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Sankar, S.

Publications and source records attributed to Sankar, S..

15 recordsLinked to original sources

Super-resolution mapping of platelet α-granules uncovers non-polarized secretion and differential retention of von Willebrand Factor and thrombospondin-1

Platelet -granules contain hundreds of bioactive proteins that regulate thrombosis, inflammation and tissue repair. The interplay between -granule secretion and platelet biomechanics is central to platelet function but remains incompletely understood. Here we combined complementary super-resolution microscopy methods, computational image simulations and quantitative single-cell analysis to investigate -granule nanoscale organization and secretion in tandem with cytoskeletal remodeling in spreading human platelets. We show that P-selectin, thrombospondin-1 (TSP1) and von Willebrand factor (VWF) occupy distinct subgranular domains and that apparent co-localization strongly depends on imaging resolution. We identify ring-like P-selectin staining as a robust signature of intact -granules and demonstrate that -granule secretion in spreading platelets was confined to the platelet cell body rather than the actively remodeling periphery. Quantitative assessment at the single-cell level showed that degranulation coincided with transitions from filopodia-rich to lamellipodial morphologies. Comparisons across adhesive substrates and perturbations by soluble agonists indicated that these processes are coordinated through overlapping signaling networks rather than direct local coupling. Analysis of secreted cargo revealed distinct extracellular fates despite no evidence for polarized secretion. TSP1 accumulated beneath platelets within diffusion barrier-restricted membrane pockets and around platelets following matrix binding, whereas VWF remained predominantly tethered to platelet membranes and formed short VWF strings. Together, our findings redefine the organization and release of platelet -granules, demonstrate an absence of secretion polarity, and establish cargo-specific retention mechanisms that may influence platelet signaling and thrombus architecture.

cell biology↗

Maternal obesity induces developmental programming of Intestinal stem cells through an IL-17A/PPAR immune-epithelial axis

Maternal obesity is associated with increased risk of sporadic colorectal cancer (CRC) in offspring, suggesting that early-life environmental exposures durably shape disease susceptibility. Intestinal stem cells (ISCs), long-lived drivers of epithelial renewal and tumor initiation, are well poised to mediate this effect; however, how maternal obesity influences ISC programming during development remains poorly understood. Using mouse models of diet-induced obesity, we show that exposure to a maternal high-fat Western diet (mHFD) during pre- and postnatal development stably programs colonic ISCs. Offspring exhibit increased ISC proliferation, enhanced self-renewal, a hypermetabolic state, and altered epithelial lineage composition that persists into adulthood despite dietary normalization. These changes are accompanied by increased tumor burden following loss of Apc heterozygosity. Mechanistically, we identify the pro-inflammatory cytokine IL-17A as a key extrinsic driver and PPARd/a nuclear receptors as intrinsic mediators of the mHFD phenotype, revealing an immune-epithelial axis that programs ISC function during early life. Together, our findings demonstrate that maternal metabolic environments durably enhance stem cell fitness, providing a mechanistic link between developmental exposure and adult disease risk.

cell biology↗

Genomic Evolution of SARS-CoV-2 Delta Variants Pre- and Post-Omicron Emergence using Alignment-free Machine Learning models

The SARS-CoV-2 Delta variant (B.1.617.2), initially classified as a variant of concern due to its enhanced transmissibility and vaccine-escape mutations, underwent further genomic changes following the emergence of the Omicron variant (B.1.1.529). This study investigates the genomic differences in Delta variant spike gene sequences collected before and after the emergence of Omicron. A total of 190 sequences were analyzed using an alignment-free approach incorporating k-mer-based feature extraction and machine learning models, including convolutional neural networks (CNN), K-means clustering, and random forest classification. The random forest model achieved 93% accuracy, with significant F1 scores, effectively distinguishing the two Delta variant groups. Comparative analysis revealed 157 persistent mutations and four vanished mutations in the post-Omicron group. Cluster analysis showed notable shifts, indicating stable yet evolving genomic patterns over time. The study demonstrates the advantage of alignment-free methods in detecting subtle sequence variations that alignment-based approaches may overlook. These findings enhance our understanding of SARS-CoV-2 evolution and provide a framework for identifying key genomic signatures relevant to public health. The methodology and insights gained offer potential applications in variant surveillance, vaccine design, and viral evolutionary studies, supporting preparedness for future SARS-CoV-2 variant emergence.

genomics↗

Diet-induced chromatin states influence intestinal stem cell memory

Intestinal stem cells (ISCs) integrate dietary cues through a metabolic-transcriptional axis, but whether these mechanisms create a lasting epigenetic memory remains unclear. Here, we investigate diet-induced chromatin adaptations in ISCs using a high-fat Western diet (HFD) mouse model. HFD broadly remodels chromatin accessibility, altering pre-existing open regulatory regions. Many differentially accessible regions (DARs) persist during the differentiation of ISCs into transient amplifying cells (TACs). Notably, HFD-induced DARs are retained following diet normalization despite phenotypic reversibility, and HFD re-exposure enhances ISC self-renewal and adenoma growth compared with naive HFD exposure. The HFD-induced chromatin changes require Ppar-d/a nuclear receptors but are independent of their transcriptional targets. Although a subset of HFD-induced DARs is maintained following Apc loss, extensive chromatin remodeling driven by tumor suppressor inactivation largely overrides diet-dependent differences in Lgr5 ISCs. Together, these findings demonstrate that ISCs retain a chromatin-based memory of dietary fat exposure.

cell biology↗

CAcnesDB: A database of Cutibacterium acnes with Integrated Functional Insights derived from Multi-modal Genome Annotation

Cutibacterium acnes is a predominant member of the human skin microbiome, generally as a beneficial or a benign inhabitant, which under specific conditions transforms into a pathogen, causing acne and associated inflammatory responses. While there is a wealth of data on the microbiology and genomics of the microbe, there is a lack of comprehensive annotation of the proteins coded by the genome, slowing progress in understanding its unique metabolic versatility and survival in host hypoxic sebaceous niches. We configured an integrated pipeline for functional annotation of the C. acnes genome, combining gene calling, domain and ontology mapping, KEGG pathways assignment, proteome-scale structural modeling, predicting Pockets and associating the small-molecule metabolites based on binding site similarity to facilitate structure-to-function annotation. Structural predictions using ColabFold covered nearly the full proteome, with 67.4% of models showing high confidence. To infer protein function, ligand-binding sites in the C. acnes modeled proteome were predicted using a consensus of three independent algorithms, PocketDepth, SiteHound, and FPocket. The resulting pockets were matched with known small-molecule binding sites in PDB to map potential ligands, resulting in the C. acnes predicted metabolome (CApM) comprising 1,954 ligands across 1,865 proteins. CAcnesDB is a comprehensive up-to-date database of the C. acnes genome, hosting functional annotation from multiple levels of input and analyses, covering 2297 protein-coding genes. Impact StatementCutibacterium acnes (C. acnes) is implicated in acne vulgaris, a common skin condition affecting millions of people worldwide, yet the absence of a unified genomic resource limits comprehensive understanding of the underlying biology. In this work, we introduce CAcnesDB, a genome-wide annotation resource built through multi-modal integration of sequence- and structure-based analyses, structural proteome models, predicted binding sites associated with small-molecule metabolites, functional classes, protein-protein interactions, and pathways. This resource consolidates enriched annotations to enable systematic exploration of C. acnes biology and pathogenic mechanisms. We showcase its utility through detailed analyses of membrane transporters and hypothetical proteins, highlighting novel functional insights into this skin microbe. Given the clinical relevance of C. acnes in skin health and its role in skincare product development, CAcnesDB represents a valuable platform for both basic research and translational applications.

bioinformatics↗

Computational prediction of cyclotides from Viola odorata as potential inhibitors against the neuraminidase of Streptococcus pneumoniae

Cyclotides are naturally occurring peptides characterized by a cyclic cystine knot, which provides them with exceptional structural stability. In addition to their stability, cyclotides exhibit diverse therapeutic activities including antimicrobial, antiviral and antitumor activities, making them promising candidates in drug discovery. However, computational studies aimed at identifying cyclotide-based inhibitors for infectious diseases remain limited. To this end, we conducted a virtual screening of cyclotides from an Indian medicinal plant Viola odorata to identify potential inhibitors against a bacterial pathogen causing respiratory infections. We compiled a library of 93 cyclotides by retrieving their structures from public domain or predicting them using the AlphaFold server. We then docked these cyclotides against the neuraminidase protein of Streptococcus pneumoniae and analyzed the interacting residues and binding energies to identify top five potential inhibitors namely, kalata S, kalata B1, cycloviolacin O15, vodo L12, and cycloviolacin O36. Thereafter, we performed molecular dynamics simulations of the protein-cyclotide complexes, and observed that the cyclotides remained stable within the complex. Altogether, this study is the first computational effort to identify potential cyclotide inhibitors against bacterial pathogen causing respiratory diseases, which can be further pursued for experimental validation to develop novel therapeutic agents for respiratory infections.

pharmacology and toxicology↗

Gametophytic epigenetic regulators MEA and DME synergistically suppress ectopic shoot formation in Arabidopsis

The gametophyte to sporophyte transition facilitates the alternation of generations in a plant life cycle. The epigenetic regulators DEMETER(DME) and MEDEA(MEA) synergistically control central cell proliferation and differentiation, ensuring proper gametophyte to sporo-phyte transition in Arabidopsis. Mutant alleles of DME and MEA are female gametophyte lethal, eluding the recovery of recessive homozygotes to examine their role in the sporophyte. Here, we exploited the paternal transmission of these mutant alleles coupled with CENH3-haploid inducer to generate mea-1;dme-2 sporophytes. Strikingly, the simultaneous loss of function of MEA and DME leads to the emergence of ectopic shoot meristems at the apical pole of the plant body axis. DME and MEA are expressed in the developing shoot apex and regulate the expression of various shoot-promoting factors. Chromatin immunoprecipitation(ChIP), DNA methylation and gene expression analysis revealed several shoot regulators as potential targets of MEA and DME. Knockdown of upregulated shoot-promoting factors STM, CUC2, and PLT5 rescued the ectopic shoot phenotypes. Our findings reveal a previously unrecognized synergistic role of MEA and DME in restricting the meristematic activity at the shoot apex during sporophytic development to orchestrate the plant architecture.

plant biology↗

CRD: a De novo Design algorithm for prediction of Cognate Protein Receptors for small molecule ligands

While predicting a new ligand to bind to a protein is possible with current methods, the converse of predicting a receptor for a ligand is highly challenging, except for very closely-related known protein-ligand complexes. Predicting a receptor for any given ligand will be path-breaking in understanding protein function, mapping sequence-structure-function relationships and for several aspects of drug discovery including studying the mechanism of action of phenotypically discovered drugs, off-target effects and drug repurposing. We use a novel approach for predicting receptors for a given ligand through de novo design combined with structural bioinformatics. We have developed a new algorithm CRD, that has multiple modules which combines fragment-based sub-site finding, a machine learning function to estimate the size of the site, a genetic algorithm that encodes knowledge on protein structures and a physics-based fitness scoring scheme. CRD has a pseudo-receptor design component followed by a mapping component to identify possible proteins that house the site. CRD is designed to cater to ligands with known and unknown complexes. CRD accurately recovers sites and receptors for several known natural ligands including ATP, SAM, Glucose and FAD. It designs similar sites for similar ligands, yet to some extent distinguishes between closely related ligands. More importantly CRD correctly predicts receptor classes for several drugs such as penicillins and NSAIDs. We expect CRD to be a valuable tool in fundamental biology research as well as in the drug discovery and biotechnology industry.

bioinformatics↗

Longitudinal monitoring of maternal care and maternal neglect

Parental care is required for offspring survival, because infants require nearly-continual oversight for extensive periods. Parents must balance caretaking with their own survival, and benefit from help provided by other experienced adults. We built a system for 24/7 long-term monitoring of wild-type or oxytocin receptor knockout (OXTR-KO) mouse mothers ( dams) over litters. Some wild-type dams had high litter survival rates, but others consistently lost pups due to neglect and hypothermia. Maternal caretaking in low-pup-survival dams improved after co-housing with an experienced dam and litter, from reorganized maternal behavior including increased nest-building. In contrast, singly-housed OXTR-KOs died in childbirth and pups died due to prolonged parturition. Co-housing with a lactating female prevented OXTR-KO maternal-infant mortality, because the other female acted as a midwife by removing and cleaning pups from the pregnant dam. Thus for single mothers that continually lose litters or die in labor, maternal-infant survival is enhanced by experienced helpers.

neuroscience↗

Fast Local Alignment of Protein Pockets (FLAPP): A system-compiled program for large-scale binding site alignment

Protein function is a direct consequence of its sequence, structure and the arrangement at the binding site. Bioinformatics using sequence analysis is typically used to gain a first insight into protein function. Protein structures, on the other hand, provide a higher resolution platform into understanding functions. As the protein structural information is increasingly becoming available through experimental structure determination and through advances in computational methods for structure prediction, the opportunity to utilize this data is also increasing. Structural analysis of small molecule ligand binding sites in particular provide a direct and more accurate window to infer protein function. However it remains a poorly utilized resource due to the huge computational cost of existing methods that make large scale structural comparisons of binding sites prohibitive. Here we present an algorithm called FLAPP that produces very rapid atomic level alignments. By combining clique matching in graphs and the power of modern CPU architectures, FLAPP aligns a typical pair of binding site binding sites at ~12.5 milliseconds using a single CPU core, ~ 1 millisecond using 12 cores on a standard desktop machine, and performs a PDB-wide scan in 1-2 minutes. We perform rigorous validation of the algorithm at multiple levels of complexity and show that FLAPP provides accurate alignments. We also present a case study involving vitamin B12 binding sites to showcase the usefulness of FLAPP for performing an exhaustive alignment based PDB-wide scan. We expect this tool will be invaluable to the scientific community to quickly align millions of site pairs on a normal desktop machine to gain insights into protein function and drug discovery for drug target and off-target identification, and polypharmacology.

bioinformatics↗

Highly dense and scalable protein arrays for single-molecule studies

Single-molecule proteomic studies are critically important for understanding the molecular origins of cellular phenotypes. However, no currently available technology can achieve both the single-molecule sensitivity and high dynamic range required to comprehensively analyze the complex mixtures of proteins in biological samples. One approach to achieve high sensitivity across a wide dynamic range would be to create a protein array that arranges billions of single molecules with regular spacing on a patterned surface. However, creating such a protein array has remained an unsolved challenge for the field. Here, we present a highly scalable method for fabricating dense single-molecule protein arrays using a specially designed DNA origami structure, protein click-conjugation, photolithography and surface functionalization. The origami-structure is enhanced via terminal deoxynucleotidyl transferase-extension, which generates brush-like projections, increasing the effective size of the origami from 88 nm to greater than 200 nm. These particles are large enough to enable super-Poisson deposition of individual protein molecules on a nano-patterned chip (>98% occupancy with only 1% of sites occupied with multiple protein molecules). This approach allowed for single-molecule protein display of 600 million protein molecules per microscope slide-sized chip with the potential to scale further with denser feature spacing. We hypothesize that this technology will ultimately enable the development of highly scalable proteomic analysis platforms that address the currently unmet need for protein measurements at single-molecule sensitivity across an exceptionally wide dynamic range of protein concentrations.

bioengineering↗

A human iPSC derived bone marrow milieu identifies a novel target against niche-conferred leukaemia proliferation and treatment resistance

Leukaemia cells re-program their microenvironment to provide proliferation support and protection from standard chemotherapy, molecularly targeted therapies, and immunotherapy. Although much is becoming known about molecules that drive niche-dependent treatment resistance; means of targeting these in the clinics has remained a key obstacle. To address this challenge, we have developed human induced pluripotent stem cell engineered niches ex vivo to reveal insights into druggable cancer-niche dependencies. We show that mesenchymal (iMSC) and vascular niche-like (iANG) cells support ex vivo proliferation of patient-derived leukaemia cells, impact dormancy and mediate therapy resistance. iMSC protected both non-cycling and cycling blasts against dexamethasone treatment while iANG protected only dormant blasts. Leukaemia proliferation and protection from dexamethasone induced-apoptosis was dependent on direct cell-cell contact and mediated by CDH2. To explore the therapeutic potential of disrupting this cell-cell interaction, we tested the CDH2 antagonist ADH-1 (previously in phase I / II for solid tumours) in a very aggressive patient-derived xenograft leukaemia mouse model. ADH-1 showed high in vivo efficacy. ADH-1/ dexamethasone combination therapy was superior to dexamethasone alone with no ADH1 conferred additional toxicity. These findings provide a proof-of-concept starting point to develop novel, potentially safer therapeutics that target niche-mediated cancer cell dependencies in haematological malignancies. SummaryCDH2 mediated niche-dependent cancer proliferation and treatment resistance is clinically targetable via ADH-1, a low toxic agent that could be potentially repurposed for future clinical trials in acute leukaemia.

cancer biology↗

Geminin is required for Hox gene regulation to pattern the developing limb

Development of the complex structure of the vertebrate limb requires carefully orchestrated interactions between multiple regulatory pathways and proteins. Among these, precise regulation of 5 Hox transcription factor expression is essential for proper limb bud patterning and elaboration of distinct limb skeletal elements. Here, we identified Geminin (Gmnn) as a novel regulator of this process. A conditional model of Gmnn deficiency resulted in loss or severe reduction of forelimb skeletal elements, while both the forelimb autopod and hindlimb were unaffected. 5 Hox gene expression expanded into more proximal and anterior regions of the embryonic forelimb buds in this Gmnn-deficient model. A second conditional model of Gmnn deficiency instead caused a similar but less severe reduction of hindlimb skeletal elements and hindlimb polydactyly, while not affecting the forelimb. An ectopic posterior SHH signaling center was evident in the anterior hindlimb bud of Gmnn-deficient embryos in this model. This center ectopically expressed Hoxd13, the HOXD13 target Shh, and the SHH target Ptch1, while these mutant hindlimb buds also had reduced levels of the cleaved, repressor form of GLI3, a SHH pathway antagonist. Together, this work delineates a new role for Gmnn in modulating Hox expression to pattern the vertebrate limb. SummaryThis work identifies a new role for Geminin in mouse limb development. Geminin is a nuclear protein that regulates gene expression to control several other aspects of vertebrate development.

developmental biology↗

In-vitro synergistic antibacterial effect of atorvastatin and ampicillin against resistant Staphylococcus spp and E.coli isolated from bovine mastitis

The colossal rise in antimicrobial resistance has led to treatment failures and so mastitis has become cumbersome to treat. The objective of this study was to evaluate the antibacterial effect of non-antibiotic drug, atorvastatin in combination with antimicrobial, ampicillin against two commonly isolated bacterial species Staphylococcus spp and E. coli from bovine mastitis. Milk samples were collected from mastitis cows, visiting Veterinary Clinical Complex. Bacterial isolation was performed using Eosin Methylene Blue (EMB) agar and Mannitol Salt Agar (MSA), followed by characterization and identification by biochemical tests and gram staining. Genotypic confirmation was done by Polymerase Chain Reaction (PCR) with subsequent screening for resistant genes-mec A, blaTEM. Antibiotic Sensitivity Test (ABST) of the isolates against 12 different antimicrobials, atorvastatin only, and combination of atorvastatin with ampicillin were performed using Kirby-Bauer disc diffusion method. Minimum Inhibitory Concentration (MIC) of ampicillin alone and ampicillin in combination with atorvastatin were determined by modified microdilution method. Staphylococcus spp (77.5%) and E.coli (35%) were the two major pathogens isolated in the current study and multi-drug resistance was observed. Among the antimicrobials, the ampicillin showed 100% resistance against Staphylococcus spp and 85.71% resistance against E. coli. Atorvastatin did not display antibacterial effect as a sole agent but displayed synergistic antibacterial activity with ampicillin. There was an average increase in Minimum Inhibitory Concentration of ampicillin for E.coli and Staphylococcus spp isolates and atorvastatin decreased the Minimum Inhibitory Concentration of ampicillin in combination. The ampicillin shows more resistance against both Staphylococcus spp and E.coli, while atorvastatin improves the effect of ampicillin in-vitro. So, atorvastatin may be combined with ampicillin for the treatment of Gram-positive and Gram-negative infections. However, further studies are required to ascertain the exact mechanism of action of atorvastatin with respect to their antibacterial effect for them to be redeployed as an antimicrobial drug in the future.

pharmacology and toxicology↗

High accuracy DNA sequencing on a small, scalable platform via electrical detection of single base incorporations

High throughput DNA sequencing technologies have undergone tremendous development over the past decade. Although optical detection-based sequencing has constituted the majority of data output, it requires a large capital investment and aggregation of samples to achieve optimal cost per sample. We have developed a novel electronic detection-based platform capable of accurately detecting single base incorporations. The GenapSys technology with its electronic detection modality allows the system to be compact, accessible, and affordable. We demonstrate the performance of the system by sequencing several different microbial genomes with varying GC content. The platform is capable of generating up to 2 Gb of high-quality nucleic acid sequence in a single run. We routinely generate sequence data that exceeds 99% raw accuracy with read lengths of up to 175 bp. Average quality scores remain above Q30 (99.9% raw sequencing accuracy) beyond 150 bp, with more than 85% of total bases at or above Q30. The utility of the platform is highlighted by targeted sequencing of the human genome. We show high concordance of SNP detection on the human NA12878 HapMap cell line with data generated on the Illumina sequencing platform. In addition, we sequenced a targeted panel of cancer-associated genes in a well characterized reference standard. With multiple library preparation approaches on this sample, we were able to identify low frequency mutations at expected allele frequencies.

genomics↗