Biology subjects

Jain, S.

Publications and source records attributed to Jain, S..

At least 19 recordsLinked to original sources

bioRxiv2026

Progressive Actomyosin Remodeling Defining a Structured Podocyte Injury Response in Nephrotic Syndrome

Nephrotic syndrome, the leading cause of chronic kidney disease worldwide, is associated with injury and eventual loss of podocytes, the specialized epithelial cells that form the final layer of the kidney's filtration apparatus. The progression from injury to loss is largely irreversible. However, some forms of nephrotic syndrome undergo remission, suggesting that injured podocytes may retain a capacity for repair, the structural basis of which remains unknown. Podocytes respond to injury by the stereotypical morphological change known as foot process effacement (FPE), which can be visualized using transmission electron microscopy. Using modified ultrastructure expansion microscopy (U-ExM) protocol combined with super-resolution microscopy, we discovered that injured podocytes exhibit a three-stage progression of FPE maturation, with kinetics determined by the degree of actomyosin contractility. Through longitudinal study of adriamycin-induced nephropathy in mice, we identified three sequential stages of actomyosin reorganization within the sarcomere-like structures (SLSs) that define the injury response: focal infiltration of myosin IIA into synaptopodin-rich foot processes (Stage 1), disordered intermingling of synaptopodin/myosin IIA (Stage 2), and the formation of highly organized periodic contractile arrays oriented perpendicular to the direction of capillary blood flow (Stage 3). Longitudinal quantification revealed predictable temporal dynamics, with mature Stage 3 predominating by day 7-9 post-injury. To determine whether this sequence is conserved in human disease, we analyzed kidney biopsies from patients with minimal change disease, focal segmental glomerulosclerosis, membranous nephropathy, and diabetic nephropathy. The same three stages were present across all four diseases, and their distribution tracked disease course: acute podocytopathies exhibited heterogeneous early-stage patterns, whereas chronic injuries converged on uniform, mature SLS organization. These findings demonstrate that podocyte injury is a graded, potentially reversible process rather than a binary switch. They identify structured actomyosin remodeling as a conserved wound response across mechanistically distinct kidney diseases and suggest that therapeutic strategies targeting specific stages of this progression could alter the trajectory of diverse glomerular diseases.

cell biology↗

bioRxiv2026

High-throughput identification of chromatin-opening transcription factors

Cell fate transitions involve major changes to the chromatin landscape, some of which are thought to deepen the basin around a newly adopted cell state, stabilizing gene expression programs that might otherwise be transient. Transcription factors (TFs) are central to this process, binding a subset of their genome-wide motif occurrences to create accessible regions that can act as cell type-specific enhancers. However, apart from a few well-studied cases, it is not clear which of the ~1,600 mammalian TFs, when newly expressed, can directly or indirectly initiate newly accessible sites, nor why only some motif occurrences gain accessibility. Here, we applied pooled CRISPR activation (CRISPRa) to upregulate endogenous TFs to physiological levels in mouse embryonic stem cells (mESCs). After screening guides targeting 240 developmental TFs for transcriptional response, we selected 60 and jointly profiled gene expression and chromatin accessibility in ~140,000 single cells. Some TFs (e.g. Cdx2, Sox10) appeared to initiate new accessibility on their own, predominantly at distal sites that are closed in mESCs but coincide with cell type-specific enhancers later in development. Others appeared to partner with "co-TFs", either by leveraging preexisting mESC heterogeneity (e.g. {uparrow}Grhl1 in Tfap2c+ mESCs [->] opening of sites bearing motifs for both), or by hierarchical activation (e.g. {uparrow}Sox7 [->] {uparrow}Gata6 [->] opening of sites bearing either or both motifs). Such dependencies shape which sites are used and which fates are reachable, and may explain the differential behavior of TFs with nearly identical consensus motifs. Thus, the capacity of a newly expressed TF to open chromatin strongly depends on the cell type, cell state and gene regulatory network it lands in. Charting these dependencies will inform how cell fate transitions are initiated in development, homeostasis and disease, and how to engineer them in silico, in vitro and in vivo.

genomics↗

bioRxiv2026

Autophagy dependent HIF1α proteostasis is compromised in models of PEX1 deficiencies

Peroxisomes, along with mitochondria, coordinate and compartmentalize oxidative metabolism in eukaryotic cells. Rare genetic disorders caused by mutations in PEX genes impair peroxisome function and cause Peroxisome Biogenesis Disorders, which are characterized by liver and neurological dysfunction, hearing and vision loss, and metabolic abnormalities. The majority of Peroxisome Biogenesis Disorders (PBDs) are caused by mutations in the gene encoding PEX1, which together with PEX6 forms a hetero-hexameric AAA-ATPase complex that drives the import of enzymes into the peroxisome lumen. One particular destabilizing mutation - PEX1G843D - results in almost 30% of all cases. Here we show that deficiencies in PEX1 lead to increased levels of the oxygen-responsive transcription factor HIF1 in normoxia, as well as a HIF1 transcriptional signature. The increase in HIF1 protein was rescued by overexpression of PEX1WT, suggesting PEX1 deficiencies modulate HIF1 signaling. The increased levels of HIF1 were not explained by defects in the oxygen responsive degradation pathway of HIF1 that relies on proline hydroxylase domain enzyme-dependent hydroxylation and von Hippel Lindau tumor suppressor protein-dependent ubiquitination. Instead, we found that PEX1 deficiency alters HIF1 proteostasis by reducing degradation through a hydroxylation- and autophagy- dependent mechanism. Notably, enhancing autophagic capacity by ULK1 agonism was sufficient to reduce HIF1 levels in PEX1 deficient cells. Lastly, we demonstrate that upon hypoxia-reoxygenation, PEX1 deficient cells are slower to reset HIF1 levels. Our results suggest that PBD patients with PEX1 deficiency may be susceptible to dysregulation of the HIF1 pathway, particularly in tissues where oxygen gradients are physiological or developmentally required.

cell biology↗

bioRxiv2026

Plasma Extracellular Vesicle Lipidomics Reveals an SMPD1-Driven Sphingomyelin Salvage Pathway Collapse in Parkinson's Disease

While lysosomal lipid dysregulation is implicated in Parkinsons disease (PD), identifying the precise enzymatic drivers remains limited by the lack of subcellularly resolved metabolic mapping. Leveraging endosome-origin plasma extracellular vesicle (PsEV) lipidomics, we identified a profound bidirectional disruption of the ceramide-sphingomyelin (SM) axis in PD, driven by asymmetric upregulation of sphingomyelin phosphodiesterase 1 (SMPD1) and sphingomyelin synthase 1 (SGMS1). BODIPY-C5 SM tracking revealed that SMPD1 perturbation severely impairs lysosomal SM turnover. Crucially, this SMPD1-driven hydrolysis forces a salvage pathway collapse, bottlenecked by SPHK1/SGPL1 downregulation, which precipitates oxidative membrane damage and PINK1/Parkin-dependent mitophagy failure. We robustly validated this multi-pathway dysfunction across orthogonal in vitro, in vivo mouse, and postmortem human brain models. Furthermore, SMPD1/SGMS1 expression distinctly stratifies clinical phenotypes, marking the aggressive Postural Instability/Gait Difficulty (PIGD) subtype. Our findings establish SMPD1-mediated lysosomal impairment and ceramide-SM imbalance as a core biochemical axis in PD pathophysiology.

neuroscience↗

bioRxiv2026

Dual MMP-9/12 Inhibition with AZD1236 Confers Neurovascular Protection and Reduces Post-Stroke Pain in Experimental Stroke Models.

Background: Stroke remains a leading cause of death and disability worldwide. Matrix metalloproteinases (MMPs), particularly MMP-9 and MMP-12, contribute to early blood-brain barrier (BBB) disruption, neuroinflammation, haemorrhagic transformation, and intracerebral haemorrhage (ICH). Intravenous thrombolysis is the only widely used pharmacological therapy for acute ischaemic stroke, but its utility is limited by narrow eligibility criteria and haemorrhagic risk. Inhibition of MMPs in the acute phase may offer a complementary neurovascular protective strategy. Methods: AZD1236, a selective dual MMP-9/-12 inhibitor, was evaluated in transient and permanent middle cerebral artery occlusion models and in a collagenase-induced ICH model in young, aged, obese, and female mice. Drug or vehicle was administered 2-6 hours after stroke onset. Outcomes included infarct or haematoma volume, BBB integrity, neurological function, and pain-related behaviours. Results: AZD1236 given within 2-4 hours after ischaemic or haemorrhagic insult significantly reduced infarct and haematoma volumes, improved short- and long-term neurological scores, and preserved BBB integrity, whereas treatment at 6 hours was largely ineffective. AZD1236 also attenuated the development of post-stroke mechanical allodynia and thermal hyperalgesia. Mechanistically, treatment reduced MMP-9 and MMP-12 activity, increased tight junction protein expression, and dampened inflammatory responses. Conclusions: Dual inhibition of MMP-9/-12 with AZD1236 confers robust neurovascular protection and mitigates post-stroke pain across clinically relevant models of ischaemic and haemorrhagic stroke. These findings provide a strong preclinical rationale for clinical evaluation of dual MMP-9/12 inhibition as an adjunctive neuroprotective strategy for acute stroke.

neuroscience↗

bioRxiv2026

Approaches to optimize cell internalization and in vivo tumor homing by aptamer-drug conjugates using SELEX

Glioblastoma (GBM) is the most common primary malignant brain tumor and is typically fatal. GBM therapies are hindered by the impermeability of the blood brain barrier (BBB), the diffuse and infiltrative nature of the tumor, and the high heterogeneity of intratumoral GBM cells. Aptamers are short, synthetic, folded single strands of RNA or DNA or analogs that bind targets with high affinity and specificity. Aptamers are developed via the principles of natural selection, permitting an unbiased approach to therapeutic development. Thus, rather than using rational design to select a target and develop a targeting moiety, cycles of Systematic Evolution of Ligands by Exponential Enrichment (SELEX) are employed in cell culture or in vivo to identify aptamers against unknown targets. Antibody drug conjugates (ADCs) have shown some efficacy for GBM but are limited by their large size and thus depend on leakiness of the BBB. We have recently applied in vivo SELEX to develop anti-GBM aptamers (six-fold smaller in mass than IgG antibodies) and to select aptamer-drug conjugates. Here we report attempts to focus aptamer selection toward internalizing drug-delivery targets and resulting challenges involving loss of tumor specificity in vivo.

biochemistry↗

bioRxiv2026

Efficient exploration of sequence space enables rapid generation of functional genome editors

The problem of how protein sequences translate into defined functions remains largely unsolved despite decades of progress. New methods to efficiently explore protein sequence space will help to shed light on these sequence-function relationships, particularly for complex protein function. Here, we describe an approach to create novel, functional proteins through the integration of deep mutational scanning, structural analysis, and evolutionary mining within prompts for a generative protein language model (PLM). We demonstrate the utility of this approach with the generation of novel compact RNA-guided nucleases. This approach is highly efficient, resulting in active nucleases with [~]40% sequence divergence relative to natural proteins and activity equivalent to or exceeding by up to [~]3X that of other compact nucleases at multiple endogenous loci in human cells. The approach described here is rapidly deployable and produces new sequences that will serve as scaffolds for further exploration of complex protein functionality, as well as substrates for novel genome engineering applications.

synthetic biology↗

bioRxiv2026

A Principled Statistical Framework for Analyzing Spatial Patterns in Spatially Resolved Multi-Omics

Emerging spatial multi-omics technologies enable the profiling of molecular variation within its tissue context, yet existing methods for identifying spatially variable features lack principled approaches to experimental design and cross-sample inference. Here, we present STORM, a principled Statistical TOol for spatially Resolved Multi-omics, for rigorously analyzing spatial patterns in spatial multi-omics research. STORM incorporates a robust and efficient nonparametric test that quantifies local deviations in molecular feature measurements to detect spatial dependence across transcriptomic and proteomic data. It further estimates an interpretable spatial effect size, supports power calculations for both spatial locations and biological replicates, and enables formal group-level comparisons. In several simulated and experimental spatial multi-omics case studies, STORM demonstrates reliable performance in detecting spatial structures while offering quantitative support for study design decisions. Overall, STORM provides a principled statistical framework that unifies spatial hypothesis testing, effect size estimation, power analysis, and experimental design for spatial multi-omics data.

bioinformatics↗

bioRxiv2026

Bone Lymphatic Endothelial Cells Form a Distinct Skeletal Population and Drive Skeletal Repair

Bone regeneration relies on specialized vascular niches, yet the contribution of lymphatic vessels across distinct skeletal sites remains poorly understood. Here, we identify bone lymphatics as an essential component of the regenerative microenvironment in the mandible and long bones. We demonstrate that bone lymphatic endothelial cells (LECs) constitute a specialized endothelial population that is transcriptionally and spatially distinct from periosteal LECs. During skeletal repair, bone LECs reactivate a regenerative transcriptional programme, and promote mandibular and fracture healing. In osteonecrosis of the jaw and periodontitis, bone lymphatic-associated signalling is disrupted, identifying impaired lymphatic function as a shared feature of mandibular disease. Therapeutic activation of VEGFC-FLT4 signalling during injury or mandibular disease restores lymphangiogenesis, enhances osteogenesis, and markedly improves bone regeneration. Together, our findings advance the paradigm-shifting role of bone lymphatics positive regulators of bone regeneration and identify lymphatic activation as a promising therapeutic strategy to enhance bone regeneration in mandibular diseases.

cell biology↗

bioRxiv2026

A geometric-to-neural cascade for cerebral microbleed detection in susceptibility-weighted MRI

Cerebral microbleeds (CMBs) are established imaging biomarkers of cerebral small vessel disease and are a defining feature of cerebral amyloid angiopathy (CAA), yet their automated detection in susceptibility-weighted imaging (SWI) remains challenging due to high false-positive rates from vessel cross-sections, iron and calcium deposits, and other hypointense mimics. We present a fully automated, three-stage cascade pipeline that combines subject-adaptive unsupervised candidate generation with two successive lightweight 3D ResNet classifiers, trained with only human-in-the-loop quality-assurance (QA) labels (yes/no per candidate) rather than dense voxel-wise segmentation masks. The candidate generation stage is performed by fitting a Gaussian Mixture Model (GMM) to each subjects SWI intensity histogram to define an adaptive low-intensity threshold, followed by anatomical masking to exclude physiologically irrelevant regions (image edges, ventricles/CSF/choroid plexus, and cerebellum), and filters candidates by size and sphericity. The model was trained and evaluated across a nested 3x5-fold cross-validation on N = 30 subjects from a publicly available labeled microbleed dataset and a CAA cohort (11,424 CMB candidate lesions) with data augmentation during training. Stage A classifies all geometric candidates as CMB or non-CMB and Stage B refines the predicted positives to suppress false positives (cascade AUC = 0.9587, sensitivity = 0.712, specificity = 0.975, PPV = 0.676, F1 = 0.693). The cascade reduces Stage A false positives by 76.8% (888/1,157 false positives eliminated) while retaining competitive sensitivity. Inference was performed on 141 SWI scans, detecting a mean 40.3 CMBs per scan and being preferred for use in 85% of high CMB cases, as evaluated by a blinded neurologist. The inference pipeline outputs binary CMB segmentation NIfTI images and radiologist-ready QA visualizations.

bioinformatics↗

bioRxiv2026

The Proposed Bone Post-Arterial Type R Capillaries Resolve into Venous and Fatty Acid-Handling Endothelial Cells

Endothelial specialization is increasingly recognized as a fundamental regulator of tissue homeostasis, yet the cellular diversity of the skeletal vasculature remains incompletely resolved. Here, we integrate large-scale single-cell transcriptomics, cross-tissue comparisons, and imaging to comprehensively define endothelial heterogeneity across the skeleton. Our analyses demonstrate that the proposed post- arterial "type R" endothelial population is not a distinct endothelial subtype but instead comprises canonical venous endothelial cells and fatty acid-handling endothelial state. RNA velocity supports a venous continuum, while the proposed type R markers FMO2, and AQP7 lack both endothelial and skeletal specificity. The fatty acid-handling endothelial state, characterized by Lpl and Cd36 is conserved across multiple skeletal sites and non-skeletal tissues, indicating a general endothelial metabolic programme. Within bone, this endothelial state expands following high-fat diet and is suppressed during injury. Together, these findings redefine skeletal endothelial heterogeneity and establish the proposed type R population as part of a venous continuum.

cell biology↗

bioRxiv2026

Organism-scale annotation with Pan-human Azimuth

Single-cell atlases now span many human tissues, but inconsistent annotations across studies limit their utility as a unified reference. We introduce Pan-human Azimuth, a supervised neural network that maps human cells from diverse tissues and datasets onto a single hierarchical organism-scale typology. Developed through NIH HuBMAP, the model is trained on a uniquely curated corpus designed to maximize diversity across tissues and technologies while enforcing uniform, interpretable annotations and stringent quality control. The use of a single organism-wide reference enables us to map tens of millions of cells in the Tabula Sapiens and scBaseCamp repositories, perform cross-tissue comparisons across thousands of samples, and identify striking tissue specialization among fibroblast states. Pan-human Azimuth naturally extends to annotating spatial transcriptomic data, recovering canonical kidney cortical structures and distinguishing glomerular states consistent with expert pathology. We release Pan-human Azimuth alongside cloud, R, and Python interfaces to facilitate standardized organism-wide single-cell analysis.

genomics↗

bioRxiv2026

Age Stratified Meta Transcriptomic Analysis Reveals Early and Core Dysregulated Pathways in Parkinson's Disease

Parkinsons disease (PD) is strongly age-associated, yet how aging reshapes PD-related transcriptional changes remains unclear. We performed an age-stratified meta-analysis of 16 bulk RNA-seq datasets (646 samples: 314 PD, 332 controls) to distinguish early-onset (<60 years) from late-onset ([≥]60 years) signatures. In the full dataset, 131 significantly (padj<0.05, |log2FC|>1) differentially expressed genes (DEGs) were observed, spanning neuronal activity-dependent genes (NPAS4, PVALB, ARC, FOSB) and immune/stress-related transcripts (IL3RA, SLC25A6, HSPA1A/B). Age-specific analyses revealed 31 DEGs in <60, dominated by large-effect changes in uncharacterized lncRNA LINC02188, pseudogene loci (MUC20P1, RPS28P7), calcium-modulating gene CALML6, lipid{square}associated gene TLCD3B, and cytoskeletal regulators (TIAM2, KCTD8). In contrast, the [≥]60 group showed 181 DEGs enriched for neuronal markers (NPAS4, PVALB) and immune-metabolic genes (FGA, NPC1L1, UPK1A, HSPA1A/B). GO/KEGG analyses indicated that the <60 signature centers on actin remodeling, filopodia, axonogenesis, and Rap1-mediated adhesion/signaling, consistent with early neurite and structural reorganization. The [≥]60 signature was enriched for blood microparticles, chemokine activity, infection-related pathways, ER protein processing, and arachidonic/ether lipid and cytokine signaling, pointing to broad immune-metabolic and proteostasis dysregulation. Cross-age comparison showed that classical PD neuronal immediate-early gene changes are largely [≥]60-driven, whereas early-onset PD involves novel lncRNA-calcium-lipid and cytoskeletal modules. These findings highlight LINC02188, TLCD3B and related cytoskeletal/lncRNA genes as novel early-onset PD-associated candidates, and NPC1L1, IL3RA and PVALB as age-amplified markers within the broader PD transcriptomic signature.

bioinformatics↗

bioRxiv2026

AI-Driven Discovery and BSL-4 Validation of Cross-Filovirus Ebola-Marburg Inhibitors and their Synergistic Combinations

Filovirus outbreaks caused by Ebola virus (EBOV) and Marburg virus (MARV), pose severe global health threats characterized by high rates of fatal hemorrhagic fever. While species-specific vaccines and therapeutic monoclonal antibodies are approved for Zaire ebolavirus, broadly-active therapeutics remain unavailable, leaving populations vulnerable to MARV and other pathogenic Ebola species, such as Bundibugyo (BDBV) and Sudan (SUDV) ebolaviruses. Here we report a computationally guided, infectious virus validated screening platform for the rapid discovery of broad-spectrum filovirus antivirals. By leveraging quantitative structure-activity relationship (QSAR) models, we screened 142,382 compounds in silico to prioritize 125 high-potential candidates. Subsequent dose-response and viability profiling identified 23 compounds exhibiting potent, low-micromolar pan-filovirus activity and favorable cytotoxicity profiles. Molecular docking indicates these compounds target conserved structural and functional domains--primarily the VP35 and L proteins--which may disrupt essential viral replication and immune antagonism. Furthermore, systematic combinatorial screening revealed three highly synergistic compound pairs, notably NCGC00113249-01 and NCGC00118008-01, demonstrating robust cross-species efficacy. By targeting conserved vulnerabilities across the filovirus family, this integrated in silico and in vitro pipeline provides a scalable framework to rapidly nominate and optimize synergistic therapeutic regimens against both endemic and emerging viral threats including BDBV. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=74 SRC="FIGDIR/small/737586v1_ufig1.gif" ALT="Figure 1"> View larger version (34K): org.highwire.dtl.DTLVardef@531939org.highwire.dtl.DTLVardef@19d1454org.highwire.dtl.DTLVardef@1a1c9e3org.highwire.dtl.DTLVardef@cd861b_HPS_FORMAT_FIGEXP M_FIG C_FIG

microbiology↗

bioRxiv2026

PEPstrMOD2: Next-generation tertiary structure prediction of chemically modified and non-natural peptides

While most existing methods are limited to predicting the tertiary structures of proteins containing only canonical residues, the PEPstrMOD server (developed in 2015) pioneered structure prediction for chemically modified and non-natural peptides. Despite its widespread use, the original framework was restricted to peptides of 7 to 25 residues and relied on older backbone-prediction algorithms. To address these limitations, we present PEPstrMOD2, which introduces three major advancements over its predecessor. First, it replaces the original in-house coordinate generation with state-of-the-art deep learning (DL) algorithms, leveraging AlphaFold2 and ESMFold for highly accurate initial structure prediction. Secondly, it greatly expands the accessible chemical space through incorporation of new, AMBER force-field compatible library of 257 post-translational modifications (PTMs), 428 non-canonical amino acids (NCAAs), and 243 terminal modifications. Lastly, through the application of native scalability of AlphaFold2 (AF2) and ESMFold (EF), PEPstrMOD2 eliminates the original restrictions of the length, enabling the structural modeling of longer, complex therapeutic peptides and small proteins. We evaluated the performance of PEPstrMOD2 against state-of-the-art methods across three distinct peptide datasets. For the AfCyc dataset consisting of 80 cyclic peptides, PEPstrMOD2 obtained a competitive average atom-level Root Mean Square Deviation (RMSD) of 2.05 [A], compared to 1.13 [A] by AlphaFold3 (AF3) and 1.82 [A] by AfCycDesign. Remarkably, for the modified peptide ModPep433 dataset, PEPstrMOD2 outperformed AF3, achieving the lower average RMSD score of 4.49 [A] against 4.67 [A] of AF3. Furthermore, in the case of the ModPep16 benchmark, PEPstrMOD2 achieved 2.50 [A] average RMSD value, which is two times more accurate than that of the original PEPstrMOD (5.84 [A]). In summary, PEPstrMOD2 provides a powerful, high-throughput, and highly accurate platform to facilitate peptide-based drug development and structural biology research. While the original PEPstrMOD was restricted to a web server interface, PEPstrMOD2 is available as both an intuitive webserver and a standalone command-line tool via GitHub, featuring Docker support for easy deployment and reproducible, large-scale modeling pipelines (https://webs.iiitd.edu.in/raghava/pepstrmod/). HighlightsO_LIPEPstrMOD2 predicts structures of chemically modified peptides using deep learning and molecular dynamics refinement. C_LIO_LISupports 928 chemical modifications through custom AMBER based force-field libraries including PTMs, NCAAs, terminal, D- as well as cyclic modifications. C_LIO_LIRemoves peptide length restrictions through AlphaFold2 and ESMFold integration. C_LIO_LIutperforms PEPstrMOD and is competitive with AF3 on different benchmark datasets. C_LIO_LIAvailable as both a web server and a standalone platform via GitHub and Docker. C_LI Authors BiographyO_LISaloni Jain is currently working as Ph.D. in Computational biology from Department of Computational Biology, Indraprastha Institute of Information Technology, New Delhi, India C_LIO_LINaman Kumar Mehta is currently working as Ph.D. in Computational biology from Department of Computational Biology, Indraprastha Institute of Information Technology, New Delhi, India C_LIO_LISahil Raina is currently working as Ph.D. in Computational biology from Department of Computational Biology, Indraprastha Institute of Information Technology, New Delhi, India C_LIO_LIPankaj Kumar is currently working as Ph.D. in Computational biology from Department of Computational Biology, Indraprastha Institute of Information Technology, New Delhi, India C_LIO_LIVarun is currently an integrated BS-MS student at Indian Institute of Science Education and Research (IISER) Pune, India. He is currently working as an intern on a project position at Department of Computational Biology, Indraprastha Institute of Information Technology (IIIT), New Delhi, India. C_LIO_LIGajendra P. S. Raghava is currently working as a Professor in the Department of Computational Biology, Indraprastha Institute of Information Technology, New Delhi, India. C_LI

bioinformatics↗

bioRxiv2026

Critical period plasticity enables credit assignment

Synaptic plasticity is often guided by instructive inputs to neural circuits, but learning only succeeds when these instructions reach neurons that mediate relevant outputs. This creates the credit assignment problem: how does a neuron receive instructions suited to its own behavioral function? Here we report a developmental mechanism that enables credit assignment by using instructive inputs to organize the downstream architecture through which learning is expressed. In the olivocerebellar learning system, the inferior olive provides instructive inputs that guide plasticity within the cerebellum. During circuit assembly in zebrafish, we find these same inputs regulate long-range cerebellar projections during a highly plastic, two-day critical period. Developmental experience caused specific maturation of projections to targets that were coactivated with olivary inputs. Mathematical theory and computational modeling show how the resulting architecture constrains later learning, such that a single input can sculpt downstream connectivity and then leverage that circuit to assign credit. Simulated learning became paradoxically more robust if we reduced plasticity after a developmental critical period, protecting key architecture from corruption during learning. Thus, instructive inputs can first build the circuits they later teach, coordinating development and learning to enable effective credit assignment.

neuroscience↗

bioRxiv2026

Discovery of cell-active small molecule inhibitors of UDP-galactose 4'-epimerase

Glycosylation depends on tightly regulated pools of nucleotide-sugars (NS), yet the mechanisms controlling mammalian NS homeostasis and their downstream effects on glycoprotein biosynthesis remain poorly understood. UDP-galactose 4'-epimerase (GALE) catalyzes the reversible interconversion of UDP-galactose/UDP-glucose and UDP-N-acetylgalactosamine/UDP-N-acetylglucosamine, making it a central regulator of glycan precursor pools and an excellent model enzyme for studying NS metabolism. Here, we report the discovery of a cell-active small molecule inhibitor of human GALE through a high-throughput chemical screening strategy. Using a coupled luminescence-based assay, we identified the FDA-approved drug disulfiram as a GALE inhibitor. Biochemical analyses demonstrated that disulfiram directly inhibits GALE through covalent modification of cysteine residues, including C153, likely via its reactive metabolite diethyldithiocarbamate. In cultured human cells, disulfiram treatment phenocopied genetic GALE deletion, reducing terminally sialylated glycans, mucin-type O-glycans, and properly glycosylated mucin-domain glycoproteins. These effects were rescued by galactose supplementation, consistent with a mechanism of on-target GALE inhibition. Similar phenotypes were observed in human lung adenocarcinoma cells, supporting a broader role for GALE in regulating glycosylation and mucin biosynthesis across tissue types. Together, these studies establish a platform for the discovery of pharmacological GALE inhibitors as new research tools, identify disulfiram as a cell-active chemical probe for studying NS regulation, and suggest that targeting GALE might modulate mucin hypersecretion in muco-obstructive diseases and mucinous cancers.

biochemistry↗

bioRxiv2026

A Single-Dose Bundibugyo Virus Vaccine Protects Macaques Within 3 Days

Bundibugyo virus (BDBV), a member of the orthoebolaviruses in the Filoviridae family, causes severe hemorrhagic disease with high case-fatality rates. Currently, there are no medical countermeasures approved for human use hampering the response to the large ongoing outbreak in the Democratic Republic of the Congo and Uganda. While vesicular stomatitis virus (VSV)-based vaccines have demonstrated fast-acting prophylactic single-dose efficacy against multiple filoviruses, it has yet to be defined for VSV-BDBV. Here, we evaluated the rapid protection by a single-dose vaccination of VSV-BDBV in nonhuman primates (NHPs). Vaccination elicited rapid innate and early adaptive immune responses and conferred complete protection from clinical disease against BDBV challenge within 3 days. Vaccinated NHPs exhibited minimal clinical signs, limited systemic inflammation, and no infectious virus was isolated from the blood at any time. Protection correlated with neutralizing antibodies and Fc effector functionality of the humoral immune response. These findings establish VSV-BDBV as a fast-acting vaccine candidate suitable for outbreak response and highlight immune mechanisms underlying rapid protection.

microbiology↗