III, hinting at a preserved regenerative profile. Additionally, while p21 expression rose with age in Foxn1^+/+ mice, it remained low in Foxn1^+/- mice, suggesting an altered senescence pathway. Intriguingly, Foxn1 also emerged as a modulator of the hypoxia response, oxidative stress levels, and cellular protection, particularly in young and middle-age mice. These effects diminished with advanced age, underscoring Foxn1's age-dependent regulatory dynamics.</p><p><strong>Conclusions: </strong>Together, these results position Foxn1 as one of key regulators of skin homeostasis and reveal its potential role in skin aging processes.</p>","PeriodicalId":9339,"journal":{"name":"BMC Biology","volume":"24 1","pages":""},"PeriodicalIF":5.4,"publicationDate":"2026-09-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13660126/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149165582","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":"Pluripotency, differentiation, and reprogramming: 20 years of induced pluripotent stem cells.","authors":"Sarah J Hainer, Stanley E Strawbridge, Sekyu Choi, Ge Guo, Masaki Kinoshita, Chengchen Zhao, Fan Zhou","doi":"10.1186/s12915-026-02712-6","DOIUrl":"10.1186/s12915-026-02712-6","url":null,"abstract":"","PeriodicalId":9339,"journal":{"name":"BMC Biology","volume":"24 1","pages":""},"PeriodicalIF":5.4,"publicationDate":"2026-08-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13505079/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148812038","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":"Peptide language pragmatic analysis and two-stage hierarchical learning framework for therapeutic peptide prediction.","authors":"Ke Yan, Siyan Lu, Shutao Chen, Yunjie Wang, Alexey K Shaytan, Zhen Li, Bin Liu","doi":"10.1186/s12915-026-02642-3","DOIUrl":"10.1186/s12915-026-02642-3","url":null,"abstract":"<p><strong>Background: </strong>Therapeutic peptides exert pivotal effects in diverse biological processes, and have attracted significant interest in the field of biomedicine in recent years. However, most existing methods often fail to adequately capture the intricate interactions among amino acid residues and the contextual dependencies within peptide sequences, which hampers the extraction of deep semantic representations and ultimately restricts predictive performance. Moreover, the task of multi-functional therapeutic peptide prediction is inherently constrained by the challenge of imbalanced multi-label classification resulting from long-tailed distribution patterns.</p><p><strong>Results: </strong>In this study, we propose a two-stage hierarchical deep learning framework, named TPpred-PepPA, for the prediction of multi-functional therapeutic peptides based on pragmatic analysis. Specifically, ProtT5 is employed to extract deep semantic representations that capture residue-level contextual information. In the first stage, a transformer-based network is utilized to perform shared representation learning, wherein the encoder model captures the intricate inter-residue interaction to characterize the contextual semantics of peptide sequences. In the second stage, the framework is fine-tuned by incorporating task-specific classifiers and optimizing the classification decision with Asymmetric Loss. Then the dynamic thresholding strategy is utilized to address the long-tail distribution problem, enabling more accurate prediction performance of multi-functional therapeutic peptide. Moreover, we adopted the SHAP analysis and motif identification to interpret feature contributions and identify key functional peptide fragments, respectively. Our experimental results indicate that TPpred-PepPA significantly outperforms all current baseline methods in identifying multi-functional therapeutic peptides and exhibits robust performance in recognizing rare functional categories.</p><p><strong>Conclusion: </strong>We developed TPpred-PepPA, a two-stage hierarchical deep learning framework based on the ProtT5 pre-trained large language model. Compared with existing methods, TPpred-PepPA achieves state-of-the-art predictive performance and provides valuable interpretability for the discovery of multi-functional therapeutic peptides. Finally, a web server has been established and is accessible at http://bliulab.net/TPpred-PepPA .</p>","PeriodicalId":9339,"journal":{"name":"BMC Biology","volume":"24 1","pages":""},"PeriodicalIF":5.4,"publicationDate":"2026-08-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13471556/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148720040","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":"Rhobot-Screen: an integrated robotic platform for functional screening of rhodopsin variants.","authors":"Takashi Nagata, Masae Konno, Daisuke R Hashimoto, Keiichi Inoue","doi":"10.1186/s12915-026-02691-8","DOIUrl":"10.1186/s12915-026-02691-8","url":null,"abstract":"<p><strong>Background: </strong>Rhodopsins are photoreceptive membrane proteins widely used as optogenetic tools in basic research and medical applications, and extensive mutational studies have been performed to improve or modify their functional properties. Recently, in the broader field of protein engineering, data-driven strategies based on machine learning have attracted increasing attention, as they enable efficient exploration of vast mutational spaces with a reduced number of experiments. Such approaches require large, consistent datasets that link predefined mutations to quantitative functional properties, which necessitates systematic construction and characterization of targeted variants rather than random mutagenesis. For rhodopsins, however, generating these datasets remains challenging due to operator-dependent, non-integrated workflows that are difficult to scale and standardize.</p><p><strong>Results: </strong>To address this limitation, we developed an automated screening platform termed Rhobot-Screen, based on a robotic liquid-handling workstation, which integrates multiple experimental steps into a standardized workflow with reduced dependence on operator-specific expertise. This platform performs site-directed mutagenesis, plasmid preparation, protein expression in bacterial and mammalian cultured cells, and functional characterization in a 96-well format through automated liquid-handling operations. For spectroscopic characterization, we established a 96-well plate-based hydroxylamine bleaching assay that determines absorption maximum wavelengths without protein purification. As a demonstration of the platform, we comprehensively mutated three established color-tuning residues in Gloeobacter rhodopsin, generating 57 single-point variants. Using Rhobot-Screen, the absorption maxima of 46 variants were successfully determined. The resulting dataset revealed position-dependent relationships between spectral shifts and amino acid physicochemical properties, with clear correlations between absorption wavelength and side-chain volume at positions 129 and 256, but not at position 226. The platform was further extended to mammalian cell-based assays for functional characterization of animal rhodopsins.</p><p><strong>Conclusions: </strong>Rhobot-Screen provides an integrated workflow in which all liquid-handling steps for systematic construction and spectroscopic characterization of rhodopsin variants are automated in a 96-well plate format under standardized conditions. By automating and standardizing multiple operator-dependent steps, the platform provides a reproducible framework for acquiring quantitative sequence-function data from predefined rhodopsin variants. This framework should support both mechanistic studies of rhodopsins and future data-driven engineering of rhodopsin functions.</p>","PeriodicalId":9339,"journal":{"name":"BMC Biology","volume":"24 1","pages":""},"PeriodicalIF":5.4,"publicationDate":"2026-08-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13445694/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148677356","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":"Publisher Correction: Sibling cooperation in boreal owls during the post-fledging dependence period.","authors":"Marek Kouba, Simona Stehlíková Sovadinová, Filip Tulis, Michal Ševčík, Jitka Bartošová, Erkki Korpimäki, Luděk Bartoš","doi":"10.1186/s12915-026-02702-8","DOIUrl":"10.1186/s12915-026-02702-8","url":null,"abstract":"","PeriodicalId":9339,"journal":{"name":"BMC Biology","volume":"24 1","pages":""},"PeriodicalIF":5.4,"publicationDate":"2026-07-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13420857/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148629532","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":"Nanopore sequencing reveals coordinated host and microbiome responses across barley genotypes.","authors":"Bennet Rohan Fernando Devasahayam, Thomas McNeil, Tesfaye Wubet, Thomas Schmutzer","doi":"10.1186/s12915-026-02688-3","DOIUrl":"10.1186/s12915-026-02688-3","url":null,"abstract":"<p><strong>Background: </strong>Barley (Hordeum vulgare L.) provides a suitable model for studying domestication-driven plant-microbiome interactions. Although wild, landrace, and modern genotypes host distinct rhizosphere communities, the extent to which roots and microbes reciprocally influence each other remains unclear. Here, we applied an integrated multi-omics approach combining long-read metagenomics, root transcriptomics, and plant genomics to understand genotype-specific host-microbiome coordination.</p><p><strong>Results: </strong>Oxford Nanopore whole metagenome sequencing (WMS) revealed genotype-associated shifts in rhizosphere communities across seasons. Functional profiling showed a conserved metabolic backbone including amino acid metabolism, energy production, and secondary metabolite biosynthesis, alongside genotype-dependent variation in carbohydrate metabolism and transport-associated pathways. Genome-resolved analysis through metagenome-assembled genomes (MAGs) further detailed the taxonomic and functional architecture of key rhizosphere lineages. Root transcriptome profiling identified extensive differential expression associated with microbial perception, signaling, defense, and metabolic processes. Integration of host and microbiome data revealed coordinated molecular patterns, indicating that barley genotypes are associated with distinct microbial assemblages and corresponding transcriptional responses.</p><p><strong>Conclusions: </strong>These findings indicate that domestication has shaped coordinated associations between barley genotypes and their rhizosphere microbiomes, reflected in both microbial community composition and host transcriptional regulation. This work provides new insights into the evolutionary tuning of plant-microbiome relationships and highlights opportunities for microbiome-informed strategies in barley improvement.</p>","PeriodicalId":9339,"journal":{"name":"BMC Biology","volume":"24 1","pages":""},"PeriodicalIF":5.4,"publicationDate":"2026-07-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13425779/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148629541","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":"Author Correction: Streptococcus suis avian expansion suggests shared antibiotic use drives host jumps.","authors":"Muriel Dresen, Gemma G R Murray, Peter Valentin-Weigand, Marcus Fulde, Lucy A Weinert","doi":"10.1186/s12915-026-02692-7","DOIUrl":"10.1186/s12915-026-02692-7","url":null,"abstract":"","PeriodicalId":9339,"journal":{"name":"BMC Biology","volume":"24 1","pages":""},"PeriodicalIF":5.4,"publicationDate":"2026-07-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13411667/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148599369","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":"Deeply conserved and expressed small ORFs in the model beetle Tribolium castaneum.","authors":"Diego Guerra-Almeida, Jonathan Javier Mucherino-Muñoz, Evenilton Pessoa Costa, Mariana Freitas Nery, Diogo Antonio Tschoeke, Rodrigo Nunes-da-Fonseca","doi":"10.1186/s12915-026-02686-5","DOIUrl":"10.1186/s12915-026-02686-5","url":null,"abstract":"<p><p>Small open reading frames (small ORFs/smORFs/sORFs) were historically overlooked due to their short length (< 100 codons) and detection challenges. It is widely accepted that small ORFs are rarely conserved across distant taxa, particularly in deeply rooted ancestors. However, growing evidence supports their biological relevance and potential roles in gene innovation. Integrating genomic, transcriptomic, and proteomic datasets, we identified and characterized 454 putative small ORFs in Tribolium castaneum. Conservation analyses revealed 230 potential orthologs within Coleoptera, 167 in insects, 85 in arthropods, 39 in eukaryotes, and six in bacteria. Conserved small ORFs displayed higher GC content (~ 44.87%), with bacterial-conserved sequences exceeding 50%. Functional enrichment revealed dozens of small ORFs associated with catalytic, transporter, structural, and regulatory roles. Binding site predictions indicated 254 small ORFs possess protein-protein interaction potential. Expression profiles across 14 RNA-seq libraries spanning multiple developmental stages showed 40.1% of small ORFs expressed (TPM > 1) in at least one sample, and 16.5% expressed in five or more libraries. Conserved small ORFs showed broader, stable expression, while lineage-specific genes displayed restricted expression, mostly in gonads or embryos. Isoformic and small CDSs (coding DNA sequences) were the most widely expressed classes. Notably, 29 small ORFs exhibited transcriptional and translational support (Swiss-Prot/Ribo-seq), 28 being small CDSs. Furthermore, 390 small ORFs had potential paralogs, some homologous to described proteins. Our findings highlight the small ORF diversity and provide a framework for distinguishing conserved small proteins from lineage-specific candidates, emphasizing the need for experimental validation to determine their functional relevance and evolutionary significance.</p>","PeriodicalId":9339,"journal":{"name":"BMC Biology","volume":"24 1","pages":""},"PeriodicalIF":5.4,"publicationDate":"2026-07-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13670568/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149191414","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}