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Dey, S.

Publications and source records attributed to Dey, S..

At least 19 recordsLinked to original sources

Structural order emerges without mechanical order inside living cells

Intracellular organization is vital for cell function, and disruption of organelle positioning is connected to severe diseases, such as cancer. Given the small length scale of cells and the importance of Brownian motion, maintaining intracellular organization requires mechanical interactions to remain stable. Here, we test the common view that intracellular organization is reflected in intracellular mechanical properties. Using the recently introduced active mechanical fingerprint, we quantify intracellular mechanical properties and active forces to create mechanical maps of patterned RPE1 cells. The organization of actin, microtubules, the Golgi apparatus, the endoplasmic reticulum, and the nucleus reveals pronounced structural polarization across the cell population. To overcome limitations of simple averages, we use a Wasserstein barycenter to calculate an optimal intracellular organization that explains all measurements with minimal cellular distortion. To our surprise, and in contrast to previous reports, we find neither a statistically significant spatial mechanical pattern nor any relevant correlation between the tested structures and intracellular mechanical properties. While there is clear local mechanical anisotropy, the large heterogeneity of mechanical values outweighs any intracellular mechanical gradient. This is further supported by large cell-to-cell variability. Thus, despite having the same genome, cells function properly while their intracellular mechanical properties vary over two orders of magnitude.

biophysics↗

Accessing Enzyme Kinetic Data and Prediction Methods at Scale

Enzyme kinetic parameters inform metabolic models, yet experimental measurements are sparse. A growing body of work predicts them from protein and substrate features, but software fragmentation hinders adoption, so downstream tools lock into the most accessible method. We present OpenKinetics Predictor (at predictor.openkinetics.org), an open-source platform integrating thirteen methods in isolated environments behind one interface. The platform optionally reports similarity between query proteins and each method's training data to contextualise reliability. A common featurisation-prediction abstraction keeps it extensible, and independent parties, including original authors, contributed many methods. We pair it with a data portal (at data.openkinetics.org) that exposes CatLog, a curated kinetic dataset, with precomputed embeddings, predicted binding sites, and standardised splits. Both offer a web interface and an API, and the GECKO modelling toolbox already calls the predictor API. As a case study, we predict across an E. coli model and find inter-predictor agreement varies with metabolic context and data availability.

systems biology↗

Genetic and structural interpretation of NLRP1 FIIND domain variants in glioma in an Indian cohort: a pilot study

Gliomas, particularly glioblastoma (GBM), are aggressive primary brain tumors associated with dysregulated NLR signaling, a pathway central to innate immunity and inflammation. NLRP1 triggers proinflammatory cytokine release and pyroptotic cell death via autoproteolytic cleavage. The FIIND missense variant rs11651270 (M1184V) may modulate this cleavage process. While NLRP1 polymorphisms are associated with various diseases and cancers, their specific impact on glioma remains to be investigated. In our study, five FIIND-domain single-nucleotide polymorphisms (SNPs) of NLRP1 rs371579423, rs58604457, rs57636751, rs11651270, and rs2301583, were investigated by Sanger sequencing in a clinical cohort of glioma patients and compared against population-matched controls from the GenomeIndia dataset (Rajasthan cohort) using genetic association models. Molecular dynamics simulations were performed to evaluate the structural effects of the missense variant rs11651270 (M1184V) in NLRP1 during pre- and post-cleavage states. The linked variants rs58604457 (G>A) and rs57636751 (C>T) exhibited complete linkage disequilibrium (r2=1.00) and were significantly associated with lower odds of glioma (odds ratio ~0.5). The missense variant rs11651270 (T>C) showed no association with glioma risk. Notably, the SNP rs2301583 had a higher allelic frequency in glioma cases despite being absent in the GenomeIndia population-based control catalogue. Molecular dynamics simulations revealed that the M1184V substitution stabilizes local FIIND architecture by preserving {beta}-strand organization through persistent interactions with neighboring residues. This study provides the first combined genetic and structural analysis of NLRP1 FIIND-domain variants in an Indian glioma cohort. These findings illustrate the potential value of integrating population-based genetic association with structural modelling to generate hypotheses and uncover potential functional mechanisms of inflammasome-gene variants in neuro-oncology.

cancer biology↗

Programmable Self-Assembly of RNA Nanostructures with >100 Unique Components

Sophisticated biomolecular functions often arise from large, precisely organized architectures, motivating efforts to construct increasingly complex structures through programmed nucleic acid self-assembly. Although RNA offers a richer repertoire of structural motifs and biological functions than DNA, RNA nanostructures constructed to date have remained substantially less complex and less scalable than their DNA counterparts, most notably DNA origami and DNA bricks, which rely on large libraries of synthetic single-stranded (ss) DNA strands. Directly adapting these strategies to RNA, however, faces two major barriers: (i) the high cost of producing large libraries of distinct synthetic ssRNA strands, and (ii) the limited stability of ssRNA under conditions commonly used for assembling multicomponent nucleic acid nanostructures. Here we present the double-stranded RNA (dsRNA) bricks approach, which addresses both barriers by adopting principles inspired by natural RNA systems: (i) many distinct RNA components ("bricks") are encoded within a single precursor transcript and released by enzymatic processing, (ii) each brick's predominantly double-stranded nature enhances stability. The resulting dsRNA bricks self-assemble through programmable branched kissing-loop interactions. Using this approach, we constructed complex two- and three-dimensional RNA nanostructures with more than 100 distinct components, representing, to our knowledge, the largest and most compositionally complex RNA nanoarchitectures reported to date. Overall, the dsRNA bricks approach establishes a scalable and robust framework for constructing complex RNA nanostructures with compositional and architectural sophistication approaching that of DNA-based systems, thereby opening new opportunities for programmable RNA materials and RNA-based devices.

synthetic biology↗

Synthetic transcriptional control in the malaria parasite Plasmodium falciparum

Malaria is responsible for over half a million deaths each year. However, our understanding of malaria parasite biology is hampered by a lack of molecular tools, particularly at the level of transcriptional control. In light of this, we have created two orthogonal systems for inducible transcriptional repression in the malaria parasite Plasmodium falciparum using bacterial repressor proteins. We achieve 200- to 800-fold repression of expression, improving on previous attempts at transcriptional regulation by two orders of magnitude and outperforming gold standard translational/post-transcriptional regulation systems. We developed automated DNA design software to apply this tool to conditional regulation of native gene expression, validating essentiality and chemogenetic interactions with both two parasite lipid kinases and PfKelch13, which is associated with artemisinin resistance. These tools can advance our understanding and engineering of malaria functional genomics, drug mechanisms, and gene regulation.

synthetic biology↗

Protein size and geometry govern mutational robustness

A fundamental question in structural biology centres around understanding protein evolution. Key to this process is mutational robustness, defined as the protein fold's ability to absorb sequence changes without collapsing its structure. Here, we show that robustness is systematically shaped by simple features such as protein size, geometry, and oligomeric state. We used Foldseek-identified (structural) homologs to quantify family size across monomers and higher homo-oligomers. We found that proteins in larger families are consistently larger in size, more compact in atomic density, and less exposed to solvent. Strikingly, homo-oligomers occupy systematically larger families than monomers, revealing quaternary structure itself as a driver of mutational tolerance, not merely a functional supplement. This signature of robustness can be further linked to increasing functional complexity in proteins; those with adaptive, multifaceted biological roles belong to larger structural families than those with specific roles, thereby linking structural flexibility directly to evolutionary versatility. In short, simple yet overlooked features of protein geometry can explain mutational robustness and evolvability, offering a structural rationale for why certain protein families have diversified extensively while others remain in evolutionary stasis.

bioinformatics↗

Edge controllability is associated with treatment response to repetitive transcranial magnetic stimulation in depression.

Repetitive transcranial magnetic stimulation (rTMS) is an established treatment for major depressive disorder (MDD), yet variability in treatment response remains a significant challenge. Network control theory provides a framework to quantify how brain networks facilitate state transitions, but prior work has focused primarily on node level metrics. Here, we investigate whether edge based controllability of the structural connectome is associated with rTMS outcomes. Twenty five patients with treatment-resistant depression underwent diffusion MRI prior to a 5 week course of high frequency rTMS targeting the dorsolateral prefrontal cortex. Structural connectomes were constructed using MRtrix3 and the Destrieux atlas, and edge based controllability metrics were computed at baseline. Controllability of specific middle frontal gyrus centered edges showed significant associations with changes in HAMD-24 scores, including connections to the superior frontal gyrus, hippocampus, angular gyrus, and orbital gyrus (r =- (0.470 - 0.597), p < 0.05). These findings suggest that edge based controllability captures circuit level properties relevant to treatment response and may inform personalized neuromodulation strategies.

neuroscience↗

PFAS triggers a SpoT-associated metabolic switch that promotes persister-like phenotype in Salmonella Typhi

Per- and polyfluoroalkyl substances (PFAS) are new pollutants in the environment whose effects on bacterias physiology is not well understood. In this study, we show that exposure to PFAS causes membrane depolarization in Salmonella enterica serovar Typhi. This works as a metabolic uncoupler that breaks down proton motive force without immediately killing the cells. This disturbance results in a significant elevation of intracellular NADH and NAD levels while preserving redox equilibrium, signifying an augmented metabolic flux. At the same time, we see that {beta}-oxidation pathways are turned on, which suggests that the cells are shifting toward breaking down fats to make up for the lack of energy. Even though there are more reducing equivalents, ATP levels go down, which is what happens when respiration is uncoupled. This puts the cells in a state of "pseudo-starvation." This metabolic stress triggers the SpoT-dependent stringent response, leading to the accumulation of (p)ppGpp. Genetic analysis employing {Delta}relA and {Delta}relA{Delta}spoT mutants confirm that SpoT is necessary for this adaptive response. Functionally, PFAS-treated populations show an enhanced proportion of persister-like cells, which connects exposure to environmental pollutant in the environment to antibiotic tolerance. Our findings reveal a previously unidentified mechanism by which PFAS alters bacterial metabolism and stress responses, facilitating persistence through membrane depolarization, metabolic reconfiguration, and stringent response activation. This study underscores the potential influence of environmental pollutants on bacterial survival mechanisms and antibiotic resistance.

microbiology↗

A transcriptomic axis aligns with in vivo functional dynamics in hippocampal inhibitory circuits

Linking molecular identity to function in vivo at single-cell resolution remains an outstanding challenge in neuroscience. Here, we bridge this gap in the mouse hippocampus with an end-to-end pipeline of cell-resolved two-photon imaging and spatial transcriptomics. CA1 interneurons exhibiting heterogeneous physiological responses during a virtual-reality navigation task were post hoc clustered by gene expression into 5 GABAergic subclasses and 14 types. Physiological responses of individual cells aligned with a transcriptomic axis, and a classifier trained on physiological features alone recovered the same ordered organization. Our approach establishes a direct, scalable framework for linking in vivo circuit dynamics to constituent cell identity, revealing a transcriptomic axis that encompasses the structural and functional diversity of hippocampal inhibitory neurons. One-Sentence SummaryTracking neurons from behavior to spatial transcriptomics links in vivo function to molecular identity in the hippocampus.

neuroscience↗

Tubulin glycylation regulates microtubule-protein interactions that are key for ciliary stability and trafficking

Tubulin glycylation, a cilia-specific posttranslational modification is emerging as a potentially key regulator of ciliary axonemal microtubules. However, insights into the functional consequences of glycylation have remained limited. Here, using in vitro reconstitution assays with unmodified or custom-glycylated tubulin, we provide a systematic mechanistic analysis of glycylation-dependent regulation of motors and microtubule-associated proteins. Our studies highlight that glycylation selectively enhances ciliary kinesin-2 motility while reducing kinesin-1 activity, suggesting a role in promoting efficient intraflagellar transport along axonemal microtubules. Moreover, glycylation protects microtubules from decay by suppressing the activities of the depolymerase MCAK and severing enzyme spastin, thereby enhancing stability. Notably, this regulation is dependent on the proportion of glycylation on the microtubule surface, coupled with concomitant reduction of glutamylation. Thus, by generating microtubule surfaces with distinct biochemical states, we establish that combinatorial modification patterns define functional microtubule properties especially in cilia. Together, our findings provide the first comprehensive mechanistic framework for tubulin glycylation in regulating molecular motors and MAPs in cilia, establishing glycylation as a key determinant of motor selectivity and microtubule stability within the axoneme.

biochemistry↗

Genome-wide association study and transcriptomics reveal the genetic architecture of alkalinity tolerance in Arabidopsis thaliana

Alkalinity stress significantly restricts global plant productivity, yet the genetic basis for plant tolerance remains largely uncharacterized. In this study, a genome-wide association study was performed using 218 diverse natural Arabidopsis thaliana ecotypes to identify the top 73 SNPs associated with alkalinity tolerance, measured by relative root length in hydroponic growth media containing NaHCO3 at pH 8.0. Prominent association peaks were localized near genes involved in lipid metabolism (GGL20), protein degradation (AT3G17570), and vesicle-mediated protein sorting (VPS13B and AT5G57210). Expression level and protein polymorphisms in these genes were associated with alkalinity tolerance. T-DNA mutants of GGL20, AT3G17570, and the chromatin-modifying gene AFR1 showed alkaline hypersensitivity, reduced root length, iron content, and rosette size, and elevated hydrogen peroxide. Conversely, mutants of the DNA repair gene ETG1 exhibited greater tolerance than wild type in hydroponics, solid media, and soil assays, confirming their role in alkalinity tolerance. Transcriptome and network analyses revealed that alkalinity responses significantly overlap with iron deficiency pathways, identifying hub genes involved in ribosome assembly and translation control. These findings provide a comprehensive map of the genetic and transcriptional landscape of alkalinity adaptation and offer promising candidate genes for engineering crops resilient to alkaline soil conditions.

plant biology↗

Structural and Metabolic Characterization of Ni(I)-inhibitors Provide a Robust Anti-Methanogenicity Scoring System

Atmospheric methane (CH4) acts as a key contributor to global warming and a short-lived climate forcer. CH4 mitigation represents the most promising means to address short-term climate change. Ruminant enteric CH4 produced by methanogenic archaea represents 27.2% of global CH4 emissions. Only a few of the direct methanogenesis inhibitors identified bear high mitigation potential hence it is important to investigate their underlying modes of action. Here, we elucidated biophysical and thermodynamic interplay between known inhibitors and cofactor F430, to determine their stoichiometric ratios and binding affinities. We leverage this prior in a robust contrastive learning approach to functionally cluster known sixteen inhibitors and 53,959 bovine-linked metabolites. We demonstrate a multi-factor optimization protocol to identify putative inhibitors with: (i) high bacterial membrane permeability, (ii) no adverse effect to ruminal fermentation, (iii) known degradation pathway, and (iv) direct commercial availability. Subsequent in vitro assays and community metabolic modeling with a first set of eight treatment molecules revealed structo-metabolic priors that tie thermodynamic signatures of inhibition to metabolic flux shifts. We established a multi-scale workflow that transforms ostensibly negative compounds into mechanistic insight, linking rumen metabolic flux shifts to MCR-F430-Ni(I) inhibition chemistry as a foundation for rational methane-mitigation design. COVER ABSTRACT O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=147 SRC="FIGDIR/small/708075v1_ufig1.gif" ALT="Figure 1"> View larger version (40K): org.highwire.dtl.DTLVardef@1d38d21org.highwire.dtl.DTLVardef@1d681d9org.highwire.dtl.DTLVardef@1e70c0corg.highwire.dtl.DTLVardef@1c8223f_HPS_FORMAT_FIGEXP M_FIG C_FIG

systems biology↗

Spatial pattern formation as a consequence of Protease Competition

Exploring the emergence of spatio-temporal patterns due to nonlinearities in gene expression is a relatively new development. In this work, we explore the effect of resource constraint on gene regulatory motif from both equilibrium and spatio-temporal standpoint, taking into consideration the degradation class of resource, protease. We have demonstrated that protease-tagged degradation can cause an emergent bistability to form in the system in a steady-state scenario. Instead of a graded linear response in protein synthesis, two Saddle-node bifurcations caused by protease competition provide a switch-like response with hysteresis, where two drastically differing protein concentrations can coexist. We next turn our attention to spatio-temporal analysis: we extend our study for a two-dimensional sheet of cells with diffusible protein molecules and report the stationary patterns.To investigate the reasons behind these non-homogeneous stationary patterns, we investigate the traveling wave solution and observe that a stationary pattern is formed by the traveling wave solution. Considering that proteases play a major role in the regulation and expression of genes in a variety of diseased scenarios, the repercussions of this spatial patterning caused by protease competition can be extensive in gene regulatory systems.

synthetic biology↗

Pseudomonas simiae-induced resistance in barley is associated with compromised JA signaling and phyllosphere microbiome responses

Interactions of plant growth-promoting rhizobacteria with plant roots can trigger induced resistance (IR) protecting above-ground tissues from disease, a process that is increasingly recognized for its potential to support sustainable crop protection strategies. Although the molecular basis of IR has been extensively studied in Arabidopsis thaliana, considerably less is known about the underlying mechanisms in cereal crops. Here, we show that Pseudomonas simae WCS417r triggers IR in barley (Hordeum vulgare), reducing the propagation of Blumeria graminis f. sp. hordei, the causative agent of barley powdery mildew. Analysis of defense-associated marker genes revealed pathogen-dependent transcriptional responses during IR: HvPATHOGENESIS-RELATED1 (HvPR1) was induced by powdery mildew but not by the bacterial pathogen Xanthomonas translucens pathovar cerealis, whereas HvPR5 responded to both pathogens, with its induction by X. translucens depending on WCS417r-IR. To improve our molecular understanding of IR, transcriptomic responses to methyl jasmonate, salicylic acid and abscisic acid were characterized and used to identify hormone-responsive genes. Notably, several jasmonate-responsive genes were suppressed during powdery mildew infection, and this suppression was more pronounced in plants undergoing IR, indicative of priming. Finally, metabarcoding of the phyllosphere microbiome demonstrated that IR was not associated with major shifts in bacterial community composition. Alpha and beta diversity remained largely unchanged, while a limited number of amplicon sequence variants differed in abundance between treatments. Together, these results show that P. simiae WCS417r induces resistance against powdery mildew in barley through priming pathogen-dependent transcriptional changes while leaving the overall phyllosphere microbiome structure largely intact.

plant biology↗

Bi-directional highways and super-seeder tissues underpin parasite dissemination in experimental visceral leishmaniasis.

Visceral leishmaniasis (VL) is a life-threatening parasitic disease caused by Leishmania donovani and L. infantum. Although VL is characterised by organ-specific immunopathology and parasitism of the spleen, liver and bone marrow, other tissues may harbour parasites without overt pathology. The mechanisms governing patterns of within-host dissemination and tissue tropism are largely unknown. We used a barcoded library of isogenic L. donovani and an ecological analysis framework to evaluate parasite population diversity across tissues and to map parasite dissemination in a murine infection model. We reveal an unexpected high degree of inter-connectivity between parasite populations demonstrating: i) continual bi-directional dissemination between viscera and skin; ii) the existence of "super-seeder" sites that act as hubs fuelling systemic spread; and iii) rerouting of dissemination "highways" following immune perturbation. These findings change our understanding of L. donovani pathogenesis, providing critical insights into infection dynamics with direct implications for relapse, treatment failure and transmission.

microbiology↗

A single-cell transcriptomic atlas of peripheral blood immune cells spanning progressive canine leishmaniosis

Dogs play a major role in sustaining transmission of Leishmania infantum to people, thus prevention and treatment of canine leishmaniosis (CanL) to reduce transmission represents an unmet public health need. Although advances have been made in understanding how immunopathology correlates to infectiousness as CanL progresses, the immune mechanisms underlying transition between disease stages and terminal decline remain ill-defined. To address this knowledge gap, we generated a comprehensive atlas of peripheral immune cells from control dogs and naturally-infected dogs using single-cell RNA sequencing. The LeishDog Atlas captures the cellular and transcriptional complexity underlying CanL, tracing shifts in immune composition and gene expression across progressive, well-defined disease stages. Notably, we identified distinct myeloid, CD4+ and CD8+ T cell phenotypes and transcriptional states associated with disease progression. This resource provides a valuable framework for understanding systemic immune dysregulation in CanL, including determinants of T cell exhaustion and myeloid cell activation, and establishes a foundation for comparative, translational, and mechanistic studies of CanL immunopathology and transmissibility.

immunology↗

Polarization MultiFocus Microscopy for volumetric super-resolution and orientation imaging of biofilaments

Accessing molecular orientation in single molecule localization microscopy (SMLM) offers valuable insights into molecular ordering and organization in biological structures. Conventional single-molecule orientation-localization microscopy (SMOLM) methods typically rely on either engineering the microscopes point-spread function (PSF) to encode the orientation information or on polarization resolved detection. While PSF engineering enables detailed orientation analysis, it often requires complex computational analysis and suffers from reduced performance in dense cellular environments due to PSF spreading and overlap. In contrast, polarization-based approaches are easier to implement and are more fit when imaging dense samples but are unable to retrieve the axial information of single molecules. To overcome this limitation, we introduce the Polarization MultiFocus Microscope (PolMFM), a novel method for simultaneously retrieving the orientation and 3D position of single molecules. PolMFM combines the orientation measurement capabilities of a 4-polarization splitting scheme with a 3-planes multifocus microscope (MFM) enabling the reconstruction of molecular 2D orientation, wobble, and axial localization in a single acquisition. Through simulations, we demonstrate that PolMFM accurately recovers both orientation and 3D position, despite PSF defocusing. Experimental validation with reference samples shows that PolMFM matches the orientation precision of 4-Polar STORM, while uniquely adding axial information. We demonstrate the power of PolMFM by resolving the orientation and 3D positions of molecules in actin filaments in fixed cells, and by revealing that chromatin in crickets undergoes major reorganization and increased ordering during spermiogenesis. These findings highlight the potential of PolMFM for high-precision, multidimensional super-resolution imaging in complex and crowded biological environments.

biophysics↗

Revisiting the Evolution of Lactase Persistence: Insights from South Asian Genomes

Lactase persistence (LP), the ability to digest lactose from milk into adulthood, is a classic example of natural selection in humans. Multiple mutations upstream of the LCT gene are associated with LP and have been previously shown to be under selection in Europeans and Africans. South Asia is the worlds largest producer of dairy, and milk and dairy products are widely consumed throughout the subcontinent. However, the origin, evolutionary history and selective pressures associated with LP in South Asia remain elusive. We assembled genome-wide data from [~]8,000 present-day and ancient genomes from India, Pakistan, and Bangladesh, spanning diverse timescales ([~]3300 BCE-1650 CE), geographic regions, and ethnolinguistic and subsistence groups. We find that the Eurasian LP-associated variant,-13.910:C>T, is widespread across South Asia, exhibiting clinal variation along north-south and east-west gradients. Ancient DNA analysis reveals that this variant first appeared in South Asia during the historical and medieval periods through Steppe pastoralist-related gene flow. Interestingly, unlike in other worldwide populations, the LP prevalence is almost entirely explained by Steppe ancestry--not selection--in most contemporary South Asians. A notable exception is the only two pastoralist groups, Toda in South India and Gujjar in Pakistan, that have unexpectedly high frequencies of-13.910*T, comparable to estimates in Northern Europeans. By performing local ancestry inference, we find significant enrichment for Steppe pastoralist ancestry around the LCT locus in these two geographically-distant pastoralist groups, indicative of strong selection. Together, these findings highlight the complex role of ancestry and natural selection in shaping the prevalence of lactase persistence on the subcontinent.

evolutionary biology↗