Biology subjects

Chai, Y.

Publications and source records attributed to Chai, Y..

At least 19 recordsLinked to original sources

bioRxiv2026

Generating a Collection of Single-Gene Deletions in the eps Operon in Bacillus subtilis Strain NCIB 3610

In the environment, bacteria mainly exist in multicellular, surface-adhered communities called biofilms. One key feature of the biofilms is a self-produced extracellular matrix that embeds cells within a structured community and contributes to their adhesion, organization, and retention. The matrix of most characterized biofilms contains three primary components: polysaccharides, protein, and extracellular DNA (eDNA). Upon biofilm induction, Bacillus subtilis produces and secretes a polysaccharide known as exopolysaccharide (EPS). The 15 genes of the epsA-O operon encode proteins that coordinate the assembly, export, and polymerization of EPS oligosaccharide (glycan) subunits. While much progress has been made to elucidate the chemical structure of EPS, further work is needed to determine the contributions of some eps genes to EPS biosynthesis experimentally. Here, we generated a collection of marker-less, in-frame deletions targeting each eps gene in the epsA-O operon in B. subtilis strain NCIB 3610 using the Cre system. Biofilm phenotypes of resulting mutants were used to assess each gene's importance to biofilm development. Impact The epsA-O single-gene deletion collection was designed to enable systematic assessment of the contribution of each eps gene to EPS production and biofilm-associated phenotypes. When combined with current knowledge of EPS structure, this collection will help clarify the roles of individual genes in EPS biosynthesis. This approach can also be easily adapted for the systematic analyses of other large, complex operons in diverse bacterial species.

microbiology↗

bioRxiv2026

Spatially Confined Phase Separation Promotes Local Tubulin Availability to Stabilize Ciliary Microtubule Growth

How microtubule (MT) growth is locally sustained within cilia remains a central unanswered question in ciliogenesis. Here we identify RAT-1 as a regulator of ciliary tubulin homeostasis and MT growth. Genetic screens in Caenorhabditis elegans show that loss of RAT-1 suppresses the toxic effects of a mutant -tubulin and restores ciliary structure, while RAT-1 deficiency reduces tubulin turnover at the ciliary tip, indicating its physiological role in tuning ciliary MT dynamics. Mechanistically, RAT-1 forms intra-ciliary condensates selectively at the distal region through an auto-inhibitory -helix and phosphorylation by the distally localized ciliary kinase. RAT-1 enriches tubulin within condensates in vivo/vitro, and cooperates with end-binding proteins to facilitate sustained MT growth in vitro. Notably, heterologous expression of worm RAT-1 reveals conserved condensate behavior within mammalian cilia. Our findings reveal a kinase-regulated mechanism controlling RAT-1 condensation within cilia and establish RAT-1 as a regulator of ciliary MT dynamics.

cell biology↗

bioRxiv2026

Integrating structural and biological evidence to rerank ESMFold2 protein-protein interactions

Large-scale protein structure prediction enables proteome-wide protein-protein interaction (PPI) screening, but distinguishing biologically meaningful interactions from spurious interfaces remains challenging. Here, we develop a scalable framework combining fast, MSA-free ESMFold2 prediction with PAE-guided domain parsing and evidence-based reranking. Three-recycle ESMFold2-Fast achieved 57% acceptable-or-better DockQ scores on FoldBench, comparable to AlphaFold2-Multimer while substantially reducing computation. PAE-guided parsing preserved 98.1% of XL-MS cross-links within parsed domain pairs. We then developed the Structure Prediction and Omics informed Classifier (SPOC)-ESMFold2, which integrates structural features with independent biological evidence to prioritize predicted interactions. SPOC-ESMFold2 achieved an AUROC of 0.93 and AUPR of 0.90, compared with 0.87 and 0.79 for a structural-only classifier. Under a 1:128 positive-to-negative ratio, SPOC-ESMFold2 achieved 17.2% recall at 5% false-discovery rate, substantially outperforming structural confidence metrics alone. This framework enables scalable PPI screening by integrating structural plausibility with orthogonal biological evidence to prioritize candidates for experimental investigation.

bioinformatics↗

bioRxiv2026

HMCES DNA-protein cross-links promote template slippage during DNA replication

During replication, nucleolytic processing of apurinic/apyrimidinic (AP) sites in single-stranded (ss)DNA is attenuated by the evolutionarily conserved 5-hydroxymethylcytosine binding, embryonic-specific (HMCES) protein. HMCES forms a covalent thiazolidine linkage with the ring-opened aldehyde form of a ssDNA AP site to stabilize the AP site and suppress the formation of DNA double-strand breaks. The resulting HMCES DNA-protein cross-link (DPC) can then be digested by the SPRTN protease and bypassed through mutagenic translesion synthesis (TLS). Here, we use Xenopus egg extracts and molecular dynamics simulations to investigate how HMCES-DPC formation influences the mutagenicity of AP site bypass. We show that SPRTN processes the HMCES-DPC to a five amino acid peptide adduct prior to TLS. Surprisingly, the mutagenicity of HMCES-DPC bypass is insensitive to the extent of DPC proteolysis and depends only on cross-link formation, which traps the AP site in a more dynamic ring-opened configuration. We further show that the spectrum of mutations produced during bypass of HMCES-adducts strongly depends on the template strand nucleotide immediately 5 of the AP site. Our data support a model in which HMCES-DPC formation increases the conformational flexibility of the DNA template, allowing template slippage and use of the 5 template nucleotide to direct insertion opposite the adducted AP site.

biochemistry↗

bioRxiv2026

A cross-modal generative model for incomplete and degradedprostate MRI with multicentre clinical validation

Missing or degraded sequences can limit prostate multiparametric MRI. We developed MSCNet, a sequence-conditioned cross-modal generative framework for reconstructing unavailable contrasts and restoring degraded acquisitions. Across ten completion tasks, task-specific MSCNet achieved mean structural similarity of 0.818 versus 0.798 for the strongest task-matched comparators; matched-capacity analyses showed larger differences in lesion fidelity and boundary preservation. In a blinded 1,000-case reader study, overall image quality met the prespecified non-inferiority criterion for DWI, ADC and T2W completion, but not T1W. In a separate 200-case diagnostic assessment, AUCs for clinically significant cancer were 0.860 with acquired images, 0.841 with MSCNet and 0.797 with baseline-generated images. A locked 186-case three-hospital cohort supported multicentre transportability. These retrospective results support quality-controlled cross-modal reconstruction as an adjunct to acquired prostate MRI.

bioengineering↗

bioRxiv2026

nELAVL phosphorylation by CDKL5 regulates inter-condensates composition and communication to promote experience-dependent maturation of the visual cortex

Mutations in Cyclin-Dependent Kinase-Like 5 (CDKL5) cause CDKL5 deficiency disorder (CDD), an X-linked neurodevelopmental condition. Through a phosphoproteomic screen, we identified the neuron-specific nELAVL family of RNA-binding proteins as direct activity-dependent substrates of CDKL5. In support of this regulatory axis, single-nuclei transcriptomics of Cdkl5 knockout (KO) cortices revealed an enriched reduction in activity-dependent mRNAs. Mechanistically, we show that nELAVL proteins undergo phase separation to form biomolecular condensates, the size of which is gated by CDKL5 phosphorylation. Loss of CDKL5 leads to enlarged nELAVL condensates, which exhibit reduced binding affinity for the target mRNA Fos, resulting in its accelerated degradation. This disruption extends to inter-condensate communication: phosphodeficient nELAVL show diminished interaction with P-bodies, which themselves become enlarged in CDD mutant iNeurons. Functionally, the absence of nELAVL phosphorylation recapitulates the deficits in experience-dependent visual function observed in Cdkl5 KO mice. Our findings establish a critical molecular mechanism by which CDKL5-mediated phosphorylation governs mRNA metabolism by tuning the properties of nELAVL condensates and their communication with other biomolecular condensates, ultimately promoting experience-dependent maturation of the visual cortex.

neuroscience↗

bioRxiv2026

A Discrete Language of Protein Words for Functional Discovery and Design

Proteins can preserve conserved functions despite extensive sequence and structural divergence, suggesting that functional organization is governed by distributed constraints not captured by conventional representations. Here we develop a hierarchical sequence-based representation framework that compresses proteins into context-dependent latent states while preserving multiscale organizational information. Using this framework, we identified previously uncharacterized ciliary proteins lacking detectable sequence and structure homology, including ADMAP1, which is required for normal sperm axonemal organization and motility in mice. Discrete latent protein states captured species-level organizational signatures correlated with major evolutionary groups and revealed expansion of intrinsically disordered regulatory environments in eukaryotes. Autoregressive sampling within this latent space further enabled design of synthetic actin-remodeling proteins that maintained robust F-actin severing activity despite extensive sequence rewiring across key functional interfaces. These findings demonstrate that distributed protein organization can be inferred directly from sequence, linking functional discovery, evolutionary analysis, and protein design within a shared representational framework.

bioinformatics↗

bioRxiv2026

Serotonergic modulation of motor subspace dynamics drives a sleep-independent quiescent state

The dorsal raphe nucleus (DRN) serotonergic (5-HT) system has been implicated in regulating sleep and motor control; however, its specific role remains controversial. In this study, we found that optogenetic activation of DRN 5-HT neurons in larval zebrafish induced a quiescent state and a reduced response to acoustic stimuli. Unlike sleep, the induced quiescent state was not accompanied by a loss of postural control, and nighttime activation of DRN 5-HT neurons led to a subsequent sleep rebound. Whole brain light field imaging combined with demixed principal component analysis (dPCA) revealed distinct neural subspaces related to DRN activation, sound responses, and motor activity. DRN 5-HT activation selectively modulated the motor-related subspace while leaving the sound-evoked subspace unaffected. Unlike DRN activation, sleep induced by mepyramine significantly altered sound-evoked neuronal activity patterns. Further analysis demonstrated that serotonin had a graded effect on the motor subspace, wherein downstream neurons responsible for particular bout types were more significantly influenced. Embedding motor population activity in a curved geometric space revealed that the degree of curvature scales with behavioral suppression across animals, providing a quantitative signature of the quiescent state. Together, these results elucidate that serotonergic modulation promotes behavioral quiescence through selective regulation of motor populations.

neuroscience↗

bioRxiv2025

TaoChongBao: A Large-Scale Caenorhabditis elegans Mutagenesis and Missense Variant Database Bridging Worm and Human Genomes

We generated and sequenced 12,069 viable Caenorhabditis elegans strains produced by ethyl methanesulfonate mutagenesis, identifying 20,315,536 variants, including 541,102 unique missense mutations across 20,914 genes. To organize and visualize this resource, we developed TaoChongBao, an open-access database and strain repository that integrates C. elegans mutation data with AlphaMissense-predicted pathogenicity scores and ClinVar clinical annotations. TaoChongBao enables users to explore worm missense variants, identify conserved residues corresponding to human pathogenic sites, and access viable strains for experimental validation. Compared with the previous Million Mutation Project in C. elegans, TaoChongBao expands mutation coverage over twenty-fold and emphasizes amino acid-altering variants. This resource provides a scalable platform for functional residuomics, variant interpretation, and comparative analyses between C. elegans and human genomes.

bioinformatics↗

bioRxiv2025

Throwing dice, but not always: bet-hedging strategy of parthenogenesis

Parthenogenesis, clonal propagation by only female, is a common asexual reproduction model. Without sexual gene recombination, it is hypothesized that the deficiency of genotypic variation and accumulation of deleterious mutations reduce the fitness of parthenogenetic lineages confronted with environmental fluctuations, which is also regarded as evolutionary dead end. There should be specific life-history strategies to explain why parthenogenesis has been existing successfully. We constructed a family pedigree for rotifer spanning six generations, comprising 1200 individuals with identical genetic background in uniform condition, tracing back to the inception of parthenogenesis from single dormant egg. The individual fitness represented by lifespan and fecundity exhibits rich variation, and seems to be determined before birth by maternal stochastic investment among clutches regardless of maternal aging. Alike to "Do not put all your eggs in one basket", this bet-hedging strategy spreads risk of environmental unpredictability. Despite the absence of sexual recombination, the phenotypic fitness failed to achieve fixation and heritability, instead demonstrating transgenerational compensation and trade-offs phenomenon. More siblings mean less children, and vice versa. This can be regarded as intrinsic and innate non-density-dependent self-regulation strategy of population, as limited by the conservation of disposable energy for allocation among offspring. Those strategies are conducive to explain the adaptability of parthenogenesis in evolution.

zoology↗

bioRxiv2025

Ultrafast fMRI detects age-related changes in harmonics of cardiac pulsations in the brain at 7 T

PurposeTo develop and apply an ultra-fast fMRI acquisition at 7 T to measure the pulsatile signals in the brain with full brain coverage and detect age-related differences. Pulsatile signals parameters provide information about the health status of the cerebrovascular system. This new acquisition provides a good mix of spatial coverage, image resolution, and temporal resolution for observing physiological signals. MethodsA partial separability MRI acquisition and reconstruction approach was used to collect 3D data acquired at 7 T with TR = 65 ms in 28 healthy adults. 8 young subjects and 14 older subjects (10 male and 12 female) had acceptable pulse plethysmography and MRI data. With full-brain coverage and 2 mm isotropic resolution, the reliability of the pulse signal (even/odd heartbeat as test/retest) within each brain voxel was computed across subjects. Within voxels of high pulse reliability, the average magnitude within 0.15 Hz of the 4 heartbeat harmonic frequencies were compared within CSF, GM, and WM between young/old and between male/female participants. ResultsIncreased first harmonic magnitude in older adults compared to young adults was detected in regions with reliable cardiac pulsations, which overlap major arteries and CSF pools. There was also a greater magnitude of the third harmonic normalized to the first in males. Brain maps of the pulse frequency and the harmonics were formed for visualization of regions of high pulsatility. ConclusionThis new approach captures the pulsatile signal with BOLD fMRI with high spatiotemporal resolution and can be sensitive to age- and sex-related differences.

neuroscience↗

bioRxiv2025

A comprehensive functional landscape of α-tubulin TUBA1A variants illuminates microtubule biology and refines clinical classification

Missense variant interpretation in highly conserved, paralog-rich gene families remains a critical bottleneck for precision medicine. Here, we developed an integrated experimental-computational platform to systematically assess the functional impact of all possible missense mutations in the -tubulin TUBA1A. Combining high-throughput comprehensive mutagenesis, high-content imaging, convolutional neural network- driven phenotyping, and machine learning-guided prediction, we quantified microtubule assembly phenotypes for every coding variant. This approach outperforms conservation-based predictors and enables functional reinterpretation of disease-associated variants. Structural mapping of the TUBA1A mutational landscape reveals distinct domains critical for GTP binding, chaperone-assisted folding or protofilament interaction, illuminating diverse mechanisms of tubulin-related diseases. Integration with ACMG-AMP guidelines demonstrates this mutational landscape improves clinical variant classification in redundant gene families. This framework is broadly applicable to other structurally conserved proteins, linking variant effect prediction to mechanistic insight and clinical translation.

genetics↗

bioRxiv2025

Understanding the genetic diversity of bacteria isolated from across the Atacama Desert

Despite being one of the driest and harshest deserts on Earth, the Atacama Desert is home to a variety of bacterial life. Microorganisms that reside here may have developed adaptations to help them survive this unique environment. In this study, we used bioinformatic and genetic methods to assess the abundance of phyla that are present in this environment and what types of adaptations individual bacteria have obtained. To assess bacterial diversity, we used 16S rRNA sequencing on soil samples and determined the relative composition of different phyla and archaea at sixteen locations. A selection of eight cultivatable organisms which produce pigments were subjected to whole genome sequencing (WGS). Using these sequences, we screened for stress-tolerance capabilities including pigment production pathways, biofilm-related genes, antibiotic production, and genome stability. We found that all strains we sequenced are predicted to produce bioactive compounds. We also found that the pigments that these bacteria produce have antioxidant, iron and ion chelating, and/or antibiotic properties. This characterization allows us to assess adaptive strategies of bacteria which is important in the fields of agriculture, biotechnology and health.

microbiology↗

bioRxiv2025

Physiological Reconstitution of Microtubule Doublets

The formation of microtubule doublets (MTDs) is a foundational step in cilia biogenesis, yet how B-tubule nucleation is initiated at the molecular level remains elusive. Here, we identify FAP53 as a crucial factor that promotes B-tubule assembly. Molecular dynamics simulations revealed that FAP53 alleviates steric hindrance from the -tubulin C-terminal tail and stabilizes B-tubule docking at the A-tubule surface. In vitro reconstitution demonstrated that recombinant FAP53 is sufficient to drive MTD formation under physiological tubulin conditions. In cultured HeLa cells, co-expression of CFAP53 and CFAP20--an inner junction protein--induced ectopic MTD-like structures in the cytoplasm. Furthermore, a structurally homologous protein in C. elegans, WFAP-53, localized to sensory cilia; however, when overexpressed, it triggered ectopic MTD formation in neuronal dendrites and concomitantly led to sensory cilia disassembly. These findings uncover a conserved mechanism of B-tubule initiation and underscore the necessity for spatially restricted expression of MTD assembly factors during ciliogenesis.

cell biology↗

bioRxiv2025

Rapid decoding of neural information representation from ultra-fast functional magnetic resonance imaging signals

High spatio-temporal resolution is crucial for neuroimaging techniques to improve our understanding of human brain function. While the fMRI signal is slow and shows a spread in latencies over space, the precision of hemodynamic response latency for each voxel is preserved and has been shown to be able to detect oscillatory hemodynamic changes approaching 1 Hz, suggesting its potential to reveal rapid neural dynamics. To examine how fast neural information can be derived from fMRI signals, we performed experiments that acquire high-field (7T) fMRI signals at an ultra-fast sampling rate (TR = 125 ms) from the visual cortex while participants observed naturalistic object stimuli. We applied multivariate pattern decoders to extract presented object-category information from the acquired signals at each sampling time after stimulus onset. Results showed that decoding accuracy rose above statistical significance less than 2 s after signal onset, faster than the peak latency of the hemodynamic response. The peak latency of the decoding accuracy was independent of variations in the hemodynamic latency of voxels used for decoding. The application of sparse decoders further revealed that rapid and accurate decoding was possible by pruning vein-rich voxels off from the multivariate voxel input to the decoders. These results suggest that a combination of ultra-fast sampling and multivariate decoding allows fast and temporally precise analysis of neural activity using fMRI signals. Significance statementFunctional magnetic resonance imaging (fMRI) is the most successful method to evaluate human brain function at fine spatial scales but is thought to lack temporal resolution because of slow hemodynamics. We challenge this conventional notion by fast sampling of fMRI signals, combined with multivariate decoding to extract information content represented in the fMRI signals. Results showed that the information content can be extracted faster than the magnitude of hemodynamic response rises, independent of the large spatial variation of hemodynamic latencies across individual voxels, and even after removing venous voxels from decoders. Our method is thus effective at filtering out slow and variable hemodynamic components, leading to the extraction of rapid and temporally precise components reflecting neuronal activity in human fMRI signals.

neuroscience↗

bioRxiv2025

Mesoscopic SCAPE Microscope with a Rescanned, Super-oblique Illumination Plane

Investigating structural and functional dynamics across large spatial scales in living organisms calls for volumetric microscopy that combines a wide field of view (FOV), high spatial resolution, and sufficient temporal resolution. Swept confocally-aligned planar excitation (SCAPE) microscopy offers a compelling balance of optical sectioning, cellular resolution, and high-speed volumetric imaging. However, extending SCAPE to mesoscopic scales has been hindered by the limited tilting angle of the oblique illumination light sheet achievable with commercial low-magnification objectives. Here, we present a mesoscopic SCAPE microscope that overcomes this constraint by implementing a super-oblique light sheet--tilted up to ~60{degrees} relative to the optical axis of a 0.5-NA primary objective--enabled by an air-to-water bridging reflector. In addition, we introduce a single-galvanometer, self-conjugating rescanning strategy that allows arbitrary customization of the optical-to-mechanical angle ratio. This innovation accommodates the reversed and modulated scan displacement of the reflected light sheet and preserves descanned epi-fluorescence detection. Together, these advancements enable our mesoscopic SCAPE microscope to achieve a lateral FOV of 5.0 mm x 2.9 mm, cellular-level spatial resolution (~9.4 m x ~5.9 m lateral, and ~6.0 m axial), and a volumetric imaging rate of 9 volumes per second.

bioengineering↗

bioRxiv2025

Decoding the Moving Mind: Multi-Subject fMRI-to-Video Retrieval with MLLM Semantic Grounding

Decoding dynamic visual information from brain activity remains challenging due to inter-subject neural heterogeneity, limited per-subject data availability, and the substantial temporal resolution gap between fMRI signals (0.5 Hz) and video dynamics (30 Hz). Current approaches face persistent challenges in addressing these temporal mismatches, demonstrate limited capacity to integrate subject-specific neural patterns with shared representational frameworks, and lack adequate semantic granularity for aligning neural responses with visual content. To bridge these gaps, we propose a framework addressing these limitations through three innovations: (1) a Dynamic Temporal Alignment module that resolves temporal mismatches via exponentially weighted multi-frame fusion with adaptive decay coefficients; (2) a Brain Mixture-of-Experts architecture that combines subject-specific extractors with shared expert layers through parameter-efficient tri-modal contrastive learning; and (3) a Multi perspective Semantic Hyper-Anchoring module that resolves cross-subject attention bias via multi-dimensional semantic decomposition, leveraging multimodal LLMs for fine-grained video semantic extraction--enabling the model to match individual attention patterns as different subjects naturally focus on distinct aspects of the same visual stimulus. This module boosts Top-10/Top-100 retrieval by 17.7%/6.6%. Experiments on two video-fMRI datasets demonstrate state-of-the-art performance, with 39%/30% improvements in Top-10/Top-100 accuracy over single-subject baselines and 27% gains against multi-subject models. The framework exhibits remarkable few-shot adaptability, retaining 97% performance when using only 10% training data for new subjects. Visualization analysis confirms this generalization capability stems from effective disentanglement of subject-specific and shared neural representations.

neuroscience↗

bioRxiv2025

Noninvasive ultrasound targeted modulation of calcium influx in splenic immunocytes potentiates antineoplastic immunity attenuating hepatocellular carcinoma proliferation

The spleen, as the largest immune organ, plays a pivotal role in modulating immune responses, particularly in the context of carcinogenesis and tumor progression. Non-pharmacological manipulation, particularly splenic ultrasound stimulation (SUS), has demonstrated significant immunomodulatory efficacy in alleviating chronic inflammatory diseases, suggesting its potential to revitalize splenic immunocompetence suppressing tumor proliferation, yet remains underexplored. This study applied low-frequency pulsed focused ultrasound (FUS) noninvasively stimulating the spleen (FUS sti. spleen) to investigate the efficacy in enhancing antitumor immunity and suppressing hepatocellular carcinoma (HCC). The results showed that FUS sti. spleen significantly suppressed tumor proliferation, achieving a suppression rate of >70% for H22-HCC and >83% for Hepa1-6-HCC, along with significantly prolonged survival. Comprehensive flow cytometry, single-cell RNA sequencing (scRNA-seq) and cytokine analyses demonstrated that SUS profoundly reshaped the splenic and intratumoral immune landscape, specifically activating cytotoxic CD8+ T cells and NK cells while suppressing immunosuppressive cell populations. Mechanistically, FUS facilitated calcium influx in splenic immunocytes, activating multiple signaling pathways, such as TNF, NF{kappa}B, MAPK, HIF-1, and ErbB, thereby counteracting tumor-driven immunosuppressive polarization while potentiating robust immune activation that impedes malignant progression and neoplastic proliferation. Leveraging above insights, we developed spleen-targeted nanodroplets encapsulating bioavailable calcium ions (STNDs@Ca{superscript 2}), which, upon FUS stimulation, undergo cavitation-mediated controlled release of Ca{superscript 2}, further amplifying immunocyte activation and tumor suppression, achieving a remarkable H22-HCC suppression rate of over 90%. This study highlights the therapeutic potential of ultrasound-mediated splenic immunomodulation, both as a standalone intervention and in synergy with STNDs@Ca{superscript 2}, as a novel and noninvasive strategy for cancer immunotherapy.

biophysics↗