Biology subjects

Singh, S.

Publications and source records attributed to Singh, S..

At least 55 records · Page 3Linked to original sources

bioRxiv2026

Lipid Droplets Direct Amyloid Assembly and β-Cell Stress through Interfacial Control of Amylin Aggregation

Islet amyloid polypeptide (IAPP, amylin) aggregation is a central pathological feature of type 2 diabetes, yet the cellular factors governing its conformational conversion remain incompletely understood. Here, we identify lipid droplets (LDs) as active modulators of amylin structure, aggregation, and {beta}-cell stress. Using artificial and native LDs, we show that amylin binds LD surfaces with high affinity and undergoes accelerated conversion into {beta}-sheet-rich conformations. LDs promote rapid nucleation while constraining fibril elongation, yielding shorter and morphologically distinct amyloid assemblies. Residue-resolved NMR mapping reveals a conserved N-terminal interaction interface, which is amplified upon removal of LD surface proteins, indicating that the LD proteome modulates peptide engagement and aggregation pathways. In {beta}-cells, lipid loading drives intracellular colocalization of amylin with LDs and reshapes transcriptional stress responses, attenuating ER stress and apoptosis while altering markers of {beta}-cell identity. Finally, systemic lipidomic profiling reveals coordinated remodeling of neutral lipid species across dysglycaemic states, linking intracellular LD dynamics with whole-body lipid metabolism. Together, our findings establish lipid droplets as dynamic scaffolds that reshape amylin aggregation pathways and associated {beta}-cell stress responses, providing a mechanistic bridge between lipid dysregulation and islet amyloidosis in diabetes. Significance StatementLipid droplets accumulate in pancreatic {beta}-cells during metabolic stress, yet their role in amylin aggregation remains unclear. Using structural, biophysical, and cellular approaches, we show that lipid droplet interfaces directly bind human amylin, reshape its aggregation pathway, and alter fibril morphology. Native lipid droplets and their associated surface proteins further modulate aggregation kinetics and peptide conformations. In {beta}-cells, lipid loading enhances amylin colocalization with lipid droplets and modifies stress and survival responses. Complementary lipidomic profiling reveals systemic remodeling of neutral lipid species across dysglycaemic states. These findings identify lipid droplets as active regulators of amyloid-associated proteostasis, linking lipid dysregulation to {beta}-cell dysfunction in type 2 diabetes.

Cell Biology↗

bioRxiv2026

Pillbox: A Leakage-Aware Foundation-Model Predictor and Lineage-Ceiling Diagnostic for Cancer Drug Response

We present Pillbox, a predictor whose pipeline is audited against the six Asiaee leakage modes with the one residual pathway shown by per-fold ablation to be non-load-bearing on hard splits. Our model combines CpGPT methylation embeddings, CLAMP drug embeddings, and per-fold-fit gene-expression principal components which are fused by Feature-wise Linear Modulation (FiLM)-conditioned graph attention on the STRING v12 protein-protein interaction graph. Then we -ensemble the model against a histogram-based gradient boosting regressor baseline. On GDSC GSE68379 (987 cell lines, 375 drugs) across seeds 42, 7, and 123, the ensemble reaches test R2 of 0.78, 0.77, and 0.76 on random, histology-blind, and site-blind splits respectively, with cell-aware lifts above the drug-mean floor of +0.054, +0.060, and +0.037. As a quantitative diagnostic for feature-stack saturation we propose the cross-architecture residual correlation, calibrated against a same-architecture-different-initialization control. On histology-blind splits the cross-architecture value of 0.939 falls short of the same-architecture ceiling of 0.974 by approximately 0.03 in residual correlation, a gap we interpret as the headroom available to architecture choice on top of the current foundation-model representation and consistent with the long-established observation that tissue lineage dominates cell-line drug response. We integrated curated mutation, methylation, and drug-target-expression channels, but these do not improve prediction once foundation-model embeddings are in place. Cross-screen validation against PRISM matches the GDSC-to-PRISM measurement reproducibility ceiling within 0.01 Spearman.

bioinformatics↗

bioRxiv2026

Sennoside A and Ceftazidime Inhibit Nucleocapsid RNA BindingAcross SARS-CoV-2, SARS-CoV, and MERS-CoV

SARS-CoV, MERS-CoV, and SARS-CoV-2 exemplify the persistent threat posed by coronaviruses, with their capacity for zoonotic spill over, rapid transmission, and high mortality, and thus underscores the urgent need for broad-spectrum antiviral strategies. The nucleocapsid (N) protein, essential for RNA binding, genome packaging, and viral replication, is highly conserved among coronaviruses but remains an underexplored antiviral target. In our earlier work, we identified two small molecules, ceftazidime and sennoside A, that bind the N-terminal domain of the SARS-CoV-2 N protein and inhibit nucleic acid binding, and identified their binding sites using NMR chemical shift perturbation assays. Here, we observed that several residues involved in inhibitor binding are conserved across betacoronaviruses, suggesting a shared druggable vulnerability. We have purified recombinant N proteins from SARS-CoV, MERS-CoV, and SARS-CoV-2, and demonstrated by electrophoretic mobility shift assays that both compounds significantly reduced RNA binding. Their inhibitory concentrations (IC50) were determined using fluorescence polarization. The docking analyses indicated that both inhibitors target the RNA-binding pocket of the N-NTD, consistent with a conserved mechanism of action. Collectively, our findings reveal a conserved RNA-binding vulnerability in coronavirus N proteins and highlights the pan-coronavirus therapeutic potential of these inhibitors.

biophysics↗

bioRxiv2026

A metabolic labelling-based lipid imaging technology establishes VPS13A as a phosphatidylethanolamine lipid transfer protein

The ability to image specific lipid subtypes within cells can have a transformative impact on the study of lipid dynamics and trafficking mechanisms. Herein, we describe a technology for imaging phosphatidylethanolamine (PE) lipids in live mammalian cells that involved screening a library of ethanolamine derivatives to identify an azido compound that efficiently metabolically labels PE. Crucially, this probe evades the cellular methylation machinery specifically labelling PE without forming labelled methylated PE and phosphatidylcholine (PC) lipids. The administration of cyclooctyne dyes to cells metabolically labelled with this probe rendered azido PE lipids fluorescent via strain-promoted click chemistry, enabling imaging. We employed this technology to image PE in various cellular organelles, visualize PE externalization during apoptosis, and discover that the VPS13A protein transports PE from the endoplasmic reticulum to the mitochondria. This technology will facilitate addressing fundamental questions in PE biology and studying dysregulation of PE dynamics and trafficking in disease states.

cell biology↗

bioRxiv2026

Pleiotropic antimalarial activities and immunomodulation exhibited by Himalayan Buransh (Rhododendron arboreum) in human and rodent malaria models

Emerging drug resistance against the malaria parasite is worrisome and necessitates the development of novel antimalarials. Himalayan Buransh (Rhododendron arboreum) is a well-known medicinal plant found in the northern states of India. In this study, we observed the pleiotropic antimalarial activities and immunomodulation exhibited by the aqueous extract of Buransh flower (AEBF). AEBF demonstrated significant IC50 values (16-29 {micro}g/ml) against the asexual stages of various P. falciparum strains (3D7, Dd2-chloroquine-resistant and C580Y-artemisinin resistant). The oral administration of AEBF (200 mg/kg) in mice, suppressed [~]80% P. berghei parasitemia, improved mean survival time (MST-23.5 days) and prevented splenomegaly. Notably, the combination of AEBF and artesunate not only cleared primary infection, but also conferred sustained immunity. This immunomodulatory effect, driven by protective IFN-{gamma} resulted in reduced parasitemia during a homologous challenge without the need for further treatment. It is important to highlight the malaria transmission blocking activity of AEBF, resulting in reduced sexual stage male gametocyte exflagellation. Furthermore, the virtual drug screening of selected bioactive constituents from Buransh flower demonstrated potent binding against multiple P. falciparum proteins, suggested a pleiotropic mode of action. Altogether, our results corroborated the first ever evidence of the multistage antimalarial potential of Buransh flower, supported by in vitro cell studies, in vivo rodent malaria model and in silico docking analyses. Based on our studys findings and the traditional use of Buransh juice as a medicinal beverage in Uttarakhand, India, we propose exploring it as an adjunct therapy for drug-resistant malaria, subject to further clinical validation.

pathology↗

bioRxiv2026

Structural analysis of de novo designed binders targeting the closed state of HSP90

Heat shock protein 90 (HSP90) assists protein folding and maturation of many important signaling proteins. In various diseases, HSP90 clients contribute to aberrant signaling, and HSP90 inhibition is being explored as a potential therapeutic approach. Commonly researched HSP90 inhibitors target the ATP-binding pocket, thereby disrupting the ATP-induced closure of HSP90. Drugs disrupting the HSP90 ATPase cycle by targeting the closed state of the chaperone have not been developed. Here, we present de novo design and selection of protein binders interacting exclusively with the closed state HSP90. Two such binders, H2 and H4, were identified that feature a similar fold and comparable affinities for HSP90 but display different binding kinetics. The structures of the HSP90 complexes with H2 and H4 were determined by cryo-EM single particle analysis, and they revealed high accuracy of the BindCraft predictions. H2 and H4 compete with p23 at one but not both symmetrical p23 binding sites on HSP90. H2 expressed in HEK293T cells moderately elevated expression of HSP70 and had no effect on the HSP90 level, suggesting muted heat shock response. Overall, this study demonstrates that the de novo binders represent novel and promising tools to probe the potential utility of HSP90 inhibition by targeting its closed state.

biochemistry↗

bioRxiv2026

Diabetes and Immunosuppression Drive Distinct Patterns of Candidozyma auris Skin Colonization and Dissemination in Mice

Candidozyma auris is an emerging, multidrug-resistant (MDR) fungal pathogen that persistently colonizes human skin and disproportionately causes invasive infections in patients with metabolic or immune dysfunction. Despite strong epidemiological links to diabetes and immunosuppression, how these host conditions shape skin colonization, immune defense, and dissemination remain poorly defined. Here, we establish complementary murine model of C. auris skin colonization under immunocompetent, immunosuppressed, and diabetic ketoacidosis (DKA) conditions. DKA mice exhibited significantly increased skin fungal burden, impaired clearance, and frequent systemic dissemination. Notably, DKA permitted dissemination despite preserved granulocyte and neutrophil recruitment to the skin, indicating a functional rather than quantitative defect in innate immunity. Consistent with this, phagocytes from DKA mice displayed impaired antifungal activity characterized by reduced phagocytosis and killing despite elevated reactive oxygen species production. Hyperglycemic and ketone-rich conditions (BHB) remodel the C. auris cell wall, reducing mannan, increasing chitin, and upregulating adhesins, thereby enhancing adhesion and inflammatory activation while impairing neutrophil killing. Together, these findings reveal host metabolic dysfunction as a primary driver of persistent C. auris skin colonization and dissemination, identify qualitative defects in innate antifungal immunity as a key determinant of invasive risk and highlight metabolic condition as a critical target for infection prevention strategies. Short SummaryThis study establishes the first physiologically relevant murine model of Candidozyma auris skin colonization under diabetic ketoacidosis and immunosuppression, revealing distinct immune dysfunction and systemic dissemination that can inform targeted antifungal strategies.

microbiology↗

bioRxiv2026

BK Channels Orchestrate Cardiac Homeostasis Through Mitochondrial Uncoupling Proteins

BK channels, coded by the Kcnma1 gene, integrate voltage and intracellular Ca2+ signals and are recognized for their roles in smooth muscle and neuronal excitability. However, their contribution to baseline cardiac physiology remains poorly defined. Here we uncover a fundamental function for BK channels in maintaining normal cardiac performance, independent of pathological stress. Using non-invasive echocardiography, transcriptional profiling, and mechanistic analyses, we demonstrate that Kcnma1 deletion disrupts ventricular function, and remodels metabolic and stress-response pathways. Transcriptomic profiling revealed selective downregulation of mitochondrial uncoupling proteins (UCPs) and suppression of the PGC-1/FOXO3a axis, without broad loss of oxidative phosphorylation components. Enhancing UCP expression restored cardiac performance, indicating that mitochondrial uncoupling and redox control constitute key downstream effectors of BK signaling. Together, these results identify a physiological role for BK channels in maintaining myocardial function and define a mitochondrial BK-UCP axis, critical for cardiac homeostasis.

cell biology↗

bioRxiv2026

Astrocytic ACSBG1 depletion improves lipid-cytokine signaling and attenuates α-Synuclein pathology in a Parkinson's disease mouse model

Astrocytes are key regulators of lipid metabolism, and dysregulated astrocytic lipid processing is implicated in Parkinsons disease (PD) pathogenesis. Our prior genome-wide screens identified ACSBG1, an astrocyte-enriched acyl-CoA synthetase, as a candidate regulator of -synuclein (-Syn) levels. However, how ACSBG1 links lipid reprogramming to inflammatory astrocyte activation and -Syn pathology remains unknown. We compared the transcriptomic, cytokine, and lipid secretomes of TNF- and IL-1 stimulated primary astrocytes from wild-type (WT) and Acsbg1 knockout (KO) mice. In vivo, we crossed Acsbg1 KO mice with a Thy1--Syn PD model to assess behavior, neuroinflammation, synaptic integrity, and -Syn levels. Following cytokine exposure, Acsbg1 KO astrocytes mounted an attenuated inflammatory transcriptional response, secreting significantly fewer inflammatory mediators (e.g., IL-6, RANTES, MIP-3) and less long-chain Sphingosine 20:1 than WT astrocytes. Importantly, exogenous Sphingosine 20:1 or cytokines from WT reactive astrocytes induced neuronal -Syn phosphorylation (pS129). In vivo, Acsbg1 deletion in Thy1--Syn mice reduced astrogliosis, rescued synaptic and behavioral deficits, and decreased total and pS129--Syn. These findings establish ACSBG1 as a key regulator of inflammatory astrocyte signaling that contributes to -Syn phosphorylation via specific cytokine and lipid mediators, identifying ACSBG1 as a novel therapeutic target for modulating astrocyte-neuron communication in PD. Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=143 SRC="FIGDIR/small/726454v2_ufig1.gif" ALT="Figure 1"> View larger version (31K): org.highwire.dtl.DTLVardef@150a3e3org.highwire.dtl.DTLVardef@137b5caorg.highwire.dtl.DTLVardef@7fe373org.highwire.dtl.DTLVardef@2d996e_HPS_FORMAT_FIGEXP M_FIG C_FIG

neuroscience↗

bioRxiv2026

CRISPR/Cas12a-Mediated Knockout of the INNER NO OUTER (INO) Gene in Musa balbisiana cv. Bhimkol

Banana (Musa spp.) is a vital staple food and cash crop cultivated in over 140 countries, providing nourishment and livelihoods to more than 400 million people worldwide. In this context, Bhimkol (Musa balbisiana, BB genome), a diploid banana variety native to Northeast India holds significant nutritional and commercial value. Its high iron and nutrient content have already been commercially validated through products like Bhimvita and Bhimshakti, which utilize fresh fruit pulp as nutrient-rich food for infants. However, Bhimkol fruits typically contain 100-150 seeds, an undesirable trait for product development. The manual removal of these seeds significantly increases production time and labour costs. Furthermore, because bananas are recalcitrant to traditional breeding, there is a constant need for rapid in vitro transformation protocols. To address these challenges, as a proof of concept, our research aims to knockout the INNER NO OUTER (INO) gene, which is responsible for ovule development. Using CRISPR/Cas12a technology, we established an efficient and reproducible in vitro regeneration and transformation system using Embryogenic Cell Suspensions (ECS). The resulting CRISPR-edited plantlets exhibited various mutations, including insertions and deletions (INDELs) within the targeted INO gene. These INDELs resulted in frameshift mutations that triggered premature stop codons. While these genetic changes are expected to render the banana seedless, phenotypic verification is currently underway to confirm the absence of seeds in mature fruit. Significance StatementDespite its superior nutritional profile, the commercial viability of the Bhimkol banana (Musa balbisiana) is restricted due to abundance of seeds (100-150 per fruit). This study employs CRISPR/Cas12a-mediated knockout the INNER NO OUTER (INO) gene in Bhimkol and expected to develop seedless fruits. The resulting plantlets exhibit targeted indels that trigger frameshift mutations, effectively disrupting ovule developmental INO gene.

plant biology↗

bioRxiv2026

Direct Synthesis of Targeted Nanosized ICG J-aggregate for Photoacoustic Imaging

Indocyanine green (ICG) J-aggregates (JAs) are self-assembled particles characterized by a sharp and strong absorption peak in the near-infrared region ([~]890 nm), enhanced photostability, low fluorescence, and high photothermal conversion efficiency, compared to monomeric ICG. These attributes make ICG-JAs promising contrast agent candidates for photoacoustic imaging (PAI). However, traditional methods for synthesizing ICG-JAs often yield particles without targeting ability, which limit their applications. Thus, to synthesize targeted nanoscale JA, complex and multi-step encapsulation and filtration processes are generally required. To solve this issue, we introduce a robust and rapid strategy for direct synthesis of targeted nanoscale ICG-JA by co-assembling ICG and ICG-azide dyes under optimized formulation conditions that do not require encapsulation. The resulting nanoscale JAAZ particles (nJAAZ) exhibit diameters of [~]120-150 nm and are amenable to direct bio-orthogonal functionalization via copper-free click chemistry for the attachment of virtually any targeting ligands and/or biomolecules. We further demonstrate the strong photoacoustic signal generation of these nJAAZ in vitro and in vivo, highlighting their potential as a modular high-performance contrast agent platform for PAI. This work establishes a scalable and tunable platform for engineering functional JAs, opening new avenues for targeted molecular imaging and theranostic applications.

bioengineering↗

bioRxiv2026

Soda-baited RNAi Yeast Insecticides as Effective Attractive Targeted Sugar Baits (ATSBs) for Mosquito Control

BackgroundAttractive Targeted Sugar Baits (ATSBs) are a promising, environmentally friendly approach for mosquito control, but the direct field application, scalability and long-term effectiveness of ATSBs across diverse mosquito species remain significant challenges. Methodology/Principal FindingsWe assessed the efficacy of a genetically engineered RNA interference (RNAi) yeast strain (Sh.463_56.10R) formulated in three sugar baits, soda (Coca-ColaTM), 10% sucrose, and a commercial mosquito bait (BaitStabTM), on Aedes, Anopheles and Culex mosquitoes. All RNAi yeast bait formulations induced significantly higher mean mortality (87-100%) compared to the control groups (0-9%; P<0.0001), but mosquitoes exhibited a higher feeding preference for RNAi yeast-soda baits, which induced mortality rates of 94-100% (P < 0.0001) recorded across all mosquito species. Additionally, to assess the competitiveness of the RNAi yeast-soda bait to other tropical sugar sources, semi-field choice assays were conducted in Trinidad, West Indies using competing flowering plants and fruits typically found in residential environments. The RNAi yeast-soda ATSB continued to perform well in the presence of competing floral and fruit sugar sources during both Aedes albopictus and Culex quiquefasciatus trials, though the presence of several fruits and flowers did reduce A. aegypti mortality, suggesting that further field testing will be necessary. The residual activity of the Sh.463_56.10R + soda formulation was retained for at least 14 months, with sustained 100% mortality in C. quinquefasciatus and 93-100% mortality in Aedes aegypti, Anopheles gambiae and Anopheles stephensi. The RNAi yeast-soda ATSB also performed well in semi-field studies performed with a prototype soda bottle feeder. Conclusions/SignificanceThis study demonstrates the potential of soda-baited RNAi yeast as a potent, long-lasting, and scalable platform for ATSB-based mosquito control as a component of integrated vector management programs. Author SummaryMosquito-borne diseases continue to affect millions of people worldwide, and current mosquito control methods face challenges such as low public uptake, insecticide resistance and environmental concerns. Here we evaluated a new and environmentally friendly approach to mosquito control using ATSBs. We tested genetically engineered species-specific yeast producing RNAi molecules capable of killing mosquitoes that feed on it. We mixed the yeast with three different sugar baits, including soda (Coca-ColaTM), 10% sucrose, and the commercial mosquito bait BaitStabTM formulation, and evaluated how well they worked against different mosquitoes. The results showed that the RNAi yeast mixed with soda was the most effective, killing up to 100% of mosquitoes in laboratory and outdoor tests. The bait remained effective in the presence of many competing natural tropical fruit and floral sugar sources. Remarkably, the bait, which can be delivered in a soda bottle feeder, stayed active for at least 14 months under simulated field conditions. These findings suggest that soda-based RNAi yeast baits could provide a practical, long-lasting and scalable tool for mosquito control and may help strengthen future strategies to reduce mosquito-borne diseases.

genetics↗

bioRxiv2026

Dynamic s-acylation of schizophrenia-linked antioxidants explicate the redox flexibility of human microglia during inflammation.

Cysteine proteome essentially regulates cellular adaptability during stress. Proteomic cysteines are reversibly modified to avoid loss through oxidation. Reversible cysteine-modifications beneficially preserve cellular stress-response mechanisms by regulating the transient activation of substrate proteins. Cysteine acylation (or s-acylation) is one such extensively documented reversible protein modification. Inflammation-responsive changes in s-acylation facilitate the plasticity of immune-partitioned brains by dynamically determining the utilization of stress-buffering (substrate) cysteine-proteins in microglia, the primary immune-reactive brain cells. However, the inflammation-responsiveness of cysteine-acylation in microglia is not elaborately measured at a large-scale. Therefore, we observed the differential (quantitative) s-acylation of proteins in cultured human (HMC3) microglia by implementing comparative MLCC-based chemoproteomic workflows. Parallelly, we characterized the molecular consequences of HMC3 cell treatment with 2-bromopalmitate, a general s-acylation inhibitor, by performing immunocytochemistry and proteomic experiments. We also identified the s-acylation-dependent microglial inflammatory responses through live spatiotemporal tracking and confocal microscopy, following treatment of microglia with PAMPs (LPS or IFNy). Finally, from our proteomic studies of postmortem human brain tissues, we confirmed major protein-causals of schizophrenia, a redox-related brain disorder, to undergo inflammation-responsive s-acylation. This report provides a first comprehensive library of cysteine-proteins differentially processed through inflammation-responsive acylation in microglia. It also outlines the inflammation-responsive s-acylation of key NRF2-antioxidants, including peroxiredoxins (especially PRDX2) and glutathione synthetase (GSS), as a biochemical signature of early-stage inflammation and oxidative-stress in microglia. More importantly, the innovative proteo-informatic workflows designed for this research work can be reliably repurposed to identify bifunctional theragnostic protein markers of many complex disorders and diseases.

biochemistry↗

bioRxiv2026

A SRC-Annexin A2 axis that couples membrane repair to microRNA export during radiation stress in glioblastoma

Repair of ionizing-radiation (IR)-induced membrane damage is essential for cell survival, and Annexin A2 (ANXA2) mediates this repair by promoting shedding of microvesicles containing both damaged lipid and ANXA2. Here, we show that coupling this process to microRNA export contributes to radiation resistance of glioblastoma, the most common adult brain cancer. Structural modeling and mutational analysis identify that ANXA2 tyrosine 23 (Y23) phosphorylation, required for its IR-induced localization to damaged membranes, is also essential for binding miR-603, a critical regulator of glioblastoma cell state. This binding is required for IR-induced miR-603 export, indicating that the repair program recruiting ANXA2 also positions it to load miR-603 into microvesicles. Mutations that abolish ROS-induced sulfenylation and activation of SRC (SRC-C185A/C245A) suppressed ANXA2-Y23 phosphorylation, microvesicle shedding, and miR-603 export. The epistatic interaction between ANXA2-Y23A, SRC-C185A/C245A, and miR-603 delineates a therapeutically targetable radiation-response network that couples membrane repair with miRNA export.

cancer biology↗

bioRxiv2026

Predicting Pain Using a Data-Driven Agent-Based Model of the Bilateral Central Amygdala

Sensory processing in the amygdala is a complex, dynamic process. Decades of surgical, electrical, pharmacological, optogenetic, and chemogenetic in vivo manipulations have revealed the nociceptive functions of anatomically- and genetically-restricted neuronal populations. In parallel, molecular and electrophysiological approaches have allowed for high-resolution, temporal examination of nociceptive-induced alterations in amygdala plasticity. Computational integration of this data is critical for future therapeutic development; in practice, these models would allow for in silico prediction of amygdala activity following injury, and in a reciprocal fashion, changes in pain-like behaviors following manipulation of discrete amygdala neuronal populations. To this end, we developed a three-dimensional computer model of the bilateral central nucleus of the amygdala (CeA). We employed agent-based modelling to integrate wet-lab data from two CeA cell populations: Calcitonin Gene-Related Peptide Receptor (CGRPR; Calcrl) expressing cells and Protein Kinase C delta (PKC{delta}; Prkcd) expressing cells. We integrated the spatial location, connectivity, neuronal activity, and electrophysiological properties of these neurons in our realistic bilateral model architecture. Our model captures properties of the amygdala that drive pain modulation, including hemisphere-specific physiological differences, and generates predictions of nociception related to bladder injury. Predictions from the model were compared retrospectively to pain outcomes during manipulation of CGRPR-expressing neurons in whole mice. These comparisons show strong alignment between our model and in vivo outcomes. Significance StatementNociceptive processing in the amygdala emerges from interactions among cell types. No framework has been developed that recapitulates this complexity. Here, we generated a 3-D agent-based computational model of the bilateral central amygdala (CeA) using data that accounts for pain-associated changes in neuronal physiology, cellular identity, anatomical positioning, and temporal specificity. The model revealed that hemispheric differences in intrinsic CeA neuronal excitability are dominant drivers of nociceptive output. Furthermore, when manipulated to mimic injury-associated plasticity, the model accurately predicted behavioral outcomes. This model is a publicly available computational tool that predicts hemisphere-targeted pain therapy efficacy. Moreover, the flexibility of this framework will allow future adaptations to other brain areas and disease contexts.

neuroscience↗

bioRxiv2026

Generative Augmentation Reveals Previously Overlooked Signals in Transcriptomic Datasets

Identifying robust gene expression signatures from transcriptomic studies with small sample sizes remains one of the most persistent challenges in computational biology. Gene expression datasets have thousands of features but only a handful of biological samples. This presents the classic p >> n imbalance, which limits statistical power and makes it difficult to discover reliable biomarkers. In imaging, generative models such as GANs, VAEs, and diffusion models have demonstrated promising applications in data augmentation, but their usefulness for omics data has not been systematically tested. More importantly, no existing framework integrates synthetic data generation, stability-aware signature discovery, and multi-source biological validation into a single pipeline. In this work, we present GeneLift, with the hypothesis that a computational pipeline of generative data augmentation, stability testing, and evaluating biological evidence will aid novel gene-signature discovery in small-cohort transcriptomic studies. We tested this hypothesis across 36 microarray datasets covering five diseases: sepsis, breast cancer, ovarian cancer, tuberculosis, and diabetes. A component-wise testing of GeneLift revealed that Gaussian Mixture Models (GMMs) outperformed deep generative approaches and faithfully reproduced gene-level distributions. By a novel approach of titrating the level of augmentation, we identified biologically meaningful gene candidates that did not appear in the original, underpowered analyses. We also developed BayesScore, a Bayesian posterior probability of gene-disease association computed from PubMed co-occurrence, which both recovers well-characterised disease genes missed by standard differential expression and surfaces candidates whose disease relevance was independently confirmed in subsequent publications, with lead times of up to 18 years between the source dataset and the first disease-specific citation. GeneLift is freely available at tavlab-iiitd/GeneLift. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=103 SRC="FIGDIR/small/720348v1_ufig1.gif" ALT="Figure 1"> View larger version (41K): org.highwire.dtl.DTLVardef@13c8aeeorg.highwire.dtl.DTLVardef@1c5277corg.highwire.dtl.DTLVardef@a35664org.highwire.dtl.DTLVardef@17cdc48_HPS_FORMAT_FIGEXP M_FIG C_FIG

genomics↗

bioRxiv2026

A MaBBX21-MaGCN5 Histone Acetyltransferase Module Regulates Flavonoid Biosynthesis to Improve Heat and UV B Stress Tolerance in Banana (Musa acuminata)

Flavonoids are important specialized metabolites that contribute to plant pigmentation, stress adaptation, and nutritional value. In banana, a major global staple crop, their accumulation is highly tissue-specific, with very low levels in the edible pulp, and the mechanisms underlying this spatial distribution remain unclear. Here, integrative transcriptomic and metabolomic analyses across vegetative and reproductive tissues reveal that light-responsive regulatory networks control tissue-specific flavonoid biosynthesis. We identified a B-box transcription factor MaBBX21 as a key positive regulator of flavonoid biosynthesis. Its overexpression enhances flavonoid accumulation, whereas knockdown leads to a reduction in flavonoid levels in banana. Mechanistically, MaBBX21 interacts with MaHY5 and directly activates anthocyanin biosynthesis genes (MaDFR2 and MaANS). It also regulates metabolic flux by binding to the MaWRKY23 promoter, promoting flavonol biosynthesis through activation of MaFLS1 while partially repressing the anthocyanin branch. In addition, MaBBX21 introduces an epigenetic layer by activating the histone acetyltransferase MaGCN5, increasing H3K9 acetylation at target promoters, including MaDFR2, MaANS, and MaBBX21 itself, thereby forming a positive feedback loop. Functionally, MaBBX21 overexpression enhances flavonoid accumulation, ROS scavenging, and tolerance to heat and UV-B stress, whereas knockdown lines show reduced metabolite levels and increased stress sensitivity. Collectively, these results define a MaBBX21-MaWRKY23/MaGCN5 regulatory axis that integrates transcriptional regulation, and chromatin modification to control flavonoid biosynthesis, providing a foundation for improving nutritional quality and stress resilience in banana.

plant biology↗

bioRxiv2026

Evaluating splicing factor and kinase network crosstalk through global phosphoproteomics

Both splicing and kinase signaling are biochemical processes that fundamentally determine and shape cell physiology. Although there has been some indication that there is an interaction between the two - splicing can alter the availability of exons encoding kinase targets and kinases can phosphorylate splicing factors - it has yet to be established the extent to which altering splicing factor expression impacts kinase signaling networks. In this work, we implemented a data-driven analysis using ENCODE RNA-sequencing data and prior work mapping post-translational modifications onto splice events to identify candidate splice factor perturbations that show extensive alterations to phosphorylation-encoding protein products. We then replicated the ENCODE knockdown experiments and performed global phosphoproteomics for two candidates, U2AF1 and SRSF3, complementing the transcription-level data. Both knockdowns showed extensive changes in phosphorylation and kinase activities, both basally and upon receptor tyrosine kinase stimulation. U2AF1 knockdown drove decreased JNK-associated cell death signaling but elevated chromosome regulation through CSNK2A1, PLK, and EIF2AK4 activity. SRSF3 knockdown, on the other hand, led to decreased cell cycle signaling through CDK and HIPK2 but increased cytoskeletal signaling through various PAKs. In addition, we found a striking enrichment of phosphorylated splicing regulators in both knockdowns that were linked to their splicing activity, such as HNRNPC, suggesting potential feedback and crosstalk between splice factors through signaling pathway activation. Importantly, comparison of differential phosphorylation measurements from this study to mRNA expression and splicing measurements from ENCODE revealed significant knockdown-dependent protein regulation, not captured by transcriptomic measurements alone, underscoring the value of phosphoproteomic profiling after splice factor perturbations. Combined, the transcriptomics and phosphoproteomics reveal deep interconnection between the two processes that are relevant to understanding cell signaling in health and disease.

systems biology↗