Biology subjects

Sun, F.

Publications and source records attributed to Sun, F..

At least 19 recordsLinked to original sources

bioRxiv2026

In situ architecture of the basal body reveals regionalized assembly and central pair microtubules nucleation

The basal body (BB) is essential for axoneme assembly and ciliary function, and its defects are associated with ciliogenesis disorders and ciliopathies (1,2). However, the molecular basis of the BB's region-specific transitions along the proximal-distal axis, and the mechanism by which ciliary central pair (CP) microtubules are nucleated during ciliogenesis, have remained largely unknown. Here, we resolve the subnanometer architecture of native BBs in mammalian multiciliated cells using cryo-electron tomography and subtomogram averaging, and identify 11 ciliary-base microtubule-associated proteins (CMAPs), including 5 previously uncharacterized core components. These CMAPs localize specifically along ciliary base that facilitate the triplet-to-doublet microtubule transition. We further identify luminal gamma-tubulin ring complexes (gamma-TuRCs) anchored to the microtubule wall via the augmin complex, and propose that they may serve as candidate nucleation sites for CP microtubules biogenesis. Together, these findings define a molecular blueprint of the BB and provide a structural framework for understanding how regional architectural specialization and luminal nucleation collectively drive ciliary assembly and how their dysfunction causes ciliopathies.

cell biology↗

bioRxiv2026

Flexible 3D multimodal organoid interface reveals functional subnetworks and coordinated circuit activity in cortical organoids

The balance between excitatory and inhibitory (E/I) neurons is fundamental to cortical function, and its disruption underlies a wide range of neurological disorders, including epilepsy, Alzheimers disease and autism spectrum disorder. Cortical organoids offer a promising model to study this balance, as they recapitulate key features of brain development, including the emergence of E/I circuitry. However, no existing technology can simultaneously resolve neuronal identity, spatial organization, and dynamic network activity within intact organoids, limiting precise interrogation of E/I circuit function. Here, we report INFORM, an INtegrated Flexible Organoid Recording Multimodal neural interface that conformally wraps organoids of any size and shape, enabling long-term recordings over 371 days with above 90% of channels detecting spikes. INFORM interface combines four distinct modalities; electrophysiology, two-photon calcium imaging, targeted electrical microstimulation, and chemical intervention to monitor and modulate neural activity across multiple spatial and temporal scales spanning from action potentials from single neurons to synchronized bursts from large-scale populations. Such high-resolution interrogation enables probing of emergence of functional connectivity in fusing assembloids and resolves spatially discrete functional subnetworks that can be selectively recruited and modulated by INFORM. Neurotransmission blockade confirms that stimulus-evoked suppression of neuronal spiking is mediated by GABAergic inputs providing direct functional evidence of the presence of inhibitory signaling in organoids. This work allows single-cell dissection of functional networks in brain organoids, providing a powerful platform for modelling and studying cortical development, neurological diseases, and the E/I imbalances underlying circuit dysfunction.

neuroscience↗

bioRxiv2026

Intranasal adenovirus type 5 influenza vaccination enhances milk antibody responses and passive transfer to neonatal ferrets

Newborns and infants are particularly vulnerable to influenza, largely due to the immaturity of their immune systems. As such, maternal immunization is a valuable strategy to enhance influenza-neutralizing antibodies in both blood and breast milk, ensuring optimal passive immunity transfer to the infant. In our pregnant and lactating ferret maternal-neonatal model, we evaluated antibody responses to an adenovirus type 5-vectored H1N1 hemagglutinin vaccine delivered enterically, intranasally, or intramuscularly. While all three routes elicited a robust antibody response compared to saline-treated controls, intranasal vaccination significantly increased influenza-specific antibodies in dam serum, upper respiratory tract secretions, and milk, and subsequent transfer to suckling kits. Our results suggest that intranasal immunization was the most effective route for inducing functional influenza-specific antibodies in both dam serum and milk, with efficient passive transfer to suckling kits. Leveraging mucosal immune induction may enhance maternal antibody responses, transfer to offspring, and downstream neonatal protection.

microbiology↗

bioRxiv2026

CryoForge: A Self-Correcting Agent for Cryo-EM Model Building That Learns When to Act and When to Stop

Automated atomic model building has accelerated cryo-EM structure determination, but different builders leave distinct residual error profiles requiring expert inspection. The post-building challenge is to decide which local interpretations are sufficiently supported by experimental evidence to be retained, corrected or rejected. Here we introduce CryoForge, an evidence-gated post-builder agent that separates repair proposal from repair acceptance. Rule and learning-based components identify candidate regions and prioritize legal actions, whereas an independent evidence gate evaluates each edit using map and half-map support, stereochemistry, connectivity and local structural context. Supported edits are retained; unsupported or conflicting modifications are rejected, rolled back, stopped or escalated for expert review. Across a resolution-stratified benchmark, 84.9% of 26,153 released trajectories yielded standard validated improvements and 3.7% yielded low-confidence partial improvements, with no quality-degrading edit retained in the final promoted models. Relative to rule-only control, learned prioritization reduced non-improving candidates and harmful actions while preserving global structural stability. External evaluations using an alternative initializer, same-team automated/manual-assisted challenge submissions and three recently released complex assemblies showed that CryoForge adapts to distinct residual error phenotypes and performs bounded, evidence-supported correction without uncontrolled remodeling. CryoForge provides a builder-independent, scalable and auditable correction layer between automated model generation and expert structural interpretation.

bioinformatics↗

bioRxiv2026

A Generalized Spatial Progress Code for Navigation in the Medial Prefrontal Cortex

Goal-directed navigation requires an internal estimate of progress toward a desired outcome, yet how the brain constructs and represents such a signal remains unclear. Here, we designed a multi-route navigation paradigm with geometrically distinct paths and imaged medial prefrontal cortex (mPFC) activity as mice performed goal-directed route choice behavior. We found that a substantial fraction of mPFC neurons fired at consistent positions along a normalized start-to-goal axis, independent of path geometry, running direction, and task context. At the ensemble level, mPFC activity reliably decoded spatial progress but carried minimal information about path identity. This progress code emerged with task familiarity and required input from the hippocampal CA1. Inactivation of either mPFC or CA1[->]mPFC projection did not disrupt learned path preference but impaired navigational fluency in trained mice. These findings reveal a hippocampal-prefrontal mechanism for representing abstract, context-generalized spatial progress within a goal-directed navigational episode, supporting fluent navigation across variable routes.

neuroscience↗

bioRxiv2026

cryoAgent: An agentic workflow for robust and adaptive end-to-end cryo-EM image processing

Cryo-electron microscopy (cryo-EM) is the mainstream method for structure determination, yet current automated workflows remain rigid and require expert intervention for failure recovery, heterogeneity analysis, and optimization. We present cryoAgent, an agentic workflow for autonomous cryo-EM image processing with adaptive tool use to address these challenges. cryoAgent improves reconstruction quality across diverse datasets, identifies a previously unreported structural state, and outperforms state-of-the-art automated workflows, advancing scalable and discovery-oriented structural biology.

biophysics↗

bioRxiv2026

Loss of C3 and CD14 reduces region-specific neuroinflammation in a murine polytrauma model

BackgroundTraumatic brain injury (TBI) together with non-cerebral injuries characterizes the TBI-polytrauma (P-TBI) constellation, which is associated with acute neurological deterioration, delirium and unfavourable prognosis. It is hypothesized that systemic inflammatory mediators my enhances the focal, cerebral neuroimmune reaction with overall detrimental consequences, in particular in terms of acute microglial reactivity. MethodsWe explored the role of the Complement factor 3 (C3) and of the TLR-co receptor cluster of differentiation (CD14) in a murine polytrauma model that involves a mild TBI together with femur fracture, blunt thorax trauma and resuscitated haemorrhagic shock, making use of mice genetically lacking either C3, CD14 or both. ResultsWe show that P-TBI results in a rapid (4h) and brain-wide induction of inflammatory cytokines, although with distinct profiles (TNF and CCL2 having brain-wide involvement and IL-1{beta} restricted to ipsilateral cortex and striatum). TNF and CCL2 mRNA as well as protein synthesis were upregulated in microglia upon P-TBI in cortex, hippocampus and striatum which was fully abolished in the C3-/-CD14-/-animals. The analysis of single-KO animals revealed that induction of TNF and CCL2 was prevented in animals lacking C3, but not CD14, in the contralateral cortex and striatum, with an abolishment in hippocampus in mice lacking both C3 and CD14. In the cortical area of focal lesion neither C3 nor CD14 affected the induction of pro-inflammatory cytokines. ConclusionThus, C3 and CD14 are dispensable for the acute cytokine response to P-TBI in the site of injury but play differential roles across the cortex, hippocampus and striatum for the induction of cytokines in the non-injured parenchyma and in particular in microglia. Thus, interventions on C3 (mainly) and/or CD14 may reduce the encephalopathy risk associated with P-TBI but not the acute response in the injury site, where additional DAMP signalling may offer redundant activation pathways.

neuroscience↗

bioRxiv2025

An Lrs14 family protein functions as a nucleoid-associated protein regulating cell cycle progression in Sulfolobales

Archaea of the order Sulfolobales possess eukaryotic-like cell cycle. The chromatin organization in these archaea is supposed to rely on nucleoid-associated proteins (NAPs). Genomes of Sulfolobales species encode multiple members of the Lrs14 protein family, which have been postulated to function as NAPs. Here, we show that one of the Lrs14 family protein, named Sul14a, is a potential key player in dynamic chromatin organization in Saccharolobus islandicus. Sul14a is transcribed in a cell cycle-dependent manner and appears to be essential for cell viability. The protein exhibits DNA-binding activity preferring AT-rich sequences and can bridge DNA in vitro. ChIP-seq analysis revealed that Sul14a is enriched at AT-rich regions of the chromatin. Overexpression of Sul14a leads to cell cycle arrest at G2 phase. High-throughput chromosome conformation capture (Hi-C) and transcriptomic analyses indicate that Sul14a overexpression results in chromatin contact reduction and global transcriptional changes. In addition, we observed that the chromatin contact pattern changes markedly between 1h and 5h after release from G2 synchronization, corresponding to the lowest and highest levels of sul14a transcription, respectively, during the cell cycle. Our results establish that Sul14a is an NAP intimately associated with chromatin dynamics and global transcriptional changes during the cell cycle in Sulfolobales.

microbiology↗

bioRxiv2025

GBoost-CTL: A novel method in multi-tissue transcriptome-wide associations studies in cross-tissue learner incorporating GWAS information

Genome-wide association studies (GWAS) have uncovered numerous genetic variants linked to complex human diseases, yet linking these variants to transcripts and tissues that drive pathology remains difficult. Multi-tissue transcriptome-wide association studies (TWAS) offer a powerful bridge, but existing analytical methods have some limitations, either by discarding important signals by separately analyzing and then aggregating results across tissues, implying imputation models in individual tissues, or fusing them with weights that ignore how much GWAS signal each tissue actually carries. Therefore, most of the existing methods do not work uniformly across different GWAS cohorts. Here, we propose GBoost-CTL - a GWAS-boosted cross-tissue learner that can overcome those aforementioned limitations. The method starts with any collection of single-tissue learners (STLs), allowing investigators to choose the most suitable imputation engine for each tissue. It then (i) allocates weights according to each STLs out-of-sample predictive accuracy and (ii) refines those weights incorporating the GWAS-derived information, so that informative tissues are automatically up-weighted while uninformative tissues are down-weighted. This dual weighting strategy lets GBoost CTL adapt to fully shared, partially shared, or highly tissue-specific regulatory architectures while preserving nominal type I error control and delivering substantially higher power than existing linear or covariance-based methods. Through extensive simulation, we have found that this dual weighting strategy lets GBoost-CTL adapt to fully shared, partially shared, or highly tissue-specific regulatory architectures while preserving nominal type I error control and delivering substantially higher power than existing linear or covariance-based methods. When applied to real data, GBoost-CTL consistently outperformed some existing multi-tissue TWAS methods (e.g., TWAS-CTL, UTMOST and PrediXcan) by identifying a greater number of disease-associated genes with more stringent p-values. Given its modular design, computational scalability, and demonstrable gains in discovery power, we believe that GBoost-CTL offers a practical tool for the analysis of multi-tissue TWAS.

bioinformatics↗

bioRxiv2025

Structural basis for BCL7B-mediated ncBAF-nucleosome engagement

The mammalian SWI/SNF family of chromatin remodelers comprises BRG1/BRM-associated factor (cBAF), Polybromo-associated BAF (PBAF), and non-canonical BAF (ncBAF) complexes, which slide and disassemble nucleosomes to regulate gene expression and chromatin structure dependent on ATP hydrolysis energy. While the chromatin engagement mechanisms of cBAF and PBAF have been structurally resolved, the molecular architecture governing ncBAF interaction with chromatin remains elusive. In this study, by integrating cryo-electron microscopy, biochemical assays and cross-linking mass spectrometry, we resolved the conformational transition of ncBAF-nucleosome complexes from nucleotide-free to nucleotide-bound states. Our analyses establish BCL7 proteins as dynamic molecular tethers connecting the ARP module to the nucleosomal acidic patch and demonstrate that BCL7B promotes ncBAF-mediated nucleosome remodeling, with BRG1-catalyzed ATP hydrolysis triggering conformational changes that modulate BCL7-mediated histone association. Structurally and biochemically, we further demonstrate that {beta}-actin within the BCL7-containing ARP module retains ATP hydrolysis activity, rendering its exposed pointed end structurally compatible with incorporation into the barbed end of nuclear actin filaments, which provides a potential molecular basis for coordinating nuclear actin networks with chromatin remodeling. Collectively, our findings unravel a dynamic role of BCL7 in regulating ncBAF-mediated chromatin remodeling and establish a distinct chromatin engagement mode of ncBAF from that of cBAF/PBAF.

molecular biology↗

bioRxiv2025

AI-HEAD: Auto-indexing for Helical assembles' diffraction and fast dynamic structure determination

Analyzing the structure of the helical assembly is very important to excavate the mechanism of base life activities such as cell morphology maintaining, cargo transportation, et. al. However, the structure determination of helical assembles still challenging due to ambiguous of helical parameters. Here, we developed automatic, fast and accurate helical parameter and structure calculation method AI-HEAD, which perform diffraction indexing and parameter calculation automatically in seconds, and determine the final structure unambiguously by sorting parameters semi-automatically. AI-HEAD is open source and also provides a user-friendly graphical interface.

biophysics↗

bioRxiv2025

Single-cell transcriptomics reveals spaceflight-induced accelerated aging and impaired recovery in the murine bone marrow

Spaceflight induces physiological changes that resemble accelerated aging, however, how age influences bone marrow response at the cellular level remains poorly understood. Here, we perform single-cell transcriptomic profiling of murine femur and humerus bone marrow from young (12-week-old) and old (29-week-old) mice that underwent a 32-day spaceflight mission followed by a 24-day Earth recovery, with age-matched ground controls. Our analysis reveals that, compared with young cohorts, old mice exhibit persistent dysregulation after spaceflight, most prominently in erythroid and B cell lineages. In erythroid cells, old flight mice show pronounced aging signatures, characterized by impaired maturation, inhibited mitophagy, and increased oxidative stress. In B cells, old flight mice show dysregulation associated with failure of the AP-1 stress-response pathway and complete collapse of the intercellular CXCL signaling network. Our findings dissect the age-dependent effects of spaceflight on the bone marrow hematopoietic and immune system at single-cell resolution, and demonstrate that spaceflight imposes a disproportionate burden on the aged hematopoietic system and blunts post-flight recovery. These insights provide candidate pathways and biomarkers for health monitoring and countermeasures in long-duration missions.

bioinformatics↗

bioRxiv2025

TWAS-CTL: A robust and efficient method for multi-tissue transcriptome-wide association studies using cross-tissue learners

The advent of transcriptome-wide association studies (TWAS) has expanded the classical genome-wide association study (GWAS) framework by integrating gene expression with genetic variation to identify trait-associated variants. While multi-tissue TWAS approaches improve statistical power over single-tissue models, existing methods often lose information during result aggregation and require intensive computation. Here, we present TWAS-CTL (Cross-Tissue Learner), a novel framework that leverages heterogeneous gene expression across tissues by adaptively reweighting and optimizing multiple single-tissue learners. Simulations demonstrate that TWAS-CTL achieves higher statistical power than the leading method, UTMOST, while maintaining proper type I error control and reducing computational time by over half. When applied to the analysis of the Genetics of Kidneys in Diabetes (GoKinD) cohort, we observed that TWAS-CTL identified more susceptible genes associated with diabetes than both UTMOST and PrediXcan, another widely used method in TWAS. These results establish TWAS-CTL as a powerful and efficient tool for cross-tissue gene expression analysis, capable of integrating heterogeneous gene-trait associations to advance genetic discovery.

bioinformatics↗

bioRxiv2025

Visible Light-Controllable Surgical Hemostatic Adhesives Enabled by Vitamin B12-Stabilized Poly(α-Lipoic Acid)

Water-resistant adhesives are indispensable for biomedical applications, from surgical wound closure to internal hemostasis. While poly(-lipoic acid)-based adhesives show promise for their strong underwater adhesion, their clinical utility has been limited by uncontrolled polymerization-depolymerization dynamics. Here we present a visible light-controllable adhesive system enabled by a simple mix of -lipoic acid (LA) and vitamin B12 (i.e., adenosylcobalamin or AdoB12)--a photolabile compound--without resorting to any chemical modification. Benign visible light irradiation facilitates the cleavage of the C-Co bond and the subsequent formation of B12-thiolate complexes that stabilize LA polymers against depolymerization. The photoresponsive LA-AdoB12 adhesive system has proven highly effective in a wide range of surgical applications, achieving (1) strong bonding in porcine skin models in vitro, (2) reliable sealing of punctured organs (lung, heart and stomach) ex vivo, and (3) immediate hemostasis in active bleeding models such as topical, esophageal, and intestinal wounds in vivo. This work highlights a simple yet powerful strategy for creating visible light-controllable bioglues well-suited for diverse surgical applications.

bioengineering↗

bioRxiv2025

Benchmarking Alignment Strategies for Hi-C Reads in Metagenomic Hi-C Data

BackgroundMetagenomics combined with High-throughput Chromosome Conformation Capture (Hi-C) offers a powerful approach to study microbial communities by linking genomic content with spatial interactions. Hi-C enhances shotgun sequencing by revealing taxonomic composition, functional interactions, and genomic organization from a single sample. However, aligning Hi-C reads to metagenomic contigs presents challenges, including the varying insert size of Hi-C paired-end reads, multi-species complexity, and gaps in assemblies. Although many benchmark studies have evaluated general alignment tools and Hi-C data alignment, none have specifically addressed metagenomics Hi-C data. ResultsHere, we selected seven alignment strategies that have been used in Hi-C analyses: BWA MEM -5SP, BWA MEM default, BWA aln default, Bowtie2 default, Bowtie2 -very-sensitive-local, Minimap2 default, and Chromap Hi-C default. We benchmarked them on one synthetic and seven real-world environments, and evaluated these tools based on the number of inter-contig Hi-C read pairs and their influence on downstream tasks, such as binning quality. ConclusionOur findings show that BWA MEM -5SP consistently outperforms other tools across all environments in terms of inter-contig read pairs and binning quality, followed by BWA MEM default. Chromap and Minimap2, while less effective in these metrics, demonstrate the highest computational efficiency.

bioinformatics↗

bioRxiv2025

Analysis of Wheat Spike Morphological Traits Using 2D Imaging

The morphological structure of wheat spikes plays a central role in wheat yield. Wheat spike morphology, closely associated with crop yield, has attracted considerable attention in the fields of genetics and breeding. However, traditional measurement methods can only measure simple traits, and precise phenotypes remain difficult to obtain, constraining the study and improvement of complex spike-related traits. This study utilized deep learning technologies to develop a pipeline, called SpikePheno, for the acquisition of precise wheat spike phenotypes. Our pipeline demonstrated high accuracy in spike segmentation, achieving a mean Intersection over Union (mIoU) of 0.948. Additionally, our method accurately identified spikelet counts, achieving an R2 of 0.9923. Using experimental data of 221 wheat cultivars from various regions of China grown in Zhao County, Hebei Province, our pipeline extracted 45 different phenotypes and studied their correlations with thousand grain weight (TGW) and spike yield. Our findings indicate that precise measurement of spike area, spikelet area, and other phenotypic traits enables a clearer understanding of the correlation between spike morphology and wheat yield. Through hierarchical clustering based on spike morphology, we categorized wheat spikes into six classes and identified phenotypic differences between these classes and their impact on TGW and yield. Furthermore, this study revealed phenotypic differences between wheat cultivars from different geographical regions and over different decades, with an increase in large-spike cultivars over time, especially in southern China. This research may help breeders understand the relationship between wheat spike morphology and yield, providing an important basis for future wheat breeding efforts.

plant biology↗

bioRxiv2025

Controllable Gap Junctions by Vitamin B12 and Light

Gap junctions, mediate rapid signal transduction between contiguous cells, which are indispensable for multicellular organisms to coordinate cellular activities across numerous physiological processes. However, precise control of gap junctions remains elusive. Herein, we present CarGAP, a single-component chemo-optogenetic tool that utilizes the C-terminal adenosylcobalamin (AdoB12) binding domain of a photoreceptor protein (i.e., CarHC) to achieve reversible control over both vertebrate and invertebrate gap junctions with spatiotemporal precision. The vertebrate CarGAP (i.e., Cx-CarGAP), created by genetically fusing connexins with CarHC in mammalian cells, can efficiently block the gap junction channels through AdoB12-induced protein oligomerization, and subsequently reinstate them via green light-induced protein disassembly. We further introduced the CarGAP system (i.e., Inx-CarGAP) to the Drosophila ovary, enabling reversible control over the heterotypic gap junctions formed by innexin2 (Inx2) and innexin4 (Inx4, also known as zero population growth, Zpg), thereby uncovering the roles of gap junctions in stem cell-niche interactions. This study illustrates CarGAP as a generalizable chemo-optogenetic tool for interrogating the functions of gap junctions in various biological contexts.

bioengineering↗

bioRxiv2025

Genetically Programmable Adhesive Protein Hydrogels for Sealing Perforating Corneal Trauma

The cornea, situated at the forefront of the eyeball, is often subjected to varying degrees of mechanical laceration injuries due to various traumatic incidents. Timely and precise suturing of corneal wounds to prevent the leakage of intraocular contents is a significant clinical challenge. Although some studies have attempted to use hydrogels to accurately cover corneal injuries, most of these hydrogels are only suitable for adhering to focal stromal defects that do not involve the corneal stroma. Here, a fully protein-based hydrogel, based on SpyTag-SpyCatcher chemistry, was investigated for repairing corneal perforating injury models in rats and rabbits. The hydrogel formation relies on covalent bonding between SpyTag (A) and SpyCatcher (B) under physiologically mild conditions, eliminating requirements for organic solvents, elevated temperatures, or photoactivation Notably, integration of recombinant mussel foot protein 3 (Mfp3) endowed the hydrogels with exceptional water-resistant adhesiveness, while maintaining their original mechanical properties and biocompatibility. This study demonstrates the great potential of Mfp hydrogels in the timely and precise repair of corneal perforating injuries in complex physicochemical environments. TeaserBioinspired protein hydrogel rapidly seals corneal perforations, minimizing scarring and inflammation without sutures in animal models.

bioengineering↗