Biology subjects

Yuan, J.

Publications and source records attributed to Yuan, J..

At least 37 records · Page 2Linked to original sources

bioRxiv2026

Vagus Nerve Stimulation Ameliorates Epilepsy via a Gut Microbiota-Butyrate-Vagus Nerve-Brain Axis

Vagus nerve stimulation (VNS) is an established therapy for drug-resistant epilepsy, yet its mechanism remains partially understood. Here, through an integrated clinical-translational approach, we demonstrate that VNS modulates the gut microbiome and alter the level of butyrate to reduce seizure susceptibility via vagus nerve-dependent signaling. In a longitudinal cohort of epilepsy patients, VNS enriched short-chain fatty acid-producing bacteria, including Akkermansia muciniphila, Prevotella, Alistipes, and Odoribacter. Among clinical responders, fecal butyrate levels decreased concomitantly with an increase in plasma butyrate concentrations. Fecal microbiota transplantation from post-VNS patients into mice reduced seizure severity and improved gut barrier integrity. In a murine model of epilepsy, VNS similarly increased the abundance of Akkermansia and plasma butyrate concentrations, decreased fecal butyrate levels, and abolished its antiseizure effects upon vagotomy. Either colonization with Akkermansia muciniphila or exogenous butyrate supplementation was sufficient to reduce seizures and anxiety-like behavior, effects that also required intact vagal signaling. Our findings define a microbiota-butyrate-vagal pathway essential for the therapeutic effects of VNS, highlighting the gut-brain axis as a target for epilepsy treatment. GRAPHICAL ABSTRACT O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=200 SRC="FIGDIR/small/707138v1_ufig1.gif" ALT="Figure 1"> View larger version (75K): org.highwire.dtl.DTLVardef@8243e6org.highwire.dtl.DTLVardef@37f0e6org.highwire.dtl.DTLVardef@a8b321org.highwire.dtl.DTLVardef@1887342_HPS_FORMAT_FIGEXP M_FIG C_FIG HIGHLIGHTSO_LIVagus nerve stimulation (VNS) remodels the gut microbiota and alter the level of butyrate. C_LIO_LIVNS enriches short-chain fatty acids-producing bacteria, specifically Akkermansia muciniphila, in both humans and mice. C_LIO_LITransplantation of VNS-conditioned microbiota confers seizure protection and restores gut barrier integrity. C_LIO_LIAkkermansia muciniphila or exogenous butyrate is sufficient to reduce seizures via a vagus nerve-dependent pathway. C_LI

neuroscience↗

bioRxiv2026

T2T Genome and Population Resequencing Reveal OfCCD4 Alleles Orchestrate Petal Color and Scent in Osmanthus fragrans

Osmanthus fragrans is prized for its floral color and fragrance, both key targets for genetic improvement. However, the lack of a complete genome assembly and comprehensive population structure hinders gene dissection and marker development for breeding. To investigate the genetic basis of color-scent interaction, a telomere-to-telomere (T2T) genome assembly is generated, and whole-genome resequencing of 100 cultivars is performed. Integrative population and metabolomic analyses reveal a trade-off: orange-red ( Aurantiacus) cultivars accumulate high /{beta}-carotene but low aromatic apocarotenoids (/{beta}-ionone), while yellow-white cultivars show the opposite pattern. Divergence mapping identifies OfCCD4 as the major underlying locus. Three alleles are characterized--functional (A), partially functional (aDel), and a frameshift null (aStop)--with aStop strictly co-segregating with the Aurantiacus phenotype. Transient and stable transformations confirm that A and aDel cleave /{beta}-carotene into /{beta}-ionone, while aStop abolishes this activity. A co-dominant PCR marker is developed based on allele-specific polymorphisms. OfCCD4 is thus established as the key regulator of the color-scent trade-off in osmanthus. The identified alleles and molecular marker enable rapid, low-cost genotyping at the seedling stage--offering particular value for marker-assisted selection in ornamental breeding, where extended juvenility makes phenotypic selection highly time- and resource-intensive.

plant biology↗

bioRxiv2026

SPCoral: diagonal integration of spatial multi-omics across diverse modalities and technologies

Spatial multi-omics is indispensable for decoding the comprehensive molecular landscape of biological systems. However, the integration of multi-omics remains largely unresolved due to inherent disparities in molecular features, spatial morphology, and resolution. Here we developed SPCoral for diagonal integration of spatial multiomics across adjacent slices. SPCoral extracts spatial covariation patterns via graph attention networks, followed by the use of optimal transport to identify high-confidence anchors in an unsupervised, feature-independent manner. SPCoral utilizes a crossmodality attention network to enable seamless cross-resolution feature integration alongside robust cross-omics prediction. Comprehensive benchmarking demonstrates SPCorals superior performance across different technologies, modalities and varied resolutions. The integrated multi-omics representation further improves spatial domain identification, effectively augments experimental data, enables cross-modal association analysis, and facilitates cell-cell communication. SPCoral exhibits good scalability with data size, reveals biological insights that are not attainable using a single modality. In summary, SPCoral offers a powerful framework for spatial multi-omics integration across various technologies and biological scenarios.

bioinformatics↗

bioRxiv2026

Glucose hypometabolism and hyperphosphorylated Tau synergistically drive neuronal necroptosis

The combination of brain glucose hypometabolism and hyperphosphorylated Tau (p-Tau) pathology is the strongest known clinical predictor of imminent cognitive decline, yet how these factors cooperate to drive dementia remains unknown. Here, we show that glucose hypometabolism synergizes with p-Tau to trigger neuronal loss through necroptosis. Under low-glucose conditions, accumulated p-Tau forms a molecular scaffold that directly recruits the necroptotic kinase RIPK1, while concomitant loss of the necroptosis checkpoint protein A20 removes a critical brake on this death pathway. This dual mechanism thereby precipitates neuronal necroptosis independent of classical TNF/TNFR1 signaling paradigm. Restoring A20 expression with acetyl-L-carnitine as a dietary supplement or preventing the p-Tau - RIPK1 interaction using a RIPK1 derived competitive peptide alleviates neuronal necroptosis and brain atrophy in a Tau transgenic mouse model. Collectively, our findings uncover a previously unrecognized metabolism-driven necroptotic signaling cascade initiated by a p-Tau-RIPK1 hub, providing mechanical insight into how glucose hypometabolism synergizes with p-Tau to drive neurodegeneration.

neuroscience↗

bioRxiv2026

Wetting-mediated extracellular phase separation drives long-range cell adhesion

Cells must efficiently locate and engage for tissue formation and immune coordination, yet classical receptor-ligand binding is limited to nanometre distances and is inherently slow [1-3]. Here, we uncover a previously unrecognised physical principle, liquid-like adhesion by phase separation (LAPS). This process creates dynamic wetting layers on cell surfaces [4, 5], functioning as "liquid bridges" that enable robust, long-range cell capture across tens of micrometres. Remarkably, this wetting-mediated attraction remains effective at nanomolar concentrations--conditions where bulk phase separation would not be expected--and facilitates high-fidelity cell sorting through competitive wetting. By integrating aqueous two-phase systems, endogenous proteins (Galectin-3, CCL5), and fluid-particle-dynamics simulations [6], we demonstrate that extracellular liquid-liquid phase separation not only mediates long-range cell capture but also acts as a physical catalyst for contact-dependent signaling. These findings establish extracellular phase separation as a key physical principle complementing molecular recognition in multicellular systems, offering new opportunities for understanding immune response, tissue morphogenesis, and therapeutic strategies targeting the extracellular environment [7, 8].

biophysics↗

bioRxiv2026

Bioarchaeological evidence for commensal brown rats (Rattus norvegicus) in early Neolithic China

Due to its commensal relationship with humans, facilitating its dispersal from its natural range in East Asia, the brown rat (Rattus norvegicus) is now one of the most cosmopolitan and invasive mammals. Brown rats are also vectors of human pathogens and the most commonly used mammalian model (after mice) for biomedical research. Despite their major role in biodiversity loss and medicine, our understanding of a likely origin for their commensal relationship with humans in China still relies on modern population genetics, without a reliable timeframe of localisation. In this research, we have tried to fill this gap using direct information from the archaeological remains of rats collected by Chinese colleagues in several archaeological sites dated between 9000 and 3500 BP. Thanks to high-resolution morphometrics and direct 14C dating, we have identified the occurrence of the brown rat (Rattus norvegicus) within the domestic area deposits of the early Neolithic site of Jiahu by 7500 cal BP, suggesting a tentative link between rice agriculture and an early commensal behaviour of this species.

zoology↗

bioRxiv2025

A Generative Foundation Model for Cryo-EM Densities

Single-particle cryo-electron microscopy (cryo-EM) enables structure determination of macromolecular complexes, yet reconstructions are often degraded by noise, anisotropic sampling and reconstruction artifacts. Correcting these effects is an ill-posed inverse problem that requires strong prior knowledge in addition to experimental data. Here we introduce cryoFM, a generative foundation model for cryo-EM densities that unifies data-driven structural priors with dataset-specific constraints within a Bayesian inference framework. CryoFM is trained in an unsupervised manner on thousands of high-quality cryo-EM maps using flow matching, learning a generalizable prior over macromolecular density distributions. Combined with explicit likelihood models describing experimental degradations, cryoFM enables flow posterior sampling, an inference-only procedure that performs denoising and restoration and refinement while remaining explicitly constrained by dataset-derived statistics. We show that this framework improves density reconstruction and refinement across diverse experimental settings, including preferred-orientation datasets and cases with strong spatial heterogeneity in signal-to-noise ratio, without introducing hallucinated features. In addition, cryoFM can be fine-tuned into conditional generative models for density post-processing, yielding maps with improved interpretability and fewer artifacts compared to existing supervised approaches. Together, cryoFM establishes generative foundation models as a principled and controllable framework for cryo-EM density reconstruction and modification.

biophysics↗

bioRxiv2025

The NuRD complex shapes RNA polymerase III activity at highly expressed tRNA gene clusters, tuning the dynamic range of cellular tRNA pools

RNA polymerase III (Pol III) produces noncoding RNAs involved in diverse cellular activities, including translation (tRNA, 5S rRNA, 7SL RNA), RNA processing (U6 snRNA, RPPH1, RMRP), and transcription regulation (7SK snRNA). In this way, Pol III activity must be broadly coupled with cellular demands for protein accumulation and growth, increasing in response to nutrient availability and decreasing during differentiation and exit from proliferation. However, the currently established mechanisms of Pol III regulation remain relatively limited, due in part to the few Pol III-centered protein-protein interaction (PPI) studies performed to date. To address this gap, we first investigated PPIs shared by multiple Pol III subunits to understand the macromolecular interactome of Pol III, with special attention directed at potential regulatory candidates. Our proteomic survey uncovers interactions between Pol III and the NuRD (Nucleosome Remodeling and Deacetylase) complex. Taken further, we show that NuRD localizes to active Pol III-transcribed genes and that its recruitment is Pol III-dependent but nonrandom, with peak occupancy and regulatory hallmarks converging on tRNA gene clusters associated with notably high expression levels. Inhibiting NuRD-associated histone deacetylase function reduces Pol III transcription at these sites, suggesting NuRD restricts Pol III and thereby modulates the global dynamic range of Pol III-derived RNA species. These findings are congruent with the transcriptionally repressive nature of NuRD and bring-to-light a new regulatory mechanism that may couple signaling events and changes in metabolic needs with the dynamic availability of specific tRNA pools.

molecular biology↗

bioRxiv2025

Noninvasive enrichment of circulating tumor biomarkers in a mouse model of diffuse midline glioma using focused ultrasound

BackgroundDiagnosing diffuse midline glioma (DMG) through invasive tissue biopsies is challenging due to the tumors eloquent location at the pons. Liquid biopsies offer a promising noninvasive alternative; however, their limited detection sensitivity and lack of information on the source of biomarkers pose great challenges. This study aimed to evaluate the feasibility and safety of using focused ultrasound (FUS) with microbubbles to enrich circulating DMG tumor biomarkers in blood and cerebrospinal fluid (CSF) using a mouse model. MethodsMurine DMG cells, transfected with enhanced green fluorescent protein (EGFP) and firefly luciferase (Fluc) genes, were orthotopically injected into the mouse brain. Magnetic resonance imaging was used to guide FUS targeting of the DMG tumor. Droplet digital PCR assays were developed to detect circulating tumor DNA (ctDNA) and RNA (ctRNA) of EGFP and Fluc in blood and CSF samples collected after FUS. ResultsFUS enhanced the plasma levels of EGFP ctRNA by 5.4-fold (p=0.0112), compared with liquid biopsy without FUS. CSF EGFP ctDNA was increased by 2.5-fold (p=0.0253), and Fluc ctDNA was increased by 2.6-fold (p=0.0253) with FUS. No brain tissue damage was associated with FUS sonication. ConclusionsThis study demonstrated the feasibility and safety of FUS in enriching tumor biomarkers in blood and CSF in a mouse model of DMG. The enrichment ratio for circulating biomarkers depends on the source (plasma vs. CSF), analyte type (ctDNA vs. ctRNA), and individual marker (EGFP vs. Fluc). These findings support the potential future application of FUS to advance the diagnosis of DMG through liquid biopsy. Key pointsO_LIddPCR assays were developed to detect plasma and CSF ctDNA and ctRNA in a mouse model of DMG C_LIO_LIFUS with microbubbles enriched ctDNA and ctRNA in the blood and CSF of a mouse model of DMG C_LIO_LIThe enrichment ratio on circulating biomarkers is dependent on the source (plasma vs. CSF), analyte type (ctDNA vs. ctRNA), and individual marker (EGFP vs. Fluc) C_LI Importance of the studyLiquid biopsy via detecting circulating tumor biomarkers holds enormous clinical value in the diagnosis of diffuse midline glioma (DMG), where the eloquent location of the tumor poses significant risks to invasive surgical tissue biopsies. However, the effectiveness of liquid biopsy is hindered by its low sensitivity and the lack of information about the source of biomarkers. This study demonstrated that noninvasive and spatially targeted FUS treatment can release tumor-derived DNA and RNA into the blood and CSF in a mouse model of DMG. This study also found that the enrichment effect of FUS on circulating biomarkers depends on the source (plasma vs. CSF), analyte type (ctDNA vs. ctRNA), and individual marker (EGFP vs. Fluc). This study opens new avenues for advancing noninvasive DMG diagnosis through FUS-enhanced liquid biopsy (sonobiopsy).

bioengineering↗

bioRxiv2025

A disease mutation reveals a non-swapped pore and rewired gating cycle of the mechanically activated PIEZO1 channel

PIEZO1 is a versatile mechanotranduction channel critical for diverse cellular and physiological processes1-3. Gain-of-function mutations, such as R2482H, which slow channel inactivation, are linked to dehydrated hereditary stomatocytosis (DHS) and iron overload4-7. PIEZO1 forms a gigantic bowl-shaped trimer comprising flattenable peripheral blades and a central pore module with a switchable cap8-12. However, the structural dynamics governing its gating process and pathogenesis remain incompletely understood. Here, we determined distinct conformational states of the DHS-associated PIEZO1-R2482H mutant in both detergents and proteoliposomes. Remarkably, the R2482H mutation in the central pore induces a conformational change that propagates [~]25 nm to the most distal blade, enabling resolution of all 38 transmembrane helices. PIEZO1-R2482H is inherently flatter than PIEZO1, lowering the gating force and energy barrier and thus explaining its heightened mechanosensitivity. While the flattened PIEZO1 has its cap in the up-state adopting an inactivated state, the flattened PIEZO1-R2482H has its cap in the down-state and twisted by [~]75{degrees}, drastically switching the pore module from a swapped to a non-swapped organization. Such twisted conformation of PIEZO1-R2482H might hinder the transition to the inactivated state, instead proceeding through a deactivation-transition state characterized by curved blades and a partially twisted cap, thereby accounting for the slowed inactivation and deactivation kinetics. Taken together, we reveal the full transmembrane topology and a non-swapped pore conformation induced by R2482H, and propose the structural dynamic model that delineates the distinct gating cycle of activation, inactivation, and deactivation for PIEZO1 and PIEZO1-R2482H.

biophysics↗

bioRxiv2025

Transcription profiling and functional analysis of spRNAs and their corresponding asRNAs in Methanosarcina mazei

Small proteins (sPs) encoded by small RNAs (sRNAs), the so-called small protein RNAs (spRNAs), and their corresponding antisense RNAs (asRNAs) have emerged as important regulatory elements in microbial stress adaptation, yet remain poorly characterized in archaea. In this study, we identified and characterized five sRNA/asRNA pairs in the methanoarchaeon Methanosarcina mazei. Expression analysis revealed condition-specific regulation of two of those pairs, spRNA23/asRNA93 and spRNA24/asRNA94, under oxidative, temperature, and osmotic stress. Overexpression of the corresponding small proteins, sP23 and sP24, revealed distinct physiological effects: both enhanced growth under high-salt conditions, while sP24 in addition supported cell size maintenance during osmotic stress, as confirmed by transmission electron microscopy. Consistently, overexpression of asRNA94 let to impaired growth under salt stress, suggesting its negative regulatory role towards sP24. The results also imply that the antisense RNA might be crucial for controlling sP24 expression under non-stress conditions. Bioinformatic analysis predicted one transmembrane domain in sP24. Membrane-association of sP24 was experimentally validated in vitro using a cell-free expression system, demonstrating sP24s integration into lipid bilayers. Conservation analysis showed that spRNA24 appears specific for M. mazei strains potentially reflecting niche adaptation, while spRNA23 is widespread within Methanosarcina. These findings demonstrate that archaeal sRNAs can encode functional small proteins, often encoded together with their respective regulatory asRNA, that contribute to environmental stress responses, overall offering new insights into the role of sRNA-derived small proteins in archaea.

microbiology↗

bioRxiv2025

Axially swept dithered light-sheet microscope to reveal cardiac morphology

Understanding cardiac microstructure and vascular networks in their entirety is critical for assessing cardiovascular development, disease progression, and therapeutic interventions. Light-sheet microscopy combined with tissue clearing enables high-resolution volumetric imaging of intact organs but faces limitations in trabeculated myocardium due to trade-offs among light-sheet thickness, effective range, and frame rate. We exploit temporal dynamics that govern illumination-detection interplay to maintain uniform resolution across specimens. Building on this, we implemented high-speed dithered light-sheet (DiLS) illumination, extending the confocal region by over 40% and enhancing the space-bandwidth product while preserving optical sectioning. Integration of DiLS with a sweeping approach establishes the axially swept dithered light-sheet (AS-DiLS), which enhances imaging throughput while preserving axial resolution and enables uniform illumination up to 12.5-millimeter range. AS-DiLS delivers near-isotropic resolution (~2.5 m) for investigating intricate ventricular trabeculae, vasculature, and extracellular matrix, providing a scalable platform for comprehensive cardiovascular morphology and topology assessment from embryos to adults. TeaserVolumetric imaging reveals microstructure and vascular networks in their entirety with near-isotropic resolution.

bioengineering↗

bioRxiv2025

Loss of miRNA-153 promotes endothelial-to-mesenchymal transition and compromises lung vascular integrity

Endothelial-to-mesenchymal transition (EndMT) is a biological process through which lung vascular endothelial cells (ECs) transdifferentiate into mesenchymal-like cells. EndMT has recently been implicated in the development and progression of pulmonary vascular remodeling in pulmonary hypertension (PH); however, its underlying regulatory mechanisms remain incompletely understood. MicroRNAs (miRNAs) are key post-transcriptional regulators of EC gene expression and cellular responses to various stimuli. Notably, microRNA-153 (miR-153) has been shown to directly target SNAI1 to modulate epithelial-to-mesenchymal transition (EMT), a process closely related to EndMT and extensively studied in cancer. Whether miR-153 also participates in EndMT regulation, however, remains unknown. In this study, we demonstrate that 72-hour hypoxic exposure induces SNAI1-mediated EndMT in human lung vascular ECs. Hypoxia also increased cell proliferation and disrupted intercellular junctions, leading to enhanced endothelial permeability. Reduced miR-153 expression was observed in both hypoxia- and TGF-{beta}1-induced EndMT, as well as in ECs isolated from PH patients exhibiting an EndMT phenotype. Similar to hypoxia, TGF-{beta}1 promoted EC permeability. Loss of miR-153 enhanced SNAI1-mediated EndMT, endothelial survival, and permeability under normoxic conditions, whereas miR-153 overexpression attenuated EndMT induced by hypoxia or TGF-{beta}1. However, miR-153 restoration did not completely recover endothelial barrier integrity disrupted by these stimuli. In conclusion, miR-153 serves as a critical regulator of EndMT, maintaining endothelial identity and barrier function. Therapeutic delivery of miR-153 may therefore represent a novel strategy to inhibit EndMT and attenuate pulmonary vascular remodeling in PH.

physiology↗

bioRxiv2025

Immune cell de novo steroidogenesis regulates inflammation resolution and recovery in acute lung injury

Effective resolution of inflammation following acute lung infection or injury is critical for restoring immune and tissue homeostasis to ensure functional recovery. Prolonged or unresolved inflammation can impair lung repair, promote fibrosis, and contribute to pulmonary dysfunction. While systemic steroid signalling is known to modulate general immune responses, the specific role of immune cell-mediated steroidogenesis in regulating lung inflammation and repair remains unknown. Here, we show that immune cell de novo steroidogenesis is essential for resolving inflammation and promoting recovery in a murine model of acute lung injury. During the resolution phase, steroid-synthesizing immune cells, predominantly basophils, are enriched in the lung. Mice with immune cell-specific ablation of de novo steroidogenesis exhibit exacerbated lung injury, impaired resolution of inflammation, and defective tissue repair. These findings reveal a previously unrecognized immunoregulatory function of immune cell-derived steroids and identify immune cell steroidogenesis as a potential therapeutic target for promoting resolution and recovery in inflammatory lung diseases.

immunology↗

bioRxiv2025

Genetics-to-structure multiscale analysis identifies disrupted calcium homeostasis as a mechanism of psychiatric disease

Neuropsychiatric disorders are highly heritable, but the molecular mechanisms linking risk variants to disease remain unclear1. Linking genetics to biological mechanisms requires integrating evidence across scales, from sequence variation to gene regulation to protein function. Here we integrate genetic, transcriptomic, and structural evidence to identify dysregulation of neuronal Ca2+ dynamics as a contributing mechanism. We analyzed single-nucleus neuronal RNA-seq data together with genome-wide association study (GWAS) heritability in a new way to identify gene expression programs enriched for psychiatric risk; genes encoding Ca2+ flux pathway genes were implicated by this analysis, a result that was then confirmed by concentrations of rare coding variants in these same genes in persons with psychiatric disorders. A critical gene in this biology, ATP2B2, encodes a Ca2+-extruding ATPase pump2 linked to neuropsychiatric disorders primarily through missense variants. To recognize specific molecular functions affected by these missense variants, we developed a 3D-neighborhood-based method that maps missense variants onto AlphaFold3-predicted protein structures and tests clustering of protein-altering variants in three-dimensional space. This approach revealed clustering of these missense changes in the Ca2+ pore and ATP:Mg2+ coordination site of ATP2B2. To validate the structural predictions arising from the genetic analysis, we determined the structure of human Ca2+-bound ATP2B2 at 2.64 [A] resolution by cryogenic electron microscopy. The structure replicated the 3D mutational hotspots identified by the genetic analysis, supporting the observation that neuropsychiatric variants cluster near specific catalytic sites of ATP2B2. In vitro experiments revealed that missense variants prioritized by the structural clustering analysis impaired ATP2B2-mediated Ca2+ extrusion in cellular and biochemical assays. Together, these findings suggest that precise regulation of Ca2+ dynamics is a contributing mechanism in neuropsychiatric disorders and establish a structure-based framework for predicting the mechanistic impact of missense variants.

genetics↗

bioRxiv2025

The role of actin dynamics in vesicle formation during clathrin mediated endocytosis

Clathrin-mediated endocytosis (CME) is an important internalization route for macromolecules, lipids, and membrane receptors in eukaryotic cells. During CME, the plasma membrane invaginates and pinches off forming a clathrin coated vesicle. We previously identified heterogeneity in this process with clathrin coated vesicles forming though multiple routes including simultaneous clathrin accumulation and membrane invagination (constant curvature; CCM) as well as membrane bending after accumulation of flat clathrin (flat to curved; FTC). The architectural dynamics of vesicle formation could be influenced by osmotic or confining pressure, membrane stiffness, fluid force, or cytoskeletal arrangement. Whether these biophysical factors regulate the heterogeneity of vesicle formation dynamics is not well understood. To address this, we investigated the interconnected roles of actin and membrane tension in CME using simultaneous two-wavelength axial ratiometry (STAR) microscopy with nanometer-scale axial resolution. First, we treated Cos-7 cells with latrunculin A (LatA) to inhibit actin polymerization and found the total number of clathrin coated vesicles increased significantly, short-lifetime curved events especially. The proportion of vesicles formed following the FTC model was reduced, the membrane curved sooner after clathrin recruitment, and vesicles were less stable in the x-y plane compared to control. Next, we disrupted actin branching by inhibiting Arp2/3 with CK-869. We found an increased delay between membrane invagination and clathrin recruitment, reduced number of curved events, increased vesicle stability and an increase in the FTC model compared to control. As loss of actin filaments also reduces membrane tension, we treated Cos7 with high osmolality to decrease membrane tension and observed similar result with LatA treated group except vesicle stability stayed unchanged. This suggested the increased curved events in LatA groups may result from reduced membrane tension. We conclude actin polymerization promotes FTC while actin branching promotes vesicle formation though the CCM.

cell biology↗

bioRxiv2025

Investigating the impacts of sidechains on de-novo protein design

De novo protein design aims to create novel protein structures and sequences, often to enable specific functions. Most current generative models operate on simplified backbone-only representations. However, in vivo and in vitro protein folding and function are largely mediated by amino acid sidechains. Given this biochemical relevance, we ask: what happens when sidechain and sequence information are introduced into a protein generative model? To address this, we developed SiBaSe, a novel generative model that simultaneously co-designs sidechains, backbones, and sequence. SiBaSe achieves design performance approaching that of state-of-the-art backbone-only models. However, analysis of design patterns reveals that, despite access to sidechain data, the model behaves similarly to a backbone-based model. This appears to arise from uncertainties in the simultaneous modeling of sequence and sidechains that are inherent to flow-based architectures and offers new insight into architectural limitations and opportunities for improving generative protein design.

bioinformatics↗

bioRxiv2025

Integrative genomic and transcriptomic analyses uncover regulatory landscape of symbiotic nitrogen fixation in soybean natural population

Symbiotic nitrogen fixation (SNF) is a key trait in legume productivity, yet the genetic and regulatory basis underlying its natural variation remains poorly understood. Here, we integrated genome, transcriptome, and chromatin accessibility data from a soybean diversity panel comprising 380 accessions, including 108 wild and 272 cultivated lines. Genome-wide association studies (GWAS) detected multiple loci for SNF traits but with limited resolution due to polygenic architecture and environmental influences. Independent component analysis (ICA) identified 136 co-expression modules; ten ICs were strongly correlated with SNF phenotypes and enriched in circadian clock components (e.g., GmLHY1a/b), lipid metabolism, or defense signaling pathways. Transcriptome-wide association studies (TWAS) linked 1,453, 806, and 178 genes to NFP, NW, and NFE traits, respectively. Among TWAS hits, 185 transcription factors were identified, with 39.0% overlapping selective sweeps, suggesting regulatory evolution under domestication. To further dissect expression regulation, we performed eQTL mapping and detected 4,654 significant eQTLs, including 1,241 local (cis), 2,505 distal (trans), and 908 mixed. By integrating ATAC-seq data from sorted nodule nuclei, we found that eQTLs, particularly local eQTLs, are significantly enriched within open chromatin regions, indicating their regulatory potential. Notably, we validated the circadian clock gene GmLHY1b as a negative regulator of nodulation using CRISPR mutagenesis and CUT&Tag. Our integrative study provides comprehensive genomic and transcriptomic resources from a diverse soybean population, offering novel insights into SNF regulatory networks and a valuable foundation for future SNF research and soybean improvement.

plant biology↗