bioRxiv : the preprint server for biology最新文献

{"title":"ProteomeScout v4: An open-source, harmonized, ecosystem for post-translational modifications.","authors":"Sam Crowl, Saqib Rizvi, Logan Campbell, Alekhya Kandoor, Kristen M Naegle","doi":"10.64898/2026.10.01.756115","DOIUrl":"10.64898/2026.10.01.756115","url":null,"abstract":"<p><strong>Motivation: </strong>There are many databases of post-translational modifications, but each has different protein and PTM coverage, making the current state of post-translational modifications difficult to obtain, assess, or harmonize. ProteomeScout has been a relational database that harmonized a myriad of resources to address this challenge. In this update, we wished to create a lightweight, sustainable open source resource for the community that retained the power of harmonization, protein visualization, and Python tools for interacting with the database.</p><p><strong>Results: </strong>ProteomeScout-v4 presents an ecosystem of open-source tools for aggregating and updating proteins and post-translational modifications and presenting the web-based and code-based access tools for interacting with the data. ProteomeScout has moved from using a complex relational database to a flat-text file format. The database file update is version controlled on FigShare and all features have processes for continuous updating, including migrating PTMs to updated protein records, when external databases are updated. The open-source nature and flexibility allow for user-based control and community-based feature integration. Fast and easy analysis is possible with the API, with example analyses provided here.</p>","PeriodicalId":519960,"journal":{"name":"bioRxiv : the preprint server for biology","volume":" ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2026-10-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13648721/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149168346","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"RSV & rhinovirus coinfection order dictates outcome via type III interferon-mediated interference in infant respiratory epithelium.","authors":"Emily M Schultz, Gina M Aloisio, Ashley Murray, Sathi Wijeyesinghe, Letisha Aideyan, Trevor McBride, David Henke, Laura Ferlic-Stark, Gauri Khade, Oluwadamilola N Oluwo, Hanning Li, Divya Nagaraj, Sarah E Blutt, Vasanthi Avadhanula, Pedro A Piedra","doi":"10.64898/2026.10.01.756024","DOIUrl":"https://doi.org/10.64898/2026.10.01.756024","url":null,"abstract":"<p><p>Coinfection with respiratory syncytial virus (RSV) and rhinovirus (RV) is the most frequently detected coinfection in infants, yet mechanisms governing viral interference and disease outcome remain poorly understood. Although infection order is a key determinant of coinfection outcome involving RSV, influenza, rhinovirus, and SARS-CoV-2, its role in RSV/RV coinfections has not been defined. Using infant-derived human nasal organoids at air-liquid interface, we demonstrate that coinfection order fundamentally determines the outcome of RSV/RV interactions. An initial RSV infection almost completely inhibits secondary RV coinfection, whereas primary RV infection only partially impairs a subsequent RSV coinfection. These distinct outcomes are accompanied by divergent temporal antiviral and pro-inflammatory responses. Mechanistically, we identify type III interferons as a sufficient mediator of RSV-induced restriction of RV, establishing a host-driven mechanism of viral interference. In contrast, partial impairment of RSV following RV infection occurs through an interferon-independent mechanism. Despite marked differences, RSV/RV coinfections do not exacerbate epithelial injury or innate immune responses beyond that induced by RSV alone, indicating RSV is the dominant driver of pathology in coinfections. Collectively, our data establishes coinfection order as a critical determinant of RSV/RV outcome and reveals novel and mechanistic insight into critical viral-host interactions in the infant nasal epithelium.</p><p><strong>Importance: </strong>This study uncovers fundamental differences in infant epithelial control of two major pediatric viral pathogens. We demonstrate for the first time that the order of coinfection fundamentally determines the outcome of RSV-RV interactions within infant respiratory epithelium. By identifying type III interferon as an important regulator of these interactions, our study suggests that differences in interferon susceptibility among respiratory viruses can heavily influence coinfection outcomes. Importantly, despite clear differences in viral interference, RSV/RV coinfections did not produce greater epithelial injury or pro-inflammatory responses than RSV infection alone. Instead, RSV consistently emerged as the dominant driver of epithelial damage and inflammation, providing a mechanistic explanation for clinical observations that RSV/RV coinfections are often not more severe than RSV infection alone.</p>","PeriodicalId":519960,"journal":{"name":"bioRxiv : the preprint server for biology","volume":" ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2026-10-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13648688/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149167796","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Disease-associated mutations directionally modulate epigenetic age in iPSC-derived tissues.","authors":"Nicholas J Skvir, Todd W Dowrey, Samuel F Cranston, Elise MacDonald, Richard Giadone, Dakota Jones, Carly S Golden, Braden Pate, Madeline Labott, Maria A Serrano, Konstantinos-Dionysios Alysandratos, Kim Vanuytsel, George J Murphy","doi":"10.64898/2026.09.30.755445","DOIUrl":"10.64898/2026.09.30.755445","url":null,"abstract":"<p><p>Reprogramming somatic cells into induced pluripotent stem cells (iPSCs) resets epigenetic age, creating a major challenge for modeling age-associated cellular states and limiting the use of iPSCs in aging research beyond the genetic component. Recent work has shown that healthy organoids can re-accumulate age-associated epigenetic states over extended culture; whether disease-associated genetic states can directionally reshape these trajectories after reprogramming remains unknown. Here, we present a reproducible, <i>in-vitro</i> approach to re-establish epigenetic aging trajectories using iPSC-derived organoid systems, as quantified by multiple epigenetic clock models. We first demonstrate that epigenetic age progressively increases with serial passaging in a lung organoid model (alveolospheres). We then show that disease-associated mutations in multiple models drive additional, cell-intrinsic shifts in epigenetic age, implicating disease state as an independent modulator of epigenetic clocks. Together, these findings reinforce that iPSC-derived organoids recapitulate epigenetic aging trajectories over time, while highlighting disease state as a potent and potentially tractable modulator of epigenetic age <i>in vitro</i>. By enabling more faithful modeling of age-associated cellular states, this approach expands the utility of iPSC-based systems for dissecting the molecular mechanisms that regulate human aging.</p>","PeriodicalId":519960,"journal":{"name":"bioRxiv : the preprint server for biology","volume":" ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2026-10-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13648741/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149172017","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Early-life adversity alters the adult blood proteome primarily in female mice.","authors":"Madison M Garvin, Ae Ra Kim, Jessica L Bolton, Yun Liang","doi":"10.64898/2026.09.28.755115","DOIUrl":"https://doi.org/10.64898/2026.09.28.755115","url":null,"abstract":"<p><strong>Background: </strong>Early-life adversity (ELA) is one of the strongest predictors of poor mental and physical health later in life, increasing an individual's risk for disorders ranging from depression to metabolic syndrome. However, whether and how ELA shapes immune memory through adulthood, subsequently affecting susceptibility to immune-associated diseases such as autoimmunity, remains elusive.</p><p><strong>Methods: </strong>To address this question, we employed a translationally and ethologically relevant mouse model of resource deprivation, the limited bedding and nesting model, to study the long-term effects of ELA on the immune system. ELA was induced by limited bedding and nesting material in the cage during postnatal days (P)2-9, which provokes fragmented and unpredictable maternal behavior in the dams, and results in chronic stress in the pups. Nucleic acid Linked ImmunoSandwich Assay (NULISA) was used to survey the proteome of adult (∼P90) mice of both sexes that experienced ELA vs. control conditions.</p><p><strong>Results: </strong>Using a novel proteomic method, we detected significant upregulation in the levels of IL-17A in the adult blood, primarily in females. Within females, ELA also upregulated IL-13 and CCL3. Three proteins, HGF, PDGFA, and WNT16, were significantly downregulated in ELA mice of both sexes.</p><p><strong>Conclusions: </strong>Being a hallmark proinflammatory cytokine, IL-17A is found to increase in patients with systemic lupus erythematosus (SLE), as well as in animals with lupus-like diseases in virtually all reports. Importantly, autoimmune diseases like SLE have a higher prevalence in women than men, and our data support this sex bias. Together, our data suggest that ELA shapes long-term immune function in a way that may increase risk for autoimmune diseases, with promise for the development of more targeted and personalized therapies for autoimmunity.</p>","PeriodicalId":519960,"journal":{"name":"bioRxiv : the preprint server for biology","volume":" ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2026-10-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13648666/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149171616","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Protective near-germline antibodies to malaria elicited by RTS,S/AS01_E vaccination in African infants.","authors":"Emma Bloch, Fiona Devys, Fabien Cannac, Monika Jain, Katrina Broadbent, Carla Sánchez, Wen-Hsin Lee, Chenjerai Jairoce, Pedro Aide, Joseph J Campo, Dídac Macià, Carlo Carolis, Ian A Wilson, Andrew B Ward, Rogerio Amino, Gemma Moncunill, Carlota Dobaño, Luis M Molinos-Albert","doi":"10.64898/2026.10.01.755937","DOIUrl":"10.64898/2026.10.01.755937","url":null,"abstract":"<p><p>Malaria is a leading cause of childhood mortality, yet infant immune responses to vaccination remain poorly understood. Here, we characterize 88 monoclonal antibodies (mAbs) directed against the <i>Plasmodium falciparum</i> circumsporozoite protein cloned from African infants immunized with the RTS,S/AS01_E malaria vaccine, identifying potent antiparasitic mAbs exhibiting molecular features resembling those observed in adults and minimal somatic hypermutation. Importantly, germline-reverted variants of four mAbs inducing sterile protection <i>in vivo</i> maintained high binding affinity and Fab-dependent parasite killing. Structural analyses revealed that a few amino acid replacements drive homotypic helical assemblies, fine-tuning parasite inhibition and protective efficacy. Thus, despite maturational constraints of early life, infants can generate potent antimalarial antibodies in a near-germline configuration, informing next-generation vaccine development for this vulnerable group.</p>","PeriodicalId":519960,"journal":{"name":"bioRxiv : the preprint server for biology","volume":" ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2026-10-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13648702/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149168636","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Developmental Convergence Across Diverse Genetic Architectures in Childhood Apraxia of Speech.","authors":"Tiffanie White, Marjan Chapi, Caitlin Raaz, Laurel Bruce, Akshit Modi, Valentin Dinu, Li Liu, Judith Klein-Seetharaman, Beate Peter","doi":"10.64898/2026.10.03.756424","DOIUrl":"10.64898/2026.10.03.756424","url":null,"abstract":"<p><p>Childhood apraxia of speech (CAS) is a neurodevelopmental disorder of speech-motor planning and programming, associated with literacy, academic, and psychosocial difficulties. We performed whole-exome sequencing in 11 families comprising 21 affected and 15 unaffected individuals with phenotyping spanning speech, language, cognition, literacy, and motor function. We identified 60 prioritized variant observations representing 22 unique variants across 20 genes with family-based segregation analysis assessed in informative relatives; 5 arose <i>de novo</i>. Our cohort included multiple affected siblings and extended relatives, with several families carrying multiple prioritized variants, suggesting cumulative or oligogenic susceptibility. Speech and literacy impairment co-occurred with oral-motor, feeding, and fine-motor difficulties. BrainSpan co-expression analysis identified <i>MECP2</i> and <i>ANK2</i> as the genes with the highest observed connectivity in the sampled postnatal network. Exploratory analysis of the KOLF2.1J perturbation atlas in undifferentiated human induced pluripotent stem cells identified a positive <i>LMO3</i> expression-response score following <i>NIPBL</i> repression and opposing <i>LMO3</i> and <i>ANK2</i> response directions within a cohesin-associated perturbation cluster. These observations motivate testing in human neural cells. Functional enrichment, protein-association, and developmental-expression analyses supported shared biological themes involving chromatin regulation, neuronal signaling, and extracellular-matrix organization. Among six families, multiple affected relatives shared prioritized variants across a unique set of several genes, demonstrating multilocus candidate profiles whose individual and combined effects may contribute to CAS susceptibility. We propose four novel CAS candidate genes-<i>LMO3</i> and <i>PCDH10</i>, previously linked to human accelerated regions, as well as <i>MYCBP2</i> and <i>PTPRS</i>. Our work provides multiple testable hypotheses for future variant-specific functional validation in speech-motor development.</p>","PeriodicalId":519960,"journal":{"name":"bioRxiv : the preprint server for biology","volume":" ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2026-10-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13648706/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149170942","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Trial-by-trial inter-areal interactions in visual cortex in the presence or absence of visual stimulation.","authors":"Dianna Hidalgo, Giorgia Dellaferrera, Giordano Ramos-Traslosheros, Will Xiao, Carlos R Ponce, Maria Papadopouli, Stelios Smirnakis, Gabriel Kreiman","doi":"10.1101/2024.12.05.626981","DOIUrl":"https://doi.org/10.1101/2024.12.05.626981","url":null,"abstract":"<p><p>State-of-the-art computational models of vision focus on fitting trial-averaged spike counts triggered by visual stimuli using overparameterized neural networks. Understanding visual cortex requires predicting the dynamic responses of neurons within and across areas, in single trials, and across different experimental conditions. Here we investigated trial-by-trial inter-areal interactions in the visual cortex by predicting neuronal activity in one area based on activity in another area, including stimulus-driven and non-stimulus-driven activity. We analyzed two datasets: calcium imaging from mouse V1 layers 2/3 and 4, and extracellular neurophysiological recordings from macaque V1 and V4. Neuronal activity could be predicted bidirectionally between L2/3 and L4 in mice, and between V1 and V4 in macaque monkeys, even in the absence of visual stimuli, with distinct contributions for bottom-up and top-down interactions. In mice, we observed a bimodal distribution of neurons, with some neurons primarily driven by visual inputs and others showing predictable activity during spontaneous activity despite lacking consistent visually evoked responses. Predictability depended on the stimulus type, intrinsic neuronal properties, receptive field overlap, and the relative timing of activity across areas. These findings provide initial steps towards computational models that capture the dynamic transformation of neuronal responses throughout visual cortex.</p><p><strong>Impact statement: </strong>Neuronal activity in one visual cortical area can be predicted from another area in single trials, with or without visual stimulation, in both mice and macaques.</p>","PeriodicalId":519960,"journal":{"name":"bioRxiv : the preprint server for biology","volume":" ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2026-10-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13648356/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149170794","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"IgG sequencing maps systemic antibody binding to oral commensals and pathobionts in health and periodontitis.","authors":"Ramin Akhi, Drake Winslow Williams, Teresa Greenwell-Wild, Andrew S Burns, Shreni Mistry, Laurie Brenchley, Nicolas Bouladoux, Ivan Vujkovic-Cvijin, Yasmine Belkaid, Akintunde Emiola, Niki M Moutsopoulos","doi":"10.64898/2026.09.28.753837","DOIUrl":"https://doi.org/10.64898/2026.09.28.753837","url":null,"abstract":"<p><p>The oral cavity harbors one of the body's most diverse microbial communities, which continuously seeds the bloodstream and gastrointestinal tract, particularly in periodontitis, a disease in which both barrier permeability and microbial burden increase. Despite this constant systemic exposure, overt bacteremia from oral organisms is rare, suggesting an active surveillance system that contains this reservoir. Here, we apply IgG-sequencing to comprehensively map mucosal and systemic antibody recognition of the oral microbiome across paired oral fluid and serum from healthy individuals and patients with periodontitis. We find that IgG-binding is only weakly predicted by microbial abundance, suggesting taxon-specific and largely conserved IgG-binding of commensals, many of them streptococci which dominate antibody recognition irrespective of disease state. Periodontitis broadens the repertoire of IgG-bound taxa to include particular disease-associated pathobionts while preserving robust targeting of health-associated symbionts. Comparison of salivary and serum antibody profiles further uncovers a subset of commensal streptococci, including species implicated in infective endocarditis, that acquire disproportionate systemic IgG binding in periodontitis. Together, these findings establish a taxon-level atlas of humoral immunosurveillance at a major mucosal-microbial interface and reveal how periodontal disease reshapes systemic antibody recognition of both pathobionts and commensals.</p>","PeriodicalId":519960,"journal":{"name":"bioRxiv : the preprint server for biology","volume":" ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2026-10-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13648604/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149169569","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Triazole Stress Induces Accelerated Degradation of <i>Aspergillus fumigatus</i> Hmg1.","authors":"Jinhong Xie, Adela Martin-Vicente, Harrison I Thorn, Uxue Perez-Cuesta, Asmita Nandi, Jarrod R Fortwendel","doi":"10.64898/2026.10.02.756251","DOIUrl":"10.64898/2026.10.02.756251","url":null,"abstract":"<p><p>Triazole antifungals inhibit the lanosterol C14-demethylase Cyp51A/B and are the first-line treatment for invasive aspergillosis caused by <i>Aspergillus fumigatus</i>. We previously proposed that triazoles impose a secondary constraint on ergosterol biosynthesis through negative feedback regulation of HMG-CoA reductase (Hmg1) through its sterol sensing domain (SSD), and SSD mutations compromise this regulation to produce resistance. The molecular mechanism underpinning this feedback remained unknown. In this study, we show that voriconazole drives accelerated protein degradation of Hmg1 and that SSD mutation abolishes this regulated degradation. Triazole-induced Hmg1 degradation is proteasome-dependent and partially requires the ERAD E3 ubiquitin ligase, HrdA, and INSIG ortholog, InsA, both conserved regulators of HMG-CoA Reductase abundance. We provide genetic evidence that the initiating negative feedback signal is not triazole acting directly on Hmg1 but lanosterol accumulation resulting from Cyp51A/B inhibition. To test whether depleting Hmg1 protein could re-sensitize resistant strains, we utilized a GFP-targeted degradation system designed to target Hmg1 for degradation without engaging its SSD. Combining this system with voriconazole treatment reduced the MIC at least four-fold in both conidia and established hyphae in susceptible and resistant strains. Together, our findings support a model wherein triazole-induced lanosterol accumulation drives HrdA/InsA-dependent accelerated degradation of Hmg1 and establish that pharmacologically inducing this secondary mechanism can enhance triazole activity in both susceptible and resistant isolates.</p>","PeriodicalId":519960,"journal":{"name":"bioRxiv : the preprint server for biology","volume":" ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2026-10-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13682438/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149240964","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Motor Occupancy Defines Emergent Mechanical States in Cardiac Myosin Ensembles.","authors":"Omayma Y Alazzam, Md Amzadul Hoque Chowdhury, Heath M Stevens, Dana N Reinemann","doi":"10.64898/2026.07.17.739215","DOIUrl":"10.64898/2026.07.17.739215","url":null,"abstract":"<p><p>Myosin II generates force through the collective action of mechanically coupled motor ensembles, yet the mechanisms by which these ensembles sense changes in motor occupancy and coordinate force generation remain poorly understood. Ensemble force production may be governed by an optimal balance between effective motor occupancy and mechanical coordination rather than by motor number alone. We reconstituted cardiac myosin ensembles and systematically perturbed effective motor occupancy using the small-molecule drugs omecamtiv mecarbil (OM), which prolongs actomyosin interactions, and mavacamten (MAVA), which reduces the number of available force-generating myosin heads. Optical trapping measurements of full-length and S1 cardiac myosin ensembles revealed that force generation depended on both myosin concentration and pharmacological perturbation. Reducing myosin concentration increased force generation in the absence of drug, while OM and MAVA produced responses that varied with the initial occupancy state of the ensemble. Low concentrations of MAVA enhanced force generation under high motor occupancy but reduced force under low motor occupancy, whereas OM produced occupancy-dependent changes in both endpoint force and force dynamics. Force traces further revealed changes in the persistence and temporal coordination of force generation. These findings support a model in which cardiac myosin ensembles operate along an occupancy-coordination landscape, where maximal force generation is achieved at an intermediate level of effective motor occupancy. Our results illuminate how changes in motor occupancy are translated into coordinated ensemble mechanics and suggest that emergent mechanical feedback through the shared actin filament may enable ensembles to collectively sense and adapt to their mechanical state.</p><p><strong>Statement of significance: </strong>Force generation by muscle emerges from the coordinated activity of myosin ensembles, yet the principles governing this collective behavior remain poorly understood. Using an in vitro force assay with full-length and truncated cardiac myosin, we systematically perturbed ensemble activity by varying myosin availability and pharmacologically altering the fraction of force-generating motors. We find that force production depends on an optimal balance of motor engagement rather than a simple increase or decrease in active motors, demonstrating that collective mechanical output arises from coordinated interactions within the ensemble. These findings reveal emergent design principles that govern molecular motor function and establish effective motor occupancy as a key regulator of collective force generation, providing new insight into the mechanisms underlying muscle contractility.</p>","PeriodicalId":519960,"journal":{"name":"bioRxiv : the preprint server for biology","volume":" ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2026-10-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13405130/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148611938","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}