Biology subjects

Zhang, N.

Publications and source records attributed to Zhang, N..

At least 55 records · Page 3Linked to original sources

bioRxiv2026

Independent Trafficking and Diverse Stability of XyG-Synthesizing Glycosyltransferases in Distinct Golgi cisternae

XyG-synthesizing glycosyltransferases (GTs) are localized in Golgi, and their protein-protein interactions suggest the formation of multiprotein complexes; however, the mechanisms underlying protein complex assembly and transportation, protein stability and degradation remain unknown. We have uncovered that protein-protein interactions among XyG-synthesizing GTs are not prerequisites for Golgi localization and different GTs are first delivered to Golgi as independent proteins. By employing the transient expression of YFP-fused GTs along with a cis-Golgi marker and generating fluorescence intensity profiles, we demonstrated the differential distribution of GTs in Golgi apparatus. We treated Arabidopsis seedlings expressing GTs with cycloheximide (CHX) to estimate half-lives, The GTs exhibit distinct half-lives, and based on their turnover rates, divided into two groups. Our findings revealed that cellulose synthase-like C4 (CSLC4), galactosyltransferase (MUR3), and fucosyltransferase (FUT1) exhibit longer stability. In contrast, XyG xylosyltransferases XXT1, XXT2, XXT5, and galactosyltransferase XLT2 are significantly shorter-living proteins. XyG-synthesizing proteins traffic independently to Golgi, exhibiting distinct sub-Golgi localization that shapes multiprotein complex assembly in specific cisternae. This spatial organization governs partner GT access and residence time for functional efficiency, while GT half-life variations regulate stability and interaction dynamics. Collectively, these factors provide a critical framework for independent operation and coordinated organization of Golgi-resident XyG-synthesizing proteins. HighlightGlycosyltransferase traffic independently to the Golgi, exhibit distinct sub-Golgi localization and variable half-lives that reveal the mechanism of protein interactions, stability, and assembly of multiprotein complexes for stepwise synthesis.

plant biology↗

bioRxiv2026

FoTO1 is an epoxide isomerase in paclitaxel biosynthesis

Paclitaxel biosynthesis is limited by the instability of taxadiene-4(5)-epoxide, which readily diverts to the non-productive byproduct 5(12)-oxa-3(11)-cyclotaxane (OCT) instead of rearranging to taxadiene-5-ol. Although FoTO1 suppresses OCT accumulation, its molecular function has been unclear. Here we identify FoTO1 as a dedicated epoxide isomerase that directs productive rearrangement. Biochemical characterization, site-directed mutagenesis, and QM/MM calculations reveal a pre-organized D68-D149 dyad that electrostatically activates epoxide ring opening and stereospecific rearrangement. Modular dissection of the C-terminal extension further reveals a functional partition between catalytic integrity and productive coupling with T5OH, mediated by specific hydrophobic contacts that enforce precise geometric complementarity at the binary complex interface. These results demonstrate how electrostatic activation and enzyme association cooperate to control the fate of a highly reactive intermediate in paclitaxel biosynthesis.

biochemistry↗

bioRxiv2026

Bacterial endosymbionts enhance fungal virulence by disrupting the disease-suppressive rhizobiome

The mechanisms by which bacterial endosymbionts (bacteria living within fungal cells) enhance the fitness and virulence of fungal pathogens remain poorly understood. Here, we report that the tomato Fusarium wilt pathogen Fusarium oxysporum f. sp. lycopersici (FOL) hosts Achromobacter sp. endosymbionts that enhance fungal virulence. This virulence potentiation is partially dependent on interactions with the native rhizosphere microbiota. We show that bacterial endosymbiont-harboring FOL reshapes the rhizosphere bacterial community during pathogen infection and decreased the abundance of disease{square}suppressive bacteria, including Streptomyces sp. taxa. This inhibitory effect is mediated by bacterial endosymbiont{square}stimulated production of beauvericin (an antibacterial cyclic hexadepsipeptide) by FOL. Together, our findings reveal a tripartite interaction in which a fungal pathogen leverages its bacterial endosymbiont to weaken rhizosphere microbiome{square}based disease suppression by inhibiting plant-protective bacterial taxa. This work highlights how cross{square}kingdom symbioses can modulate pathogen ecology and virulence in soil environments.

microbiology↗

bioRxiv2026

pertTF: context-aware AI modeling for genome-scale and cross-system perturbation prediction

Predicting genetic perturbation responses at a single-cell level is central to building models for cell state and disease. However, existing approaches are limited on predicting phenotypic outcomes beyond expression changes and generalizing predictions across genome-scale perturbations in biologically relevant contexts. Here we introduce pertTF, a transformer-based single-cell genetic perturbation model. pertTF was trained from a unique dataset capturing single cell expressions profiles of 30 full gene knockouts across 14 relevant cell types during human pancreatic development and beta-cell differentiation. pertTF outperforms current methods in predicting expression changes of perturbing unseen genes in unseen cellular contexts. In addition, pertTF infers perturbation-induced shifts in cell identity and population composition, an important phenotypic outcome of perturbation in many physiology and disease settings. Through transfer learning, pertTF operates in physiologically relevant systems, including primary human islets, where large-scale perturbation experiments are challenging. The generalizability of pertTF is further demonstrated by in silico pooled and single-cell CRISPR screens, capturing critical regulators of stem cells and early pancreatic cell development. These results establish pertTF as a framework for integrating large-scale single-cell perturbation data with AI models to predict genetic perturbation effects across cellular systems and disease contexts.

bioinformatics↗

bioRxiv2026

The Meatball Matchup: Plant vs. Animal Proteins on Campus

Institutional dining halls increasingly serve plant-based meat products, yet it remains unclear how consumers perceive these products relative to animal-based options in real-world settings. This study compares consumer sensory perceptions of two plant-based meatballs (soy, soy-wheat) and two animal-based meatballs (beef, beef-mushroom) among university dining hall patrons (n = 116), complemented by instrumental Texture Profile Analysis. Animal-based meatballs received significantly higher ratings for moistness, meatiness, fattiness, and tastiness (all p < 0.001), with the meatiness gap being the largest ({Delta} = 1.40 on a 5-point scale). Texture analysis revealed that animal-based samples were significantly harder, more cohesive, and chewier than plant-based samples. In contrast, consumers perceived no differences in chewiness or hardness between categories, revealing a disconnect between instrumental and sensory measures. Just-About-Right penalty analysis identified insufficient savoriness as a universal improvement target across all products, including beef. Flavor and texture emerged as the dominant drivers of dining choice, while sustainability and animal welfare ranked lowest in importance. These findings suggest that sensory parity--particularly in moistness, meatiness, and savoriness--may drive acceptance of plant-based meat more strongly than sustainability messaging. Data and code are available at https://github.com/LivingMatterLab/AI4Food

bioengineering↗

bioRxiv2026

Multiscale confidence quantification for virtual spatial transcriptomics with UTOPIA

Virtual spatial transcriptomics (ST) methods predict gene expression or cell types from histology images, extending molecular readouts beyond the limited regions or samples directly measured by ST platforms. However, the statistical reliability of these predictions remains unclear. Here, we present UTOPIA, a model-agnostic framework for multiscale confidence quantification in virtual ST. UTOPIA assigns statistically calibrated confidence scores to predictions across spatial resolutions and biological granularities, ranging from single genes to metagenes and from specific cell types to broader cell classes. UTOPIA controls false discovery rates for detecting genes, metagenes, or cell types while accounting for local tissue context. We show that prediction confidence depends critically on both spatial resolution and biological granularity, with reliable inference often emerging only at coarser, biologically meaningful scales. Across multiple ST platforms and in both in-sample and out-of-sample settings, UTOPIA enhances interpretability, prevents false biological conclusions, and enables more trustworthy downstream analyses of virtual ST.

genomics↗

bioRxiv2026

Distributed neural signatures of discomfort induced by transcranial magnetic stimulation

Transcranial magnetic stimulation (TMS) is a cornerstone tool for causal inference in human brain function and an increasingly used neuromodulation therapy, yet it induces well-recognized discomfort that may systematically bias measured outcomes. Despite its ubiquity, a critical gap remains in understanding how TMS-induced discomfort is represented across the brain and to what extent it contributes to TMS-evoked neural responses. Using concurrent TMS-fMRI across 11 cortical targets, we collected an unprecedented dataset (165 participants; 1,535 runs) spanning healthy participants and those with elevated affective symptoms. Cross-validated multivariate modeling revealed that TMS-induced discomfort engages distributed cortical and subcortical regions across sensorimotor, attentional, default mode, and limbic networks, with both shared and group-specific patterns. Discomfort-related activity accounted for approximately 12% and 25% of TMS-evoked responses in healthy and elevated-symptom groups, respectively, and varied systematically across stimulating sites. These findings identify TMS-induced discomfort as a substantial and previously under-characterized component of TMS-evoked neural responses, underscoring the need to explicitly measure and model it. By providing a whole-brain map of regional contributions associated with TMS-induced discomfort and an analytic framework to dissociate direct neuromodulatory effects from discomfort-related responses, this work improves the interpretability of TMS-evoked signals and supports more rigorous causal inference and therapeutic applications.

neuroscience↗

bioRxiv2026

Metabolic exchange and siderophore sharing underlie emergent biofilm synergism

Biofilm communities exhibit emergent properties that exceed the sum of contributions from individual members of the community. Here, we describe a multilayered metabolic interaction that drives enhanced biofilm formation among three bacterial species from the plant rhizosphere. Comparative metatranscriptomic and metabolomic analyses reveal that Bacillus velezensis-secreted 5-aminovaleric acid promotes the growth of the other community members, Burkholderia contaminans and Acinetobacter baumannii. In return, B. contaminans supplies branched-chain amino acids for B. velezensis. Branched-chain amino acids and cell-cell signaling acyl-homoserine lactones from B. contaminans induce biosynthesis of the siderophore bacillibactin in B. velezensis, that is further enhanced by A. baumannii. In exchange, the B. velezensis-secreted siderophore promotes the growth of B. contaminans in iron-limited conditions, which benefits the multispecies biofilm community in vitro and promotes plant growth performance in iron-depleted soil. Our study reveals the molecular mechanisms underlying an emergent rhizosphere biofilm community function and demonstrates its importance in plant-microbe interactions.

microbiology↗

bioRxiv2026

Experimental Time Points Guided Transcriptomic Velocity Inference

Time-series single-cell RNA sequencing enables longitudinal tracking of biological processes, yet cellular trajectory reconstruction informed by experimental time remains challenging. Existing trajectory inference methods either perform de novo reconstruction without leveraging experimental time points, or prioritize transitions between time points while paying less attention to intra-time-point dynamics. To reconcile experimental time points with local precision, we present CellDyc, a semi-supervised learning framework that leverages experimental time-point supervision to reconstruct transcriptomic velocities and recover an intrinsic gene-embedded time. CellDyc consistently outperforms existing approaches in reconstructing cellular trajectories across development, disease, and reprogramming contexts. Biologically, CellDyc provides novel insights, such as resolving temporal heterogeneity in erythroid maturation and quantitatively demonstrating that the immunosuppressive environment delays monocyte differentiation in glioblastoma. CellDyc integrates seamlessly with downstream tools like CellRank and remains robust even when only inferred temporal information is available. Collectively, CellDyc offers a rigorous, data-driven solution for deciphering time-resolved cellular dynamics.

bioinformatics↗

bioRxiv2026

Unwinding of RNA G-quadruplexes induces mouse and human totipotency

Totipotent stem cells (TotiSCs) have significant application prospects in regenerative medicine and assisted reproductive technologies. The mRNAs of totipotency-related genes are rich in G-quadruplex (G4) structures, while the G4 density of pluripotency-related genes mRNAs is relatively low, suggesting a potential functional link between RNA G4s and the totipotent state. Nevertheless, how G4s are involved in the establishment or maintenance of mouse and human totipotency remains poorly understood. Here, we demonstrate that FC3, a small-molecule RNA G4 unwinder, enables efficient induction and maintenance of mouse and human TotiSCs (mG4TotiSCs and hG4TotiSCs). These FC3-induced TotiSCs closely recapitulate the molecular features of 2-cell-stage blastomeres via transcriptomic and epigenomic profiling. Functionally, both mG4TotiSCs and hG4TotiSCs exhibit totipotent capacity: they differentiate into embryonic and extraembryonic lineages in vitro and in chimeric embryos; moreover, they autonomously self-organize into blastocyst-like structures without exogenous signalling. Mechanistically, we identify that Gata2 mRNA, a G4-containing transcript, is essential for FC3-mediated reprogramming. Genetic disruption of Gata2 would abolish totipotency induction. Collectively, RNA G4 unwinding is a new regulatory axis governing totipotency acquisition and maintenance, providing insight into the functional interplay between nucleic acid secondary structures and cell fate plasticity.

cell biology↗

bioRxiv2026

Microbubble-Enhanced Focused Ultrasound Improves Targeted Adeno-Associated Virus Delivery in Brain Tumors Quantified by PET Imaging

Gene therapy using adeno-associated virus (AAV) vectors shows promise for cancer treatment through molecular intervention, yet achieving sufficient and targeted delivery to brain tumors via systemic administration remains limited by the biological barriers. Here, we investigate whether microbubble-enhanced focused ultrasound (MB-FUS) improves targeted delivery of systemically administered AAV9 to orthotopic gliomas, using quantitative PET imaging of 64Cu-radiolabeled AAV9 vectors and fluorescent reporter expression to assess biodistribution and functional efficacy. At 21 hours after injection, 64Cu-AAV9 accumulation was 3.2-fold higher in FUS-treated tumors compared to non-FUS-treated tumors (n=3, p=0.004). Quantitative PCR analysis of tumor tissue at the same timepoint confirmed a 6.4-fold increase in genome copies in FUS-treated tumors (p=0.0003). The enhanced vector delivery translated to a 5.3-fold increase in optical reporter protein expression in FUS-treated compared to control tumors (p=0.0002) at 17 days post-treatment. These results establish that MB-FUS enables spatially-targeted AAV delivery with quantifiable enhancement in both acute vector biodistribution and downstream transgene expression. The integration of radiolabeled AAV with PET imaging provides a non-invasive methodology for real-time assessment of vector delivery and optimization of treatment protocol for brain cancer gene therapy. HighlightsO_LIMB-FUS enables targeted systemic AAV delivery to brain tumors. C_LIO_LIMB-FUS enhanced vector delivery translates to increased transgene expression in gliomas. C_LIO_LIPET imaging of radiolabeled AAV allows non-invasive tracking of gene therapy vectors. C_LIO_LIReal-time imaging validates spatially-controlled gene delivery for brain cancer. C_LI

bioengineering↗

bioRxiv2026

The genetic repertoire of the deep sea: from sequence to structure and function

The deep sea as the largest and maybe most hostile environment on Earth is still underexplored especially regarding its genetic repertoire. Yet, previous work has revealed significant habitat-specific deep-sea biodiversity. Here, we present an integrated deep-sea genetic dataset comprising 502 million nonredundant genes from 2,138 samples and 2.4 million predicted structures, and used it to link specific protein structures with genetic variants associated with life in the deep sea and to assess their biotechnology potential. Combining global sequence analysis with biophysical and biochemical measurements revealed unprecedented sequence diversity, yet substantial structural conservation of proteins. Especially proteins involved in replication, recombination, and repair were identified to be under rapid evolution and with specialized properties. Among these, a structurally divergent helicase exhibited advantages in controlling nanopore sequencing speed. Thus, our work positions the deep sea as a unique evolutionary engine that generates and hosts genetic diversity and bridges genetic knowledge with biotechnology.

bioinformatics↗

bioRxiv2026

Ultrasound-Mediated Gene Therapy in Alzheimer's Disease Validated through In Vivo PET Imaging

Efficient, spatially selective delivery of adeno-associated virus (AAV) therapeutics to deep brain structures remains a major challenge to gene therapy for Alzheimers disease (AD), owing to limited transport across the blood-brain barrier (BBB) and poor penetration to target neurons. Here, we establish an integrated, noninvasive imaging and therapy platform that combines microbubble-enhanced focused ultrasound (MB-FUS) with positron emission tomography/computed tomography (PET/CT) to transiently modulate the BBB, enhance region-specific AAV delivery following systemic dosing, and longitudinally track transduction in vivo. Optimized MB-FUS achieved targeted hippocampal delivery of systemically administered AAV9 in healthy mice, resulting in a 10-fold enhancement of neuronal transduction as compared to non-FUS controls. Importantly, longitudinal PET reporter gene imaging in the 5xFAD AD model demonstrated robust brain AAV transduction that remained stable for at least seven months. Finally, to assess therapeutic impact, we used brain-derived neurotrophic factor (BDNF) as a test cargo. MB-FUS-facilitated delivery elevated BDNF expression in targeted regions and produced short-term improvements in synaptic signaling in 5xFAD mice. Collectively, these results highlight MB-FUS as a next-generation delivery platform to overcome barriers to AAV therapeutic delivery in Alzheimers disease and position longitudinal PET assessment as a critical, translatable tool for monitoring and optimizing gene therapy.

bioengineering↗

bioRxiv2026

Mechanical, rheological, and sensory characterization of lion's mane mushroom steak

Mushrooms are increasingly recognized as delicious, nutritious, and sustainable foods, with an intrinsic umami flavor and fibrous microstructure that can approximate meat-like texture. Among them, lions mane mushroom has emerged as a promising candidate for whole-cut meat alternatives. Yet, its mechanical, rheological, and sensory properties remain largely unquantified. Here we show that a minimally processed lions mane mushroom steak exhibits distinctive mechanical, rheological, and sensory characteristics that position it favorably among existing meat alternatives. Despite its pronounced fibrous morphology, lions mane steak behaves predominantly as an isotropic material under both mechanical loading and rheological testing, with elastic stiffnesses of E = 33.2 kPa and E = 34.8 kPa in-plane and cross-plane. A fundamental challenge in alternative protein development is to understand how these measurable physical properties relate to human texture perception. In a complementary sensory survey, n = 21 participants ranked lions mane steak as more fatty, fibrous, moist, and meaty than eight animal- and plant-based comparison meats. Strikingly, our perceived sensory softness correlates inversely with our experimentally measured mechanical stiffness ({tau}=-0.60, p = 0.02) and rheological loss modulus ({tau}=-0.56, p = 0.03). Taken together, our results demonstrate that lions mane steak combines favorable mechanical performance with desirable sensory attributes and provide a mechanistic link between physics and taste. Our findings highlight lions mane mushroom as a compelling whole-cut alternative protein and underscore the value of integrated mechanical-sensory characterization for rational food design.

bioengineering↗

bioRxiv2026

Curcumin Promotes Myelin Repair after Spinal Cord Injury via Spatially Selective Regulation of CLASP2 Phosphorylation

Spinal cord injury (SCI) remains a devastating neurological disorder, where limited axonal regeneration and inefficient remyelination severely restrict recovery. Although curcumin has recognized neuroprotective properties, its mechanism in myelin repair is unclear. Here, we identify a phosphorylation-dependent cytoskeletal pathway as a key target of curcumin. In a mouse spinal cord transection model, curcumin treatment improved hindlimb motor function, reduced fibrotic scarring, and increased myelin basic protein (MBP) in the injured region. Phosphoproteomic profiling revealed cytoskeletal regulation as a major process affected by curcumin, with CLASP2 emerging as a critical target. Curcumin enhanced CLASP2 phosphorylation at Ser1025, a modification that strengthened Golgi association and increased EB1 distribution at the cell periphery, thereby promoting microtubule anchoring without altering global stability. This spatially selective regulation provides a novel mechanism by which curcumin fine-tunes cytoskeletal organization to support remyelination. Analysis of published single-cell sequencing data further showed CLASP2 enrichment in myelin-forming cells, underscoring its relevance. Unlike prior studies emphasizing anti-inflammatory or antioxidant effects, our findings reveal a defined molecular mechanism linking curcumin to cytoskeletal remodeling and myelin repair, highlighting its potential as a safe and accessible therapeutic candidate for SCI.

cell biology↗

bioRxiv2026

Chromatin context-dependent deacetylation by the asymmetric Rpd3L

The regulation of gene expression requires precise control of chromatin-associated complexes that respond to diverse structural and epigenetic cues. The Rpd3 Large (Rpd3L) complex is a Sin3 histone deacetylase (HDAC) complex that dynamically adapt to chromatin states to reinforce transcriptional silencing, yet the mechanisms governing the catalytic activation in chromatin context-dependent manner remain unclear. Here we present the cryo-EM structure of Rpd3L bound to both mono- and di-nucleosome substrate at near-atomic resolution, uncovering a substrate-guided allosteric activation mechanism. Rpd3L adopts an asymmetric architecture, in which the proximal catalytic module anchors the first nucleosome, while the Sin3 PAH domains engage linker DNA to reposition a second nucleosome. This spatial configuration brings the distal catalytic module into proximity with chromatin and unlocks its latent deacetylase activity. Biochemical and mass spectrometry analyses confirm that dual nucleosome engagement selectively enhances Rpd3L activity and broadens substrate specificity. Together, these findings establish a hierarchical mechanism by which Rpd3L interprets histone modifications and nucleosome organization to modulate its enzymatic output at promoter regions. Our study provides a framework for understanding higher-order chromatin repression mechanisms by chromatin-regulation complexes and co-repressors.

molecular biology↗

bioRxiv2026

CELLWHISPER: INFERENCE OF DIRECT CELL-CELL COMMUNICATION FROM SPATIAL TRANSCRIPTOMICS

AbstractDirect, contact-dependent cell-cell communication shapes tissue physiology and disease. Spatial transcriptomics offers a unique opportunity to infer such communication mechanisms, but the few existing tools for such inference are prone to high error rates due to spatial structure in distribution of cell types and gene expression. We present CellWHISPER, a statistical framework for inferring contact-mediated cell-cell communication, including gap junctions and ligand-receptor mechanisms, from single-cell resolution spatial data. CellWHISPER achieves strict error control via a specialized hypothesis-testing procedure that accounts for the confounding effects of cell- type-specific expression and spatial organization. Its use of an exact closed-form significance score obviates expensive permutation testing and enables scalable analysis of large tissues an extensive signaling compendia. To uncover salient communication patterns, CellWHISPER also includes a latent variable model that distills recurrent patterns into maps of mutual preferences among cell types and signaling genes. Applied to mouse brain STEREO-seq and Xenium datasets, CellWHISPER identifies cell type-specific gap-junction coupling and yields a comprehensive connexin-interaction map. We experimentally confirmed Connexin 43-mediated interfaces among astrocytes, microglia and endothelial cells, which were among the highest- ranked predictions; in contrast, existing approaches fail to prioritize these confirmed interactions. Differential analysis of an Alzheimers disease model versus wild-type identifies preserved astroglial coupling but increased microglia-associated gap-junction communication. In summary, CellWHISPER disentangles direct cell-cell communication from structural proximity, enabling statistically robust and computationally scalable inference from spatial transcriptomics, leading to the discovery of tissue- and disease-associated contact-mediated signaling programs.

bioinformatics↗

bioRxiv2026

Context-Dependent Motor Feedback Underlies Choice-Related signals in Visual Cortex

Choice-related neural activity, reflecting trial-by-trial correlation with subjects perceptual choice, is commonly observed in sensory cortices and has been implied in sensory readout. Recent studies suggest an alternative source from motor-reporting, yet its precise nature remain elusive due to limitations in conventional experimental paradigms. Here we quantitatively identified motor component by training macaques to discriminate visual motion directions via making saccade to spatial-independent, colored choice targets appeared under two contexts: at stimulus onset, or after its offset. Neural recordings in visual areas MT/MST revealed a dominant motor-related choice signal when the saccade goal was known in advance; this signal vanished with delayed target onset. By comparing with downstream sensory-motor transformation areas and employing a recurrent network model, we demonstrated that this motor component reflected feedback. Our work clarifies that a major portion of "decision" activity in sensory neurons is attributable to motor-reporting processes, highlighting the profound influence of behavioral context.

neuroscience↗