Biology subjects

Maity, D.

Publications and source records attributed to Maity, D..

10 recordsLinked to original sources

bioRxiv2026

Self-generated oxygen limitation drives coral outcomes during marine heatwaves

Marine heatwaves cause massive, but often patchy coral bleaching. Why neighboring colonies often respond differently remains unresolved. Here, we show that interactions between metabolic demand and flow-mediated resupply generate heterogeneous oxygen microenvironments inside branching corals under heat stress. During the 2023 and 2024 Red Sea heatwaves, high-frequency in situ measurements revealed hypoxic to near-anoxic interbranch conditions despite well-oxygenated surrounding seawater. In 2023, neighboring colonies developed divergent oxygen regimes preceding paling and bleaching; in 2024, stronger and earlier thermal stress was associated with recurrent nighttime near-anoxia before tissue disintegration and mortality. A physics-based three-dimensional fluid-metabolism model reproduced these patterns. Oxygen depletion and coral impacts emerged when metabolic oxygen demand exceeded flow-mediated resupply. Organism-scale variability in oxygen regimes may explain divergent coral fate under shared heatwave exposure.

ecology↗

bioRxiv2026

Sphingomyelin-Cholesterol Synergy as a Lipid Chaperone Driving Cytolysin A Pore Formation

Bacterial pathogens rely on pore-forming toxins (PFTs) to breach host barriers, a feat that requires water-soluble monomers to spontaneously metamorphose into membrane-inserted pores. In the extracellular milieu, these toxins must navigate complex folding landscapes without ATP-dependent chaperones. Here, we show that the synergistic interplay of host sphingomyelin (SM) and cholesterol (CHOL) acts as an intrinsic "lipid chaperone" that drives the conformational maturation of the bacterial toxin Cytolysin A (ClyA). Using leakage assays on vesicles and suspended lipid bilayer (SuLBs) arrays, atomistic molecular dynamics (MD) simulations, cell membrane permeabilization assays and biophysical measurements, we demonstrate that SM-CHOL synergy accelerates the rate-limiting unfolding of the toxins membrane bound {beta}-tongue motif into a reactive "molten globule" intermediate and guides its subsequent refolding into functional -helical conformation crucial for pore formation. We identify conserved lysine residues (K175 and K206) as critical molecular sensors that detect this specific lipid signature to drive productive transformation. This assembly process reciprocally remodels the host membrane and dismantling liquid-ordered domains, suggesting a mechanical coupling between toxin folding and the disruption of host lipid homeostasis. Our findings establish a paradigm of lipid-mediated chaperoning, revealing how pathogens co-evolve to exploit host lipid complexity to overcome the energetic barriers of membrane insertion.

biophysics↗

bioRxiv2025

Targeting RARβ With a Stable Retinoic Acid Mimic Promotes Neurite Outgrowth, Neurogenesis, and Behavioral Recovery

Injury to the adult central nervous system triggers minimal axonal regeneration, partly due to the limited activation of intrinsic growth programs. Retinoic acid (RA) signaling has been shown to promote modest regenerative responses, but its clinical utility is restricted by poor biochemical stability and short-lived receptor engagement. Here, we report a tribenzamide-based small molecule DM04, that recapitulates RA-like transcriptional and phenotypic effects and enhances regenerative outcomes, independent of canonical RARE-dependent transactivation. DM04 promoted neurite outgrowth in primary neurons, upregulated canonical RA-responsive genes, and supported neural induction from human iPSCs. In a murine spinal injury model, DM04 treatment improved motor recovery. Transcriptomic analysis revealed shared target gene activation between RA and DM04, along with unique enrichment of extracellular matrix remodeling pathways. These findings establish DM04 as a small molecule based approach with dual efficacy in injury and developmental contexts, acting through a mechanism distinct from canonical RAR transactivation, and highlight its promise as a candidate for further preclinical investigation in neural repair.

neuroscience↗

bioRxiv2025

Prion protein-derived cell-penetrating peptide inhibits type II diabetes-associated islet amyloid polypeptide aggregation and cytotoxicity

Islet amyloid polypeptide (IAPP) is a 37-residue peptide hormone co-packaged and co-secreted with insulin by pancreatic {beta}-cells. A pathological hallmark of type II diabetes is the self-assembly of IAPP into {beta}-sheet rich amyloid fibers, which is associated with {beta}-cell impairment. Previously, we showed that a cell-penetrating peptide (CPP) construct, consisting of a hydrophobic signal sequence coupled to a polycationic nuclear localization signal (NLS)-like sequence, exhibited potent anti-prion activity and antagonism of Alzheimers disease-associated amyloid-{beta} (A{beta}) peptide aggregation and neurotoxicity. Here, we have extended this approach towards type II diabetes by assessing the efficacy of the CPP construct, designated as NCAM1-PrP, in inhibiting IAPP oligomerization, fiber formation and associated cytotoxicity. Using complementary in vitro and in silico experiments, we show that NCAM1-PrP effectively modulates IAPPs toxic structures into non-toxic conformations. This study underlines the potential of our designed CPP-based therapeutic approach as a versatile tool in the battle against amyloid-associated pathologies.

biochemistry↗

bioRxiv2023

Next-Gen Profiling of Tumor-resident Stem Cells using Machine learning

Tumor-resident stem cells, also known as cancer stem cells (CSCs), constitute a subgroup within tumors, play a crucial role in fostering resistance to treatment and the recurrence of tumors, and pose significant challenges for conventional therapeutic methods. Existing approaches for identifying CSCs face notable hurdles related to scalability, reproducibility, and technical consistency across different cancer types due to the adaptable nature of CSCs. In this context, we introduce OSCORP, an innovative machine-learning-driven approach. This methodology quantifies and identifies CSCs, achieving almost 99% accuracy using biopsy bulk RNAseq data. OSCORP leverages genetic similarities between normal and cancer stem cells. By categorizing CSCs into four distinct yet dynamic potency states, this approach provides insights into the differentiation landscape of CSCs, unveiling previously undisclosed facets of tumor heterogeneity. In evaluations conducted on patient samples across 22 cancer types, OSCORP revealed clinical, transcriptomic, and immunological signatures associated with each CSC state. It has emerged as a comprehensive tool for understanding and addressing the complexities of cancer stem cells. Ultimately, OSCORP opens up new possibilities for more effective personalized cancer therapies and holds the potential to serve as a clinical tool for monitoring patient-specific CSC changes during treatment or follow-up care.

cancer biology↗

bioRxiv2023

Methotrexate-modulated talin-dynamics drives cellular mechanical phenotypes via YAP signalling

Methotrexate is a well-known antineoplastic drug used to prevent cancer aggravation. Despite being a targeted therapeutic approach, its administration comes with the risk of cancer recurrence, plausibly through its proven off-target effect on focal adhesions. Since FA dynamics is dependent on force transmission through its constituent proteins, including talin, methotrexate might affect the mechanical activity of these proteins. Here we have combined single-molecule studies, computational dynamics, cell-based assays, and genomic analysis to unveil the focal adhesion-regulating role of methotrexate central to its effect on talin dynamics and downstream pathways. Interestingly, our single-molecule force spectroscopic study shows that methotrexate modulates the bimodal force distribution of talin in a concentration-dependent manner. Steered molecular dynamics reveal that methotrexate-talin interactions alter talin mechanical stability exposing their vinculin binding sites. Finally, we found that methotrexate-regulated talin-dynamics remodel cancer cell mechanical phenotypes like cell polarity, adhesion, and migration by regulating talin-vinculin association-mediated YAP signaling. These results further correlate with genomic analysis of methotrexate-treated patients, demonstrating its clinical importance. Taken together, these findings disseminate the effects of methotrexate-modulated mechanosensitivity of adhesion proteins on cellular events.

cell biology↗

bioRxiv2022

Profiling emergent behaviors from single-cell motility

Cell motility plays an essential role in many biological processes as cells move and interact within their local microenvironments. Current methods for quantifying cell motility typically involve tracking individual cells over time, but the results are often presented as averaged values across cell populations. While informative, these ensemble approaches have limitations in assessing cellular heterogeneity and identifying generalizable patterns of single-cell behaviors, at baseline and in response to perturbations. In this study, we introduce CaMI, a computational framework designed to leverage the single-cell nature of motility data. CaMI identifies and classifies distinct spatio-temporal behaviors of individual cells, enabling robust classification of single-cell motility patterns in a large dataset (n=74,253 cells). This framework allows quantification of spatial and temporal heterogeneities, determination of single-cell motility behaviors across various biological conditions, and provides a visualization scheme for direct interpretation of dynamic cell behaviors. Importantly, CaMI reveals insights that conventional cell motility analyses may overlook, showcasing its utility in uncovering robust biological insights. Together, we present a multivariate framework to classify emergent patterns of single-cell motility, emphasizing the critical role of cellular heterogeneity in shaping cell behaviors across populations. TeaserA computational framework to identify and classify single-cell motility patterns and phenotypic heterogeneity across biological conditions.

bioengineering↗

bioRxiv2021

Mechanical Compression Creates a Quiescent Muscle Stem Cell Niche

Skeletal muscles can regenerate throughout life time from resident Pax7-expressing (Pax7+) muscle stem cells (MuSCs)1-3. Pax7+ MuSCs are normally quiescent and localized at a niche in which they are attached to the extracellular matrix basally and compressed against the myofiber apically3-5. Upon muscle injury, MuSCs lose apical contact with the myofiber and re-enter cell cycle to initiate regeneration. Prior studies on the physical niche of MuSCs focused on basal elasticity6,7, and significance of the apical force exerted on MuSCs remains unaddressed. Here we simulate MuSCs mechanical environment in vivo by applying physical compression to MuSCs apical surface. We demonstrate that compression drives activated MuSCs back to a quiescent stem cell state, even when seeded on different basal elasticities. By mathematical modeling and manipulating cell tension, we conclude that low overall tension combined with high edge tension generated by compression lead to MuSC quiescence. We further show that apical compression results in up-regulation of Notch downstream genes, accompanied by increased levels of nuclear Notch. The compression-induced nuclear Notch is ligand-independent, as it does not require the canonical S2-cleavage of Notch by ADAM10/17. Our results fill the knowledge gap on the role of apical tension for MuSC fate. Implications to how stem cell fate and activity are interlocked with the mechanical integrity of its resident tissue are discussed.

biophysics↗

bioRxiv2020

Protein mimetic amyloid inhibitor potently abrogates cancer-associated mutant p53 aggregation and restores tumor suppressor function

Missense mutations in p53 are severely deleterious and occur in over 50% of all human cancers. The vast majority of these mutations are located in the inherently unstable DNA-binding domain (DBD), many of which destabilize the domain further and expose its aggregation-prone hydrophobic core, prompting self-assembly of mutant p53 into inactive cytosolic amyloid-like aggregates. Screening an oligopyridylamide library, previously shown to inhibit amyloid formation associated with Alzheimers disease and type II diabetes, identified a tripyridylamide, ADH-6, that potently abrogates self-assembly of the aggregation-nucleating subdomain of mutant p53 DBD. Moreover, ADH-6 effectively targets and dissociates mutant p53 aggregates in human cancer cells, which restores p53s transcriptional activity, leading to cell cycle arrest and apoptosis. Notably, ADH-6 treatment substantially shrinks xenografts harboring mutant p53 and prolongs survival, while exhibiting no toxicity to healthy tissue. This study demonstrates the first successful application of a bona fide small-molecule amyloid inhibitor as an anticancer agent.

cancer biology↗

bioRxiv2019

Trans-epithelial Fluid Pumping Performance of Renal Epithelial Cells and Mechanics of Cystic Expansion

Using a novel microfluidic platform to recapitulate fluid absorption activity of kidney cells, we report that renal epithelial cells can actively generate hydraulic pressure gradients across the epithelium. The fluidic flux declines with increasing hydraulic pressure until a stall pressure, at which the fluidic flux vanishes--in a manner similar to mechanical fluidic pumps. The developed pressure gradient translates to a force of 50-100 nanoNewtons per cell. For normal human kidney cells, the fluidic flux is from apical to basal, and the pressure is higher on the basal side. For human polycystic kidney disease (PKD) cells, the fluidic flux is reversed from basal to apical with a significantly higher stall pressure. Molecular studies and proteomic analysis reveal that renal epithelial cells are highly sensitive to hydraulic pressure gradients, developing different expression profiles and spatial arrangements of ion exchangers and the cytoskeleton in different pressure conditions. These results, together with data from osmotic and pharmacological perturbations of fluidic pumping, implicate mechanical force and hydraulic pressure as important variables during morphological changes in epithelial tubules, and provide further insights into pathophysiological mechanisms underlying the development of high luminal pressure within renal cysts.

biophysics↗