Biology subjects

Wu, Y.

Publications and source records attributed to Wu, Y..

At least 271 records · Page 15Linked to original sources

bioRxiv2025

The Ral small GTPase is an essential regulator of Exocyst complex function in secretion.

Ral GTPases have long been proposed as regulators of the metazoan Exocyst, a conserved secretory vesicle-tethering complex, but direct evidence for this role has been scarce. In contrast, the well-studied yeast Exocyst relies on multiple Rab GTPases to regulate function, but yeast do not encode Ral. Using Caenorhabditis elegans we demonstrate that endogenous RAL-1 directly engages the Exocyst through conserved binding sites in its subunits. Loss of RAL-1 disrupts dendritic arborization of PVD sensory neurons, impairs vesicle trafficking, and causes broad developmental defects, acting both cell-autonomously in neurons and non-autonomously through supporting epithelial cells. Structure-guided genome editing of RAL-1-Exocyst interfaces produced synthetic phenotypes, underscoring the physiological importance of these contacts. Taken together, our findings establish RAL-1 as a bona fide regulator of the metazoan Exocyst in vivo and suggest that Ral-Exocyst interactions operate in parallel with other secretory pathways. More broadly, this work positions C. elegans as a powerful system to dissect Ral- Exocyst mechanisms across molecular, cellular, and developmental scales.

cell biology↗

bioRxiv2025

ARP2/3 complex mediates the neuropathology of PTEN-deficient human neural cells downstream of mTORC1 and mTORC2 hyperactivation

Mutations in the phosphatase and tensin homolog (PTEN) gene are linked to severe neurodevelopmental disorders. Loss of PTEN causes hyperactivation of both mechanistic target of rapamycin (mTOR) complexes, mTORC1 and mTORC2. Recent studies have shown that this dual hyperactivation is required for the neuropathology observed in PTEN-deficient human stem cell-derived neural cells. However, the molecular effectors that integrate these synergistic signals remain unknown. Here, we identify the actin-regulating ARP2/3 complex as a critical point of convergence downstream of mTORC1 and mTORC2. We show that concurrent hyperactivation of both complexes drives increased filamentous actin and elevated levels of the ARP2/3 complex subunits in PTEN-deficient human neural precursors and neurons. Pharmacological or genetic inhibition of ARP2/3 is sufficient to rescue multiple disease-relevant phenotypes, including neural precursor hyperproliferation, neuronal hypertrophy, and electrical hyperactivity, without affecting the upstream mTORC1 or mTORC2 hyperactivation. Together, these findings reveal the PTEN-mTOR-ARP2/3 signaling axis as a core mechanism of neuropathology and highlight ARP2/3 inhibition as a potential therapeutic strategy for PTEN-related neurodevelopmental disorders.

neuroscience↗

bioRxiv2025

Serratia marcescens Outer Membrane Vesicles rapidly paralyze Drosophila melanogaster through triggering apoptosis in the nervous system

The pathogenicity of Gram-negative bacteria is mediated by multiple virulence factors that likely include secreted Outer Membrane Vesicles (OMVs) that can act as a cargo for delivery of enzymes or toxins to target tissues. Here, we have studied the effects on the host of OMVs prepared from one of the most potent pathogens of Drosophila melanogaster, Serratia marcescens. OMV injection leads to the apparent demise of flies within few hours. We identify a number of host defenses that somewhat protect it from the action of OMVs, namely the systemic humoral immunity pathway Immune deficiency, Prophenol Oxidases 1&2, and the redox active enzymes Dual oxidase, NADPH-oxidase, and Nitric Oxygen Synthase. In contrast, unidentified hemocyte function(s) and the circulating protease Hayan promote the pathogenicity of OMVs. Mechanistically, we find that OMVs promote the activation of the JNK pathway and the transient expression of the pro-apoptotic genes head-involution defective and reaper in at least neurons. Our data suggest that mitochondrially-derived reactive oxygen species promote neuronal cell death that leads to the paralysis of OMV-injected flies. We identify the metalloprotease PrtA as a major virulence factor of OMVs and show that the injection of purified PrtA mimics most of the effects of OMVs. Finally, our data further indicate that PrtA contributes to the pathogenicity of injected Serratia marcescens. This study underscores the potential for OMVs to act as virulence factors that efficiently target the nervous system in vivo despite the blood brain barrier.

immunology↗

bioRxiv2025

Mechanistic Insights into Sex Differences in Atrial Electrophysiology and Arrhythmia Vulnerability through Sex-specific Computational Models.

Atrial fibrillation (AF), the most common cardiac arrhythmia, is characterized by notable sex differences in clinical presentation, treatment response, and outcomes. Although prevalence is similar between sexes, women often experience more severe symptoms, higher rates of adverse drug effects, and reduced treatment efficacy. To investigate the underlying sex-specific AF mechanisms, we developed and validated male and female human atrial cardiomyocyte models that integrate known sex-based differences in electrophysiology and calcium (Ca2+) handling under normal sinus rhythm (nSR) and chronic AF (cAF) conditions. While the model parameterizations were based on limited human data, and the assumptions may not capture the full spectrum of clinical variability, the models reproduced key reported sex-dependent differences in human atrial cardiomyocyte action potential (AP) and Ca2+ transient (CaT) dynamics. Simulations revealed that both sexes exhibited shortened effective refractory periods and wavelengths in cAF vs. nSR. However, females were more prone to delayed afterdepolarizations (DADs), while males were more susceptible to AP duration (APD) and CaT amplitude (CaTAmp) alternans. Population-based modeling identified distinct parameter associations with arrhythmia mechanisms, whereby DAD vulnerability was associated with enhanced ryanodine receptor sensitivity to Ca2+ (in females), and alternans in males correlated with reduced L-type Ca2+ current maximal conductance. Pharmacological simulations revealed sex-specific responses to antiarrhythmic therapies. In males, multiple drug combinations proved effective in restoring APD at 90% repolarization (APD90), CaTAmp, and reducing alternans susceptibility, whereas females responded to only one combination improving APD90 and CaTAmp but with minimal impact on DAD risk. These findings underscore the need for sex-specific therapeutic strategies and support the use of computational modeling in guiding precision medicine approaches against AF. Key pointsO_LIAtrial fibrillation (AF) is a common heart rhythm disorder that presents differently in males and females, but how the underlying mechanisms differ in males and females is not fully understood. C_LIO_LIWe developed and validated computer models of male and female human atrial cardiomyocytes that incorporate known sex differences in ion channels and calcium handling under normal sinus rhythm and AF conditions. C_LIO_LIUnder normal rhythm, males and females showed distinct electrical activity, which became less pronounced in AF. In AF, both sexes showed reduced effective refractory period and wavelength and depressed calcium transients. Males were more susceptible to electrical alternans, while females showed a greater tendency for calcium-driven delayed afterdepolarizations. C_LIO_LISimulated drug treatments showed greater benefit in male models, particularly with combinations targeting multiple potassium channels, while female models showed limited response. These results highlight the need for sex-specific approaches to treating AF and may help guide future drug development. C_LI

physiology↗

bioRxiv2025

Multi-omics reveals lipid metabolism, mitochondrial and extracellular matrix dysregulation of diabetic cardiomyopathy in the human heart

Diabetic cardiomyopathy (DbCM) is a condition characterized by myocardial dysfunction in diabetes. Although the clinical recognition of DbCM is increasing, its underlying molecular mechanisms remain poorly understood. We aimed to conduct a comprehensive multi-omics analysis of heart tissue from cardiomyopathy patients (both with and without diabetes),alongside tissue from healthy donors, by integrating transcriptomic, 4D-DIA proteomic, and full-spectrum widely targeted metabolomic data. Differential analyses revealed a significant metabolic pattern in patients with DbCM, characterized by increasing utilization of triglyceride-derived fatty acids. Correlation analyses highlighted impaired BNIP3L-mediated mitophagy as a potential contributor to the disruption of fatty acid metabolism and mitochondrial dysfunction in DbCM. Protein interaction and fibrotic trichrome analyses showed that patients with DbCM had impaired cardiac matrix repair compared to patients with cardiomyopathy without diabetes. These findings provide a system-level understanding of DbCM and reveal molecular signatures driving its progression, offering insights for targeted therapeutic strategies against diabetic heart disease.

bioinformatics↗

bioRxiv2025

Paclitaxel Alleviates Pulmonary Arterial Hypertension by Modulating Macrophage M2a Polarization via the NF-κB Pathway

BackgroundPulmonary arterial hypertension (PAH) is primarily associated with vascular remodeling, in which macrophage polarization is considered to play a major role. Paclitaxel(PTX) has been shown to modulate macrophage polarization in tumors. We investigated whether PTX could alleviate PAH by altering macrophage polarization, particularly M2a macrophages. MethodsTo establish PAH, rats underwent left pneumonectomy followed by monocrotaline (MCT) injection. In vitro, THP-1 cells were differentiated into macrophages using PMA and polarized with LPS+IFN-{gamma} (M1), IL-4 (M2a), or IL-10 (M2c), followed by PTX intervention. Hemodynamic parameters (mPAP) and right ventricular hypertrophy index (RVHI) were measured. Pathological changes were assessed via HE staining. Single-cell RNA sequencing analyzed macrophage subsets in lung tissues. Macrophage polarization and NF-{kappa}B pathway activity were evaluated using immunohistochemistry, qPCR, cytokine profiling and Western blot. ResultsIn a severe PAH model induced by left pneumonectomy plus monocrotaline, pulmonary interstitial macrophages initially exhibited a predominant M1-polarized phenotype in the early stage, which transitioned to an M2a-polarized phenotype in the later stage and eventually stabilized. Low-dose PTX alleviated severe PAH by reducing perivascular macrophage infiltration. Cytological studies confirmed that PTX inhibited M2a polarization via suppression of NF-{kappa}B, thereby attenuating its proliferative effects on pulmonary arterial smooth muscle cells (PASMCs). ConclusionM2a macrophages play a crucial role in PAH progression. PTX may alleviate PAH by suppressing M2a polarization via the NF-{kappa}B pathway.

immunology↗

bioRxiv2025

SnakeAltPromoter Facilitates Differential Alternative Promoter Analysis

BackgroundAlternative promoter usage regulates isoform diversity in mammals, playing critical roles in development, disease, and cellular reprogramming. While Cap Analysis of Gene Expression (CAGE) enables precise transcription start site mapping, its high cost and limited coverage hinder scalability. In contrast, RNA-seq is abundant across biological contexts; several algorithms (ProActiv, Salmon, DEXSeq) infer promoter activity from these data, yet no unified, reproducible framework exists to execute, benchmark, and compare them or to scale alternative promoter analyses across large compendia. ResultsWe developed snakeAltPromoter, an end-to-end Snakemake workflow that ingests raw FASTQ files, performs quality control and alignment, quantifies promoter activity using three complementary strategies (junction-based, transcript-based, and first-exon-based), classifies promoters into major, minor/alternative, and inactive categories, and conducts both differential promoter activity and usage analysis. Crucially, snakeAltPromoter integrates a systematic benchmarking module against matched CAGE profiles to reveal method-specific strengths and limitations. ProActiv showed the highest concordance with CAGE in promoter classification, activity and differential analysis, Salmon was robust at low coverage and intronless cases. Overall, the complete workflow recovered a majority of CAGE-validated active promoters and processed a 50 M-read RNA-seq sample in around 2h on a 32-core node, demonstrating both accuracy and scalability. ConclusionssnakeAltPromoter is, to our knowledge, the first reproducible framework that pairs comparative method evaluation with scalable differential alternative promoter analysis. It provides concrete guidance for method selection under different experimental scenarios and enables high-throughput mining of promoter-level regulation from public RNA-seq repositories. Code and example data are freely available at https://github.com/YidanSunResearchLab/SnakeAltPromoter.git.

bioinformatics↗

bioRxiv2025

BIN1 deficiency leads to DNA damage and neuronal insulin resistance through ATM dysregulation

The major neuronal isoform of the AD risk gene BIN1 is specifically reduced in patients. In the present work, we demonstrate that BIN1 is necessary for intact insulin signaling and its loss leads to cellular-level insulin resistance. Persistently activated mTORC1 feedback inhibits the insulin signaling; meanwhile, ATM-dependent DNA Damage Response decreases the expression of multiple insulin signaling pathway members. Unexpectedly, nuclear ATM activation is accompanied by autophagic degradation of the cytoplasmic ATM, rendering neurons susceptible to oxidative stress, which predisposes oxidative DNA damage, DNA strand breaks, and ATM-dependent DNA Damage Response. Treating BIN1-deficient mice with rapamycin or liraglutide to improve the insulin response, or with the natural antioxidant alpha-lipoic acid to attenuate oxidative stress, both effectively preserved the spatial cognitive ability. Lastly, we reanalyzed a single-cell transcriptomic dataset from human neurons and identified positive correlations between levels of BIN1 and the insulin signaling, as well as neuronal activity. Together, this work revealed an ATM-centered mechanism that globally damages neuronal health in BIN1-deficient pyramidal neurons, which could be a driving force in the AD disease course.

cell biology↗

bioRxiv2025

Embodied Intelligence Unlocks Autonomous Microscopy

Advanced microscopy is a cornerstone of modern science, yet its potential is constrained by a reliance on manual operation, which struggles with the complexity and reproducibility of long-term experiments protocols. While scripting offers a degree of automation, it lacks the generalizability to adapt to new samples or dynamic biological events. A fundamental challenge is the absence of an intelligent system that can interpret high-level scientific intent and ground it in the physical actions of the microscope. To bridge this gap, we introduce an Embodied Intelligent Microscope System (EIMS) with hierarchical reasoning structure that reimagines the microscope autonomous control. This system leverages the advanced reasoning of large models to interpret complex user commands and decompose them into actionable steps. To solve the critical grounding problem, we constrain the models output to the feasible action space, effectively serving as the models "hands and eyes" in the physical world. We demonstrate that our system achieves zero-shot generalization on complex, multi-step protocols and successfully automates challenging biological missions requiring expert-level judgment, such as capturing the sparse spatiotemporal events of cell mitosis and locating scatteredly distributed organoids. This work establishes a new paradigm for scientific instrumentation--fusing high-level intent understanding with grounded, dynamic execution--and provides a generalizable framework for deploying embodied intelligence to accelerate autonomous scientific discovery.

bioengineering↗

bioRxiv2025

PRMix: Primary Region Mix Augmentation and Benchmark Dataset for Precise Whole Mouse Brain Anatomical Delineation

The architecture of the mouse brain shares remarkable similarities with the human brain, making it an essential model for studying brain pathologies, synaptic diversity, and regional specialization. A key step in such studies involves registering molecular images to reference brain atlases, a process hindered by the difficulty of accurately delineating brain regions. Toward this, we have curated a collection of high-resolution, dual-fluorescence microscopy images, termed as dual-fluorescence mouse brain microscopy (DMBM) dataset, complemented by expert annotations of 118 subregions. This dataset provides unprecedented insights into the molecular and structural complexity of the mouse brain. However, its full potential for detailed whole-brain analysis is compromised by challenges such as boundary ambiguity and sample scarcity in existing automated segmentation methods, prompting the development of the primary region mix (PRMix) augmentation method. PRMix is specifically designed to expand these datasets, enhance the realism of synthetic data and minimize overlap between adjacent regions. Our approach, together with the curated dataset, achieves superior segmentation performance across the mouse brain compared with existing methods, setting a new benchmark in brain imaging research. Code and data are available at https://git-pages.ecdf.ed.ac.uk/dmbm-datasets-5c13cd/.

neuroscience↗

bioRxiv2025

Light-Activated Nucleic Acid Amplification Systems Using Photo-caged DNA Polymerase or Primers

Precise control over nucleic acid amplification is essential for achieving reliable, quantitative, high-throughput, and multiplexed molecular diagnostics, particularly in point-of-care and field settings. However, conventional isothermal amplification methods, especially rapid assays at ambient temperature such as recombinase-aided amplification (RAA), suffer from spontaneous initiation and lack of synchronization across parallel reactions. Here, we report light-activatable RAA systems employing two distinct photocaging strategies to achieve spatiotemporal control. In the first, a photocaged DNA polymerase was engineered via site-specific incorporation of p-azido-L-phenylalanine and conjugation with a 2-nitrobenzyl-modified ssDNA blocker through click chemistry. This approach offers high stability, making it advantageous for long-term storage and lyophilized formats. In the second, 5'-nitrobenzyl-modified primers were synthesized to block hybridization or extension until UV activation, offering operational simplicity and rapid integration into existing workflows. Both strategies independently suppressed background activity in the dark and restored full amplification efficiency upon 365 nm UV exposure. The systems exhibited high sensitivity, low background, and compatibility with portable diagnostics. A custom-built device integrating UV activation and real-time fluorescence detection enabled seamless, on-demand operation. This modular platform provides flexible light-gated amplification solutions, allowing the selection of polymerase- or primer-based caging according to storage stability or workflow requirements, thereby advancing precise and field-ready molecular diagnostics.

molecular biology↗

bioRxiv2025

HSV-1 infection induces brain cofilin hyperphosphorylation in the 5xFAD Alzheimer's Disease mouse model

Alzheimers disease (AD) is a degenerative neurological disease characterized by various biological signatures, including synaptic dysfunction, {beta}-amyloid plaques, hyperphosphorylated Tau, cofilin-actin rods, and Hirano bodies, all of which are linked to the actin cytoskeleton and its regulators. Additionally, the presence of herpes simplex virus type 1 (HSV-1) in the brains of AD patients has long been suggested as a contributing factor for AD. However, mechanisms by which HSV-1 accelerates AD pathogenesis remain poorly understood. Here we report that HSV-1 infection induces hyperphosphorylation of cofilin in the brains of 5xFAD mice. Cofilin is an actin depolymerizing factor, and its S3 phosphorylation inactivates cofilins activity to depolymerize actin filaments. These findings facilitate the understanding of impacts of HSV-1 infection on the development of Alzheimers disease and have implications in AD therapeutics.

microbiology↗

bioRxiv2025

CircRNA-based, non-integrated, in vivo panCAR-mediated B cell immune resetting in mouse models and non-human primates

B cell immune resetting, defined as the comprehensive depletion and subsequent reconstitution of B cells, represents a pivotal therapeutic approach for B cell-associated disorders. Recently, chimeric antigen receptor T cell (CAR-T) therapy has demonstrated substantial clinical efficacy in treating B cell malignancies and autoimmune diseases. However, this approach remains constrained by its reliance on lymphodepleting conditioning regimens, high invasiveness, high costs, and the risk of severe cytokine release syndrome (CRS). Antibody-based therapies, including monoclonal antibodies and T cell-engager (TCE) bispecific antibodies, suffer from suboptimal tissue penetration, resulting in inadequate B cell depletion in lymphoid and peripheral tissues, and subsequent rapid resurgence of pathogenic B cells. Here, we engineered highly stable circular RNAs (circRNAs) encoding anti-CD19 CAR (circRNA-CAR), which demonstrated prolonged and enhanced CAR protein expression compared to conventional linear mRNAs. By employing immune cell-tropic lipid nanoparticles (LNPs) for in vivo delivery, circRNA-CAR facilitated the generation of panCAR immune cells (including CAR-T, CAR-NK, and CAR-macrophages) in both murine models and cynomolgus monkeys. Compared to rituximab or teclistamab, in vivo panCAR induced more extensive B cell depletion across multiple tissue compartments in mice. Moreover, in vivo panCAR mediated robust B cell depletion, eliminated autoreactive antibodies, and restored renal function by alleviating proteinuria in a systemic lupus erythematosus (SLE) murine model. It also effectively reduced IgE antibody levels, decreased eosinophil activity, and improved lung pathology in an asthma murine model. Notably, in vivo panCAR-mediated B cell depletion significantly attenuated aging-associated phenotypes in 17- month-old aging mice, remarkably outperforming both rituximab and teclistamab. In cynomolgus monkeys, in vivo panCAR achieved sustained B cell depletion lasting approximately 40 to 50 days, followed by reconstitution of a naive B cell repertoire. Collectively, circRNA-based in vivo panCAR enables complete B cell immune resetting, offering a versatile and promising therapeutic platform for a broad spectrum of B cell- and antibody-mediated disorders.

immunology↗

bioRxiv2025

Single-cell mass accumulation reveals bacterioplankton growth rate in native seawater

AO_SCPLOWBSTRACTC_SCPLOWThe growth of marine microbial communities drives biogeochemical cycling of carbon and other elements, yet the growth rates of individual species within complex ocean ecosystems remain poorly understood. In particular, the coexistence of a large diversity of copiotrophic bacteria, which are capable of fast growth but typically remain at low abundance, has been interpreted as a feast or famine existence. Here we show that contrary to the notion of infrequent growth, Vibrio bacteria exhibited consistent growth rates in coastal ocean samples, despite representing only a small fraction of the total community. These observations were enabled by a suspended microchannel resonator (SMR), which we adapted to function as a single-cell chemostat. By maintaining a continuous supply of native seawater around each trapped cell, we prevented nutrient depletion and used the SMRs high mass precision to resolve growth rates that are otherwise undetectable. Vibrio species displayed significantly larger cell mass and faster growth than other community members across samples collected at different temporal intervals from days to years. Surprisingly, their growth was consistently limited by carbon, contrary to the expectation that heterotrophic bacteria in the euphotic zone would be limited by nitrogen and phosphorus due to competition with algae. The correlation between cell mass and growth rate of Vibrionaceae in seawater followed established growth laws derived from laboratory conditions, suggesting that growth physiology observed in pure cultures is applicable to wild bacterial populations. Overall, our findings suggest that rare species may play a disproportionately large role in the marine carbon cycle, with rapid biomass turnover driven by a combination of high growth rates balanced by intense predation.

microbiology↗

bioRxiv2025

Mechanosensitive channel PIEZO1 enhances endometrial decidualization via BECN1-dependent autophagy

The mechanosensitive ion channel PIEZO1 plays critical roles in physiological and pathological processes in response to various types of mechanical forces, including shear stress, stretch, and extracellular matrix (ECM) stiffness. Decidualization is crucial for a successful pregnancy, characterized by the differentiation of fibroblastic endometrial stromal cells into round, secretory decidual cells, along with the rapid remodeling of the ECM. Herein, we report that PIEZO1 plays a crucial role in enhancing decidualization in response to extracellular matrix (ECM) stiffness and cell contraction. Uterine-specific knockout of Piezo1 using Pgr-Cre in mice results in subfertility due to decidualization impairment in mid-late pregnancy. Silencing of PIEZO1 in human endometrial stromal cells also results in impaired decidualization. Treatment with the PIEZO1 agonist Yoda1 enhances decidualization in both in vivo and in vitro models. Stromal cells growing on ECM with 25 kPa stiffness display a better decidualization response than cells seeded on softer 2 kPa surface or harder surface of the regulator petri dish, and this difference is abolished by null of Piezo1. Consistent with PIEZO1 as a Ca2+ modulator, blocking of intracellular Ca2+ or pCaMKII significantly inhibits Yoda1-enhanced decidualization. Further investigation reveals that BECN1-dependent autophagy acts as the downstream of PIEZO1. Silencing of Beclin1 abolishes Yoda1-induced decidualization, while Tat-BECN1 fully rescues impaired decidualization caused by the lack of PIEZO1. Finally, the lower expression of PIEZO1 is associated with impaired decidualization in the endometrium of endometriotic baboons. In conclusion, we have uncovered a novel mechanism of decidualization that is regulated by PIEZO1-mediated mechanotransduction, providing further insight into decidualization studies. Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=187 HEIGHT=200 SRC="FIGDIR/small/668790v1_ufig1.gif" ALT="Figure 1"> View larger version (68K): org.highwire.dtl.DTLVardef@2d25faorg.highwire.dtl.DTLVardef@186e56org.highwire.dtl.DTLVardef@1f3f61borg.highwire.dtl.DTLVardef@1a26bb7_HPS_FORMAT_FIGEXP M_FIG C_FIG

physiology↗

bioRxiv2025

Development of Dendritic Cell Membrane-Coated Nanoparticles for Antigen-Specific T Cell Engagement

Dendritic cell (DC) membrane-coated nanoparticles (DCmPs) hold significant potential for antigen-specific therapies. DCmPs carry key DC membrane proteins that facilitate DC-T cell interaction, such as major histocompatibility complex (MHC), costimulatory CD80/86, and adhesive molecules ICAM-1. However, our current understanding of the impact of the coating processes and the composition of the final products is very limited, significantly hindering the development of DCmP-based therapy. Here, using DC2.4 cell membrane proteins and poly (lactic-co-glycolic acid) (PLGA) nanoparticles, we comprehensively characterized and compared the compositions and functions of DCmPs produced using sonication, extrusion, and a newly developed combined coating approach (sonication coating following by extrusion process). The combined coating approach achieved relatively high level of protein coating and exerted superior control over the diameter and uniformity of DCmPs relative to sonication and extrusion. We also developed a characterization strategy by leveraging the homotypic interactions between DCmPs and DC2.4 cells and determined that about 80% of PLGA particles are coated with membrane proteins and both unbound proteins and uncoated particles similarly present in the final products after the three coating processes. Because DC2.4 cells exclusively express MHC class I molecules, DCmPs showed preferentially bind to cognate B3Z CD8+ T cells over DOBW CD4+ T cells, confirming that DCmPs bind to T cells in an antigen-specific fashion. Furthermore, we demonstrated that DCmPs can activate B3Z CD8+ T cells in vitro, similar to DC2.4 cells. These findings demonstrate a new coating approach that potentially improves size control over membrane-coated particles and a characterization strategy for detailed analysis of coated particle composition, having important and broad implications for the therapeutic development of DCmPs and other membrane-coated particle technology.

bioengineering↗

bioRxiv2025

Serotonin shapes the temporal window for associative fear learning

Fear learning is a critical adaptive mechanism that enables the association of an environmental cue (the conditioned stimulus, CS) with a potential threat (the unconditioned stimulus, US), even when these events are temporally discontiguous. When associations are instead formed between unrelated cues and threats, the maladaptive learning process can give rise to neurological disorders. Therefore, maintaining accurate temporal boundaries for forming such associations is crucial for distinguishing real threats from irrelevant stimuli. Despite its importance, the mechanisms defining this precise time window remain poorly understood. Here, we report that serotonin plays a crucial role in modulating the associable interval in trace fear conditioning. Specifically, we show that serotonergic projections from the dorsal raphe nuclei (DRN) to the CA1 region of the ventral hippocampus (vCA1) dynamically regulate the association of discontiguous CS and US. Mechanistically, we demonstrate that sustained serotonin release in the vCA1 maintains the ensemble activity of 5-HT2C receptor-expressing pyramidal neurons, facilitating the association between temporally separated events. In contrast, when the trace interval exceeds the associable window, transient serotonin release fails to drive vCA1 neuronal ensemble activity, thus preventing maladaptive learning. These findings highlight a key role for serotonin in regulating the temporal precision of fear learning and reveal the DRN-vCA1 serotonergic pathway as a potential therapeutic target for related disorders.

neuroscience↗

bioRxiv2025

Identification of the bona fide active center of influenza A virus polymerase acidic protein as the antiviral target

The influenza virus PA protein, a core subunit of RNA polymerase, is critical for viral replication and a key antiviral target. Contrary to the prevailing view that its endonuclease active site resides in the N-terminal domain (PAn, residues 1-319), we identified a C-terminal truncation (PAc, 320-716) of H1N1 PA that retained high endonuclease activity, while PAn showed minimal activity. Crystal structural analysis revealed that PAc binds substrate RNA via the YDS motif (residues 393-395), with mutations abolishing RNA association. Surprisingly, baloxavir acid (BXA), a known PA inhibitor, specifically targeted PAc rather than PAn, supported by molecular docking showing higher binding affinity to PAc. Mutations at PAc-BXA interaction sites identified F707A as a potential drug resistance mutation. Virtual screening targeting PAc identified methotrexate as potent inhibitors (EC50 < 100 nM), which effectively suppressed viral replication in vitro and alleviated symptoms in influenza-infected mice. Our findings redefine PAs catalytic architecture and establish PAc as a novel platform for antiviral discovery, offering strategies to combat drug resistance through structure-guided inhibitor design.

microbiology↗