Biology subjects

Han, G.

Publications and source records attributed to Han, G..

At least 19 recordsLinked to original sources

bioRxiv2026

In situ loading of biologics on and tissue redirection of circulating extracellular vesicles with an anchoring nanobody

Extracellular vesicles (EVs) are promising nanocarriers of therapeutic macromolecules, but ex vivo production, cargo loading and quality control constrains clinical translation. Here we demonstrate that NEV3, an EV-anchoring nanobody identified by phage display, binds EVs from multiple sources through interactions involving fibronectin and loads diverse proteins onto EVs, resulting in enhanced intracellular delivery and biological activities in vitro and in vivo. Conjugating NEV3 to target proteins hijacks circulating EVs, prolonging circulation and altering tissue distribution in vivo. When fused with an GFP nanobody or protein A, NEV3 enabled simultaneous capture and loading of circulating GFP or immunoglobulin G (IgG) antibodies on endogenous EVs with enhanced intracellular delivery in vitro and redistribution to liver in vivo. Intravenous protein A-NEV3 significantly reduced circulating IgG and anti-dsDNA antibodies in systemic lupus erythematosus mice with improved survival and reduced pathologies. Intravenous anti-transferrin receptor-protein A-NEV3 redirected circulating EVs to muscle and alleviated muscle pathologies in dystrophin-deficient mdx mice. Our study demonstrates that NEV3 enables in situ loading of protein therapeutics and tissue-specific delivery of circulating EVs, providing a modular strategy for loading cargo onto and redirecting circulating EVs in vivo.

bioengineering↗

bioRxiv2026

A spatial topology atlas of type I myofibers in porcine skeletal muscle reveals local slow-oxidative niches associated with meat quality traits

Skeletal muscle metabolism and meat quality are usually interpreted through myofiber type composition, fiber size, and histochemical state. Whether the spatial topology of myofibers constitutes an independent phenotype layer remains poorly quantified. Here, using succinate dehydrogenase (SDH)-stained cross-sectional images from multiple pig breeds and more than 40 skeletal muscle sites, we established a multiscale spatial phenotyping framework for type I myofibers. To enable scalable instance-level quantification, we developed an improved Mask R-CNN segmentation workflow, trained with SAM-assisted and manually corrected annotations, and optimized for dense, small, irregular, and variably stained muscle fibers. This framework captures single-fiber morphology and staining, local contact, connected-cluster architecture, diffusion-ring neighborhoods, and global tissue configuration. Type I myofiber abundance was separable from spatial organization capacity: some muscles formed stronger-than-expected local connectivity and clustering despite modest type I fiber abundance. Spatial transcriptomic integration further showed that slow-oxidative genes and functional modules were non-randomly organized and formed local high-expression domains in type I fiber-enriched, high-contact neighborhoods. Across muscle sites and breeds, skeletal muscles displayed distinguishable type I fiber spatial topology identities, which were remodeled by breed background in a muscle-specific manner. In samples with matched meat-quality measurements, spatial topology features improved the explanation of pH, meat color, conductivity, and intramuscular fat. These results suggest that skeletal muscle should be modeled as a spatially organized tissue system rather than a simple mixture of fiber types.

bioinformatics↗

bioRxiv2026

Long-Term Grazing Drives Compositional Shifts in Root-Associated Microbial Communities of Desert Steppe Plants

Grassland microbial communities are central to mediating ecosystem function and stability, yet how long-term grazing reshapes root-associated microbiomes across contiguous soil-root habitats remains poorly understood. This limits our ability to identify robust microbial bioindicators for grassland health monitoring. In this study, we investigated the community assembly and functional variation of root-associated microbiomes of Stipa breviflora, a dominant perennial clonal grass in desert steppes, across a 17-year continuous grazing experiment with four grazing intensity treatments (no grazing, light, moderate, and heavy grazing). We show that grazing intensity induces niche-specific restructuring of microbial communities, with the most profound compositional and functional shifts occurring in the rhizosphere, followed by root endophytic compartments and bulk soil. Light and moderate grazing significantly enriches the phylum Bacillota in rhizosphere and endophytic compartments, whereas the genus Pseudomonas dominates ungrazed grassland soils and is markedly depleted under grazing conditions. Microbial community responses to grazing follow a unimodal intermediate disturbance pattern, with moderate grazing triggering the strongest microbial community differentiation, enhanced microbial network connectivity and modularity, and the highest abundance of grazing-responsive microbial biomarkers. Notably, grazing-induced microbial community variation is decoupled from intraspecific phenotypic changes in S. breviflora. Our findings demonstrate that long-term grazing acts as a strong selective filter partitioning core beneficial microbial taxon, establishing Bacillota and Pseudomonas as complementary bioindicators for evaluating desert steppe ecosystem health. This study advances the understanding of plant-microbe interactions under anthropogenic disturbance and provides microbiome-based insights for sustainable grassland management.

microbiology↗

bioRxiv2026

Virtual-cell verification enables self-auditing AI discovery for immune rejuvenation

Artificial-intelligence agents propose drug-discovery hypotheses faster than experiments can test them, yet their conclusions are rarely verified, against the underlying biology, the predicted perturbation, or the agent's own scoring logic. We close this verification gap with an agentic framework built on three verifiers. First, PACE, a phenotype verifier, resolves immune aging into ten directionally scored, cell-type-resolved gene-set modules, selected for cross-cohort stability across four PBMC cohorts, and outperforms five established aging clocks in an independent in-house aging cohort of 434 elderly donors. Second, CellQ, a virtual-cell verifier built with multi-modal LLM, compresses each single-cell transcriptome into eight discrete tokens aligned to a language model's vocabulary through residual vector quantization; it attains state-of-the-art perturbation prediction and uniquely resolves the weak, module-level shifts that differential-expression recovery misses. Third, an Analyzer-Planner-Auditor agent verifies its own scoring logic: screening 110 compounds in primary human PBMCs, it found aged-down modules more reversible than aged-up modules and revised its objective from an equal-weight mean to a balance-constrained minimum, a self-correction that generalized to an independent 13-compound T-cell assay. By verifying its predictions and its own objective against experiment, the framework points beyond hypothesis-generating AI toward self-correcting AI scientists whose objectives could continuously evolve.

bioinformatics↗

bioRxiv2026

A gavage-fomite based method to generate mouse models with natural microbiota

Laboratory-raised specific pathogen-free (SPF) mice have been indispensable for fundamental immunology research, yet their reliability in predicting human clinical outcomes has been questionable. A major factor contributing to this disconnect is the sanitized housing environment, which deprives laboratory mice of physiological microbial exposure critical for immune maturation. Various approaches have been developed to introduce microbes to SPF mice, aiming to mimic human-like microbial experiences and engender adult human-like immune traits. However, some of these methods, specifically the pet store mice cohousing approach suffer from significant variability in pathogen exposure driven by the uncontrolled nature of microbial exchange and is associated with heightened mortality. Here we present an alternative gavage-fomite (GaF) method that exposes mice to a similarly diverse array of pathogens and commensal as the pet store cohousing method while limiting mortality. GaF-treated mice exhibited consistent gut microbial composition, robust immune maturation characterized by mucosal T-cell distribution, elevated serum inflammatory cytokines, and a splenic immune transcriptional signature closely aligned with that of adult humans. Furthermore, these mice demonstrated enhanced protection against a virulent bacterial challenge. The simplicity, and effectiveness of the GaF method for generating mice with natural microbiota, may support broader use of these models in basic and translational immunological research across institutions.

immunology↗

bioRxiv2026

Aberrant CD4+ T cell refeeding response impairs neuro-immune crosstalk in Parkinson's disease

T cells modulate disease associated neuroinflammation in Parkinsons disease (PD). We report that circulating CD4+ T cells from people with PD have a dysregulated transcriptional and cytokine response to fasting and refeeding and an altered metabolic profile. The CD4+ T cell secretome mediates a metabolic program in neurons that is impaired in PD, revealing dysfunctional neuro-immune signalling that may contribute to disease pathology.

neuroscience↗

bioRxiv2026

SPSID: A single-parameter shrinkage inverse-diffusion for denoising gene regulatory networks

Inferring gene regulatory networks (GRNs) from expression data is a fundamental problem in systems biology, but its accuracy is often undermined by structural noise arising from transitive correlations. These indirect interactions can obscure the true regulatory architecture, leading to a high rate of false positives. To address this, we introduce SPSID (Single-Parameter Shrinkage Inverse-Diffusion), a novel and robust network denoising framework. SPSID employs a principled spectral filter, built upon a shrinkage-regularized inverse-diffusion operator, to mathematically distinguish direct, one-step interactions from multi-step, indirect paths. This approach guarantees numerical stability and, through a fixed default parameter, effectively eliminates the need for data-dependent tuning. We conducted a comprehensive evaluation of SPSID on both extensive simulations and the gold-standard DREAM5 benchmark. The results demonstrate that SPSID outperforms state-of-the-art baseline methods in both AUROC and AUPR, exhibiting good stability across diverse network conditions. Furthermore, it functions as a post-processing tool, elevating the performance of multiple upstream GRN inference methods. By providing a computationally efficient and parameter-free solution to filter structural noise, SPSID offers a readily applicable tool for uncovering the underlying topology of complex biological networks with greater fidelity.

bioinformatics↗

bioRxiv2025

Stationary and germ layer-specific cellular flows shape the zebrafish gastrula

During gastrulation, a sequence of complex processes transforms the blastula into a multi-layered embryo. Fixed sample analysis has revealed much about how genetic signaling cascades determine the major body axes and organize cell fate patterns into the germ layers: ectoderm, mesoderm, and endoderm. In toto live imaging of vertebrate development highlights that embryogenesis is a dynamic process that involves on the order of ten thousand cells, but hurdles related to data handling have hampered quantitative analysis. Therefore, our understanding of the rich physical aspects of multilayered tissue reconfigurations remains incomplete. Here, we reveal that modules of stationary and germ-layer-specific tissue flows shape the zebrafish gastrula. We combine in toto live imaging with tissue-specific markers and image analysis to reveal the global shape of the enveloping layer (EVL), epiblast, and mesoderm over time. A user-friendly tissue cartography pipeline based on the Blender 3D software moves into the reference frame of individual tissue layers. We find distinct tissue flow patterns in the enveloping layer (EVL), epiblast, and mesoderm, respectively. The instantaneous tissue flow of these germ layers is organized in a temporal sequence of hours-long, constant flow patterns. This suggests that a sequence of stationary tissue flow modules transports cells to their destination during gastrulation. Mathematical decomposition suggests that epiblast flow is strongly influenced by a superposition of rotational flow in the mesoderm, and divergent flow in the EVL. Molecular and cellular complexity notwithstanding, these results hint at surprisingly, tractable physical processes that underlie vertebrate gastrulation, and set the stage for investigations of how morphogens orchestrate dynamics.

developmental biology↗

bioRxiv2025

Light on its feet: Acclimation to high and low diurnal light is flexible in Chlamydomonas reinhardtii

Chlamydomonas acclimates to repeated low (LL) or high light (HL) days by changing the abundance of photosynthetic complexes and the ultrastructure of its thylakoid membranes. These phenotypes persist through the night phases, suggesting a readiness for the daylight environment that is routinely experienced despite the intervening dark periods (Dupuis & Ojeda et al. 2025). Here, we investigate how prior acclimation impacts algal fitness upon a change in daylight intensity and how quickly Chlamydomonas can reprogram its photoprotective strategy in a diurnal context. We performed a systems analysis of synchronized populations acclimated to diurnal LL when subjected to HL days and of populations acclimated to diurnal HL when subjected to LL days. In the latter case, diurnal photoacclimation decreased fitness during the first day at a new light intensity: HL-acclimated cells barely increased in size over the first LL period, and they failed to complete a cell cycle. However, although LL-acclimated cells showed severe photodamage after 6 hours of HL, they recovered chloroplast form and function later that afternoon and successfully divided at nightfall. These cells rapidly altered their thylakoid membrane ultrastructure, increased their photoprotective quenching capacity, and decreased their inventory of photosystem and antenna proteins by the end of the first HL day. Transcriptomic and proteomic analyses revealed rapid induction of thousands of genes, including those encoding proteases, chaperones, and other proteins involved in the chloroplast unfolded protein response. These results show that the alga is highly flexible and competent to rapidly acclimate to changes in diurnal light intensity.

plant biology↗

bioRxiv2025

Field evaluation of non-invasive sampling for monitoring nine swine pathogens in the Republic of Korea

BackgroundNon-invasive sampling methods, such as swine oral fluid (OF) and fecal boot (FB) sampling, have gained attention due to their animal welfare considerations, ease of collection, and cost effectiveness. However, comparative data regarding non-invasive and standard sampling methods remain limited, particularly in the Republic of Korea, where research on OF and FB sampling is sparse. Therefore, we investigated representative pig pathogens, including six porcine respiratory pathogens and three gastrointestinal pathogens, using OF and FB samples for pathogen surveillance across commercial farms in the Republic of Korea. MethodsThe results from targeted polymerase chain reaction (PCR) assays for major respiratory and gastrointestinal pathogens obtained using OF and FB samples were compared with those obtained from standard samples. Non-invasive samples included 30 OF ropes and 30 FBs collected from nine farms, and 360 standard samples (blood, fecal, oral, and nasal swabs) were also collected. PCR assays for the nine pathogens were conducted, and the results from OF, FB, and combined OF+FB were compared with those from standard samples at the pen level. ResultsOF sampling showed superior test concordance with respiratory pathogens than gastrointestinal pathogens, and FB sampling demonstrated superior detection of gastrointestinal pathogens compared with OF sampling. Additionally, the combination of OF+FB sampling improved the detection concordance for all nine target pathogens investigated. ConclusionsWe demonstrated the feasibility and potential applicability of OF and FB sampling under field conditions in Korean pig farms. Therefore, this study supports OF and FB sampling as useful tools for swine pathogen monitoring in both research and practical field applications.

microbiology↗

bioRxiv2025

Decoding functional genes across species with annotation-independent machine learning

Dissecting the genetic basis of complex traits across species is a challenge for traditional low-throughput, species-specific methods. To overcome these limitations, we introduce a computational framework that integrates cross-species comparative genomics and machine learning to identify functional genes for shared phenotypes, independent of prior annotation. Our method links orthologous gene group (OG) profiles to specific traits, enabling the powerful discovery of functional genes across diverse evolutionary clades. For plant-arbuscular mycorrhizal symbiosis, a notoriously difficult system, our model pinpointed a regulatory network by identifying 27 core plant-AM symbiosis genes among its top 50 candidate OGs, including the critical receptor SYMRK. The approach also proved highly effective for identifying functional genes related to the tested vertebrate skeletal development and multiple bacterial traits. Most notably, for bacterial motility, our model not only identified 63 known motility genes from the top 100 candidate OGs (of which 78 are present in Escherichia coli) but also guided the experimental validation of three novel essential genes. This annotation-independent strategy represents a paradigm shift in functional genomics, offering a scalable and universal engine to decode the genetic architecture of complex traits and illuminate the vast functional dark matter across the tree of life.

genomics↗

bioRxiv2025

Epithelium intrinsic zinc sensor controls immune homeostasis with gut microbes via regulation of Tuft cell lineage

Zinc is an essential micronutrient crucial for cell proliferation, differentiation, and apoptosis, yet its precise role in the constantly renewing intestinal epithelium remains unclear. We generated mice lacking the Zn-dependent transcription factor Metal-responsive Transcription Factor 1(MTF1{Delta}IEC) in intestinal epithelial cells. MTF1{Delta}IEC mice exhibited altered metal homeostasis and acute susceptibility to Zn supplementation. Transcriptional and cellular analyses revealed increased inflammatory immune responses to microbes in MTF1{Delta}IEC mice. Mechanistically MTF1 deletion resulted in the loss of Tuft cell lineages compromising barrier function against commensal microbes and pathogens. Ex vivo experiments demonstrated that at a cellular level, Zn treatment skewed the cellular composition from proliferating to differentiated cells. Specifically, we show that Zn sensing via MTF1 is required for IL-13 dependent induction of Tuft cells. Our findings underscore critical role of Zn in maintaining intestinal immune homeostasis through differentiation of specialized cell lineages, highlighting importance nutrient sensing in the constantly remodeling epithelial barrier.

immunology↗

bioRxiv2025

Gut bacteria gatekeep host-specific colonization of a commensal fungus that boosts type 2 immunity

Naturalized, wilded, wildling, and dirty/pet store mouse models represent a spectrum of approaches designed to make laboratory mice more immunologically and physiologically similar to wild or human contexts by increasing their exposure to naturally occurring microbes and pathogens. In this study, we screened the gut mycobiome of pet store mice, and identified Kazachstania pintolopesii as a dominant fungus in pet store mice across various geographical locations. K. pintolopesii strains isolated from mice in geographically distinct pet stores stably colonize the gastrointestinal tract of laboratory mice, independent of gut bacterial composition, maintaining high fungal burdens for extended periods. K. pintolopesii rapidly became the dominant fungus in the mouse gut in conventional, antibiotic, and germ-free settings, outcompeting other non-murine fungal strains. Pet store-derived K. pintolopesii exhibited unique immunological properties distinct from typical anti-fungal responses. Unlike C. albicans colonization, K. pintolopesii did not induce circulating neutrophil expansion or Th17 cell populations in the gut mucosa. When administered systemically, K. pintolopesii-infected mice showed 100% survival with minimal fungal burden in kidneys, contrasting sharply with lethal C. albicans infections. Adaptive immune deficiency (Rag1 knockout mice) did not affect K. pintolopesii colonization or host response, indicating that B and T cell-mediated immunity does not restrain this fungus. K. pintolopesii colonization provided no cross-protection against systemic candidiasis further establishing lack of immune activation. These findings demonstrate that K. pintolopesii establishes a benign host-fungal relationship through neutrophil-independent mechanisms, avoiding classical anti-fungal immune activation while maintaining stable gut colonization. Instead, it selectively induces strong type 2 mucosal immune responses, increasing tuft and goblet cell counts and stimulating Th2 and group 2 innate lymphoid cell (ILC2) populations. This immune profile confers notable protection against intestinal nematode infection, demonstrated by reduced Heligmosomoides polygyrus egg counts. Altogether, K. pintolopesii serves as an exemplary model for commensal mycobiota, revealing distinct mechanisms for host tolerance and immune modulation.

microbiology↗

bioRxiv2024

Assessment of DNA methylation from a single genomic region of ELOV2 is sufficient to predict chronological age

Estimation of chronological age is particularly informative in forensic contexts. Assessment of DNA methylation status allows for the prediction of age, though the accuracy and ease of manipulation may vary across different models. In this study, we started with a carefully designed discovery cohort recruiting more elderly subjects than other age categories, to diminish the effect of epigenetic drifting. We analyzed DNA methylation from a single genomic region of ELOV2, which was sufficient to construct an age-prediction model comprising 15 CpG sites. This model is further validated by an independent cohort as well as a multi-center test using trace dried bloodstains. The nature of our analytical pipeline, when combined the assessment of a single genomic locus with high-throughput sequencing, can easily be scaled up with low cost. Taken together, we propose a new age-prediction model featuring accuracy, ease of manipulation, high-throughput, and low cost. This model can be readily applied in both classic and newly emergent forensic contexts that require age estimation.

genetics↗

bioRxiv2024

Tim-3 promotes viral infection by suppressing USP25-TRAF3-IRF7 signaling pathway

Tim-3, an immune checkpoint inhibitor, plays key roles in maintaining immune homeostasis and is involved in viral evasion. However, the precise role of Tim-3 in viral infection remains to be determined. USP25 is one of the deubiquitinating enzymes that serves to initiate antiviral immunity by deubiquitinating TRAF3 and triggering the anti-viral signaling pathway. Here we found that Tim-3 specific knockout in myeloid cells leads to enhanced anti-viral immunity in mice with VSV encephalitis by increasing type I interferon response. Mechanistically, Tim-3 inhibits the expression of USP25 via STAT1, interacts with USP25 but does not regulate its post-translational modification, and as a result, Tim-3 inhibits USP25 mediated deubiquitination of TRAF3, promotes k48-linked ubiquitination and degradation of TRAF3, and then inhibits the phosphorylation of IRF7, finally down-regulates the interferon response. These findings provide new insights into the function of Tim-3 in antiviral immunity and its related clinical significance.

immunology↗

bioRxiv2024

Structures of PSI-FCPI from Thalassiosira pseudonana in high light provide convergent evolution and light-adaptive strategies in diatom FCPIs

Diatoms achieve great survival success in the fluctuating oceanic environment, rely on fucoxanthin chlorophyll a/c-binding proteins (FCPs) to complete light harvesting and quenching, which provide about 20% primary productivity on earth. We report two cryo-electron microscopic structures of photosystem I (PSI) with 13 or 5 FCPIs respectively at 2.78 [A] and 3.20 [A] resolution from Thalassiosira pseudonana under high light conditions. 8 Lhcr FCPIs are found detached from the PSI-13FCPI supercomplex under high light conditions, remaining 5 FCPIs are stably combined with the PSI core including Lhcr3, RedCAP, Lhcq8, Lhcf10, and FCP3 subunits. The specific pigment network in this centric diatom T. pseudonana demonstrates a higher proportion of Chlorophylls a, diadinoxanthins, and diatoxanthins but fewer fucoxanthins compared with the huge PSI-FCPI from another centric diatom Chaetoceros gracilis, thus exhibiting more efficiency in energy transfer and dissipation among FCPI antennas. These results reveal the assembly mechanism of several types of peripheral FCPIs and corresponding light-adaptive strategies in T. pseudonana, as well as the convergent evolution of the diatoms PSI-FCPI structures.

plant biology↗

bioRxiv2024

Three pollen QTLs are sufficient to partially break stylar unilateral incompatibility of Solanum pennellii

[bullet] In tomato clade, both self-incompatibility(S-) locus-dependent and -independent mechanisms are present in unilateral incompatibility (UI). Several stylar UI factors mediating S-locus-independent mechanism have been gradually uncovered, however, related pollen UI (pui) factors still await more studies. [bullet]Quantitative trait loci (QTL) mapping, comparative transcriptomics and introgression lines (ILs) /inbred backcross lines (BILs)-based functional analysis were applied for identification and functional validation of pui QTLs between self-compatible (SC) Solanum lycopersicum and SC S. pennellii LA0716. [bullet]In addition to the reported pui10.1 (SpFPS2), two pui QTLs (pui6.2 and pui12.1) were identified. Pollen tubes of cultivated tomatoes introgressed with three pui loci could partially break the stylar UI response in LA0716 styles. Furthermore, a conserved function of pui12.1 was found in the styles of SC S. habrochaites LA0407 and SC S. chmielewskii LA1028. Three candidate genes linked to pui6.2 and pui12.1 were screened for further analysis. [bullet]This study reveals a potential synergistic relationship of the three pui QTLs in breaking stylar UI response of LA0716 and will advance our understanding of the genetic mechanisms underlying UI in the tomato clade. HighlightOur data revealed that breaking the stylar unilateral incompatibility of Solanum pennellii LA0716 requires not only the reported pollen UI (pui) factor but also another two pui QTLs identified in this study.

plant biology↗

bioRxiv2024

PIGOME: An Integrated and Comprehensive Multi-omics Database for Pig Functional Genomics Studies

In addition to being a major source of animal protein, pigs are important model for the study of development and diseases in humans. During the past two decades, thousands of high-throughput sequencing studies in pigs have been performed using a variety of tissues from different breeds and developmental stages. However, the multi-omics database specifically used for pig functional genomic research is still limited. Here, we present a user-friendly database of pig multi-omics named PIGOME. PIGOME contains seven types of pig omics datasets, including whole-genome sequencing, RNA-seq, miRNA-seq, ChIP-seq, ATAC-seq, bisulfite-seq, and MeRIP-seq, from 6,901 samples and 392 projects with manually curated metadata, integrated gene annotation, and quantitative trait locus information. Furthermore, various explore and browse functions have been established for user-friendly access to omics information. PIGOME implemented several tools to visualize genomic variants, gene expression, and epigenetic signals of a given gene in the pig genome, enabling efficient exploration of spatial-temporal expression/epigenetic pattern, function, regulatory mechanism, and associated economic traits. Collectively, PIGOME provides valuable resources for pig breeding and is helpful for human biomedical research. PIGOME is available at https://pigome.com.

bioinformatics↗