Biology subjects

Wang, D.

Publications and source records attributed to Wang, D..

At least 217 records · Page 12Linked to original sources

bioRxiv2025

SIMIT-seq: a bead-free, scalable microfluidic platform for single cell mRNA sequencing with ultrahigh cell-indexing rate

SIMIT-seq is a bead-free, scalable microfluidic platform designed for high-efficiency single-cell mRNA sequencing. Conventional microfluidic-based single-cell RNA sequencing platforms rely heavily on barcoded beads and intricate co-encapsulation schemes, often constrained by double Poisson limitations and the complexities of bead synthesis. In contrast, SIMIT-seq eliminates the need for beads entirely by employing a deterministic, orthogonal barcoding strategy within a two-dimensional micro-well array. This platform achieves an impressive single-cell indexing rate of 96.6% without the need for complex microfluidic operations. Here, we describe the design and fabrication of the SIMIT-seq platform, outline its workflow for transcript capture and library preparation, and demonstrate its application in profiling K562 cells. Our results validate both the high fidelity of molecular barcode immobilization and the systems capability to support downstream single-cell mRNA sequencing. SIMIT-seq offers a cost-effective and scalable alternative for single-cell transcriptomics, providing a promising foundation for future single-cell omics applications.

bioinformatics↗

bioRxiv2025

Development a computational framework for risk evaluation of emerging flu viruses based on genomic sequences and AI

The recent resurgence of highly pathogenic avian influenza H5N1 viruses in North America and Europe has heightened global concerns regarding potential influenza pandemics. Despite significant progress in the surveillance and prevention of emerging influenza viruses, effective tools for rapid and accurate risk assessment remain limited. Here, we present FluRisk, an innovative computational framework that integrates viral genomic data with artificial intelligence (AI) to enable rapid and comprehensive risk evaluation of emerging influenza strains. FluRisk incorporates a curated database of over 1,000 experimentally validated molecular markers linked to key viral phenotypes, including mammalian adaptation, mammalian virulence, mammalian transmission, human receptor-binding preference, and antiviral drug resistance. Leveraging these markers, we developed three state-of-the-art machine learning models to predict human adaptation, mammalian virulence, and human receptor-binding potential, all of which demonstrated superior performance compared to traditional approaches such as BLAST, prior models, and baseline classifiers. In addition, a reference-based method was implemented to provide preliminary estimates of human transmissibility and resistance to six commonly used antiviral drugs. To facilitate broad accessibility and practical application, we developed a user-friendly web server that integrates both the molecular marker atlas and predictive tools for influenza virus phenotyping (available at: http://www.computationalbiology.cn/FluRisk/#/). This computational platform offers a valuable resource for the timely risk assessment of emerging influenza viruses and supports global influenza surveillance efforts.

bioinformatics↗

bioRxiv2025

Population analysis and immunologic landscape of melanoma in people living with HIV

PurposeTo dissect the clinical and immunological features of people living with HIV (PLWH) diagnosed with melanoma, who have consistently shown worse outcomes than HIV-negative individuals (PLw/oH) with the same cancer. Experimental DesignWe analyzed electronic health records from 1,087 PLWH and 394,437 PLw/oH with melanoma. Demographic and clinical characteristics were compared. Spatial immune transcriptomics (72 immune-related genes) was performed on melanoma tumor samples (n=11), with downstream validation using multiplex immunofluorescence (n=15 PLWH, n=14 PLw/oH). ResultsPLWH were diagnosed at a younger age, had greater representation of Hispanic and Black individuals, and showed reduced survival. They also had a markedly increased risk of brain metastases. PLWH experienced significant delays in initiating immune checkpoint inhibitor (ICI) therapy and had worse post-ICI survival, even after balancing covariates. Spatial transcriptomics revealed a more immunosuppressive tumor microenvironment in PLWH, with increased transcription of immune checkpoints (PD1, LAG3) and reduced antigen-presentation markers (HLA-DRB, B2M), with distinct spatial distributions in tumors and surrounding microenvironments. Multiplex immunofluorescence demonstrated features of an exhausted CD8 T cell compartment, including enrichment of PD1intLAG3- and PD1intLAG3 subpopulations, and a significant accumulation of myeloid-derived suppressor cells (CD11b HLA-DR- CD33). ConclusionsMelanoma in PLWH is associated with distinct clinical and immunological features, including delayed ICI treatment, reduced survival, and an immunosuppressive microenvironment with exhausted CD8 T cells and expanded myeloid-derived suppressor cells. These findings suggest that chronic HIV infection may impair antitumor immunity in melanoma. Targeting the pathways identified here may improve therapeutic responses and outcomes in this population. Statement of translational relevanceThis study reveals critical barriers to effective melanoma treatment in people living with HIV (PLWH). Despite receiving immune checkpoint inhibitors (ICIs), PLWH face delayed therapy initiation, a greater likelihood of brain metastases, and significantly higher long-term mortality, even after adjusting for demographic covariates. Transcriptional immune profiling further uncovers a tumor microenvironment enriched in immunosuppressive myeloid-derived suppressor cells and CD8 T cell populations with features of exhaustion. These findings suggest that poorer outcomes in PLWH stem not only from delayed care, but also from distinct targetable mechanisms of immune dysfunction. For example, strategies to reverse MDSC accumulation in the tumor or tailored ICI regimens could enhance immune responsiveness and improve treatment efficiency. By defining the clinical and immunological features of this population, this work highlights opportunities for precision immunotherapy tailored to PLWH with melanoma, with direct implications for improving survival and reducing disparities.

cancer biology↗

bioRxiv2025

Senescence-induced reparative fibroblasts enable scarless wound healing in aged murine skin.

It has been reported that elderly individuals exhibit reduced scarring during the wound healing process compared to younger adults. However, the underlying mechanisms responsible for this phenomenon remain poorly understood. Here, we revealed that aged mice exhibited more pronounced regenerative outcomes compared to young mice, characterized by increased hair follicle numbers and collagen fiber features closer to normal skin. Single-cell sequencing identified a reparative fibroblast subpopulation (Prss35+Fib) enriched in the aged group, which promotes regeneration through communication with epithelial cells, macrophages, and T cell subpopulations via PTN and EREG signaling. Spatial transcriptomics validated this communication pattern by elucidating cell proximity and locating the regenerative niche in the upper dermis. Finally, EREG treatment significantly enhanced regenerative outcomes in young mice, while the small wound model of aged mice, lacking the reparative fibroblast and EREG signaling, failed to achieve regeneration. Collectively, our findings advance the understanding of regenerative plasticity in aging and provide new insights for designing scarless therapeutic strategies.

cell biology↗

bioRxiv2025

SND1 Impairs Calcium Homeostasis in Right Ventricular Failure by Binding and Destabilizing SERCA2a in Cardiomyocytes

BackgroundRight ventricular failure (RVF) is a major contributor to a poor prognosis in patients with pulmonary arterial hypertension (PAH); however, its underlying molecular mechanisms remain incompletely understood. We identified a significant upregulation of the cardiac fetal gene SND1 in the right ventricular myocardium of RVF rats. This upregulation may be a key component of cardiac fetal reprogramming and play a critical role in RVF progression. However, the precise molecular mechanisms by which SND1 contributes to RVF remain unelucidated. MethodsRat models of PAH were established by intraperitoneal injection of monocrotaline (MCT). The pulmonary artery pressure and right ventricular function of rats were assessed using transthoracic echocardiography combined with right heart catheterization. Weighted gene co-expression network analysis (WGCNA) of proteomic data identified a significant association between SND1 upregulation and RVF progression. Calcium transient and contractility measurements in single cardiomyocytes were performed to evaluate the effect of SND1 on sarcoplasmic reticulum (SR) function. Liquid chromatography with mass spectrometry/mass spectrometry analysis combined with co-immunoprecipitation (Co-IP) was used to identify sarcoplasmic/endoplasmic reticulum Ca2+-ATPase 2A (SERCA2a) as the protein interacting with SND1. The effect of SND1 on the progression of RVF was validated using cardiomyocyte-specific SND1 conditional knockout rats. ResultsProteomic and molecular analyses revealed that the cardiac fetal gene SND1 is reactivated in RVF and may contribute to disease progression. In vitro, SND1 knockdown in neonatal rat ventricular myocytes (NRVMs) enhanced contractility, improved calcium transient amplitude and velocity, and increased cell survival under calcium overload. Mechanistically, SND1 interacts with SERCA2a and promotes its proteasomal degradation, impairing SR calcium reuptake. SND1 knockdown restored SERCA2a stability. In vivo, cardiomyocyte-specific SND1 knockout improved right ventricular function, reduced SERCA2a degradation and apoptosis, and increased survival in RVF rats. ConclusionOur study revealed that SND1 reactivation (a fetal gene) contributes to the progression of RVF by promoting SERCA2a degradation and impairing calcium handling. Targeted suppression of SND1 enhances cardiomyocyte contractility and survival, highlighting SND1 as a potential therapeutic target for improving right ventricular function in PAH. Clinical perspectiveO_ST_ABSWhat Is New?C_ST_ABSO_LIThis study identifies SND1, a reactivated fetal gene, as a key contributor to right ventricular failure (RVF) progression in pulmonary arterial hypertension (PAH). C_LIO_LISND1 interacts with SERCA2a, promoting its proteasomal degradation, which disrupts sarcoplasmic reticulum calcium reuptake and weakens cardiomyocyte contractility. C_LIO_LICardiomyocyte-specific SND1 deletion restores SERCA2a levels, improves calcium handling, enhances right ventricular function, and increases survival in RVF rats. C_LI What Are the Clinical Implications?O_LIThe reactivation of fetal genes such as SND1 is not just a marker but a pathogenic driver in maladaptive right ventricular remodeling. C_LIO_LITargeting SND1 represents a novel therapeutic approach to improve right ventricular contractility and prevent heart failure progression in patients with PAH. C_LIO_LIThese findings may inform the development of gene- or protein-targeted therapies aimed at stabilizing SERCA2a and preserving right heart function in high-risk populations. C_LI

cell biology↗

bioRxiv2025

Synergistic roles of Aquaporin 5 and Intra- and Extracellular Carbonic Anhydrases In facilitating CO2 Diffusionacross the Xenopus Oocyte Plasma Membrane

Key PointsO_LIAccording to Ficks law, transmembrane CO2 flux (JCO2) is the product of membrane permeability (PM,CO2) and transmembrane concentration gradient ({Delta}[CO2]): JCO2=PM,CO2{Delta}[CO2]. Previous work separately showed that (1) human aquaporin-5 (hAQP5) enhances PM,CO2, and (2) intracellular and (3) extracellular carbonic anhydrases (CAs) enhance {Delta}[CO2] by consuming accumulated or replenishing lost CO2. We now examine interactio ns among #1-#3. C_LIO_LIWe assess CO2 fluxes--produced by addition/removal of extracellular CO2/[Formula]--using microelectrodes to monitor extracellular-surface pH (pHS) and intracellular pH (pHi) of Xenopus oocytes heterologously expressing hAQP5, injected with human CA II (hCA II), and/or exposed to extracellular bovine CA (bCA). C_LIO_LIEnhancing effects on CO2 fluxes are synergistic among hAQP5, hCA II, and bCA, any of which can become rate limiting, depending on the status of the other two. C_LIO_LICO2/[Formula] addition transiently increases pHS ({Delta}pHS), hCA II augments {Delta}pHS ({Delta}{Delta}pHS), and hAQP5 enhances {Delta}{Delta}pHS ({Delta}{Delta}{Delta}pHS)--a novel tool to assess potential CO2 channels. C_LI CO2 diffusion across plasma membranes depends on both membrane CO2 permeability (PM,CO2) and transmembrane CO2 concentration gradient ({Delta}[CO2])--Ficks law. Human aquaporin-5 (hAQP5) accelerates CO2 diffusion by increasing PM,CO2, whereas carbonic anhydrases (CAs) accelerate CO2 diffusion by enhancing CO2 consumption/production and thus {Delta}[CO2]. Here, we systematically assess functional interactions among a gas channel and intra-/extracellular CAs. On Day 1, we inject Xenopus oocytes with cRNA encoding hAQP5 (control: H2O). On Day 4, we inject hCA II protein in "Tris" buffer (control: "Tris"). We assess CO2 fluxes by introducing extracellular 1.5% CO2/10 mM [Formula] and using microelectrodes to measure (1) maximal extracellular-surface pH increase {Delta}pHS, (2) maximal rate of pHS relaxation (dpHS/dt)Max, and (3) maximal rate of intracellular-pH decrease (dpHi/dt)Max. By itself, hCA II minimally increases {Delta}pHS--measured "trans" to added cytosolic CA (CAi)--even at highest doses (100 ng/oocyte). However, hAQP5 alone triples {Delta}pHS, an effect further doubled by increasing hCA II. By itself, bovine erythrocyte CA (bCA) in the extracellular fluid doubles (dpHi/dt)Max magnitude--meas ured "trans" to added extracellular CA (CAo)--an effect further doubled by hAQP5. Note: pH measureme nts "cis" to added CAs--pHS for bCA, (dpHi/dt)Max for hCA II--are overwhelmed by enzymatical ly-produced/consumed H+, and cannot provide intuitive insight into CO2 fluxes. Our "trans" pH measurements: (1) confirm synergy between CAo and CAi; establish synergy between hAQP5 and both (2) CAo and (3) CAi; and show that enhancement of {Delta}pHS by CAi ({Delta}{Delta}pHS) is a useful tool for assessing CO2 permeability of membrane proteins (e.g., hAQP5).

physiology↗

bioRxiv2025

Spatial Clustering of Interface Residues Enhances Few-Shot Prediction of Viral Protein Binding

AO_SCPLOWBSTRACTC_SCPLOWPredicting protein binding affinities across large combinatorial mutation spaces remains a critical challenge in molecular biology, particularly for understanding viral evolution and antibody interactions. While combinatorial mutagenesis experiments provide valuable data for training predictive models, they are typically limited due to experimental constraints. This creates a significant gap in our ability to predict the effects of more extensive mutation combinations, such as those observed in emerging SARS-CoV-2 variants. We present PROXICLUST, which strategically combines smaller combinatorial mutagenesis experiments to enable accurate predictions across larger combinatorial spaces. Our approach leverages the spatial proximity of amino acid residues to identify potential epistatic interactions, using these relationships to optimize the design of manageable-sized combinatorial experiments. By combining just two small combinatorial datasets, we achieve accurate binding affinity predictions across substantially larger mutation spaces (R2 {approx} 0.8), with performance strongly correlated with capture of high-order epistatic effects. We validated our method in five different protein-protein interaction datasets, including binding of SARS-CoV-2 receptor binding domain (RBD) to various antibodies and cellular receptors, as well as influenza RBD- antibody interactions. This work provides a practical framework for extending the predictive power of combinatorial mutagenesis beyond current experimental constraints, offering applications in viral surveillance and antibody engineering.

molecular biology↗

bioRxiv2025

Histone 3 lysine 36 trimethylation by SETD2 shapes an epigenetic landscape in intestinal stem cells to orchestrate lipid metabolism and prevent cell senescence.

The self-renewal capacity of intestinal stem cells (ISCs) declines with aging, leading to a loss of homeostasis and an increased susceptibility to intestinal diseases. Despite the established significance of lipid metabolism and epigenetic regulation in ISC function, the molecular mechanisms that connect these processes to aging-related ISC dysfunction remain elusive. Here, we demonstrate that Histone 3 lysine 36 trimethylation (H3K36me3) caused by SETD2 is critical for ISC stemness. We found that H3K36me3 deficiency results in reduced ISC proliferation and differentiation, disrupts fatty acid oxidation (FAO) metabolism, and induces ISC senescence. Mechanistically, the loss of H3K36me3 triggers the activity of the SWI/SNF chromatin remodeling complex and leads to increased chromatin accessibility and enhancer activation, which alters FAO- and senescence-related gene expression. Importantly, we discover that metabolic intervention can prevent the senescence of ISC due to H3K36me3 deficiency. Our findings reveal a crucial role for H3K36me3 in maintaining the epigenetic landscape that orchestrates FAO metabolism and determines intestinal stem cell functions, emphasizing the role of FAO as a key modulator between H3K36me3 and ISC aging, suggesting that metabolic intervention may help mitigate age-related ISC dysfunction.

cell biology↗

bioRxiv2025

Molecular interplay between ComEC domains leads to efficient DNA translocation during natural transformation

Naturally competent bacteria can take up and incorporate free DNA from their environment using complex machinery that is endogenously encoded. This process is called natural transformation and is a key mechanism in the spread of antibiotic resistance amongst bacteria, including many human pathogens. All competent bacteria require ComEC to transport the transforming DNA across the cytoplasmic membrane. In addition to the transmembrane competence domain predicted to form the DNA channel, most ComEC orthologues additionally contain an oligonucleotide binding (OB) domain and {beta}-lactamase-like domain. Here, we provide in-depth characterisation of the nuclease activity of the {beta}-lactamase-like domain and the DNA binding activity of the OB domain, and present high-resolution structures of both domains. We show that the in vitro nuclease activity of the {beta}-lactamase-like domain is enhanced when the OB domain is encoded on the same polypeptide chain. Additionally, we identify a pin loop within the {beta}-lactamase-like domain responsible for melting the DNA duplex prior to cleavage of the non-translocating strand, and a DNA channel lined with aromatic residues that guide the uncleaved translocating strand through ComEC. On the basis of our biochemical, structural and functional characterisation, we provide a mechanistic model for how ComEC achieves the simultaneous tasks of DNA degradation and translocation, central to the natural transformation process.

microbiology↗

bioRxiv2025

Behavioral Efficacy of AAV FOXG1 Gene Replacement Therapy in a Mouse Model of FOXG1 Syndrome

FOXG1 syndrome is a severe neurodevelopmental disorder characterized by microcephaly, profound intellectual disability with communication deficits including lack of speech, impaired social interaction, increased anxiety, hyperkinetic/dyskinetic movements, seizures and abnormal sleep patterns. Mutations in a single allele of the FOXG1 gene cause disease, likely due to loss-of-function. However, current therapies do not target this root cause of FOXG1 syndrome and have little to modest therapeutic benefit on only a small subset of symptoms. To date, the therapeutic potential of restoring FOXG1 levels in the brain with adeno-associated virus (AAV) FOXG1 gene replacement therapy has only been reported in a Foxg1fl/+;NexCre mouse model that lacks one Foxg1 allele but does not express mutant FOXG1, and with only neuroanatomical endpoints evaluated. Here, in a FOXG1 mouse model that contains a highly prevalent, patient-specific Q84P mutation, we describe the beneficial effects of AAV human FOXG1 gene replacement therapy administered by intracerebroventricular (ICV) injection at postnatal day 6 (P6) on several behavioral deficits that are relevant to key features of human FOXG1 syndrome. Our studies demonstrate that AAV FOXG1 gene replacement therapy is a promising approach for the treatment of a subset of functional deficits in human FOXG1 syndrome.

neuroscience↗

bioRxiv2025

The multiomics landscape of small peptides encoded by long non-coding RNA-derived sORFs in rice

Long non-coding RNAs (lncRNAs), representing the non-coding RNA regions, constitute a significant portion of the genomes in complex organisms. Recent studies suggest that some lncRNAs have the capability to encode peptides. However, the presence of the lncRNA-derived sORFs-encoded polypeotides (LSEPs) in plants is not well understood. In this study, we developed a multi-omics approach that encompasses transcriptomics, translatomics (Ribo-seq), and proteomics to identify of LSEPs in rice. Among the 2764 identified lncRNAs, 42.69% were found to be bound by the ribosome, indicating a potential for encoding. Optimized small peptide extraction protocol was further developed, and the small peptides from rice leaves were extracted and subjected to LC-MS/MS analysis, leading to the identification of a total of 403 LSEPs across four constructed search databases. This work confirms the peptide-coding ability of lncRNAs in plants. Collectively, our study establishes an efficient multi-omics method for identifiying small peptides encoded by lncRNAs, which may be valuable for large-scare screening of LSEPs in plants.

plant biology↗

bioRxiv2025

Respiratory Airway Secretory Cells act as Immune Sentinels in Human Distal Airways

Pulmonary immunity in the human distal respiratory airways is essential for lung function but remains poorly explored, mainly due to limited physiologically relevant models. Here, we develop distal lung organoids containing respiratory airway secretory (RAS) cells, a recently identified epithelial population unique to the distal airways of humans and large mammals, using human pluripotent stem cells (hPSCs). Lineage tracing identified RAS cells as descendants of SOX9brightNKX2-1bright progenitors. Single-cell transcriptomics elucidated that RAS cells exhibited a distinct immune-competent phenotype with enriched genes associated with viral host entry and pattern recognition receptor signaling. Functionally, RAS cells infected by respiratory syncytial virus (RSV) exhibited enhanced antiviral activity marked by upregulation of interferon-stimulated genes (ISGs) and complement component 3 (C3). In contrast, bacterial flagellin or Pseudomonas aeruginosa (PAO1) triggered a TLR5-driven immune response in RAS cells, inducing complement system activation, a response suppressed by selective TLR5 inhibition. Notably, in chronic obstructive pulmonary disease (COPD), RAS cells displayed dysregulated immune activation, characterized by elevated expression of adaptive immune mediators. Together, our findings identify RAS cells as previously unrecognized sensors and effectors of mucosal immunity in the human distal airways and reveal their roles in viral infection, bacterial stimulation, and chronic inflammatory lung disease, providing potential therapeutic targets for respiratory diseases.

cell biology↗

bioRxiv2025

Targeting processive transcription for Myc-driven circuitry in medulloblastoma

AO_SCPLOWBSTRACTC_SCPLOWO_ST_ABSBackgroundC_ST_ABSMedulloblastoma is the most common malignant brain tumor of childhood. The highest-risk tumors are driven by recurrent Myc amplifications (Myc-MB) and experience poorer outcomes despite intensive multimodal therapy. The Myc transcription factor defines core regulatory circuitry for these tumors and acts to broadly amplify downstream pro-survival transcriptional programs. Therapeutic targeting of Myc directly has proven elusive, but inhibiting transcriptional cofactors may present an indirect means of drugging the oncogenic transcriptional circuitry sustaining Myc-MB. MethodsIndependent CRISPR-Cas9 screens were pooled to identify conserved dependencies in Myc-MB. We performed chromatin conformation capture (Hi-C) from primary patient Myc-MB samples to map enhancer-promoter interactions. We then treated in vitro and xenograft models with CDK9/7 inhibitors to evaluate effect on Myc-driven programs and tumor growth. ResultsEight CRISPR-Cas9 screens performed across three independent labs identify CDK9 as a conserved dependency in Myc-MB. Myc-MB cells are susceptible to CDK9 inhibition, which is synergistic with concurrent inhibition of CDK7. Inhibition of transcriptional CDKs disrupts enhancer-promoter activity in Myc-MB and downregulates Myc-driven transcriptional programs, exerting potent anti-tumor effect. ConclusionsOur findings identify CDK9 inhibition as a translationally promising strategy for the treatment of Myc-MB. KO_SCPLOWEYC_SCPLOW PO_SCPLOWOINTSC_SCPLOWO_LICDK9 is an intrinsic dependency in Myc-driven medulloblastoma C_LIO_LIDual CDK9/7 inhibition disrupts Myc-driven transcriptional circuitry C_LIO_LICDK9 inhibitors should be developed as pharmaceutical agents for Myc-MB C_LI IO_SCPLOWMPORTANCEC_SCPLOWO_SCPCAP C_SCPCAPO_SCPLOWOFC_SCPLOWO_SCPCAP C_SCPCAPO_SCPLOWTHEC_SCPLOW SO_SCPLOWTUDYC_SCPLOWMedulloblastoma is the most common malignant brain tumor of childhood, and outcomes for high-risk subgroups remain unsatisfactory despite intensive multimodal therapy. In this study, we pool multiple independent CRISPR-Cas9 screens to identify transcriptional cofactors such as CDK9 as conserved dependencies in Myc-MB. Using Hi-C from primary patient samples, we map Myc enhancer-promoter interactions and show that they can be disrupted using inhibition of transcriptional CDKs. CDK9 inhibitor treatment depletes Myc-driven transcriptional programs, leading to potent anti-tumor effect in vitro and prolongation of xenograft survival in vivo. With a large number of CDK9 inhibitory compounds now in clinical development, this study highlights the opportunity for clinical translation of these for children diagnosed with Myc-MB.

cancer biology↗

bioRxiv2025

Fast in vivo deep-tissue 3D imaging with selective-illumination NIR-II light-field microscopy and aberration-corrected implicit neural representation

Near-infrared II (NIR-II) microscopy, which enables in vivo deep-tissue visualization of vasculature and cell activities, has been a promising tool for understanding physiological mechanisms. However, the volumetric image speed of the NIR-II microscopy is hindered by scanning strategy, causing limitations for observing instantaneous biological dynamics in 3D space. Here, we developed a NIR-II light-field microscopy (LFM) based on selective-illumination and self-supervised implicit neural representation (INR)-reconstruction, which allows ultra-fast 3D in vivo imaging (100 volumes/s). Through integrating INR with view-wise aberration correction, we could conquer the artifacts induced by the angular subsampling and refractive index variation, achieving single-cell resolution at a volume of 550 m diameter and 200 m thickness. The volumetric selective-illumination overcomes the influence of out-of-focus background, together with the low scattering advantage of NIR-II wavelength, extending the imaging depth to 600 m. The developed aberration-corrected implicit neural representation reconstruction (AIR) NIR-II LFM showcases its capability by monitoring hemodynamics of mouse brain under norepinephrine and flow redistribution of ischemic stroke in 3D vasoganglion, as well as noninvasively tracking immune cell activities inside subcutaneous solid tumor through intact skin. This approach represents a significant advancement in 3D in vivo imaging, holding great potential in biomedical research and preclinical studies.

neuroscience↗

bioRxiv2025

Few-Shot Viral Variant Detection via Bayesian Active Learning and Biophysics

The early detection of high-fitness viral variants is critical for pandemic response, yet limited experimental resources at the onset of variant emergence hinder effective identification. To address this, we introduce an active learning framework that integrates protein language model ESM3, Gaussian process with uncertainty estimation, and a bio-physical model to predict the fitness of novel variants in a few-shot learning setting. By benchmarking on past SARS-CoV-2 data, we demonstrate that our methods accelerates the identification of high-fitness variants by up to fivefold compared to random sampling while requiring experimental characterization of fewer than 1% of possible variants. We also demonstrate that our framework benchmarked on deep mutational scans effectively identifies sites that are frequently mutated during natural viral evolution with a predictive advantage of up to two years compared to baseline strategies, particularly those enabling antibody escape while preserving ACE2 binding. Through systematic analysis of different acquisition strategies, we show that incorporating uncertainty in variant selection enables broader exploration of the sequence landscape, leading to the discovery of evolutionarily distant but potentially dangerous variants. Our results suggest that this framework could serve as an effective early warning system for identifying concerning SARS-CoV-2 variants and potentially emerging viruses with pandemic potential before they achieve widespread circulation.

bioinformatics↗

bioRxiv2025

Macroscopic cerebral energy efficiency corresponds to neuron reorganization in awake and anesthetized mice

Non-invasive imaging of brain function and energy supply is crucial for diagnosing and treating brain disorders. Conventional imaging struggles to capture altered relationships between energy supply and utilization caused by brain diseases. A novel method, which can be translated to human patients, is to calculate relative power (rPWR) and relative cost (rCST) to assess cerebral energy efficiency. However, whether rPWR/rCST can track individual changes and neural activity remains unproven. Our study compared these non-invasive measures with invasive two-photon microscopy in awake and anesthetized mice. We found that rPWR/rCST distributions were similar between awake mice and humans, but changed in anesthetized mice, indicating a shift in the brains economic balance. Furthermore, changes in rPWR/rCST were linked to the reorganization of microscopic neural networks, observed with two-photon microscopy. Our work highlights the potential of rPWR/rCST for medical applications, and that neural network reorganization is linked to the brains economic balance.

neuroscience↗

bioRxiv2025

Characterization of the gut mycobiome in patients with non-alcoholic fatty liver disease and correlations with serum metabolome

BackgroundThe relationship between the gut mycobiome and non-alcoholic fatty liver disease (NAFLD) is largely unexplored. MethodsIn this study, we used a publicly available shotgun metagenomic sequencing dataset of fecal samples to compare the gut fungal communities of 90 NAFLD patients with those of 90 healthy controls. We examined their correlations with gut bacterial communities, host serum metabolite s, and the interactions of key taxa within these networks. ResultsOur results revealed a remarked dysbiosis in the gut mycobiome of NAFLD patients, cha racterized by a significant increase in four fungal taxa, including Pseudopithomyces sp. c174, Muc or sp. c176, Aspergillus sp. c25, and uncultured Ascochyta c213. Multi-omics analysis showed that the gut mycobiome significantly contributes to the host serum metabolome. Pseudopithomyces s p. c174 was notably associated with some beneficial blood metabolites, such as glycoursodeoxycholic acid and alpha-linolenic acid, whereas the NAFLD-enriched pro-inflammatory phenylacetic acid was linked to Aureobasidium sp. c170 and Basipetospora sp. c193. Network analysis revealed significant alterations in the gut microbiome of NAFLD patients, highlighting the potential roles of Alternaria alternata c42, Penicillium sp. c5, and uncultured Malassezia c303. Moreover, predictive models that integrated both bacterial and fungal taxa improved prediction accuracy, emphasizing the crucial role of gut fungi in NAFLD. ImportanceNon-alcoholic fatty liver disease (NAFLD) is a widespread liver condition with limited treatments. While gut bacteria have been extensively studied in NAFLD, the role of gut fungi (the mycobiome) remains poorly understood. This study fills that gap by characterizing gut fungal communities in NAFLD patients and linking these changes to their blood metabolite profiles. We found that NAFLD patients show distinct fungal imbalances, which correlate with key metabolic alterations in the host. These findings expand our understanding of NAFLD by spotlighting gut fungi as important contributors to disease progression. This insight opens new avenues for potential biomarkers and therapies targeting the gut-liver axis. ConclusionsOur findings provide a comprehensive understanding of the link between the gut mycobiome and NAFLD progression, which is essential for guiding future therapeutic research.

microbiology↗

bioRxiv2025

Spatial transcriptomics elucidates the central role of cerebral vasculatures in the progression of Japanese encephalitis

The cellular and molecular mechanisms underlying the neuropathology of Japanese encephalitis virus (JEV) remain obscure. Herein, we designed Stereo-seq chips to simultaneously capture the in situ transcriptomes of both the host and JEV, constructing a comprehensive spatiotemporal pathological landscape for Japanese encephalitis (JE). This study reveals the central role of the vascular system in JE pathogenesis, particularly the meninges, which displayed the strongest signal of inflammation and cell death in the JEV-infected brain. The activation of the Ackr1+ endothelial cells, disruption of the blood-brain barrier, the migration of JEV-infected monocytes, secretion of immune factors by the infected cells, and the occurrence of pyroptosis and necroptosis form a positive feedback loop, resulting in an increasing influx of immune cells and tissue damage. JEV infection leads to neurological impairments, which may be attributed to the interaction between viral proteins and host cellular factors such as Stat1, Stat3, Nfkb1, and Sp1. As the vascular system serves as a central receiver and amplifier of inflammatory signals, regulating inflammation within the vascular system is essential in mitigating JE progression.

immunology↗