Biology subjects

Zhu, Y.

Publications and source records attributed to Zhu, Y..

At least 145 records · Page 8Linked to original sources

bioRxiv2026

Construction and Immunogenicity Detection of Canine Parvovirus-like Particles Fusion with Canine Febrile Antigen Epitopes

This study aimed to design and evaluate the immunogenicity of a dual-valent virus-like particles (VLP) vaccine that can simultaneously target Canine distemper virus (CDV) and Ca nine parvovirus virus (CPV).By bioinformatic analysis, conserved antigen epitopes of the three major functional proteins of CDV were screened and inserted into CPV-VP2 proteins by two different methods to construct recombinant expression plasmids CDPV1 versus CDPV2.Thr ee-dimensional structure, hydrophobicity and stability predictions of the two recombinant proteins showed that their hydrophobicity were 0.233 and 0.251, and their structural stability scores were 0.77 and 0.78, respectively.Recombinant plasmids were co-transformed with molecular chaperone pTf16 to be expressed in E. coli BL21(DE3), respectively, and the optimal expression conditions were determined after optimization: 0.25 mmol/L IPTG, 2 g/L L-arabinose in duction, and culture at 25{degrees}C for 16 h.Purified recombinant proteins can self-assemble in vitro to form VLPs about 23.5 nm in diameter with a hemagglutination titer of 1:29.The mouse immune test showed that the hemagglutination inhibition titer peaked on the 7th day after the third immunization, and the neutralizing Antibody level could reach up to 1:28.The CPV VLP s constructed in this institute carrying CDV antigen epitopes were able to successfully assemble in vitro and were well immunogenic, providing experimental basis for the development of a canine polyvalent vaccine.

immunology↗

bioRxiv2026

THIK-1 channel mediates microglial glucose sensing and modulates AgRP neurons

Microglia play essential roles in maintaining energy homeostasis, and their dysfunction contributes to metabolic disease. Although high-fat diet (HFD) exposure induces microglial activation, the underlying mechanisms remain poorly defined. Here, we identified a previously unrecognized role for THIK-1 channel in mediating glucose sensing of microglia in arcuate nucleus of the hypothalamus (ARH), during HFD-induced obesity. Pharmacological inhibition of THIK-1 channel with tetrapentylammonium (TPA) suppresses feeding and attenuates body-weight gain in diet induced obese mice. Mechanistically, inhibition of agouti-related peptide (AgRP) neurons is indispensable for TPA-induced hypophagia. Moreover, THIK-1 inhibition promotes microglial phagocytosis of perineuronal nets (PNNs), leading to reduced AgRP neuronal activity and feeding suppression. Together, these findings establish THIK-1 as a critical glucose sensor in hypothalamic microglia and uncover a microglia-dependent pathway through which overnutrition modulates AgRP neuronal activity via PNN remodeling to regulate energy balance, highlighting THIK-1 as a potential therapeutic target for treatment of diet-induced obesity.

neuroscience↗

bioRxiv2026

LoopBin, a VaDE-based neural network for chromatin loop classification

Classifying chromatin loops from 3D genomics data according to their epigenetic and structural attributes is important for inferring their functional roles. Currently, such classification typically relies on the manual intersection of epigenomic signal peaks and loop anchor locations. To automate this, remove peak-calling biases and include information inherent to 3D genomics signal structure, we developed LoopBin, a framework based on a variational deep embedding (VaDE) neural network. We applied LoopBin to kilobase-resolution Micro-C data and segmented tens of thousands of loops into clusters with distinct features using minimal histone modification and transcription factor-binding data. These features were indicative of apparently distinct biological function by each subgroup of loops. Therefore, LoopBin can provide insights into the dynamic shifts in loop classification that can occur upon perturbation of cell homeostasis or signaling.

bioinformatics↗

bioRxiv2026

Exercise-Induced Epoxy-Eicosanoids Promote Cardiomyocyte Proliferation and Post-Infarction Repair via NR4A1

BACKGROUNDMyocardial infarction (MI) causes irreversible cardiomyocyte loss that exceeds the adult hearts regenerative capacity, leading to adverse remodeling and heart failure. While exercise provides cardiovascular protection, the mechanisms underlying exercise-induced cardiac repair remain unclear. METHODSPlasma levels of free fatty acids and polyunsaturated fatty acid metabolites were quantified by liquid chromatography-tandem mass spectrometry (LC-MS/MS). RNA sequencing was performed to identify differentially expressed genes and enriched pathways. NR4A1 was knocked down in mice via tail vein injection of AAV9 carrying shRNA targeting NR4A1 (AAV9-shNR4A1). The role of 17,18-EEQ was evaluated by continuous subcutaneous infusion via osmotic minipump; the involvement of the cAMP-PKA-CREB axis was assessed using specific pharmacological inhibitor. Molecular analyses included ELISA, immunofluorescence staining, QPCR, and western blotting. Additionally, clinical samples were collected from 36 endurance-trained athletes and 30 sedentary individuals (age 18-22, male) for comparative analysis. RESULTSHere we demonstrate that preventive aerobic training promotes post-MI cardiomyocyte proliferation and confers cardioprotection by reducing fibrosis area and improving cardiac function. Targeted lipidomics revealed that exercise elevates circulating epoxyeicosatetraenoic acids (EEQs), particularly 17,18-EEQ; osmotic pump delivery of 17,18-EEQ mimicked the protective effects of exercise, reducing infarct burden and enhancing proliferation markers (Ki67, pH3, Aurora B). Transcriptomic analysis identified NR4A1 as the most prominent up-regulated mRNA under exercise induction; AAV9-mediated NR4A1 knockdown abolished exercise-mediated cardioprotection and proliferative benefits, establishing NR4A1 as essential for exercise-driven repair. Phosphoproteomic profiling revealed that 17,18-EEQ activates the PKA-CREB pathway to induce NR4A1 expression; pharmacological inhibition of adenylyl cyclase, PKA, or CREB phosphorylation reversed EEQ-mediated cardioprotection and proliferation, confirming pathway necessity. Dietary supplementation with eicosapentaenoic acid (EPA), the metabolic precursor of 17,18-EEQ, amplified exercise-induced cardioprotection by enhancing EEQ biosynthesis. CONCLUSIONOur study identifies 17,18-EEQ as an exercise-derived exerkine that promotes cardiomyocyte proliferation and post-MI repair through a PKA-CREB-NR4A1 signaling axis, advancing our understanding of exercise cardioprotection and myocardial regeneration mechanisms while providing novel therapeutic targets for cardiac intervention. What IS New?O_LIAerobic exercise enhances post-myocardial infarction cardiac repair by upregulating the cardio-protective lipid mediator 17,18-EEQ and its downstream effector NR4A1. C_LIO_LI17,18-EEQ promotes cardiomyocyte proliferation and cardiac repair through activation of the cAMP-PKA-NR4A1 signaling axis. C_LIO_LICombining aerobic exercise with omega-3 fatty acid supplementation synergistically improves cardiac remodeling and functional recovery after ischemic injury. C_LI What Are the Clinical Implications?O_LITargeting endogenous cardiomyocyte proliferation represents a promising therapeutic strategy for cardiac regeneration after ischemic injury. C_LIO_LIDietary supplementation with omega-3 fatty acids may be a clinically feasible approach to amplify exercise-induced cardioprotection and improve outcomes after myocardial infarction. C_LI

physiology↗

bioRxiv2026

Spatial transcriptomics reveals organizational properties of mouse spinal cord and alterations in neuropathic pain

The spinal cord integrates diverse somatosensory inputs and executes motor outputs through anatomically and functionally distinct circuits. Here, we employed spatially resolved single-cell transcriptomic profiling of the adult mouse spinal cord to gain insights into the organizational logic of the spinal cord. Our results reveal distinct spatial and laminar distributions of neuronal subtypes, including axial level and sex-specific differences. Many neuronal subtypes exhibit close spatial proximity, implicating regionally specific patterns of connectivity and circuit functions. Additionally, neuronal subtypes within the dorsal horn exhibit a wide range of predicted cell-cell communication motifs, as assessed by the spatial distribution of neuropeptide-and other ligand-receptor pairs. Finally, we identified several neuronal subtypes with altered transcriptomic and predicted cell-cell communications in a model of neuropathic pain. This spatially resolved cellular and molecular map of the spinal cord will facilitate the decoding of circuit mechanisms underlying somatosensory and motor functions in health and disease.

neuroscience↗

bioRxiv2026

Threshold-Free Neural Network Models for Swim Bout Detection of Larval Zebrafish

Accurate detection of swim bouts is essential for decoding motor behavior in larval zebrafish, yet conventional threshold-based methods rely on subjective cutoffs and per-experiment tuning. To address this limitation, we developed threshold-free deep learning models operating on tail-curvature time series: an offline model for post hoc analysis and an online model for real-time detection. Both improved precision over threshold-based methods, particularly for low-amplitude bouts. Using the offline model, we show that a head-fixed, closed-loop preparation largely preserves naturalistic swimming kinematics. Repeated trials reduced bout frequency and increased interbout interval, whereas genetic background primarily affects bout duration and maximum amplitude; notably, casper larvae lacked the late-trial decline observed in wildtype and nacre. We further show that detector choice can alter inferred behavioral outcomes. Together, these results establish a high-throughput framework for robust and reproducible analysis of zebrafish swimming behavior across experimental conditions.

bioengineering↗

bioRxiv2026

Early multi-omic signatures and machine learning models predict cardiomyocyte differentiation efficiency and enable robust hPSC differentiation to cardiomyocytes

Protocols for generating cardiomyocytes (CMs) from human pluripotent stem cells (hPSCs) have existed for nearly two decades, yet manufacturing variability in terminal cell identity continues to limit clinical translation. To uncover the origin of fate divergence during hPSC-CM differentiation, we performed temporal transcriptomics, proteomics, and metabolomics of high and low efficiency differentiations. We identified significant early multi-omic divergence between differentiation batches and key pathways underlying fate divergence at critical differentiation stages included Wnt, MAPK, and glucose metabolism. Machine learning models trained on early candidate gene markers predicted hPSC-CM purity better than models using canonical cardiac development markers. Lastly, multi-omic insights informed perturbations, including Wnt and MAPK inhibition, which produced higher CM purities and yields. Our results showcase multi-omic analysis coupled with machine learning models as a powerful tool to identify cell fate determinants and enable robust manufacturing of complex cell products such as hPSC-derived cell therapies. TeaserMulti-omic analysis of hPSC-CM differentiation efficiency reveals early predictive features and enables robust differentiation.

cell biology↗

bioRxiv2026

Synaptic mitochondrial oxidative stress drives individual variability in age-related cognitive decline in mice

Aging leads to cognitive decline with considerable individual variability, yet the biological mechanisms remain unclear. Here we performed ultrastructural and proteomic analyses of the medial prefrontal cortex (mPFC) alongside behavioral assessments of attentional set shifting in mice across age groups. Although reduced synaptic density did not consistently lead to cognitive decline, proteomic analyses of synaptosomes and whole tissue revealed that the molecular signatures associated with individual variability in cognitive decline were distinct from those associated with chronological aging, and that synaptic mitochondria and their proteins were more abundant in aged mice with greater cognitive decline. Moreover, treatment with the mitochondria-targeted antioxidant MitoQ reduced the abundance of synaptic mitochondrial proteins, including pro-apoptotic proteins, and mitigated age-related cognitive decline. These findings demonstrate that synaptic mitochondrial oxidative stress in the mPFC, distinct from chronological age-related processes, contributes to individual variability in age-related cognitive decline and offers a potential target for prevention and intervention.

animal behavior and cognition↗

bioRxiv2026

Aging Converts Microglial Repopulation into Maladaptive Reprogramming that Exacerbates Cognitive Deficits

Background and PurposeAging has been associated with neuroinflammation and cognitive decline. Microglial repopulation after pharmacological depletion has been proposed as a strategy to alleviate microglia-driven neuropathology. However, the effects of microglial repopulation on age-related cognitive decline remain largely unexplored. In the present study, we examined how microglial repopulation affects the transcriptomic profiles of cortical microglia and the decline in prefrontal cortex-dependent cognitive function in aged mice. Experimental ApproachYoung and aged male C57BL/6J mice were used in this study. Microglial depletion was induced by treatment with PLX3397, a CSF1R inhibitor, followed by microglial repopulation after drug withdrawal. Microglia isolated from the entire cerebral cortex were subjected to bulk RNA-sequencing analysis. The visual discrimination test followed by the response direction test was conducted to assess sensory learning and attentional set shifting abilities, respectively. Key ResultsRepopulated cortical microglia in aged, but not young, mice exhibited aberrant gene expression patterns, including reduced expression of microglial identity genes, reprogramming of innate and adaptive immune-related gene expression, and derepression of neuronal gene expression. Furthermore, microglial repopulation selectively impaired visual discrimination learning and attentional set shifting in aged mice. Conclusion and ImplicationsThese findings demonstrate that aging converts microglial repopulation into maladaptive reprogramming that exacerbates cognitive decline, possibly through aberrant gene expression programs. Therefore, the therapeutic potential of this approach must be carefully evaluated with respect to specific behavioral domains and disease contexts, including aging.

neuroscience↗

bioRxiv2026

Glucokinase links metabolism and lineage plasticity in neuroendocrine prostate cancer via interaction with AKT1

Cancer cells frequently rewire their metabolism to sustain growth and survival under stress. Despite the critical role of metabolic adaptation in tumorigenesis, how specific metabolic enzymes regulate lineage plasticity remains unclear. Here, through FDG-PET imaging and transcriptomic analyses, we reveal markedly elevated glucose uptake in neuroendocrine prostate cancer (NEPC) and identify glucokinase (GCK) as a MYCN-induced metabolic enzyme. Beyond its metabolic role, GCK is indispensable for maintaining the neuroendocrine lineage of prostate cancer cells by establishing a functional circuit with AKT1 through reciprocal regulation--AKT1 binds and phosphorylates GCK at S373, whereas GCK phosphorylates AKT1 at S473. Pharmacological disruption of this AKT1-GCK axis suppresses tumor growth in NEPC mouse models and patient-derived xenografts. Altogether, our findings uncover both the metabolic and noncanonical kinase functions of GCK and establish the AKT1-GCK axis as a key link between metabolic reprogramming and neuroendocrine lineage transition in prostate cancer.

cancer biology↗

bioRxiv2026

Parthenogenote-Derived Brain Unveils the Critical Role of Paternal Genome in Neural Development

Genomic imprinting, an epigenetic mechanism that governs parent-of-origin-specific gene expression, is essential for mammalian development, yet its role in late-stage development remains unclear due to the lethality of parthenogenetic (Pg) embryos. Here, we establish cell replacement with parthenogenote-derived cells (CReP), a blastocyst complementation strategy that enables survival and tissue-specific contribution of Pg-derived cells. Brain-targeted CReP showed that Pg-derived cells can participate in neural development but fail to maintain neuronal-glial balance due to aberrant activation of Notch signaling caused by the loss of the paternally expressed gene Dlk1. Restoration of Dlk1 normalized Notch activity and rescued neuronal differentiation. These findings reveal a critical role of the paternal genome, through Dlk1-mediated regulation of Notch signaling, in ensuring neural stem cell expansion and balanced cell fate decisions. The CReP model provides a powerful platform for investigating genomic imprinting and parental genome contributions in development and disease.

developmental biology↗

bioRxiv2026

Organoid Profiler: Automated, high-throughput and quantitative morphological characterization uncovers conserved longitudinal developmental kinetics in microfluidics-engineered organoids

Three-dimensional organoid systems have emerged as transformative tools in biomedical research, yet their translation into standardized high-throughput screening platforms is impeded by stochastic fabrication variability and a lack of scalable quantitative analytics. Here, we present a unified framework integrating microfluidic droplet engineering with Organoid Profiler, an automated deep-phenotyping pipeline designed to capture longitudinal morphological kinetics. By processing over 10,000 longitudinally tracked images across murine lung and liver and human cerebral models, we show that this platform achieves human-level segmentation precision (r = 0.99) while uncovering conserved developmental dynamics obscured in manual cultures. We identify a distinct biphasic "remodeling-to-expansion" trajectory in microfluidic organoids, characterized by an initial compaction phase underpinned by the transcriptional upregulation of focal adhesion pathways, followed by exponential expansion. We further demonstrate a "shape relaxation" phenomenon where tissues converge to spherical equilibrium regardless of initial geometry, indicating intrinsic self-organization. Multi-modal profiling confirms that microfluidic organoids exhibit superior viability, homogeneity (area variability [≤] 5% upon fabrication, [≤] 15% across development) and biological fidelity, retaining physiological levels of immune and stromal niche components often lost in conventional culture. This study establishes morphological metrics as reliable, non-invasive proxies for tissue health and molecular maturity, providing a standardized foundation for quantitative organoid biology.

bioengineering↗

bioRxiv2026

A plug-and-play ROI imaging module and deep-learning denoising framework extend three-photon microscopy to 1.7 mm depth

Three-photon microscopy (3PM) has extended optical imaging beyond the reach of two-photon microscopy (2PM), but its practical depth remains far below theoretical predictions because of low photon efficiency and severe noise contamination. Here we present an integrated hardware and software solution that addresses these limitations. We developed a plug-and-play region-of-interest (ROI) imaging module that selectively excites neuron-occupied regions to improve power efficiency and reduce photothermal stress. The module incorporates frame-partitioned accumulative (FPA) imaging for high signal-to-noise ratio (SNR) structural acquisition, automated neuron segmentation, and motion-robust registration for stable recordings. Complementing this, OptiCal is a cascaded deep-learning framework that removes mixed noise including periodic, motion-induced, and random components. Together, these innovations enable high-fidelity imaging to 1.7 mm depth, extending the practical limit of 3PM by about 400 {micro}m while maintaining low excitation power. Our results reveal reliable calcium activity and behavior-correlated dynamics in deep medial prefrontal cortex of awake mice.

neuroscience↗

bioRxiv2025

Kilohertz-rate two-photon voltage imaging of population dynamics in vivo

Understanding how neural circuits compute requires capturing voltage dynamics across large neuronal populations with millisecond resolution in vivo. However, two-photon voltage imaging remains fundamentally limited by a trade-off among imaging speed, field of view, and excitation efficiency. We introduce HS2PM, a hybrid scanning two-photon microscope that overcomes this bottleneck, enabling kilohertz-rate imaging over a 650 x 524 m2 field of view at single-cell resolution while preserving the photon efficiency of single-point excitation. HS2PM stably records deep-layer membrane potentials from over 160 neurons simultaneously, with minimal photobleaching and phototoxicity. It resolves both spikes and subthreshold voltage dynamics in vivo, revealing how these jointly shape sensory adaptation and population coding. Beyond voltage imaging, HS2PM supports high-speed fluorescence lifetime and vascular flow imaging, establishing a multimodal platform for dissecting fast circuit dynamics with precision previously inaccessible to optical methods.

neuroscience↗

bioRxiv2025

Primate-specific adaptation of Ku protects transcriptomic integrity by suppressing Alu-mediated alternative splicing

Accurate pre-mRNA splicing is essential for the transfer of genetic information but faces unique challenge in higher primates due to the massive expansion of intronic Alu elements1-3. While studying Ku, the Ku70/Ku80 heterodimer best known for initiating non-homologous end-joining (NHEJ) by encircling DNA ends4, we discovered that Ku expression increased markedly during primate evolution in parallel with Alu expansion5. Ku binds double-stranded RNA (dsRNA) stem-loops, including those at the antisense Alu (asAlu) elements within introns5. Here, we show that Ku-depletion in human cells has a broad impact on splicing largely independent of cell-cycle states, NHEJ, or innate immune signaling, significantly affecting ~8-10% of quantifiable alternative splicing events. Mechanistically, Ku directly binds exonic asAlu to prevent their aberrant inclusion and binds asAlu within inverted-repeat Alu (irAlu) pairs flanking canonical exons to prevent exon skipping6. Among human tissues, Ku expression in the brain is consistently ~50% lower, correlating with more permissive expression of Alu-derived splice variants, particularly those encoding mitochondrial proteins and RNA-binding factors. Correspondingly, heterozygous Ku loss in patient causes developmental delay, neurological dysfunction, and acidosis. Together our findings identified Ku as a critical suppressor of Alu-associated alternative splicing co-opted during evolution with implications for primate brain function and human disease.

molecular biology↗

bioRxiv2025

Genome-wide profiling of RNA 2'-O-methylation in neurons and identification of orphan snoRNA targets

We have compared genome-wide patterns of RNA 2-O-methylation (Nm) between two isogenic pairs of neurons. Each pair includes one line harboring a small deletion of orphan box C/D snoRNAs (SNORD116s) from the paternal chr15q11-q13 region. One isogenic pair also differs in expression of SNORD113/114 snoRNAs from chr14q32.2. Wild-type and modified cells were differentiated into cortical neurons, and genome-wide patterns of Nm identified. Neurons display a distinctive signature of rRNA modification compared to undifferentiated stem cells. We further identified thousands of shared Nm sites in mRNAs, lncRNAs and small RNAs. Most sites do not exhibit canonical complementarity to snoRNAs, but a number exhibit strong complementarity to U3 snoRNA, not previously shown to direct Nm. Evidence from cross-linking and sequencing of hybrids (CLASH) suggests that U3 is proximally associated with a subset of 2-O-methylation events. Finally, we identify a number of apparent canonical targets of SNORD113, SNORD114 and SNORD116 snoRNAs. These data present a comprehensive characterization of the Nm landscape in neurons and, for the first time, allow the assignment of Nm sites targeted by specific orphan snoRNAs associated with neurodevelopmental and other disorders.

molecular biology↗

bioRxiv2025

Structural studies suggest CCDC127 as a novel membrane contact site protein in the mitochondrial intermembrane space

Mitochondria feature a sophisticated membrane architecture, with a planar mitochondrial outer membrane (MOM) and a folded inner membrane (MIM). Due to the remarkable adaptability of mitochondria, a proteinaceous network in the intermembrane space (IMS) was proposed to confer both stability and flexibility. However, components of such scaffolds, tentatively termed the mitoskeleton, have remained largely elusive. The mitochondrial contact site and organizing system (MICOS), a central organizer of mitochondrial membrane architecture, was suggested to participate in mitoskeleton formation. Here, we structurally characterize the coiled-coil domain-containing 127 (CCDC127) protein, a putative interactor of MICOS. We show that CCDC127s amino-terminal transmembrane region is anchored in the MOM and the bulk soluble part exposed to the IMS. A crystal structure of CCDC127s central coiled-coil displays a parallel dimer which further oligomerizes into tetramers. We demonstrate that the carboxy-terminal helical bundle (CHB) domain dimerizes to create a peripheral membrane-binding site. Supported by electron microscopy data, we propose a structural model of CCDC127 as intramitochondrial membrane contact site protein mediating the structural organization of the IMS as part of the mitoskeleton.

molecular biology↗

bioRxiv2025

A multi-tiered microDicer with hierarchical blades achieves protein-preserving microdissection down to 10 microns

To study tissue heterogeneity at the sub-millimeter scale, laser capture microdissection (LCM) has been the leading technology for isolating regions of interest (ROI) for downstream molecular profiling. As the ROI approaches cellular dimensions ([~]10 m), laser-induced photothermal damage and challenges in capturing microtissues in conventional LCM can compromise protein preservation and quantitative fidelity. This work introduces multi-tiered Dicers, fabricated by two-photon polymerization, to mechanically dissect tissue slices into uniform microtissues down to 10 m. The hierarchical blade architecture limits instantaneous blade-tissue engagement and lowers the cutting force relative to single-tier designs. For benchmarking, proteomic analysis is performed on ethanol-fixed human squamous cell carcinoma microtissues generated by Dicers and by LCM. Under identical Nanodroplet Processing in One pot for Trace Samples (nanoPOTS) and liquid chromatography-mass spectrometry (LC-MS) conditions, Dicers yield more peptides and proteins than LCM, with the largest gains at 10-20 m spatial resolution. Confocal imaging shows catapult-associated cavities in LCM-generated microtissues. This material loss, along with membrane-limited protein extraction, likely reduces protein coverage. In contrast, multi-tiered Dicers enables reproducible microdissection down to 10 m while maintaining high protein coverage. With spatial registration of microtissues under development, Dicers have potential to complement LCM for next-generation spatial proteomic workflows.

bioengineering↗