Biology subjects

Zhang, Z.

Publications and source records attributed to Zhang, Z..

At least 415 records · Page 23Linked to original sources

bioRxiv2025

Graph pangenome reveals structural variation dynamics during cucumber breeding

Structural variants (SVs) represent a significant yet underexplored component of plant genome diversity. Analyzing SV dynamics is important for understanding their contributions to phenotypic variation and their influence on genome evolution. Here, we present a graph-based pangenome for cucumber, constructed from 39 reference-level genome assemblies. The pangenome captures 171,892 high-confidence SVs and enables genotyping of these SVs across 443 cucumber accessions, representing diverse geographic origins and spanning wild progenitors, landraces, and modern cultivars. Our analyses reveal that during cucumber domestication, a substantial portion of mildly deleterious SNPs are retained, whereas SVs are consistently purged, highlighting their potentially highly deleterious nature. During the geographic expansion of cucumber, a reduction in SV burden and a younger age of SVs than SNPs were observed, suggesting stronger purifying selection acting on SVs. Additionally, notable gene flow from wild population to African and European populations was detected, resulting in an increased SV burden, potentially due to hitchhiking effects. Importantly, incorporating SV burden into genomic prediction models improved the prediction accuracy for several agronomically important traits. This study illuminates the dynamics of SVs during cucumber domestication and improvement, highlights the complex interplay between SVs and selection pressures, and underscores the extensive implications of SVs for future cucumber breeding.

plant biology↗

bioRxiv2025

A T-cell Intrinsic Role for APOL1 Risk Alleles in Allograft Rejection

African Americans have an increased risk of kidney disease due to exonic variants in Apolipoprotein-L1 (G1 and G2). These prevalent variants have also been linked with kidney rejection, but outside of association with African ancestry, underpinning causal mechanisms are unknown. We investigated T-cell function using transgenic mice with physiologic expression of wild type (G0-), G1-, or G2-APOL1. Mice with variant APOL1 showed greater CD8+T-cell activation with expansion of a central memory (TCM) subset. Stimulated G1-CD8+T-cells showed enhanced proliferation and cytokine production, which reversed with APOL1 inhibition. In MHC-mismatched cardiac transplants, G1-mice demonstrated greater CD8+T-cell infiltration and reduced survival. Bulk transcriptome of G1-CD8+T-cells, and single-cell transcriptome of graft infiltrating TCMs, showed enrichment of canonical T-cell receptor (TCR) pathways including Ca2+-signaling. G1-CD8+T-cells demonstrated baseline ER-Ca2+ depletion followed by sustained increases in cytosolic-Ca2+ upon TCR stimulation. G1-CD8+T-cells were more sensitive to Ca2+ chelation, or store-operated Ca2+ entry inhibition, and relatively resistant to calcineurin antagonism vs. G0-CD8+T-cells. Analogously, in a kidney transplant cohort, APOL1-variant recipients developed rejection when they had elevated peripheral TCMs before transplantation and despite significantly higher tacrolimus levels vs G0/G0-AAs with rejection. In summary, we unravel an excitatory T-cell intrinsic mechanism for APOL1 exonic variants, causally linking them with kidney rejection.

immunology↗

bioRxiv2025

AtlasAgent: Vision language model and Agent-guided Framework for Evaluation of Atlas-scale Single-cell Integration

As single-cell omics transitions into the era of AI-virtual cells (AIVC), where large-scale single-cell data integration becomes prevalent, the computational demands of integration evaluation emerge as critical scalability bottlenecks. Traditional integration evaluation pipelines, requiring metrics like k-nearest-neighbor batch effect test (kBET) and Local Inverse Simpsons Index (iLISI) employed by state-of-the-art scIB method, often demand large computational resources and long runtimes, making them infeasible for large scale integration studies. Herein, we present AtlasAgent, the first vision-language model (VLM)-powered and AI agent framework to accelerate atlas-scale integration evaluation at unprecedented speed and scale. We systematically evaluate batch correction quality, biological signal preservation and overcorrection risks using chain-of-thought reasoning in conjunction with few-shot and zero-shot prompting strategies. AtlasAgent completes evaluation within 32 seconds, in contrast to scIBs runtime of 5.55 hours in GPU, while identifying the scIB-determint best integration methods within the top-3 in 88.3% of the time, lowering evaluation time from hours to seconds while preserving alignment with domain expert reasoning. AtlasAgent pioneers the use of VLMs to realize scalable and rapid integration evaluation at atlas scale.

bioinformatics↗

bioRxiv2025

Correlated protein-RNA associations reveal a requirement for HNRNPU in long-range Polycomb recruitment by the lncRNAs Airn, Kcnq1ot1, and Xist

The lncRNAs Airn and Kcnq1ot1 recruit Polycomb Repressive Complexes (PRCs) and repress genes over multi-megabase genomic intervals, but how they interact with proteins to direct repression remains poorly understood. We conducted formaldehyde-linked RNA-immunoprecipitations of 27 proteins from trophoblast stem cells, using a protocol exhibiting similar signal-to-noise and post-lysis reassociation ratios as CLIP and CLAP. Patterns of protein associations across Airn and Kcnq1ot1 were more similar to each other than to nearly all other transcripts and partitioned to extents that mirrored degree of repression each lncRNA induced, implying connections to mechanism. Indeed, HNRNPU, an essential protein that helps Xist localize to chromatin, was enriched within and required to direct PRC-catalyzed modifications by Airn and Kcnq1ot1, without being required for their localization. Our study provides insights into the role of HNRNPU in lncRNA-mediated gene regulation and reports architectures of protein association across Airn and Kcnq1ot1 relative to the transcriptome at large. Author summaryMammalian genomes express thousands of long noncoding RNAs (lncRNAs). While most remain functionally uncharacterized, a handful are known to regulate genes via epigenetic pathways. Whether or not these known regulatory lncRNAs operate through shared or divergent mechanisms remains unclear. To gain insight, we compared RNA-protein associations across three known regulatory lncRNAs -- Airn, Kcnq1ot1, and Xist -- relative to the broader transcriptome, using a protocol to immunoprecipitate RNA from formaldehyde-crosslinked cells. Benchmarking of our RNA-immunoprecipitation protocol against methods called CLIP and CLAP revealed similar results and complementary strengths among methods. We discovered similarities in RNA-protein associations between Airn and Kcnq1ot1 that nominated them as mechanistically important. One such protein, HNRNPU, was required for Airn and Kcnq1ot1 to coordinate long-range recruitment of Polycomb complexes, without giving the appearance of being required to tether either lncRNA to chromatin, as HNRNPU has been proposed to do for Xist. Our study identifies RNA-protein associations that correlate with long-range gene regulation by lncRNAs and provides new perspectives on the potential mechanisms through which HNRNPU participates in lncRNA-mediated epigenetic control. We also benchmark a protocol to recover RNA-protein interactions that is simple to execute and has complementary strengths relative to other methods.

molecular biology↗

bioRxiv2025

Fully Automated and Scalable Pipeline for Macaque Brain Registration

With the rapid development of various whole-brain ex vivo imaging technologies, there is a growing need to develop cross-modal 3D image registration methods to integrate multimodal imaging datasets. While comprehensive cross-modality registration tools such as D-LMBmap and mBrainAligner have been successfully implemented for mouse brains, macaque whole-brain registration presents unique challenges. These include more pronounced non-uniform deformations in larger ex vivo specimens, greater modality-specific contrast differences relative to standard space, and increased inter-individual variability. To address these challenges, we developed Macaca-Star, which incorporates deep learning models and self-individual MRI to tackle cross-modal and ex vivo sample deformation challenges in macaque whole-brain registration. Macaca-Star provides fully automated alignment of fMOST and 2D fluorescent slice images to the NMT MRI standard space, allowing for comprehensive integration of anterograde axonal projections and retrograde-traced neuronal soma profiles.

neuroscience↗

bioRxiv2025

Tracking breast cancer progression using Methylscape

Cancer progression is intricately driven by epigenetic reprogramming, where aberrant DNA methylation patterns reshape gene regulation and cellular phenotypes. These alterations include promoter hypermethylation of tumour suppressor genes and global hypomethylation, collectively fuelling oncogenesis and disease advancement. We previously introduced the Methylscape--a distinct cancer-specific DNA methylation landscape characterized by clustered promoter hypermethylation and gene body hypomethylation--that enhances DNAs physical affinity for gold surfaces. In this study, we demonstrate that Methylscape can be leveraged to monitor cancer progression. Using a breast cancer epithelial-mesenchymal transition (EMT) model, we observe an increase in Methylscape enrichment of mesenchymal-state DNA during EMT, suggesting that this method can sensitively detect subtle epigenetic remodelling linked to tumour progression. Using a gold-based DNA desorption enrichment strategy coupled with methylation sequencing and qPCR, we show that hypermethylated regions are preferentially enriched. Finally, we developed a low-cost, disposable screen-printed electrode platform for stage-specific breast cancer monitoring. Together, these findings establish Methylscape as a promising biophysical biomarker for non-invasive and real-time monitoring of cancer progression, advancing its potential for clinical translation.

bioengineering↗

bioRxiv2025

CNA detection from spatial transcriptomics using SpaCNA

Spatial transcriptomics (ST) enables genome-wide profiling of gene expression while preserving spatial context, yet accurate detection of copy number alterations (CNAs) in tumor ST data remain challenging. Here we present SpaCNA, a spatial-aware computational framework that integrates multi-modal spatial information to improve CNA detection. SpaCNA constructs adjacency graphs using spatial proximity and H&E stained image similarity, refines the raw gene expressions, and implements a Hidden Markov Random Field model for robust CNA state inference. Through extensive benchmarking on simulated data and multi-cancer cohorts, SpaCNA demonstrates superior accuracy and outperforms existing methods in CNA detection and tumor region identification. In real-world applications to breast cancer and colorectal cancer, SpaCNA reveals spatially distinct subclones with context-dependent interactions within the microenvironment. Additionally, applied to a 3D ST dataset of head and neck squamous cell carcinoma, SpaCNA uncovers clone-specific CNAs associated with therapeutic resistance biomarkers across multiple slices. By facilitating precise spatial mapping of CNAs and tumor architecture, SpaCNA significantly enhances our understanding of intratumoral heterogeneity and spatial evolutionary patterns.

bioinformatics↗

bioRxiv2025

An efficient beet severe curly top virus-based VIGS vector in Beta vulgaris

Sugar beet (Beta vulgaris L.) is one of the most important sugar crops worldwide. However, studies on sugar beet gene functions are still lagging compared to other crops due to the lack of an effective genetic manipulation. In this study, we generated an infectious clone of beet sever curly top virus (BSCTV) and engineered it into a VIGS vector. BSCTV-BvPDS can induce strong and persistent bleached PDS-silencing phenotype in 8 tested sugar beet varieties. We further efficiently silenced B. vulgaris MYB1 gene that regulating the betalain pathway in sugar beet by BSCTV-based VIGS system. Finally, we used this system to silence the effector CbNip1 of Cercospora beticola through cross-kingdom RNAi, resulting in reduced disease symptoms in sugar beet plants. Therefore, the BSCTV VIGS system can be used to study sugar beet-pathogen interactions. In summary, we have established an easy and efficiency BSCTV-based VIGS vector in sugar beet. This system will be an attractive tool for functional genomic studies for sugar beet.

plant biology↗

bioRxiv2025

O-GlcNAcylation-Ubiquitin Crosstalk of METTL1 Drives m7G Epitranscriptomic Collapse and Lipid Metabolic Reprogramming in Diabetic Cardiomyopathy

BackgroundMetabolic remodelling and memory in cardiomyocytes is a pivotal mechanism underlying cardiomyopathy pathogenesis. Clinical observations demonstrate persistent progression of hyperglycaemia-induced multiorgan damage following blood glucose stabilization, which is predominantly mediated through epigenetic regulation. While prior studies have identified epigenetic contributions to hyperglycaemic myocardial injury, the involvement of RNA methylation-particularly N7-methylguanosine (m7G) modification-in this regulatory network remains undefined. MethodsClinical specimens were collected from diabetic patients, and cardiomyocyte-specific METTL1 and ob/ob knockout murine models were established in parallel. Multiomic profiling (proteomics, glycoproteomics, ubiquitinomics, m7G-MeRIP sequencing, and metabolomics) was systematically conducted. The molecular mechanisms governing METTL1 regulation via O-GlcNAcylation and ubiquitination were elucidated through integrated in vitro and in vivo assays. A DUB siRNA library and computational strategies combining molecular docking with molecular dynamics simulations were employed for screening drugs targeting METTL1 O-GlcNAcylation, followed by in vivo therapeutic validation. ResultsComparative analysis of diabetic murine and human samples revealed strong METTL1 downregulation in cardiomyopathy contexts. Tamoxifen-inducible METTL1 knockout mice presented exacerbated diabetic cardiomyopathy phenotypes, confirming its cardioprotective function. Multiomic integration demonstrated that METTL1-mediated m7G modification critically regulates cardiomyocyte fatty acid metabolism. Mechanistically, hyperglycaemia was found to induce O-GlcNAcylation at the METTL1-T268 residue, suppressing m7G methyltransferase activity by 38% (p < 0.01). Subsequent investigations revealed that USP5 deubiquitinase activity is impaired under hyperglycaemic conditions, leading to accelerated METTL1 degradation. Notably, administration of the first-in-class small drug HIT106265621 significantly attenuated cardiomyopathy-associated pathological alterations in ob/ob mice in vivo. ConclusionHyperglycaemia promotes METTL1 O-GlcNAcylation, which impedes USP5-mediated deubiquitination, consequently reducing cardiomyocyte METTL1 protein levels and m7G modification. METTL1 deficiency drives diabetic cardiomyopathy progression through fatty acid metabolic dysregulation, inflammatory activation, and myocardial hypertrophy. Pharmacological inhibition of the OGT-METTL1 interaction using HIT106265621 has therapeutic potential for metabolic cardiomyopathy intervention.

pathology↗

bioRxiv2025

GatorST: A Versatile Contrastive Meta-Learning Framework for Spatial Transcriptomic Data Analysis

IntroductionRecent advances in spatial transcriptomics (ST) technologies have revolutionized our understanding of cellular functions by providing gene expression profiles with rich spatial context. Effectively learning spatial representations is crucial for downstream analyses and requires robust integration of spatial information with transcriptomic data. While existing methods have shown promise, they often fail to adequately capture both local (neighbor-level) and global (tissue-wide) spatial contexts. Moreover, they tend to rely heavily on augmentation strategies, which can introduce noise and instability. ObjectivesThis study aims to introduce and demonstrate a novel, versatile framework called GatorST, which explicitly combines graph-based modeling with advanced learning strategies to generate spatially informed representations of ST data. GatorST is designed to improve various downstream tasks, including identification of spatial domains, gene expression imputation, batch effect removal, and trajectory inference. MethodsGatorST constructs a spot-spot graph by connecting each node to its k nearest spatial neighbors and extracts two-hop neighborhood subgraphs to capture local context. At the global level, gene expression profiles are clustered using soft K-means to generate pseudo-labels, which serve as weak supervision signals within a contrastive learning framework. This process encourages the alignment of embeddings with shared pseudo-labels while separating those with different labels. GatorST further adopts an episodic training strategy inspired by meta-learning, wherein each episode consists of a support set for contrastive optimization and a disjoint query set for embedding classification, guided by the pseudo-labeled data. This design enables the model to classify unseen samples based on learned embeddings, thereby enhancing its generalization to new spatial contexts. ResultsComprehensive comparisons with fifteen state-of-the-art methods across fourteen spatial transcriptomics datasets demonstrate that GatorST consistently achieves superior performance in identifying spatial domains, imputing gene expressions, and removing batch effects. The results showcase the versatility and strong generalization capabilities of GatorST across diverse tissue types and experimental settings. ConclusionGatorST effectively integrates spatial topology and global gene expression through graph-based modeling, pseudo-labeling, and contrastive meta-learning. This framework generates biologically meaningful representations and significantly improves key downstream tasks, including spatial domain identification, gene expression imputation, batch effect removal, and trajectory inference.

bioinformatics↗

bioRxiv2025

Bromodomain protein IBD1 bridges histone acetylation and H2A.Z deposition to fine-tune transcription and prevent hyperactivation in Tetrahymena thermophila

Eukaryotic gene expression is dynamically regulated through the interplay between histone modifications and chromatin remodeling, yet how these processes are coordinated remains incompletely understood. Here, we identify IBD1 as a critical adaptor that bridges histone acetylation and SWR-mediated H2A.Z deposition. We demonstrate that the bromodomain of IBD1 recognizes histone acetylation, specifically H3K9/14 di-acetylation to recruit the SWR complex subunit ARP6, ensuring precise H2A.Z incorporation into chromatin. Genetic disruption of IBD1, either by deletion or bromodomain mutation, attenuates H2A.Z occupancy at target loci, confirming its essential role in H2A.Z deposition. Strikingly, perturbation of the histone acetylation-IBD1-H2A.Z axis triggers transcriptional hyperactivation, revealing a dual function of H2A.Z in sustaining basal transcription while preventing aberrant gene induction. This defines a novel regulatory paradigm in which IBD1 couples acetyl-mark decoding to SWR-dependent H2A.Z deposition, establishing transcriptional homeostasis. Our findings resolve a central ambiguity by demonstrating that H2A.Z acts as a repressive buffer in highly acetylated regions, counterbalancing the inherent activation potential of acetylation. This study provides a framework for investigating H2A.Z functions and reveals new perspectives on how chromatin modifications and histone variants interplay in transcriptional regulation.

genetics↗

bioRxiv2025

Thermogenic Adipose ADH5 Counteracts Age-related Metabolic Decline

Aging-associated decline in brown adipose tissue (BAT) function and mass contributes to energy and metabolic homeostasis disruption. Alcohol dehydrogenase 5 (ADH5) is a major denitrosylase that prevents cellular nitro-thiol redox imbalance, an essential feature of aging. However, the functional significance of BAT ADH5 in the context of aging is largely unknown. Here, we aimed to investigate the role of BAT ADH5 in protecting against age-related metabolic dysfunction. We show that aging elevates BAT protein S-nitrosylation modification and downregulates ADH5 in mice. Furthermore, BAT ADH5-deletion accelerates BAT senescence and aging-associated declines in metabolic homeostasis and cognition. Mechanistically, we found that aging inactivates BAT Adh5 by suppressing heat shock factor 1 (HSF1), a well-recognized proteostasis regulator. Moreover, pharmacologically enhancing HSF1 improved age-related BAT senescence, metabolic decline, and cognitive dysfunction. Together, these findings suggest that the BAT HSF1-ADH5 signaling cascade plays a key role in protecting against age-related systemic functional decline. Ultimately, unraveling the role of thermogenic adipose nitrosative signaling will provide novel insights into the interplay between BAT nitric oxide bioactivity and metabolism in the context of aging. HighlightsO_LIAging elevates general protein S-nitrosylation while downregulating ADH5 expression in BAT. C_LIO_LILoss of thermogenic adipose tissue ADH5 accelerates BAT senescence and exacerbates aging-associated metabolic and cognitive dysfunctions. C_LIO_LIDisruption of HSF1-activated Adh5 in BAT contributes to aging-associated metabolic and cognitive impairments. C_LIO_LIPharmacological targeting of BAT HSF1 alleviates aging-related BAT senescent and systemic declines. C_LI

physiology↗

bioRxiv2025

Multiparametric Correlative Topographical and Volumetric Fluorescence Microscopy

Live-cell imaging of cell surface topography and intracellular architecture is essential for understanding cellular function. However, conventional approaches often involve trade-offs between resolution, invasiveness, and volumetric coverage. Here, we present an integrated Scanning Ion Conductance Microscope and single-objective Oblique Plane Microscope (SICM-OPM) system that enables simultaneous non-contact topographical imaging and volumetric fluorescence imaging within the same live cell. Beyond correlative live imaging, the platform supports nanomechanical mapping with tens-of-nanometres resolution, fluorescence-guided localised molecular delivery via the SICM, and benefits from reduced photobleaching due to light-sheet excitation. We demonstrate this platforms capabilities by visualising imipramine-induced T-tubule remodelling in live cardiomyocytes, revealing subsurface detubulation while surface morphology remains preserved. Additionally, we show precision delivery of fluorescent cargos--including dextrans and -synuclein--into diatom and mammalian cells, alongside localised stiffness mapping to evaluate mechanical responses. We believe this technique opens new avenues for correlative structural, functional, and biophysical studies in live cells, with broad relevance to cell biology, neurodegeneration, and mechanobiology.

biophysics↗

bioRxiv2025

Simultaneous epigenomic profiling and regulatory activity measurement using e2MPRA

Cis-regulatory elements (CREs) have a major effect on phenotypes including disease. They are identified in a genome-wide manner by analyzing the binding of transcription factors (TFs), various co-factors and histone modifications in DNA using assays such as ChIP-seq, Cut&Tag and ATAC-seq. However, these assays are descriptive and require high-throughput technologies, such as massively parallel reporter assays (MPRAs), to test the functional activity and variant effect on these sequences. Currently, technologies that can simultaneously analyze both the regulatory function of a specific sequence and the TFs, cofactors and epigenomic modifications that determine it do not exist. Here, we developed enrichment followed by epigenomic profiling MPRA (e2MPRA), a novel technology that utilizes lentivirus-based MPRA to enrich for the integration of specific CREs into the genome followed by Cut&Tag or ATAC-seq targeted specifically for these sequences. This method allows to simultaneously analyze in a high-throughput manner regulatory activity, protein binding and epigenetic modification of thousands of candidate CREs and their variants. We demonstrate that e2MPRA can be used to dissect the epigenetic functions of TF motifs arranged in synthetic enhancers, as well as to analyze the effect of enhancer sequence variants on epigenetic modifications. In summary, this technology will increase our understanding of the regulatory code, its effect on the epigenome and how its alteration can lead to a variety of phenotypes including human disease.

genomics↗

bioRxiv2025

Development of a method for large-scale single-molecule analysis of tau proteoforms

Proteins exist as diverse proteoforms resulting from a combination of genetic variation, alternative splicing, and post-translational modifications. Current methods struggle to capture this complexity at the single-molecule level. Here we introduce Iterative Mapping of Proteoforms (IMaP), a method that enables the massively-parallel interrogation of millions to billions of single-protein molecules through iterative probing with fluorescently labeled antibodies. Using 12 site-specific antibodies, the method is capable of measuring 212 (4,096) potential proteoform groups. We used IMaP to measure proteoform group profiles of the tau protein, a key player in neurodegenerative diseases, using two pan anti-tau antibodies (Tau-13, Tau-216), three isoform-specific antibodies (Anti-0N, Anti-2N, Anti-4R), and seven phosphosite-specific antibodies (Anti-pT181, Anti-pS202+pT205, Anti-pT205, Anti-pS214, Anti-pT217, Anti-pT231, and Anti-pS396). The method demonstrates high sensitivity (detecting proteoforms at 0.1% abundance), high reproducibility (median CV <5.5%), and broad dynamic range (>3 orders of magnitude), outperforming conventional techniques in resolving closely related proteoform groups. We demonstrated that the method can be used on relevant biological samples by examining various neuronal models (iNeuron cells, organoids, MiBrains, and mouse brains) and human samples. This examination revealed 130 distinct tau proteoform groups with as many as six phosphorylation events. The non-random distribution of these phosphorylation events suggests ordered and site-specific modification processes rather than random, stochastic accumulation. Certain combinations of phosphorylation events were more abundant than others; for example, pT217 preferentially co-occurred with pT181. In validating the applicability of the assay to human disease samples, we noted a specific pattern of multiple phosphorylation events in an advanced Alzheimers disease patient that suggests a sequential pathway of pathological tau modification. Iterative Mapping of Proteoforms provides insights into proteoform complexity at the single-molecule level, with significant implications for understanding protein regulation in neurodegenerative diseases and beyond.

biochemistry↗

bioRxiv2025

Competing Programs Shape Cortical Sensorimotor-Association Axis Development

The neocortex is organized along a dominant sensorimotor-to-association (S-A) axis, anchored by modality-specific primary sensorimotor areas at one end and transmodal association areas that form distributed networks supporting abstract cognition at the other. The developmental mechanisms shaping this axis remain elusive. Here, we present converging multispecies evidence supporting the Multinodal Induction-Exclusion in Network Development (MIND) model, in which S-A patterning is governed by competing processes of induction and exclusion, driven by opposing transcriptomically-defined identity programs emerging from different nodes. Key molecular and connectional features of association cortices arise through pericentral programs, originating around fronto-temporal poles and partially regulated by retinoic acid. They progress inward toward central territories of the naive neocortex along fronto-temporally polarized trajectories. Central programs are induced through interactions between topographically separated first-order sensorimotor thalamocortical inputs and the neocortex, promoting the formation of primary areas while excluding pericentral programs. Influenced by SATB2 and ZBTB18, these evolutionarily conserved programs compete for the same territory and create spatial compartmentalization of axon guidance, cell-cell adhesion, retinoic acid signaling, synaptogenesis, Wnt signaling, and autism risk genes. Notably, PLXNC1 and SEMA7A exhibit anti-correlated expression and repulsive functions in shaping cortico-cortical connectivity along the S-A axis. These processes of induction and exclusion establish an S-A equilibrium and topography in which primary sensorimotor areas emerge as focal islands within the broader ocean of distributed associative networks. The MIND model provides a unifying framework for understanding experimental, evolutionary, and clinical phenomena, revealing induction and exclusion as antagonistic complementary principles shaping the S-A axis and processing hierarchies.

neuroscience↗

bioRxiv2025

A Novel 'Three-in-one' Mucosal Vaccine Elicits Broad Protection against Three Distinct Clusters of ACE2-using Sarbecoviruseses

With the persistent risk of coronavirus epidemics, the development of universal vaccines is urgently needed and challenging to achieve. In this study, we aimed to design a multivalent immunogen to provide broad protection against diverse ACE2-using sarbecoviruses, which pose a significant threat to global health. Our analysis revealed that the receptor-binding domains (RBDs) of ACE2-using sarbecoviruses segregate into three antigenically distinct clusters, including one cluster that encompasses viruses related to SARS-CoV-2. Based on these findings, we engineered a three-in-one immunogen, designated as 3Rs-NC, which incorporates representative RBDs from all three clusters. 3Rs-NC preserved the natural epitope configuration of each monomeric RBD component, and efficiently elicited high levels of neutralizing antibodies against representative viruses and closely related sarbecoviruses. When administered intranasally with flagellin-based mucosal adjuvant KFD, 3Rs-NC induced robust and durable RBD-specific serum IgG and mucosal IgA responses in mice. Furthermore, KFD-adjuvanted 3Rs-NC conferred sustained protection in both the upper and lower respiratory tracts against SARS-CoV-2 Omicron BA.1 and SARS-like coronavirus WIV1. Additionally, 3Rs-NC immunization protected mice from lethal challenge of SARS-like coronavirus rRsSHC014S, with more efficient protection observed in female mice than male mice. This needle-free three-in-one vaccine represents a promising candidate for a universal mucosal vaccine against ACE2-using sarbecoviruses and could serve as a foundational component of three-in-one vaccine series to form a comprehensive coronavirus vaccine package. HighlightO_LInovel three-in-one immunogen 3Rs-NC induced a high level of neutralizing antibodies against three distinct ACE2-using Sabecovirus clusters. C_LIO_LIadministration of 3Rs-NC plus KFD adjuvant (3Rs-NC+KFDi.n) generated potent and long-lasting RBD-specific serum IgG and mucosal IgA. C_LIO_LI3Rs-NC+KFDi.n provided long-term protection in both upper- and lower-respiratory tracts in mice. C_LIO_LI3Rs-NC+KFDi.n could serve as a foundational component for next-generation coronavirus vaccine strategies. C_LI

immunology↗

bioRxiv2025

Structures of MmpL complexes reveal the assembly and mechanism of this family of transporters

We co-expressed the MmpL5 transporter and MmpS5 adaptor proteins in Mycobacterium smegmatis and defined their structures from these detergent-solubilized crude membranes. Data generated from these samples allowed us to simultaneously solve three distinct classes of membrane protein complexes to high resolutions. We observed that MmpL5 presents as a monomer in complex with the cytosolic meromycolate extension acyl carrier protein M (AcpM) in a molar ratio of 1:1, where these AcpM-MmpL5 complexes closely pack together to generate regular two-dimensional arrays. We also identified MmpL5 as a trimer that interacts with MmpS5 and AcpM in a molar ratio of 3:3:3 to assemble the tripartite complex AcpM-MmpL5-MmpS5 that spans both the inner and outer membranes of the mycobacterium. In addition, we discovered that MmpL5 and AcpM are able to form the trimeric AcpM-MmpL5 complex in a molar ratio of 3:3. The structural data reveal that the full-length MmpL5 trimer is capable of spanning the entire mycobacterial cell envelope to transport substrates. However, this assembly requires the presence of MmpS5 to stabilize secondary structural features of the MmpL5 periplasmic subdomains.

microbiology↗