Biology subjects

Das, A.

Publications and source records attributed to Das, A..

At least 55 records · Page 3Linked to original sources

bioRxiv2025

δ2-Protocadherins organize parallel indirect basal ganglia circuits

The basal ganglia (BG) contain multiple parallel neural circuits, each of which may control different behaviors. However, how the distinct parallel BG circuits are molecularly organized is not known. Here we show that two {delta}2-protocadherins (PCDHs), PCDH17 and PCDH10, which are homophilic cell-adhesion molecules, establish and define two distinct indirect BG circuits that regulate different behaviors. PCDH17 and PCDH10 are expressed in a complementary expression pattern in the BG, anatomically defining two parallel indirect BG connections. Indirect pathway-specific Pcdh17 and Pcdh10 conditional knockout (cKO) mice show impaired establishment of the indirect BG circuits in a region-preferential manner. Finally, the Pcdh17-cKO mice show defects in task learning, while the Pcdh10-cKO mice show defects in motor/sensory habituation. These results identify PCDH17 and PCDH10 as the molecular organizers for two distinct indirect BG circuits regulating different behaviors and reveal the molecular mechanisms for organizing parallel BG circuits. TeaserDistinct protocadherins organize parallel indirect basal ganglia circuits that regulate task learning or sensorimotor habituation

neuroscience↗

bioRxiv2025

Traumatic Conditioning Induces a Combination of Anesthesia Resistant Memory and Protein Synthesis Dependent Long-Term Memory in Adult Drosophila

Stressful experiences elicit long-lasting memory trace that often persists for life-time. Though storage of experience dependent memory is key to survival, post-traumatic memories are detrimental to the physical and emotional wellbeing. The generation of any form of long-term memory culminates from synaptic plasticity and potentiation through persistent change in protein synthesis. Drosophila has been a robust model for the study of memory mechanisms; olfactory memory paradigms have been enormously successful in elucidating neuroanatomical, molecular, physiological and signalling pathways underlying the process. Long-term memory (LTM) has been induced by protein synthesis dependent mechanisms followed by a post-learning consolidation process whereas a medium-term anaesthesia resistant memory (ARM) is mediated by the Radish protein in flies. Here we present a novel and simple memory paradigm in adult flies for inducing sustained stress-induced memory paradigm, where a single attractive odorant is associated with an aversive stimulus-copper sulfate, which provides bitter taste as well as sustained malaise due to toxicity. We find that the elicited memory is a combination of ARM and LTM which is dependent on the number of training cycles. The eight-cycle training paradigm leads to robust, CREB and protein synthesis dependent memory persisting for about 7 days. The mushroom body (MB) Kenyon cells neurons as well as the dopaminergic input neurons (PPL1 subset) are involved in the formation of memory mediated by enhanced calcium as well as synaptic elaboration in the {gamma} subset of the MB neurons.

neuroscience↗

bioRxiv2025

Cyclic AMP compartmentalization drives signal specificity to control vector colonization and mammalian host infection by American trypanosomes

Cyclic AMP (cAMP) signaling is crucial for environmental sensing and response to stress conditions in trypanosomatids. However, the mechanisms driving the specificity of cAMP signals remain poorly understood in these protozoan parasites. We recently identified two putative cAMP microdomains in Trypanosoma cruzi, the causative agent of Chagas disease. Here, considering the localization of three phosphodiesterases, PDEC at the contractile vacuole complex (CVC), and PDEB1 and PDEB2 along the flagellum, we modulated their expression to functionally characterize the flagellar tip (FT) and the CVC as individual cAMP microdomains, named FT-cAMP and CVC-cAMP, respectively. We generated PDE knockout and overexpression cell lines to selectively alter cAMP signals generated in each compartment. Our results indicate that FT-cAMP mediates cell adhesion, metacyclogenesis, host cell invasion, and intracellular replication, while CVC-cAMP is required for osmoregulation and epimastigote proliferation. In addition, ablation of flagellar PDEB1 and PDEB2 enhanced the parasites ability to colonize the hindgut of the triatomine vector, whereas PDEC-KO parasites were impaired in their establishment in the insects hindgut. The observed phenotypes were compartment-specific, demonstrating functional segregation between the two cAMP microdomains. Our data provide robust evidence on the presence of compartmentalized cAMP signals in T. cruzi, linking the role of locally synthesized cAMP pools to specific cellular responses during the parasites life cycle. Author summaryChagas disease is a life-threatening infectious disease caused by the protozoan parasite Trypanosoma cruzi, which is spread through the feces of infected kissing bugs. The parasite survives in challenging environments as it transitions between the insect vector and the mammalian host by differentiating into distinct developmental forms. cAMP is a universal second messenger that mediates specific cellular processes in the life cycle of T. cruzi. However, the spatial-temporal dynamics of cAMP signal remain largely unexplored in trypanosomes. We previously reported several cAMP signaling proteins in two compartments of T. cruzi: the contractile vacuole complex (CVC) and the flagellar tip (FT). In this study, we characterized the individual functions of these microdomains. We specifically disturbed cAMP signaling in these compartments by modulating the expression of their resident phosphodiesterases. We observed that the FT microdomain is specifically involved in parasite differentiation, host cell invasion, intracellular replication, and vector colonization, while the CVC microdomain is important for osmoregulation and parasite survival within the kissing bug. Our results unequivocally demonstrate that T. cruzi utilizes specific cAMP pools to address different environmental challenges. These findings highlight cAMP signaling as an essential pathway that could be further explored for the development of novel antiparasitic interventions.

cell biology↗

bioRxiv2025

Trehalose-mediated activation of Mitf corrects autophagy defects and ameliorates neurodegeneration in MPS VII

Mucopolysaccharidosis type VII (MPS VII) is a progressive lysosomal storage disorder caused by {beta}-glucuronidase ({beta}-GUS) deficiency, featuring pronounced neurodegeneration. The Drosophila model of MPS VII, generated by deleting the fly {beta}-GUS ortholog CG2135, exhibits hallmark neuropathological features, including dopaminergic neuron loss, brain vacuolisation, and impaired locomotor performance. Using this CG2135-/- fly, we recently showed that impaired autophagosome formation and their turnover led to abnormal accumulation of damaged mitochondria and lipofuscins in the brain. In this study, we investigated the molecular basis of this autophagy defect and found that Mitf (the TFEB homolog), the transcriptional regulator of autophagy, is markedly downregulated in CG2135-/- fly brains, accompanied by reduced expression of its target genes, including LAMP1, CLN3, and v-ATPase subunits. Guided by these observations, we assessed whether boosting Mitf activity could ameliorate neuropathology. Interestingly, oral trehalose treatment reactivated Mitf and its downstream autophagy gene network in CG2135-/- fly brains, restoring autophagosome biogenesis, reducing lipofuscin accumulation, and alleviating apoptosis. Trehalose treatment also improved locomotor performance, indicating a clear mitigation of neurodegeneration. These findings demonstrate that Mitf dysregulation drives autophagy impairment in MPS VII fly brain and highlight Mitf activation as a promising therapeutic strategy to alleviate neurological pathology.

cell biology↗

bioRxiv2025

Synthetic Biology Driven Melanin Deposition for Wood Coating

Pigments are widely utilized in industries such as textiles, cosmetics, food, and packaging. However, conventional synthetic pigment production relies on petroleum-based feedstocks, consumes significant energy, and involves toxic chemicals raising environmental and safety concerns. Natural pigments offer a sustainable and biodegradable alternative, yet their large-scale application is hindered by limited availability, batch variability, and geographical dependence. To overcome this, microbial biosynthesis has attracted attention as a controllable and scalable route for pigment production independent of environmental fluctuations. Nevertheless, most existing approaches retain multistep workflows - pigment synthesis, extraction, purification, and application. This compromises process efficiency and reproducibility. Herein, we present a whole-cell biocatalytic approach for melanin synthesis and deposition, wherein recombinant E. coli expressing tyrosinase is employed to convert L-tyrosine into melanin through copper-dependent oxidative polymerization. By harnessing intact microbial cells as self-contained biocatalytic units, this system bypasses the need for enzyme extraction and purification. Prior to applying the culture media containing melanin on material surfaces such as cotton and wood, the process conditions were optimized to enhance melanin yield. Subsequently, the material surfaces incubated in the melanin culture medium were characterized for their surface morphology and chemical modifications through scanning electron microscopy, Fourier transform infrared spectroscopy, and X-ray photoelectron spectroscopy. The color fastness properties of the material were also evaluated in the presence of water and detergents and subsequently improved through post-treatment processes. In addition, the melanin-coated cotton demonstrated enhanced photothermal performance compared to uncoated controls. All these taken together, this work establishes a simplified and potentially scalable route toward sustainable pigment production and direct application through enzyme-driven in situ biocatalysis on various material surfaces.

bioengineering↗

bioRxiv2025

Population genomic structure of sorghum landraces across landscape, environment and culture

The spread of staple crops to diverse environments over time and their current genetic structure may reflect historical dispersal by humans, sustained human preference for particular traits, and adaptation to local environments. Sorghum is a drought-tolerant crop native to Africa cultivated by hundreds of millions of smallholders globally. Here we examined the ecological context of population-genomic structure of 1,806 sorghum landraces across Africa and Eurasia to infer the relative contribution of environmental and cultural factors to sorghum genetic diversity across different relative time periods. Sorghum landraces were spatially and linguistically structured at a large-scale and within subregions, following a pattern of isolation by distance. Within regions, much of genomic structure was best explained by a mechanistic model of human travel time. In our assessment of hierarchical linguistic structure, we found that language families explain 4% of genomic variation while individual languages explain 13% of genomic variation, suggesting the importance of human culture and relationships in gene flow and selection. Variance partitioning showed that travel time, language, and climate explain up to 27% of genomic variation among landraces. We also observed regional differences in the degree of genetic relatedness across space and time in our assessment of shared ancestry. East Africa showed particularly strong geographic turnover in genomic composition and haplotype sharing, while West Africa showed substantial haplotype sharing even over large distances, signifying some rapidly spreading lineages. Thus, space, travel time, and culture likely capture important forces controlling sorghum genomic variation, but these factors operate heterogeneously over space.

plant biology↗

bioRxiv2025

Hidden Spirals Reveal Neurocomputational Mechanisms of Traveling Waves in Human Memory

While traveling waves are often described as planar propagations across cortex, recent theoretical work predicts that more complex spatial patterns, including spiral dynamics, could organize large-scale neural computations but remain difficult to detect in the human brain. To investigate this, we analyzed direct brain recordings from humans performing a working memory task. To characterize traveling wave patterns, we used independent component analysis, and showed that traveling waves propagated along the cortex in complex spatial patterns that correlated with behaviors such as memory encoding, maintenance, and retrieval. We then developed a novel computational framework based on coupled phase oscillators to model these distinct wave patterns. This computational approach revealed hidden spirals that were not visible in the original recordings. The center of these hidden spirals shifted across the cortex to distinguish separate behavioral states, such as memory encoding and retrieval. Together, these findings reveal that cortical traveling waves are governed by latent spiral attractor dynamics and suggest that rotating wave architectures provide a fundamental neurocomputational mechanism for flexible human memory processing.

neuroscience↗

bioRxiv2025

Omega-3 Fatty Acid Derived Neuroactive Lipids - Docosahexaenoyl-Glycine and Its Epoxide Metabolites are Multifunctional Lipid Mediators

Lipid mediators derived from {omega}-3 and {omega}-6 polyunsaturated fatty acids (PUFAs) support neurological health in part through their oxidative and non-oxidative transformation into a diverse array of bioactive molecules. Among these are lipidated neurotransmitters, formed via conjugation of neurotransmitters with fatty acids such as arachidonic acid (AA) or docosahexaenoic acid (DHA). Previous studies links these lipidated neurotransmitters to beneficial outcomes in neurological diseases. Here, we focus on two such endogenous lipidated neurotransmitters, arachidonoyl glycine (NA-Gly) and docosahexaenoyl glycine (DHA-Gly) and demonstrate their further biotransformation by cytochrome P450 enzymes into epoxidized metabolites. These metabolites are structurally multifunctional, combining both epoxide and glycine moieties. In lipopolysaccharide-stimulated microglial cells, we observe increased formation of NA-Gly and DHA-Gly, correlating with their anti-inflammatory effects. Functionally, these lipidated glycines are selective and act as inverse agonists of G protein-coupled receptor 55 (GPR55) and selectively potentiate transient receptor potential vanilloid 4 (TRPV4), but not TRPV1 or TRPM3 channels. Together, our findings identify NA-Gly, DHA-Gly, and their epoxide derivatives as multifunctional lipid mediators with anti-inflammatory properties and selective receptor modulation, positioning them as potential therapeutic leads in neuroinflammation and reinforce the critical side role of glycine in brain function. SignificanceLipidated neurotransmitters derived from omega-3 and omega-6 polyunsaturated fatty acids (PUFAs) contribute to neurological health through their conversion into a diverse array of bioactive signaling molecules. In this study, we study docosahexaenoyl glycine (DHA-Gly) and demonstrate their further enzymatic transformation by cytochrome P450 epoxygenases into epoxidized derivatives. These structurally distinct metabolites exhibit anti-inflammatory activity in microglial cells and interact with GPR55 and TRPV4, but not TRPV1 or TRPM3. Our findings highlight a new class of multifunctional lipid mediators with therapeutic potential for targeting neuroinflammation and related neurological disorders.

biochemistry↗

bioRxiv2025

Stabilized Full-Length Measles Fusion Protein Elicits Potent Immunity and Protection In Vivo

Measles virus (MeV) is a highly contagious pathogen that causes significant morbidity and mortality in populations with low vaccination coverage. Infection typically leads to immune amnesia and, in rare cases, fatal neurological disease. While current live-attenuated vaccines are highly effective, they primarily elicit neutralizing antibodies against the hemagglutinin (H) glycoprotein, with a less robust response to the fusion (F) protein, a key protein for viral entry. To improve the immunogenicity of the F protein, we designed and characterized stabilized, prefusion MeV F protein antigens. We engineered both soluble ectodomains (FECTO) and full-length, membrane-embedded proteins (FFL) with mutations that confer thermal stability. Cryo-electron microscopy confirmed that these engineered antigens faithfully maintain the native prefusion conformation. When evaluated in a cotton rat model, immunization with either FECTO or FFL constructs induced neutralizing antibodies and elicited protection against viral challenge. The most stable full-length construct (FFL 3M) elicited a more potent neutralizing antibody response than its ectodomain counterpart. Importantly, no evidence of vaccine-enhanced respiratory disease was observed. These findings establish that a thermostable, full-length F protein is a superior immunogen to its soluble ectodomain. This work presents a promising candidate for next-generation, non-replicating measles vaccines intended to complement current vaccination strategies and provide a safe option for immunocompromised individuals and others who cannot receive live-virus vaccines. One-Sentence SummaryA prefusion-stabilized, full-length measles Fusion glycoprotein immunogen induces strong neutralizing responses and offers protection against challenge with wild-type virus.

immunology↗

bioRxiv2025

Template switching by coronavirus polymerase requires helicase activity and is stimulated by remdesivir and molnupiravir

Polymerase template switching is an essential mechanism in coronaviruses (CoVs) that enables both sub-genomic (sg) RNA synthesis and increases genomic diversity via RNA recombination. Despite its importance, the molecular mechanism of CoV polymerase template switching remains unclear. Using magnetic tweezers, we show that the CoV non-structural protein (nsp) 13-helicase drives polymerase template switching, followed by copy-back RNA synthesis. This activity requires nsp13-helicase ATPase activity and a duplex RNA downstream of the CoV polymerase. This novel function of nsp13-helicase is targeted by the nucleotide analogs remdesivir and molnupiravir, whose incorporation in the nascent strand increases CoV polymerase template switching probability, leading to defective RNA production. We propose a novel mechanism of action where incorporation of these analogs dramatically reduces full length genome copy number by stimulating polymerase template switching. Our study further demonstrates nsp13-helicases central role in CoV replication and how this enzyme function can be indirectly targeted by analogs.

microbiology↗

bioRxiv2025

Harnessing cGAS-STING signaling to counteract the genotoxic-immune nexus in tauopathy

Tauopathies are progressive neurodegenerative disorders characterized by aberrant tau aggregation, cognitive decline, and persistent neuroinflammation, yet the mechanisms driving neuroinflammation and disease progression remain incompletely understood. Here, utilizing human postmortem AD brains and a mouse model of tauopathy, we report that genotoxic stress-induced cyclic GMP-AMP synthase (cGAS)-stimulator of interferon genes (STING) immune pathway form a self-amplifying loop that fuels neuropathology and cognitive deficits. Targeted disruption of this cycle through either genetic deletion of cGAS or pharmacological inhibition of STING restores immune homeostasis and attenuates tau pathology and cognitive deficits. Our results showed a significant accumulation of DNA double-strand breaks (DDSBs) and impaired DNA repair function, alongside elevated cGAS-STING signaling and type I interferon (IFN-I) responses in human AD brains compared to non-AD. In the PS19 transgenic (PS19Tg) mouse model of tauopathy, we found significantly elevated levels of DDSBs and altered expression of DNA repair proteins during early stages of disease, which preceded the dysregulation of cGAS-STING signaling and emergence of significant neuropathology in the later stage. Interestingly, genetic deletion of cGAS shifted microglial polarization from a pro-inflammatory M1 phenotype toward an anti-inflammatory M2 state, accompanied by a reduction in IFN-I signaling and improved cognitive performance in PS19Tg mice. Pharmacological STING inhibition reshaped the transcriptomic landscape, revealing selective regulation of pathways governing synaptic plasticity, and immune responses. This transcriptional reprogramming was accompanied by suppression of inflammatory responses, reduction in synaptic pathology, and attenuation of tau pathology in PS19Tg mice, underscoring STING as a therapeutic target for tauopathy. In conclusion, our findings reveal that genotoxic-immune crosstalk drives neuroinflammation and tau pathology and identify a conserved, druggable cGAS-STING axis that can be targeted to impede or slow disease progression in tauopathies. O_FIG O_LINKSMALLFIG WIDTH=184 HEIGHT=200 SRC="FIGDIR/small/678980v1_ufig1.gif" ALT="Figure 1"> View larger version (53K): org.highwire.dtl.DTLVardef@1339c89org.highwire.dtl.DTLVardef@16a1d5borg.highwire.dtl.DTLVardef@1ad4631org.highwire.dtl.DTLVardef@db4615_HPS_FORMAT_FIGEXP M_FIG C_FIG

neuroscience↗

bioRxiv2025

A complete diploid human genome benchmark for personalized genomics

Human genome resequencing typically involves mapping reads to a reference genome to call variants; however, this approach suffers from both technical and reference biases, leaving many duplicated and structurally polymorphic regions of the genome unmapped. Consequently, existing variant benchmarks, generated by the same methods, fail to assess these complex regions. To address this limitation, we present a telomere-to-telomere genome benchmark that achieves near-perfect accuracy (i.e. no detectable errors) across 99.4% of the complete, diploid HG002 genome. This benchmark adds 701.4 Mb of autosomal sequence and both sex chromosomes (216.8 Mb), totaling 15.3% of the genome that was absent from prior benchmarks. We also provide a diploid annotation of genes, transposable elements, segmental duplications, and satellite repeats, including 39,144 protein-coding genes across both haplotypes. To facilitate application of the benchmark, we developed tools for measuring the accuracy of sequencing reads, phased variant call sets, and genome assemblies against a diploid reference. Genome-wide analyses show that state-of-the-art de novo assembly methods resolve 2-7% more sequence and outperform variant calling accuracy by an order of magnitude, yielding just one error per 100 kb across 99.9% of the benchmark regions. Adoption of genome-based benchmarking is expected to accelerate the development of cost-effective methods for complete genome sequencing, expanding the reach of genomic medicine to the entire genome and enabling a new era of personalized genomics.

genomics↗

bioRxiv2025

Circular RNA Pde4dip regulates myogenesis by interacting with Zfp143 mRNA: A novel regulatory axis

Many transcriptional and post-transcriptional regulators tightly regulate skeletal muscle myogenesis, including recently discovered circular RNAs (circRNAs). In this study, we used a crosslinking-based sequencing method called CliPP-Seq, wherein we performed AMT-mediated Cross-Linking of RNA-RNA duplexes followed by Poly-A RNA Pulldown and sequencing to identify mRNA-interacting circRNAs in the mRNA samples of mouse C2C12 myoblasts and myotubes. BLAST analysis of the circRNAs with mRNAs identified their potential interacting partners. Interestingly, silencing of the circular RNA Pde4dip (circPde4dip) altered the target mRNA Zfp143 (zinc finger protein 143) expression and suppressed the differentiation of C2C12 myoblasts into myotubes. In summary, we identified unexplored mRNA-interacting circRNAs and their possible role in muscle cell differentiation, specifically the circPde4dip-Zfp143 mRNA interaction as one of the key regulators of myogenesis. HighlightsO_LIIdentified mRNA-associated circRNAs in differentiating C2C12 myoblasts C_LIO_LIThe first report identifying the regulation of myogenesis by circRNA-mRNA interaction C_LIO_LIcircPde4dip regulates C2C12 differentiation by interacting with Zfp143 mRNA C_LI

molecular biology↗

bioRxiv2025

Insular Traveling Waves Link Distributed Neural Dynamics to Human Memory Performance

The insula is a critical brain region that plays a foundational role in adaptive human behaviors, with diverse subregions performing distinct functional roles. However, explaining how these insular subregions interact to support behaviors is elusive. Using direct recordings from humans performing a spatial episodic memory task, we show that traveling waves within the insula modulate neuronal interactions across insula subregions, by propagating in distinct spatial patterns during specific phases of memory. In addition to traveling plane waves, insula waves also propagated in complex, heterogenous spatial patterns across task conditions. Insular traveling waves correlated with memory success, highlighting the critical role of insular traveling waves in orchestrating memory performance. Our study suggests that insular traveling waves are a key mechanism for modulating interactions and neural coding across regions to support memory processing and potentially a biomarker for investigating dysfunctions in neurological disorders.

neuroscience↗

bioRxiv2025

Spatial Single-Cell Atlas Reveals KSHV-Driven Broad Cellular Reprogramming, Progenitor Expansion, Immune and Vascular Remodeling in Kaposi's Sarcoma

Kaposis sarcoma (KS) is a highly inflammatory, angiogenic tumor driven by Kaposis sarcoma-associated herpesvirus (KSHV), yet the origins of tumor cells and mechanisms of progression remain unclear. Here, we present the first spatial single-cell atlas of KS, profiling 256 samples across patch, plaque, and nodular lesions and normal controls. We identify CD34 progenitor lymphatic endothelial cells (LECs) as the primary targets of KSHV, whose clonal expansion drives tumor growth. KSHV infection induces widespread cellular reprogramming across the tumor microenvironment, including LECs, vascular endothelial cells, fibroblasts, and macrophages, generating hybrid phenotypes that support angiogenesis, inflammation, and immune modulation. KSHV macrophages are enriched in tumor-proximal niches, further promoting a proangiogenic, immunosuppressive environment. Spatial analysis reveals evolving tumor-associated niches, with a core-to-periphery gradient correlating with infection, immune modulation, and cellular remodeling. We identify disease progression predictive signatures, offering mechanistic insights into KS pathogenesis and potential new therapeutic strategies by reprogramming the tumor microenvironment. Highlights CD34+ progenitor lymphatic endothelial cells are the primary KSHV target cells, with their clonal expansion driving Kaposis sarcoma growth. KSHV infection reprograms broad cell types into hybrid identities, and drives tumor-specific niche and vascular remodeling, endothelial plasticity, and immune modulation. KSHV-reprogrammed macrophages drive inflammation, angiogenesis, and immune modulation. Spatially resolved molecular and cellular signatures predict Kaposis sarcoma progression, offering novel therapeutic strategies targeting the tumor microenvironment.

cancer biology↗

bioRxiv2025

Repurposing Melatonin in dual-mode for Wilson disease therapy as a Copper Chelator and an antioxidant agent

Loss-of-function mutations in copper-ATPase ATP7B underlie Wilson disease (WD), a disorder characterized by hepatic copper accumulation and severe hepato-neuropathology. Existing chelation therapeutics remove excess copper but lack intrinsic antioxidant capacity and frequently cause systemic toxicity. Here we evaluate melatonin, an FDA-approved indoleamine with antioxidant and putative metal-chelating activity, as a candidate therapeutic for WD. In ATP7B-/- hepatocytes, melatonin restored copper-induced reactive oxygen species (ROS) to basal levels, reduced apoptosis twofold, and attenuated Nrf2 nuclear translocation leading to reduction of Hemoxygenase-1 abundance. Live-cell ratiometric analysis of GSSG/GSH using GRX1-roGFP2 expressed in melatonin-treated ATP7B-/- hepatocytes revealed a significant reduction in intensity-ratio, indicating an effective mitigation of copper-induced glutathione oxidation. Isothermal calorimetric titration revealed moderate Cu2+ affinity (K ITC=4.54 x 103 M-{superscript 1}), rationalized by MD-simulations showing an interaction energy of 18.5 x 10-3 kcal{middle dot}mol-{superscript 1} via amide-Cu{superscript 2} coordination. In-cellulo studies also revealed that copper-induced vesicularized ATP7B reinstates to Golgi in melatonin-treated hepatocytes. In vivo, melatonin treatment reduced copper-induced oxidative stress in zebrafish embryos and lowered copper burden in Caenorhabditis elegans WD model. Our studies revealed that encapsulation of melatonin within an engineered polymeric nanocapsules having dithiol linkers, susceptible to cleavage by GSH, extended melatonins circulatory half-life ten-fold and enhanced its ROS-scavenging efficacy three-fold relative to free melatonin. This work introduces a unique dual-function therapeutic strategy that integrates antioxidant activity with copper chelation, simultaneously addressing copper overload and redox imbalance. Repurposing melatonin, with its established clinical safety, offers rapid and cost-effective translational pathway toward WD-therapy while providing a generalizable platform for redox- and metal-associated disorders.

cell biology↗

bioRxiv2025

Active flows drive clustering and sorting of membrane components with differential affinity to dynamic actin cytoskeleton

Several cell membrane proteins, including signalling receptors and cell adhesion receptors, bind to contractile cortical F-actin at the cytoplasmic leaflet. Interaction with contractile actomyosin and associated actin flows drives these proteins into nanoscale clusters and mesoscopic assemblies of physiological relevance. In the context of diverse actin-binding membrane proteins, we ask how a specific composition of the local cluster/assembly may be achieved. Using in vitro reconstitution together with kinetic Monte Carlo simulations our studies reveal that an interplay between differential actin-binding affinity, protein-protein interactions and actomyosin remodelling leads to specific molecular patterning within a cluster and sorting between clusters. We show that in the lamellipodia of spreading cells in vivo, actin flows also result in the sorting of high and low-affinity actin-binders. This affinity-based sorting mechanism provides an attractive means for locally controlling cell membrane composition via engagement with the active cortical meshwork beneath.

cell biology↗

bioRxiv2025

MutAIverse: An AI-Powered, Mechanism-backed Platform for Discovering Novel DNA Adducts and their precursor Genotoxins

Genotoxin exposure leads to DNA adduct formation, potentially causing mutations if unrepaired. Current DNA adductomics platforms or analytical workflows are limited by incomplete spectral libraries, reliance on experimentally validated adducts, limited cellular contexts, and inefficient computational methodologies. We introduce MutAIverse, an advanced AI-driven DNA adductomics analysis platform that overcomes these limitations by leveraging intracellular mechanistic modeling of genotoxin bioactivation to construct a comprehensive DNA adduct library and offers advanced spectral mapping. MutAIverse integrates experimentally validated and chemically valid putative DNA adducts, enabling interpretable retrograde tracking to parental genotoxins. Validation of MutAIverse against experimental MS/MS datasets demonstrated the detection of both known and novel adducts. Furthermore, application to in-house generated DNA adductomics data from tissue biopsies of smokeless tobacco-induced head and neck cancer patients revealed selective enrichment of both novel and known DNA adducts; a subset of them was validated using MS/MS analysis. Collectively, MutAIverse provides a robust, end-to-end, and interpretable platform for advanced DNA adductomics analysis.

bioinformatics↗