Biology subjects

Chen, Y.

Publications and source records attributed to Chen, Y..

At least 181 records · Page 10Linked to original sources

bioRxiv2026

Wide dynamic range of contrast-encoding in neural responses in macaque V1

The dynamic range of contrast-encoding in the early visual system has been investigated at both single-neuron and population levels in animals using oriented stimuli such as gratings and Gabor patches. However, contrast-encoding of unoriented stimuli such as Gaussians has been less explored, even though such stimuli can evoke a large population response. In studies that employ Gaussians, contrast response functions (CRFs) of neurons and neural populations in primary visual cortex are typically characterized across a limited range of Weber contrasts up to 100%, which may not adequately reflect the statistics of contrast in natural scenes. Indeed, our analysis shows that locations with contrasts far exceeding 100% Weber contrast are ubiquitous in natural scenes. Thus, our current understanding of contrast encoding remains incomplete in the context of natural environments. Here, we measured spiking activities of individual neurons using electrophysiology and population responses using calcium imaging in V1 of fixating macaques while Gaussian stimuli were presented over a wide range of Weber contrasts, up to 900%. Both the average spiking response and the average population response continued to increase robustly above 100% Weber contrast. Only a small minority of neurons saturate below 100% Weber contrast. These results demonstrate that the dynamic range of contrast-encoding in V1 is broader than previously assumed and aligns more closely with the statistics of contrast in natural scenes. Significance StatementThe dynamic range of contrast-encoding in V1 has typically been characterized using only a limited range of contrasts, often excluding the high contrasts commonly found in natural scenes. We measured contrast response functions of individual neurons and neural populations in V1 across a much wider range of contrasts. We found that the responses of the majority of neurons, as well as the overall population, increased robustly up to extremely high contrasts. These findings suggest that the dynamic range of contrast encoding in V1 extends well beyond the commonly tested range.

neuroscience↗

bioRxiv2026

ROS Impair Mitophagy via PARylation of PINK1

Mitophagy is the process of selective autophagic clearance of damaged mitochondria and is closely implicated in neurodegenerative disease. PTEN-induced kinase 1 (PINK1) and a RBR E3 ubiquitin-protein ligase (Parkin) constitute a positive feedback loop in mitophagy initiation. It is known that reactive oxygen species (ROS) modulate mitophagy, while the exact regulatory mechanism remains largely elusive. Here, we found that exogenously applied ROS effectively block mitophagy induced by acute mitochondrial damage agents, which could be reversed by antioxidants. Mechanistically, ROS activate poly(ADP-ribose) polymerase 1 (PARP1), and suppression of PARP1 eliminates the inhibitory effect of ROS on mitophagy. Notably, PARP1 directly interacts with PINK1 and mediates its PARylation at residue E417, thereby negatively regulating PINK1 function. Collectively, our study identifies PARylation as a new form of post-translational modification of PINK1 and reveals a novel mechanism underlying the regulatory role of ROS in mitophagy by PARP1 activation and PARylation of PINK1. In briefGao et al. demonstrate that exogenous ROS inhibit mitophagy. Mechanistically, ROS activate PARP1, which mediates PARylation of PINK1, a central regulator of mitophagy, leading to its functional impairment. This study reveals a novel regulatory mechanism of ROS on mitophagy through PARP1 activation and identifies PARylation as a novel form of post-translational modification of PINK1. HighlightsO_LIROS block PINK1-Parkin-mediated mitophagy. C_LIO_LIROS activate PARP1. C_LIO_LIPARP1 suppression eliminates the inhibitory effect of ROS on mitophagy. C_LIO_LIPARylation of PINK1 by PARP1 impairs its activity and mitophagy. C_LI

Cell Biology↗

bioRxiv2026

Full-length structure of the anti-viral and pro-tumor DNA deaminase APOBEC3B

Human APOBEC3B (A3B) restricts virus infections by catalyzing the deamination of cytosines to uracils in single-stranded DNA. A3B also contributes to mutagenesis and genome instability in cancer cells, driving tumor evolution and detrimental outcomes including therapy resistance and metastasis. A3B comprises tandem globular deaminase domains, with a multifunctional amino-terminal domain (NTD) and a catalytically active carboxy-terminal domain (CTD). Although individual domain structures have been studied, the structure of full-length A3B has remained elusive. Here, we report the cryoEM structure of wildtype A3B in complex with the natural antagonist BORF2 (the large subunit of the Epstein-Barr virus ribonucleotide reductase). The two domains of A3B bridge a novel BORF2 dimer interface, showing a unique domain positioning that distinguishes A3B from the related dual-domain retrovirus restriction factor APOBEC3G (A3G). Mutational analyses suggest that the unique NTD-CTD interaction regulates A3B deaminase activity. The BORF2 dimerization interface is stabilized by primary interactions with A3B-CTD and secondary contacts with A3B-NTD, as well as by A3B CTD-CTD dimerization. This matrix of interactions supports a molecular mechanism for A3B neutralization in which BORF2 binding leads to deaminase sequestration in large aggregates. The full-length wildtype A3B structure also provides a platform for future anti-viral and anti-cancer drug development efforts.

biochemistry↗

bioRxiv2026

High-resolution photocatalytic crosslinking of protein neighborhoods using contact-dependent antibody mapping (contactMAP)

Photo-proximity labeling proteomics (PLP) has emerged as a powerful method for rapid and temporal mapping of transient and fragile protein-protein interactions, especially those in membranes. Numerous catalysts can trigger highly reactive diffusive biotinylated probes to label protein neighborhoods at various length scales. Photocatalysts can also trigger protein crosslinking, predominantly between neighboring tyrosines or between histidine and lysine residues. We have exploited this sidechain directed crosslinking for photo-PLP, in a method we call contactMAP. Using biotinylated antibody binders to photocrosslink Her2 or EGFR neighborhoods, contactMAP enriched high resolution maps of these cancer-associated protein neighborhoods in a manner that rivals or outperforms established photo-PLP methods. ContactMAP is an extraordinarily simple and democratic photo-PLP labeling method with broad applications for probing biomolecular interactions in complex mixtures.

Cancer Biology↗

bioRxiv2026

Energy Metabolizes in Male Bone Marrow Mesenchymal Stem Cells Aging Process

Senescence human bone marrow mesenchymal stem cells (BMSCs), vulnerable to age-related defects, is poor in tissue regeneration. Cells in bone marrow accumulated senescent contributing to the development of metabolic energy regulation hold prospects for therapeutic advances. This study aimed to evaluate energy metabolic changes in male bone marrow mesenchymal stem cells senescence process. Our research established cell specific surface marker and enzymes expression level changes, as well as ECAR and OCR resonance. Notably, CD14, HLA-DRB1 and CD90 upregulated, glycolysis-related genes are increased, tricarboxylic acid cycle-related genes are decreased. We firstly identified links between time-dependent cell aging process and energy metabolism in BMSCs.

cell biology↗

bioRxiv2026

Entanglement-governed protein networks enable mechanically adaptive artificial skin for transplantation-scale skin replacement

Artificial skin substitutes that simultaneously achieve mechanical robustness, regenerative bioactivity, and transplantation-scale tissue integration remain challenging to engineer. Here we report a mechanically adaptive bilayer artificial skin based on entanglement-mediated protein networks. By integrating protein chain entanglement, flexible molecular linkers, and photo-triggered intermolecular crosslinking, we establish a hierarchically organized protein matrix with enhanced toughness, structural adaptability, and regenerative compatibility. Spatial biofunctionalization further enables integration of an antibacterial Zn{superscript 2}-coordinated epidermal layer and a regenerative CLP-EGF-functionalized dermal layer within a unified construct. The engineered skin promotes cellular proliferation through PI3K-AKT-mTOR activation, exhibits sustained antibacterial activity, and supports large-area full-thickness skin replacement covering approximately 40% of the dorsal skin surface in mice. The construct further accelerates diabetic wound repair and extracellular matrix remodeling in vivo. These findings establish entanglement-mediated protein engineering as a strategy for mechanically adaptive regenerative biomaterials and provide a platform for transplantation-scale skin regeneration.

bioengineering↗

bioRxiv2026

Functional orthogonality of WRN inhibitor resistance enables alternating therapy and mutation-tolerant inhibitor design in MSI-H cancers

Werner syndrome helicase (WRN) is a synthetic-lethal vulnerability in microsatellite instability-high (MSI-H)/mismatch repair-deficient (dMMR) cancers1-5, and non-covalent and covalent WRN inhibitors are now entering clinical development6-9. A central unresolved question is whether resistance to one WRN inhibitor class inevitably compromises the target, or instead creates actionable vulnerabilities to an alternate modality. Here we generated ten stable acquired-resistance models across three MSI-H cell lines using the non-covalent inhibitor HRO761 and the covalent inhibitor VVD-214. Whole-exome sequencing, biochemical reconstitution and isogenic knock-in models identified recurrent on-target WRN missense mutations as dominant resistance drivers, but with sharply modality-specific spectra: HRO761 resistance clustered at G729/F730/I852, whereas VVD-214 resistance concentrated at E846. These mutations impaired inhibitor engagement and abolished the canonical WRN inhibitor (WRNi)-induced pharmacodynamic cascade, including WRN reduction, DNA damage response (DDR) activation and G2/M arrest. Crucially, most resistance mutations retained biochemical, cellular and in vivo sensitivity to the alternate inhibitor modality, revealing a functional orthogonality that enabled a 7-day cyclic alternating regimen to delay tumour regrowth in xenografts. We further identified F730L as an engineered cross-resistant bottleneck model and used structure-guided, artificial intelligence (AI)-enabled optimization to generate GBA-007, a proof-of-concept mutation-tolerant WRN inhibitor candidate with promising activity against F730L in vitro and in vivo. Thus, clinically relevant WRN inhibitor classes impose distinct on-target resistance trajectories that can be exploited through schedule design, while cross-resistant bottlenecks can be addressed by rapid mutation-aware inhibitor engineering.

Cancer Biology↗

bioRxiv2026

Validation of MHPC512: A Publicly Available Special-Purpose Supercomputer for Molecular Dynamics Simulations of Biomolecular Systems

MHPC512 is a massively parallel, special-purpose supercomputer designed primarily for atomic-level molecular dynamics (MD) simulations of biomolecular systems. It comprises 512 processor units interconnected by a high-speed three-dimensional torus network and employs a custom chip architecture that uses 35-bit fixed-point arithmetic to accelerate computation while controlling precision loss within an acceptable margin. The preprocessor is compatible with GROMACS and AMBER input formats and supports widely used biomolecular force fields (including CHARMM, AMBER, and OPLS/AA), the Neutral Territory method for short-range nonbonded interactions, the k-space Gaussian Split Ewald method for long-range electrostatics, and multiple thermostats, barostats, and integrators. We present a three-tier validation protocol--comparing static energy and virial components, examining ensemble distributions (NVE, NVT, NPT), and evaluating long-time statistical properties--demonstrating that MHPC512 reproduces results consistent with GROMACS and AmberTools. Application examples, including bulk water, dipeptide conformational sampling, folding of fast-folding peptides, membrane-protein systems, lipid self-assembly, and GPCR conformational transitions, further confirm its reliability. MHPC512 has been deployed at multiple supercomputing centers and is publicly accessible, representing a significant advance in high-throughput, large-scale biomolecular MD simulations.

Molecular Biology↗

bioRxiv2026

Outbred Drosophila populations reveal diet-dependent genetic effects on development time

Metabolic effects of genetic variation often depend on diet, yet the loci underlying diet-dependent developmental responses remain incompletely defined. Here we combine multi-trait phenotyping of Drosophila Genetic Reference Panel lines with genome-wide mapping in newly developed Drosophila Recombinant Populations. High sugar causes genotype- and life-stage-dependent changes in metabolic and life-history traits, with development time emerging as a highly heritable, sugar-sensitive phenotype. Mapping in 16 outbred advanced intercross populations reveals distinct association landscapes under low- and high-sugar diets, with a concentrated low-sugar signal, a more distributed high-sugar pattern, and identified genotype-by-diet loci including tap, Eip75B and Cerk. Functional perturbation supports diet-dependent effects for several prioritized candidates. Allele-frequency analyses identify operationally defined thrifty-like variants associated with delayed development under high sugar and relatively earlier development under low sugar; these variants are enriched for cell-adhesion, neurodevelopmental, and morphogenetic processes. Together, these results establish an outbred Drosophila framework for dissecting how dietary sugar remodels the genetic architecture of development time.

genetics↗

bioRxiv2026

HOMED enables hierarchical and multimodal optimization of DNA methylation deconvolution across tissues

Cellular heterogeneity is a major confounder in bulk DNA methylation data for epigenome-wide association studies. Existing reference-based DNAm deconvolution methods often ignore hierarchies among related cell types and may generalize poorly across datasets due to limited variability in reference profiles. We developed HOMED (Hierarchically Optimized Methylation Deconvolution), a framework that integrates cell-lineage hierarchies, single-cell RNA sequencing-guided deconvolution, and paired bulk RNA-seq/DNAm data for CpG signature optimization. Across simulated and real peripheral blood mononuclear cell, lung, and placental datasets, HOMED consistently yielded the highest PCCs and lowest RMSEs, outperforming existing scRNA-seq-guided DNAm deconvolution methods, improving accuracy, resolution, and cross-tissue generalizability.

bioinformatics↗

bioRxiv2026

Structured and flexible representations in medial-frontal cortex support goal-directed navigation

Humans and animals plan actions to achieve goals in worlds that are complex and continually changing. While planning is critically dependent on the prefrontal cortex in humans, little is known about its cellular underpinnings. Mechanistic understanding has been limited by a scarcity of controlled animal experiments in which subjects must flexibly plan novel behaviours on every trial. Here we characterise the neural representations and dynamics of mouse medial frontal cortex (mFC) during flexible navigation in structured environments. We trained mice to navigate complex mazes, to goals that changed location on every trial. Optogenetic silencing established that mFC was necessary for efficient navigation. mFC activity was dominated by two factorised components: (i) a structured representation of subjects position within the maze that formed an efficient code for behavioural trajectories, and (ii) a flexible representation of the shortest path-distance to the current goal. Both representations oscillated within local field potential (LFP) theta cycles, processing from further to closer to the goal at a systematic offset. These data suggest a computation in which mFC evaluates possible futures by their distance-to-goal to update a structured behavioural policy.

neuroscience↗

bioRxiv2026

Conserved TIR-only proteins drive transcriptional defense and basal immunity in dicot and monocot plants

Toll/interleukin-1/resistance (TIR) domain NADase enzymes signal in plant immunity by producing ribosylated nucleotide second messengers which activate EDS1 dimer-helper NLR pathways to restrict pathogen growth. Members of a small, distinctive group of TIR-only proteins are conserved between dicots and monocots, yet their functions remain poorly understood. Here, we show that conserved TIR-only proteins in Arabidopsis and barley share a fundamental enzymatic role in promoting basal defense against virulent filamentous pathogens, independently of NLR mediated effector-triggered immunity. Metabolite analysis of transiently expressed Arabidopsis and barley TIR-only proteins revealed their capacity to produce ribosylated cyclic nucleotides in vivo. By comparing phenotypes of tir-only and eds1 pad4 CRISPR mutants in the two species, as well as adr1 mutants in barley, we established that the TIR-only proteins promote PAMP-triggered transcriptional defenses associated with pathogen restriction. Barley possesses just one essential TIR-only enzyme and mutations of the two conserved TIR-only members in Arabidopsis were not compensated for by numerous other TIR-domain genes in the basal immune response. These findings suggest that conserved TIR-only proteins make a crucial contribution to TIR basal defense signaling networks of Arabidopsis and barley. We propose that a shared function in transcriptional defense regulation could explain the evolutionary retention of this discrete TIR-only group across monocot and dicot lineages.

plant biology↗

bioRxiv2026

Rab8a-positive vesicles transport Wnt8a along cytonemes in zebrafish embryogenesis.

Wnt signalling is a conserved pathway that orchestrates key developmental processes by regulating cell fate, proliferation, and tissue organisation. While the production and secretion of Wnt ligands are well characterised, less is known about how lipid-modified Wnts are delivered for long-range communication. Recently, cytonemes - actin-based signalling filopodia - have been identified as transporters of Wnts over distances to target specific cells in embryogenesis. Here, we characterise Rab8a-dependent vesicular trafficking as a crucial step in this process. Using human cell lines and zebrafish embryos, we show that Wnt ligands, such as Wnt8a, are transported with their carrier protein Wntless (Wls) in Rab8a-positive vesicles along cytonemes, where they fuse at the tips to enable hand-over and signal activation in neighbouring cells. Disruption of Rab8a function results in the intracellular retention of Wnt8a, reduces Wnt spreading and paracrine signalling, and alters embryonic patterning, consistent with reduced Wnt/{beta}-catenin function. Conversely, Rab8a activation enhances Wnt8a dissemination, leading to increased long-range signalling and, consequently, patterning defects in embryogenesis. Our findings uncover a dedicated intracellular trafficking route for Wnt delivery to and along cytonemes, offering new insights into how the spatial precision of Wnt spreading in vertebrate tissues is achieved.

developmental biology↗

bioRxiv2026

Tracing the Evolutionary Origin of Interferon to Basal Chordates and Unveiling Its Antiviral Functionality in Jawless Vertebrates

Interferons (IFNs) are essential mediators of antiviral defense in vertebrates, having gradually replaced the RNA interference (RNAi) antiviral mechanism that predominates in invertebrates and plants. To date, IFNs have been identified exclusively in jawed vertebrates, leaving the origin of IFN-based antiviral mechanisms largely mysterious. In this study, by conducting a genome-wide screening of IFN homologs accross various species, we successfully identified seveal IFN homologs from agnatha and lancelet, but not other invertebrates. Notably, both agnatha and lancelet IFN homologs have ability to induce a set of interferon-stimulated genes (ISGs)-like genes, thus tracing the origin of IFN to basal chordate. Using VSV infected peripheral blood mononuclear cells (PBMCs) of Japanese lampreys, we found that lamprey IFNs have antiviral functionality by inducing the expression of hundreds of ISGs through interacting with a heterodimeric complex composed of CRFB7 and CRFB14. In addition to robustly mediating antiviral responses in monocytes, lamprey IFNs exert their effects on variable lymphocyte receptor B (VLRB)+ cells by remodeling the cytokine/chemokine networks to orchestrate antiviral innate and adaptive immunity. Furthermore, cross-species functional comparison of Dicer revealed that changes in residues essential for dsRNA processing occurred concurrently with the evolution of the IFN system. Collectively, these findings uncover the evolutionary origin of IFN and underscore its ancient roles in antiviral response and immune regulation, especially in the takeover of the RNAi antiviral mechanism during the early evolution of vertebrates. Significance StatementInterferons (IFNs) represent a hallmark of vertebrate antiviral immunity, yet their origin has remained elusive. Here, we reported bona fide IFN ligands and cognate receptors in both lamprey and lancelet, two key species placed at the transition from invertebrates to vertebrates. Using the VSV infection model, we further demonstrated the roles of lamprey IFN in antiviral defense and immune regulation. We also found that substitutions in residues essential for Dicer mediated dsRNA processing coincided with the emergence of the IFN system. Collectively, our findings provide key insights into the evolutionary origin of IFN-based immunity and its gradual replacement of RNAi as the dominant antiviral strategy in vertebrates.

evolutionary biology↗

bioRxiv2026

Visibly Transparent, Near-Infrared Absorbing Nanofluids Enable High-Efficiency and Safe Laser Lithotripsy

Laser lithotripsy (LL) is the gold standard for urinary stone management yet maximizing ablation efficiency while maintaining procedural safety remains clinically challenging. Here, we present a visibly transparent, near-infrared (NIR)-absorbing ITO@SiO2 nanofluid irrigation strategy that significantly enhances LL efficiency without compromising endoscopic visibility. By spectrally matching the absorption profile of ITO@SiO2 with the clinical Holmium:YAG laser wavelength, ablation efficiency improved by >200% in the bench-top spot treatments and >100% in the hydrogel kidney model. Mechanistic investigations revealed that the enhanced optical absorption of the nanofluid modifies bubble dynamics and synergistically amplifies photothermal/microexplosion effects and cavitation damage. Importantly, both in-vitro hydrogel and in-vivo porcine kidney models demonstrated a substantial thermal safety margin (maximum temperatures <35 {degrees}C) and excellent acute biocompatibility, with no evidence of thermal tissue injury. Integrating seamlessly into established clinical workflows without requiring stone pretreatment, this strategy offers a highly translatable, safe, and efficient platform for next-generation endoscopic lithotripsy.

bioengineering↗

bioRxiv2026

Brain states recur across diverse narrative contexts during longitudinal viewing

What does the brain do during the continuous, varied experience of watching a story unfold? One account holds that the brain traverses a finite repertoire of recurring states, but whether that repertoire is a stable property of the individual or is reshaped by each new experience has not been tested across diverse naturalistic content within the same person. We characterized the dynamic brain-state repertoire in six individuals who watched the television series Friends across its six seasons during fMRI (up to [~]146 episodes, [~]54 hours per person). For each individual we fit a sticky hierarchical Dirichlet process hidden Markov model across all episodes, discovering brain states (recurring whole-brain activity patterns with characteristic coupling) without pre-specifying their number. Each individuals brain visited roughly forty-five states arrayed along a continuous recurrence gradient, from states active in nearly every episode to episode-specific ones, with no sharp division between them. The repertoire was heterogeneous in why its states recurred: a minority locked to scan-run structure, the majority remaining eligible for content. Transitions were organized by the functional-connectivity similarity between states (per-individual Spearman {rho} = 0.33-0.55) and, in most individuals, respected resting-state network boundaries. Episode content was associated with which states the brain occupied moment to moment. The recurrence ordering discovered in Friends transferred to state occupancy during other social-narrative films (five of six individuals) and attenuated as stimuli departed from that class, weakening for visual-only reading and audio-only listening. Across diverse narrative experience, the dynamic repertoire is a property of the individual: content varies which states are visited and when, not which states exist.

neuroscience↗

bioRxiv2026

Distance Mapping and Variable-Specific Geometry of Goal-Relevant Frames in the Retrosplenial Cortex

Goal-directed navigation requires animals to continuously update their position relative to an unmarked goal. Here, we recorded retrosplenial cortex (RSC) activity in freely moving rats during goal-directed navigation and random foraging. We found that RSC neurons encoded the Euclidean distance to the goal, and that this distance representation was selectively biased toward the goal during navigation. This goal-biased signal could not be explained by non-uniform behavioral sampling alone. Task engagement selectively enhanced allocentric head-direction representations anchored to a landmark cue, whereas egocentric boundarybearing signals showed no detectable task-related enhancement and no detectable goalcentered spatial organization in this task context. Mixed-selective RSC population activity further exhibited variable-specific separability-smoothness geometry: distance-to-goal showed high local smoothness and decoding performance, whereas egocentric boundary bearing showed stronger macro-scale separability. These task-related spatial representations persisted under reduced visual input, suggesting contributions from memory and self-motion signals. Together, these findings indicate that RSC organizes goal-relevant spatial representations in a task-dependent manner.

neuroscience↗

bioRxiv2026

Phosphorylation-dependent regulation of Hsp70 chaperones stimulates client recruitment

Molecular chaperones of the Hsp70 family play essential roles in maintaining proteostasis, particularly under conditions of cellular stress. Posttranslational modifications of Hsp70, collectively termed the chaperone code, are emerging as critical regulators of chaperone function, yet their mechanistic contributions remain incompletely understood. Here, we investigate the functional significance of a conserved phosphorylation site in Hsp70, corresponding to serine 326 in yeast Ssa1 and serine 329 in human HSPA8. We demonstrate that DNA double-strand break stress increases cellular reliance on Hsp70 activity in yeast, highlighting a role for chaperones in the DNA damage response. Loss of Ssa1 serine 326 phosphorylation impairs multiple Hsp70-dependent functions, including prion sequestration and glucocorticoid receptor maturation, indicating that this modification is required for optimal chaperone activity. Extending these findings to human cells, we show that the homologous HSPA8 serine 329 residue is necessary for efficient clearance of polyglutamine aggregates. Mechanistically, a phospho-deficient HSPA8-S329A mutant exhibits reduced client-binding capacity. Together, our findings identify a conserved phosphorylation event that enhances Hsp70 function by promoting client engagement, providing new insight into how the chaperone code regulates proteostasis across species.

molecular biology↗