Biology subjects

Tan, Y.

Publications and source records attributed to Tan, Y..

At least 37 records · Page 2Linked to original sources

bioRxiv2026

The Origin and Evolution of Protein Synthesis: A Co-Adaptation Flexible-Rigid Docking Model Based on First-Principles Reasoning

Although the "RNA world" hypothesis suggests that RNA played a crucial role in the origin of life [7], the functional framework of RNA in prebiotic protein synthesis and the mechanisms of genetic code formation during the prebiotic period remain poorly understood. Here, using the prebiotic "primordial soup" as a model, we reconstructed the detailed steps that would yield a protein with a stable ordered amino-acid sequence in the "primordial soup" at the prebiotic period. In the "primordial soup", a large number of medium- to large-sized biomolecule-like substances--such as RNA-like and protein-like molecules of various sizes and shapes, as well as related polymers like amino-acid-RNA-like etc.--did generate and accumulate. Moreover, protein-like and RNA-like molecules formed even more intricate complexes. These complexes bound free mRNA-like molecules through complementary base pairing. Subsequently, with an extremely low probability, two adjacent amino-acid-RNA-like molecules became bound to this free mRNA-like molecule, and their amino acids underwent a condensation reaction by the complexes, producing peptides and eventually proteins or polypeptides. This free mRNA-like molecule exhibits a certain flexible structure, whereas the super-large complexes formed by protein-like and RNA-like molecules (which possess certain activities) and the amino-acid-RNA molecules exhibit relatively rigid structures. Long-term evolution and mutual selection led to the emergence of proteins with stable amino acid sequences and moderate catalytic activity. In this way, the nucleotide information embedded in such mRNA-like molecules indirectly express through protein synthesis--a process we term the "A Co-Adaptation Flexible-Rigid Docking Model", where flexible mRNA-like molecules dock onto rigid complexes to enable ordered peptide formation. Finally, we show how trinucleotide codons emerge naturally from the flexible-rigid docking constraints.

evolutionary biology↗

bioRxiv2026

Deep learning-guided design of hydrolases for crystalline PET depolymerization

Poly(ethylene terephthalate) (PET), a ubiquitous polyester used in packaging and textiles, persists in the environment due to its high crystallinity and stability, contributing substantially to global plastic pollution. Enzymatic depolymerization by PET hydrolase (PETase) offers a chemically precise and environmentally sustainable route to convert PET into its monomeric building blocks, enabling recycling. However, practical implementation remains hindered by the rigid, crystalline architecture of PET, which restricts enzyme access and necessitates energy-intensive pretreatment to enable efficient depolymerization. In addition, most PETases achieve only partial depolymerization with low terephthalic acid (TPA) yields and accumulate inhibitory intermediates, while limited thermostability and slow surface kinetics further restrict efficiency. To overcome these barriers, we report VenusPETase, an engineered variant of KbPETase designed using PET-Flow, a state-of-the-art computational framework for PETase engineering. Compared with KbPETase, VenusPETase exhibits a 3.4-fold increase in hydrolytic activity, up to a 27-fold improvement after heat treatment of protein, and a 12 {degrees}C enhancement in thermostability. VenusPETase exhibits rapid degradation across a wide crystallinity range (8%-50%) at 50 {degrees}C, effectively spanning the entire spectrum of commercial PET products. Moreover, VenusPETase outperformed nine high-performance PETases under their respective optimal conditions and degraded untreated PET substrates across 8%-50% crystallinity, producing TPA as over 95% of the released products with minimal intermediate accumulation. X-ray crystallography and molecular dynamics simulations suggest that dynamic modulation, elevated surface electrostatic potential enhance the interaction of VenusPETase with crystalline PET, thereby lowering the hydrolytic energy barrier and improving catalytic performance. We also demonstrate that untreated, postconsumer-PET from nine different products can all be degraded by VenusPETase. The recovered monomers can be directly repolymerized into virgin-quality PET, demonstrating a closed-loop enzymatic recycling process. In a 100 L bioreactor, VenusPETase completely depolymerizes post-consumer crystalline PET (28% crystallinity) within 24 h under 50 {degrees}C. These results establish VenusPETase as a robust biocatalyst that enables efficient, closed-loop recycling of crystalline PET under mild conditions.

biochemistry↗

bioRxiv2026

Information-dependent eye-hand coordination emerges from active vision

In daily activities, humans rely on visual information to plan hand movements, making the extraction of task-relevant information through eye gaze a key aspect of motor control. Behavioral studies have revealed characteristic saccade-pursuit patterns, likely governed by shared neural circuits, which enable an efficient reduction of task-related uncertainty. However, a unifying computational principle explaining the emergence of these patterns in continuous tasks such as reading or driving is still lacking. Here we propose a dual stochastic model predictive control formulation of active vision, in which eye movements are continuously controlled to minimize task-relevant uncertainty and build an internal model used for hand movement planning. Through experiments manipulating the amount, density, and difficulty of future visual information, we show how eye movement patterns adapt to the information context while maintaining an invariant extraction horizon. A saccade-pursuit pattern naturally emerges from the model, which accurately predicts both eye and hand movement features observed in experiments. These results provide a principled framework for understanding the continuous regulation of human eye movements and open new perspectives for applications in robotic assistance and active perception.

neuroscience↗

bioRxiv2026

COLOR-3D: a versatile tool for revealing novel 3D histological features

Hematoxylin and eosin (H&E) has been the fundamental method for visualising tissue morphology. Recent advances in tissue clearing and microscopy have enabled the observation of tissue morphology in 3D, but incomplete penetration of nucleic acid dyes has remained the bottleneck. To address this, we develop a new staining chemistry called Cyclodextrin and Organic solvent-assisted deep Labelling of ORgans in 3D (COLOR-3D), which attains the best penetration depth and homogeneity among state-of-the-art methods. We also demonstrate the scalability of COLOR-3D and its compatibility with other staining modalities. To bridge the gap between 3D histology and its wider application in biomedical research and histopathology, we develop a computational pipeline to convert 3D fluorescence images into bright-field H&E images, enabling the creation of a 3D atlas of both normal tissues and pathological specimens. Apart from qualitative observation of tissue morphology, COLOR-3D also enables quantitative analysis for studying biological phenomena. In the mouse liver, we discover rare populations of tetranuclear hepatocytes as well as m16n, t4n and t8n hepatocytes. We also propose the first structural model of the liver lobule based on 3D histology. With a more complete penetration, we reveal the following aging-related changes in tissue microarchitecture, including an increase in extreme nuclear polyploidy, and the disruption of vasculature and portal triad.

pathology↗

bioRxiv2026

Toward CT-based Tractography: Presurgical White Matter Tract Mapping in Intracerebral Hemorrhage

Presurgical mapping of key white matter (WM) fiber tracts is crucial for intracerebral hemorrhage (ICH) surgery, but it currently relies on tractography from diffusion MRI (dMRI), which has limited applicability in urgent or resource-constrained settings due to long scan times and limited MRI availability. To bridge this gap, we developed a deep learning approach designed to reconstruct critical fiber tracts directly from routinely acquired CT scans, focusing on the corticospinal tract (CST) due to its high clinical relevance. By training a novel network on a curated dataset of 150 paired CT-dMRI scans (101 ICH patients and 49 healthy subjects), we enabled the direct mapping of the CST from CT images alone, bypassing the traditional requirement for dMRI. Our results demonstrate that the CT-derived tracts achieve high anatomical plausibility, with neurosurgeon expert assessments yielding a Likert score of 3.64. Furthermore, the clinical relevance of these reconstructions was validated by a significant correlation between CT-derived tract integrity and patient motor scores (r = 0.726, p = 3.731x 10-7). These findings suggest that in complex clinical scenarios, particularly where dMRI signal quality is compromised by lesion-induced distortion, this CT-based mapping may serve as a useful anatomical reference. Overall, by enabling CT-based WM mapping, our method potentially offers a practical route to gain the key advantages of tractography in resource-limited or time-critical settings

neuroscience↗

bioRxiv2026

AI-enabled virtual immunopeptidomics links quantitative neoantigen presentation to immunogenicity

Effective anti-tumor T cell response depends on both neoantigen quality (non-selfness) and quantity (abundance). However, existing methods for neoantigen prioritization largely overlook peptide abundance because it is difficult to measure and model. To bridge this gap, we developed epiVIP, a deep learning framework that predicts the abundance of individual HLA-I peptides using widely available (sc)RNA-seq data. Trained on 1.7 million immune peptides paired with gene expression profiles, epiVIP demonstrated strong generalizability across unseen samples. Analyzing 33,711 neoantigens from clinical datasets revealed a compensatory relationship between abundance and non-selfness in determining antigenicity, providing quantitative support for the TCR avidity theory. Importantly, abundance independently predicted tumor reactivity and patient survival across multiple neoantigen vaccine cohorts and immune checkpoint blockade cohorts. Mechanistic interpretation of epiVIP further identified directional regulation of MAGEA3 epitope presentation by PSME4, which was validated experimentally using T cell functional assays. Together, these findings established AI-enabled virtual immunopeptidomics as a powerful strategy to improve cancer immunotherapy.

bioinformatics↗

bioRxiv2026

Machine learning cross-platform proteomic imputation enables protein quality scoring and replication of epidemiological associations

High-throughput affinity-based proteomics has advanced biomedical research, yet fundamental, persistent discordance between mainstream platforms (SomaScan and Olink) routinely undermines the replication of findings. This platform-driven non-replication complicates downstream biological validation and biomarker prioritization. Here, we develop a machine learning-based framework for cross-platform protein value imputation to resolve this translational bottleneck. Using paired proteomic data measured by both SomaScan and Olink from 5,325 participants of the Multi-Ethnic Study of Atherosclerosis, we developed models to impute cross-platform measurements and applied them to two independent and demographically distinct cohorts (Cardiovascular Health Study [N=3,171] and UK Biobank [UKB; N=41,405]) for external validation. Our bi-directional model 1) established an imputation performance-based protein fidelity index, validated against gold-standard measurements from Atherosclerosis Risk in Communities study (N=101) and Nurses Health Study (N=54), 2) enabled imputation of platform-exclusive protein measurements, and 3) facilitated calibration of overlapping proteins. We demonstrate the utility of this framework through three applications: 1) fidelity-informed analyses enhanced the replication of biomarker discovery, 2) recovery of SomaScan signals that were previously inaccessible in UKBs original Olink measurements, and 3) improved replication performance for overlapping proteins. Our study offers a translational roadmap that allows researchers to achieve reliable epidemiological replication, target specific assays for future optimization, and prioritize biological signal over platform noise.

bioinformatics↗

bioRxiv2026

Multimodal profiling reveals the centromedian nucleus of thalamus as a dynamic hub orchestrating staged consciousness recovery

Consciousness recovery from general anesthesia represents a fundamental brain state transition. The absence of objective, continuous metrics to monitor the shift from unconsciousness to full awareness has left its dynamic, multidimensional nature unresolved, fracturing consciousness theoretical framework and posing clinical risks due to unreliable assessment of emergence. To address this, we developed a multiscale framework integrating AI-driven behavioral analysis, continuous neuro-physiology recording, and whole-brain functional imaging. This decodes recovery into three hierarchical stages, reflex restitution, level restoration, and content re-establishment, each with unique multimodal signatures. We identified heart rate stabilization as a potential noninvasive biomarker for the restoration of consciousness level. Crucially, the centromedian nucleus of thalamus acts as a dynamic hub, actively orchestrating staged whole-brain reconfiguration via stage-dependent network routing. These findings resolve the temporal orchestration of consciousness recovery, ground disparate theories within a unified mechanistic sequence, and open transformative paths for real-time monitoring and neuromodulation in anesthesiology. HighlightsA multimodal framework decodes consciousness recovery into three hierarchical stages Recovery stages span from reflex restitution, to level restoration, and finally to content re-establishment Heart rate stabilization serves as a noninvasive biomarker for consciousness level restoration The CM paces this staged reconfiguration as a dynamic network hub In BriefZhang et al. develop a multiscale framework that delineates consciousness recovery from anesthesia as a three-stage process, identifies heart rate stabilization as a biomarker for the restoration of consciousness level, and reveals the CM as a dynamic hub orchestrating this progression. These findings clarify the temporal orchestration of consciousness recovery, pave the way for real-time monitoring and neuromodulation in anesthesiology and other fields.

neuroscience↗

bioRxiv2026

Structural Mechanism of TRPC3 Channel Activation by the Moonwalker Mutation

TRPC3 is a calcium-permeable, non-selective cation channel that is activated by DAG. It is expressed in several tissues, especially in the cerebellum, and has been implicated in various human diseases. Despite recent progress in understanding the structural mechanism of TRPC3, how the channel opens remains elusive. Here, we present structures of hTRPC3 in an agonist-free resting state, determined using a DAG-binding site mutant. We also present the structure of hTRPC3 in a DAG-bound open state, determined using a constitutively active "moonwalker" (T561A) mutant. These structures, together with electrophysiological results, reveal that the T561A mutation activates hTRPC3 by disrupting a polar interaction with N652. A newly formed {pi}-bulge in S6 leads to rotation and outward tilting of the lower half of S6, resulting in dilation of the pore and thus channel opening. Agonist DAG stabilizes hTRPC3 in the open conformation. BTDM exerts its inhibitory effect by pushing S5 and S6 back to the center to close the pore, while preserving the {pi}-bulge. These results shed light on the opening mechanism of hTRPC3.

biophysics↗

bioRxiv2026

Inducible Impairment of Polymerase Gamma Activity in Cardiomyocytes Promotes Severe Cardiomyopathy with Cardiac Hepatopathy

Mitochondrial dysfunction is a hallmark feature of heart failure (HF) and cardiomyopathy, with substantial human and preclinical evidence suggesting that congenital mitochondrial defects can directly drive these conditions. Despite these strong links, not all individuals with mitochondrial disease develop cardiomyopathy, and therefore the precise mitochondrial defects that initiate cardiac pathology in this setting remain incompletely understood. Here, we describe a novel mouse model that induces progressive deterioration in mtDNA integrity specifically in cardiomyocytes. This model was generated through a post developmental, cardiomyocyte specific deletion of the exonuclease domain of Polymerase Gamma (PolG), impairing its ability to repair mtDNA. Strikingly, from just 16 weeks post-induction these mice displayed progressive worsening of cardiac output, ejection fraction, global strain and blood pressure culminating in premature death at 28-30 weeks post-mutation. Morphologically, these mice displayed cardinal features of hypertrophic cardiomyopathy with enlarged hearts, ventricles and cardiac fibrosis - but little evidence of congestive HF. We also demonstrate using various transcriptional and proteomic readouts, that signalling pathways characteristic of cardiomyopathy were activated. Interestingly, prior to substantial declines in cardiac function, we detect robust activation of the integrated stress response (ISR) in PolGMut mice, and major rewiring of mitochondrial folate metabolism pathways, suggesting that these pathways underpin the developing pathology. Lastly, we also observed a striking hepatopathy phenotype in mutant mice reminiscent of that observed in patients with HF, a condition not robustly recapitulated previously in other mouse models. Thus, our data establish a direct link between mtDNA instability leading to chronic activation of the ISR and rewiring of folate metabolism in cardiomyocytes, subsequently driving a severe cardiac phenotype associated with hepatopathy.

physiology↗

bioRxiv2026

Regulation of the Balance between Concentric and Eccentric Cardiac Hypertrophy by a CDC14A-KMT5A Signaling Pathway

BackgroundDepending upon the type of pathological stress, the heart undergoes concentric or eccentric remodeling. This structural change is associated with diastolic and/or systolic ventricular dysfunction reflecting differentially altered cardiomyocyte morphology, ultrastructure, metabolism, contractility, and survival, as well as interstitial myocardial fibrosis. Despite an association of both concentric and eccentric remodeling with heart failure and sudden death, the molecular mechanisms resulting in abnormal cardiac geometry remain poorly understood. A better understanding of the basic mechanisms conferring these contrasting forms of remodeling should inform novel approaches to preserve normal cardiac structure and function in cardiovascular disease. The protein phosphatase Cell Division Cycle 14A (CDC14A) and its substrate the lysine methyltransferase KMT5A are identified herein as key regulators of the balance between concentric and eccentric pathological cardiac remodeling. MethodsThe regulation of adult rat ventricular myocyte morphology by CDC14A and KMT5A was studied in vitro following gain and loss of function by expression of wild-type and mutant proteins and RNA interference (RNAi). Epigenomic regulation by KMT5A was studied by mapping histone 4 lysine 20 mono-methylation (H4K20me1) modified chromatin sites and correlating them with gene transcription. Regulation of pathological cardiac remodeling in vivo was demonstrated by CDC14A and KMT5A RNAi using adeno-associated virus (AAV) mediated cardiomyocyte-specific small hairpin RNA (shRNA) expression in mice. ResultsCDC14A inhibited the growth in width of cultured adult myocytes stimulated by -adrenergic receptor activation or by serum response factor. KMT5A was downregulated by CDC14A in cardiomyocytes and was required for myocyte growth in width. -adrenergic stimulation of KMT5A-dependent H4K20 mono-methylation across transcription units correlated with regulation of gene transcription. Accordingly, AAV-expressed KMT5A shRNA induced eccentric remodeling and cardiac dysfunction in wild-type mice. Conversely, expression of Cdc14A shRNA improved systolic function and cardiac structure and inhibited pathological gene expression in the Tpm1 E54K mouse with Dilated Cardiomyopathy. ConclusionsCDC14A-KMT5A-dependent epigenomic regulation of gene transcription constitutes a molecular switch that determines concentric versus eccentric cardiac remodeling. These findings identify CDC14A as a potential therapeutic target for the treatment of dilated cardiomyopathy and other forms of heart failure with reduced ejection fraction. Clinical PerspectiveO_ST_ABSWhat is newC_ST_ABSO_LIA function is identified for the first time for the protein phosphatase CDC14A in the heart, regulation of cardiomyocyte morphology and overall cardiac geometry in pathological cardiac remodeling. C_LIO_LIThe lysine methyltransferase KMT5A is shown to mediate the effects of CDC14A in the adult cardiomyocyte by regulating H4K20 mono-methylation, such that reduced KMT5A expression promotes a phenotype resembling Dilated Cardiomyopathy. C_LIO_LIH4K20me1 epigenomic modification is identified as a regulator of cardiac structure and function. C_LI Clinical implicationsO_LICDC14A loss of function experimentation in vivo, resulting in improved cardiac structure and function in a mouse model of Dilated Cardiomyopathy, suggests that CDC14A is a novel therapeutic target for heart failure with reduced ejection fraction. C_LI

cell biology↗

bioRxiv2026

ChromSkills enables interpretable and reproducible agentic chromatin data analysis

High-throughput assays generate diverse chromatin datasets that require flexible workflows and context-dependent parameter choices. Although large language models (LLMs) can assist analysis, unconstrained LLM-based execution often exhibits unstable behavior and limited reproducibility. We present ChromSkills, a curated library of domain-specific analytical Skills for agentic chromatin data analysis on the Claude Code platform. ChromSkills encodes expert-informed decision logic and parameter-selection rules as modular, human-readable Skills and couples them with structured tool interfaces to enable reproducible execution and interpretable workflow composition from natural-language task descriptions. Across representative chromatin analysis tasks, ChromSkills consistently selected appropriate tools and parameters across repeated runs and improved execution stability and token efficiency when using Model Context Protocol-based tools. Together, ChromSkills provides a practical framework for trustworthy AI-enabled, agentic chromatin data analysis by guiding LLMs with transparent, reusable domain knowledge.

bioinformatics↗

bioRxiv2026

Multi-omics Insight into Cardiac Myofibril Remodeling in Post-Prandial Burmese Pythons

Burmese pythons exhibit rapid cardiac remodeling in response to a dramatic increase in metabolic rate during digestion. Here, we performed single-myofibril mechanics measurements and myosin heavy chain metabolic assays to evaluate the impact of feeding on the cardiomyocyte sarcomere - the fundamental molecular unit of muscle contraction - using two experimental paradigms: normal feeding (one meal per month) and frequent feeding (eight meals per month). Myofibril tension and rate of relaxation increased during digestion in both paradigms, while frequent feeding was further associated with slower myofibril activation kinetics and faster myosin heavy chain ATP turnover. To identify molecular changes at the sarcomere and gain potential mechanistic insight, we performed multi-omics analyses. RNA sequencing identified increased expression of some sarcomere genes during digestion; however, proteomics analysis suggested a delay in sarcomere protein synthesis at the peak of remodeling, as expression of many sarcomere proteins decreased. Analysis of post-translational modifications (ubiquitinomics, phospho-proteomics, acetylomics) identified hundreds of significantly regulated sites on sarcomere proteins during digestion, including many on the tension-regulating titin and myosin heavy chain proteins. Our results detail the molecular underpinnings of cardiac remodeling in digesting Burmese pythons and suggest that natures solution for rapidly increasing cardiac contractility is a post-translational sarcomere tuning program.

molecular biology↗

bioRxiv2025

scCotag: Diagonal integration of single-cell multi-omics data via prior-informed co-optimal transport and regularized barycentric mapping

Recent advances in high-throughput single-cell technologies have enabled characterization of cellular states across distinct omics layers, yielding complementary insights into the organization of biological systems. To jointly leverage these disparate modalities, computational methods have been developed to align non-overlapping cell populations profiled in different omics layers, a task known as diagonal integration, thereby facilitating more fine-grained biological interpretations. However, existing integration approaches unrealistically assume that all cells are alignable and treat prior-knowledge-derived feature correspondences as fully reliable, retaining them unrefined throughout the alignment process. In this work, we introduce scCotag, a co-optimal transport (COOT)-based deep learning frame-work for diagonal integration of single-cell multi-omics data, to address these limitations. scCotag first infers cell alignment and feature correspondence with prior-informed COOT in an iterative manner, and then leverages the resulting transport plans to jointly learn cell and feature embeddings via regularized barycentric mapping and graph reweighting. Systematic benchmarking on human brain, bone marrow, and blood single-cell RNA-seq and ATAC-seq datasets demonstrates the overall superior performance of scCotag over state-of-the-art methods in both cell alignment accuracy and embedding accuracy. In particular, scCotag excels in simulated imbalance scenarios where not all cells are alignable. Applying scCotag to data in postmortem brains of Alzheimers disease (AD) and non-AD (NoAD) patients further yields more fine-grained biological interpretation of regulatory mechanisms. Together, these results demonstrate that scCotag provides a robust framework for single-cell diagonal integration and regulatory inference.

bioinformatics↗

bioRxiv2025

Mitochondria redistribution organizes the immunosuppressive tumor ecosystem

Hostile conditions in the tumor microenvironment restrict cellular respiration, yet mitochondrial metabolism remains indispensable for tumor growth and the activity of immunosuppressive cells. How tumor ecosystems sustain mitochondrial output has been unclear. Here, we show that cancer cells resolve this paradox by acting as hubs of intercellular mitochondrial redistribution. Using mitochondrial reporter systems, we demonstrate that cancer cells import host-derived mitochondria, integrate them into their endogenous network, and subsequently relay these hybrid organelles to neighboring immune cells. Mitochondria redistribution reprograms recipient neutrophils, macrophages, and CD4+ T cells into highly suppressive states but drives CD8+ T cell exhaustion. Within cancer cells, fusion of incoming mitochondria induces filamentous P5CS assembly, enhances biosynthetic output, and enables the refurbishment of damaged organelles into fully functional units. Disrupting mitochondrial redistribution collapses the immunosuppressive ecosystem and impairs tumor growth. Thus, cancer cells do not hoard resources but orchestrate a redistribution program that fortifies their own metabolic resilience, derails anti-tumor immunity, and sustains immunosuppressive partners. HIGHLIGHTSO_LITumor cells regulate their ecosystem by redistributing mitochondria C_LIO_LIRedistributed mitochondria expand immunosuppressive cells but exhausts CD8+ T cells C_LIO_LIMitochondria fusion within cancer cells, which precedes redistribution, optimizes metabolic output by triggering conformational changes in P5CS C_LIO_LIMitochondria fusion allows cancer cells to incorporate and refurbish seemingly incompetent host-derived mitochondria, improving efficiency in the tumor ecosystem C_LI

cancer biology↗

bioRxiv2025

Inhibition mechanism of pancreatic KATP channels by centipede toxins

The pancreatic ATP-sensitive potassium (KATP) channel acts as a crucial metabolic sensor by regulating insulin secretion to maintain whole-body energy homeostasis. Gain-of-functional mutations in this channel lead to neonatal diabetes mellitus, a rare disorder in which certain mutants demonstrate resistance to standard sulfonylurea therapy. Recent studies have identified a centipede toxin, SpTx1, as a potent inhibitor of both human pancreatic KATP channels and their gain-of-functional mutants. This toxin stimulates insulin secretion, offering a promising therapeutic strategy for neonatal diabetes. Nevertheless, the molecular mechanism by which SpTx1 inhibits the KATP channel has remained elusive. Here, we report the crystal structure of SpTx1 and the cryo-electron microscopy (cryo-EM) structure of the KATP channel in complex with SpTx1. Our results demonstrate that SpTx1 binds to the extracellular surface of the Kir6.2 pore-forming subunit of the KATP channel. Multiple interactions at the SpTx1-Kir6.2 interface underpin the high affinity and specificity of SpTx1 for human Kir6.2. We show that SpTx1 inhibits potassium currents by physically blocking the ion conduction pore. Furthermore, a structure-guided search identified another centipede toxin, Sm3a, as a novel KATP channel blocker. Together, these findings provide key insights into the inhibitory mechanism of centipede toxins against the human Kir6.2-containing KATP channel and establish a foundation for developing these toxins into potential therapeutics targeting KATP channel-related diseases.

biophysics↗

bioRxiv2025

DAXX governs the silencing of LINE1 during spermatogenesis in mice

The suppression of transposable elements in germline is critical for safeguarding fertility. Here we identify that the DAXX, a potent transcription repressor and an H3.3 chaperone, is indispensable for transposable elements silencing during spermatogenesis. Male mice with conditional knockout of Daxx in germ cells mediated by Ddx4-cre display delayed meiotic progression, deformed and reduced production of sperms, and an age-dependent decline in fertility. The ablation of DAXX results in activation of evolutionarily young LINE1 and ERVs subfamilies. Mechanistically, DAXX interacts with DMAP1 to maintain DNA methylation of LINE1 in meiotic cells. In summary, this study identifies DAXX as a previously unknown regulator of spermatogenesis and demonstrates that it functions as an epigenetic regulator to maintain the silencing the young LINE1 by DNA methylation.

developmental biology↗

bioRxiv2025

Ultra-wide-field, deep, adaptive two-photon microscopy

Observing the activity patterns of large neural populations throughout the brain is essential for understanding brain function. However, capturing neural interactions across widely distributed brain regions from both superficial and deep cortical layers remains challenging with existing microscopy technologies. Here, we introduce a state-of-the-art two-photon microscopy system, ULTRA, capable of single-cell resolution imaging across an ultra-large field of view (FOV) exceeding 50 mm{superscript 2}, enabling deep and very wide field in vivo imaging. To demonstrate its capabilities, we conducted a series of experiments under multiple imaging conditions, successfully visualizing brain structures and neuronal activities spanning a spatial range of over 7 mm from superficial layers to depths of up to 900 m, while covering a volume of 45.24 mm3 in the mouse brain. This versatile imaging platform overcomes traditional spatial constraints, providing a powerful tool for comprehensive exploration of neuronal circuitry over extensive spatial scales with cellular resolution.

neuroscience↗