Biology subjects

Kar, A.

Publications and source records attributed to Kar, A..

16 recordsLinked to original sources

bioRxiv2026

A Retro-Inverso Peptide that Inhibits Formation and Disrupts Preformed α-Helical Amyloid and Staphylococcus aureus Biofilms

Combatting biofilm-associated methicillin-resistant Staphylococcus aureus (MRSA) infections remains a formidable challenge, largely due to bacterias heightened resistance to antibiotics and evasion of the hosts immune responses. Inhibiting biofilm formation or promoting biofilm dissolution is believed to disrupt the protective matrices and expose bacterial cells to immune clearance or antimicrobial treatments. Cross- helical amyloid fibrils of phenol-soluble modulins are the key structural components of the MRSA biofilm. In this study, we present a novel retro-inverso peptide that successfully inhibits cross- amyloid formation, induces disassembly of pre-formed fibrils of the biofilm-forming modulin peptide, and efficiently disperses MRSA biofilm biomass in a dose-dependent manner. The biophysical studies of the interaction of the designed peptide and modulins have suggested a mechanism for the biofilm disruption. The findings highlight the potential of the proteolytically resistant mirror-image peptide as a promising therapeutic agent for the treatment of biofilm-associated MRSA infections.

biophysics↗

bioRxiv2026

Innovative Methods for Prenatal Cannabis Exposure: Vapor Inhalation Chamber and Metabolite Quantification in Prairie Voles and Rats

The increasing prevalence of cannabis use, including among pregnant women, highlights the critical need for a deeper understanding of prenatal cannabis exposure. This study aimed to develop a standardized cross-species inhalation exposure protocol to administer the principal psychoactive component of cannabis, {Delta}9-tetrahydrocannabinol (THC), to prairie voles (Microtus ochrogaster) and laboratory rats (Rattus norvegicus), and to investigate the distribution of THC in maternal and fetal tissues following prenatal exposure. Using an established e-cigarette system for delivering vaporized THC, we administered THC to pregnant prairie voles and rats. THC concentrations were measured in maternal plasma and fetal brain tissue using LC-MS/MS (Liquid Chromatography coupled with Tandem Mass Spectrometry). In both species, THC levels were compared across groups to evaluate the impact of fetal position on THC uptake. We found that THC readily crossed the placental barrier in both species, resulting in significantly higher concentrations of THC in the fetal brain within the THC-exposed groups compared to the vehicle controls. Interspecies comparison revealed higher THC concentrations in rat fetal brain tissue compared to prairie voles. No significant effects of fetal position on THC levels were found for either species. The findings confirm placental transfer of THC and reveal species-specific patterns of THC distribution. Additional studies were then carried out in voles to compare plasma and brain THC levels in maternal and virgin adult prairie voles. Maternal brain THC concentrations were significantly higher than fetal brain concentrations in prairie voles. Strong positive correlations were observed between plasma and brain THC concentrations in both maternal and virgin adult prairie voles. This study establishes a translational model for investigating prenatal cannabis exposure using an aerosolized administration method in voles compared to established methods in rats. The standardized protocol and results provide a foundation for future research into the developmental consequences of prenatal cannabis exposure and offer crucial insights for informing public health policies and clinical practices in response to the global increase in cannabis use.

neuroscience↗

bioRxiv2026

Mettl3-catalyzed m6A methylation determines CD8+ T cell differentiation fate in tumor

The heterogeneity in patient responses to immune checkpoint blockade (ICB) is dictated by the relative abundance of exhausted CD8 T cell (Tex) subsets with distinct therapeutic responsiveness. Progenitor exhausted (pTex) cells remain sensitive to ICB, whereas terminally exhausted (tTex) cells are refractory; however, the molecular cues that bias differentiation toward these divergent fates remain poorly defined. Here, we identify the RNA methyltransferase Mettl3 as a central regulator of Tex fate. Across murine tumor models, human T cells, and adoptive transfer systems, Mettl3 expression is selectively enriched in tTex cells and inversely correlated with TCF1 pTex populations. Mechanistically, Mettl3 drives terminal exhaustion by stabilizing DNMT3B transcripts via mA modification, enforcing CpG methylation and chromatin compaction at memory-associated loci. Inhibition of the Mettl3-Dnmt3b axis reprograms chromatin accessibility toward memory-like states, thereby preserving progenitor potential and effector function. Consequently, T cells lacking Mettl3-Dnmt3b activity persist longer, mount robust recall responses, and achieve superior tumor control with enhanced responsiveness to PD-1 blockade. These findings establish the Mettl3-mA-Dnmt3b axis as a molecular rheostat of CD8 T cell fate, coupling epitranscriptomic regulation to epigenetic remodeling, and reveal a tractable pathway to improve the durability of cancer immunotherapy.

immunology↗

bioRxiv2025

Integrated ambient modeling and genetic demultiplexing of single-cell RNA+ATAC multiome experiments with Ambimux

Single cell technologies have advanced at a rapid pace, providing assays for various molecular phenotypes. Droplet-based single cell technologies, particularly those based on nuclei isolation, such as simultaneous RNA+ATAC single-cell multiome, are susceptible to exogenous ambient molecule contamination, which can increase noise in cell type-level associations. We reasoned that genotype-based sample multiplexing can provide an opportunity to infer this ambient contamination by leveraging DNA variation in sequenced reads. Thus, we developed ambimux, a likelihood-based method to estimate ambient fractions and demultiplex single-cell multiome experiments using genotype-level data. Ambimux models the ambient or nuclear probability at the read level and thus can classify empty droplets and estimate droplet-specific ambient molecule fractions in each modality. We first evaluated our method using simulated data sets across a range of parameters. We found that ambimux closely estimated the ground truth droplet contamination fractions in the RNA (MAE=0.048) and ATAC (MAE=0.042) modalities. As a result, ambimux maintained high specificity (>95%) and was able to correctly assign singlets at considerably high ambient fractions (up to 60%) for both RNA and ATAC modalities. In comparison with models that do not consider ambient contamination, these only maintained similar sensitivity levels at considerably lower ambient fractions (up to 25%). We then generated a real data set of seven visceral adipose tissue biopsies run on a single 10x Multiome channel. We ran ambimux and detected 4,986 singlets, capturing similar numbers as other methods. Then, we sought to evaluate the fidelity of the ambient fraction estimates from ambimux. We split singlets into ambient-enriched (>5% contamination in both modalities) or nuclear-enriched (<5% in both) droplets and performed gene-peak linkage analysis. Low ambient droplets resulted in more significant hits with gene-peak links enriched at the transcription start site relative to high ambient droplets, suggesting that the ambient droplets identified by ambimux hamper the identification of biologically meaningful signals. In summary, we developed a joint single-cell multiome demultiplexing method, ambimux, that accurately models and estimates ambient molecule contamination in each modality.

bioinformatics↗

bioRxiv2025

Insights into gallbladder cancer pathogenesis from a living organoid gallbladder cholangiocyte biorepository

Gallbladder cancer (GBC) while rare worldwide has a high prevalence in India. Pathogenesis is unclear and outcomes poor. Gallbladder cholangiocyte organoids (GCOs) or gallbladder carcinoma organoids (GBCOs) were developed and serially propagated from surgically resected gallbladder tissues with benign or malignant diseases, respectively. Patient derived organoids (PDOs) were derived from 15 normal; 58 inflamed; 12 xanthogranulomatous cholecystitis (XGC); 5 pre-invasive neoplasm and 13 invasive malignant gallbladder pathologies. Protocol optimisation achieved 58% (69/119) success in organoid generation and expansion. Organoids maintained tight junction integrity; P-gp pump and enzymatic activity; preserved tissue-specific gene and protein marker expression; histological features and genetic variations. Cryopreserved organoids from 62 patients with primary tissue and high-quality DNA, RNA and protein derivatives have been banked. In gene expression analyses of tissue, XGC samples clustered with malignant subtypes, separate from benign pathologies. Derived XGC organoids showed a similar clustering. Enriched hallmark pathways in XGC support neoplastic change through chronic inflammation. PDOs generated from different gallbladder pathologies are a promising model to investigate the pathogenesis of GBC. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=199 SRC="FIGDIR/small/651639v1_ufig1.gif" ALT="Figure 1"> View larger version (69K): org.highwire.dtl.DTLVardef@465f3dorg.highwire.dtl.DTLVardef@16c5f0org.highwire.dtl.DTLVardef@11d4807org.highwire.dtl.DTLVardef@163d072_HPS_FORMAT_FIGEXP M_FIG C_FIG

cancer biology↗

bioRxiv2025

CD8 T lymphocytes redeploy embryonic cell cycle control mechanisms to facilitate rapid cell proliferation

Rapid proliferation and expansion of cytotoxic CD8 T lymphocytes is crucial for adaptive immunity against viral infection. CD8 T cell cycles complete cell division cycles in <6 hours, representing a physiological extreme for somatic mammalian cells. Embryonic stem cells also rapidly divide and have been shown to utilize specialized cell cycle control mechanisms that differ from somatic fibroblasts, including subdued periodicity of cyclin proteins. CD8 T cell cycle control remains poorly understood compared to embryonic and other somatic cell types. Here, we tested whether CD8 T cells utilize similar control mechanisms to embryonic stem cells to promote rapid cell cycles. We used mass spectrometry-based proteomics to comprehensively measure protein abundances in G1, S and G2&M phases somatic mouse CD8 T cells, mouse embryonic stem cells (mESC) and mouse fibroblasts (NIH3T3). We isolated cell cycle phases using PRIMMUS, thereby avoiding potential artefacts due to arrest-based synchronization. We discovered striking similarities between mESC and CD8 T cells. Similar to mESC, Cyclin E1 was expressed at high levels and constitutively across the cell cycle in CD8 T cells. Overall, cyclins and cell cycle regulated proteins were present in higher abundance in CD8 T cells and mESC as compared with NIH3T3 cells. Additionally, CD8 T cells express high levels of Emi1/Fbxo5 to promote S-phase entry. Interestingly, Emi1 deletion unexpectedly resulted in changes in markers of CD8 T cell phenotype, suggesting an association between cell cycle control and immune function. Thus, we show several adaptations of cell cycle control of embryonic stem cells are redeployed in somatic T cells to promote rapid cell cycles.

cell biology↗

bioRxiv2024

Cellular moonlighting function of Hsp20 directs morphological and pathogenic development in Ustilago maydis

Ustilago maydis Hsp20 is involved in the pathogenicity of the fungus. In this study we have investigated the molecular basis of contribution of Hsp20 to U. maydis pathogenicity. Through biochemical studies we have demonstrated environment-dependent oligomeric plasticity associated with Hsp20. Hsp20 was also found to form higher order oligomers that undergo phase separation in vitro. Within cells Hsp20 was found to form distinct punctate structures that we believe play a pivotal role in its function. These punctate structures were demonstrated to sequester proteins such as actin and septin within it. Absence of Hsp20 was found to significantly affect key cellular processes like endocytosis, budding, cell polarity determination and mating in U. maydis cells. The deletion mutant failed to sporulate and complete pathogenic life cycle. This study presents a comprehensive understanding of the pathogenic development of U. maydis in reference to the moonlighting function of Hsp20 within the cell.

microbiology↗

bioRxiv2024

Single-cell DNA methylome and 3D genome atlas of the human subcutaneous adipose tissue

Human subcutaneous adipose tissue (SAT) contains a diverse array of cell-types; however, the epigenomic landscape among the SAT cell-types has remained elusive. Our integrative analysis of single-cell resolution DNA methylation and chromatin conformation profiles (snm3C-seq), coupled with matching RNA expression (snRNA-seq), systematically cataloged the epigenomic, 3D topology, and transcriptomic dynamics across the SAT cell-types. We discovered that the SAT CG methylation (mCG) landscape is characterized by pronounced hyper-methylation in myeloid cells and hypo-methylation in adipocytes and adipose stem and progenitor cells (ASPCs), driving nearly half of the 705,063 detected differentially methylated regions (DMRs). In addition to the enriched cell-type-specific transcription factor binding motifs, we identified TET1 and DNMT3A as plausible candidates for regulating cell-type level mCG profiles. Furthermore, we observed that global mCG profiles closely correspond to SAT lineage, which is also reflected in cell-type-specific chromosome compartmentalization. Adipocytes, in particular, display significantly more short-range chromosomal interactions, facilitating the formation of complex local 3D genomic structures that regulate downstream transcriptomic activity, including those associated with adipogenesis. Finally, we discovered that variants in cell-type level DMRs and A compartments significantly predict and are enriched for variance explained in abdominal obesity. Together, our multimodal study characterizes human SAT epigenomic landscape at the cell-type resolution and links partitioned polygenic risk of abdominal obesity to SAT epigenome.

genomics↗

bioRxiv2023

Automated segmentation by deep learning of neuritic plaques and neurofibrillary tangles in brain sections of Alzheimer's Disease Patients

Alzheimers Disease (AD) is a neurodegenerative disorder with complex neuropathological features, such as phosphorylated tau (p-tau) positive neurofibrillary tangles (NFTs) and neuritic plaques (NPs). The quantitative evaluation of p-tau pathology is a key element for the diagnosis of AD and other tauopathies. Assessment of tauopathies relies on semi-quantitative analysis and does not consider lesions heterogeneity (e.g., load and density of NFTs vs NPs). In this study, we developed a deep learning-based workflow for automated annotation and segmentation of NPs and NFTs from AT8-immunostained whole slide images (WSIs) of AD brain sections. Fifteen WSIs of frontal cortex from four biobanks with different tissue quality, staining intensity and scanning formats were used for the present study. We first applied an artificial intelligence (AI-)-driven iterative procedure to improve the generation of pathologist validated training datasets for NPs and NFTs. This procedure increased the annotation quality by more than 50%, especially for NPs when present in high density. Using this procedure, we obtained an expert validated annotation database with 5013 NPs and 5143 NFTs. As a second step, we trained two U-Net convolutional neural networks (CNNs) for accurate detection and segmentation of NPs or NFTs. The workflow achieved a high accuracy and consistency, with a mean Dice similarity coefficient of 0.81 for NPs and 0.77 for NFTs. The workflow also showed good generalization performance across different patients with different staining and tissue quality. Our study demonstrates that artificial intelligence can be used to correct and enhance annotation quality especially for complex objects, even when intermingled and present in high density, in brain tissue. Furthermore, the expert validated databases allowed to generate highly accurate models for segmenting discrete brain lesions using a commercial software. Our annotation database will be publicly available to facilitate human digital pathology applied to AD.

neuroscience↗

bioRxiv2022

Cell overgrowth during G1 arrest triggers an osmotic stress response and chronic p38 activation to promote cell cycle exit

Cell size and the cell cycle are intrinsically coupled and abnormal increases in cell size are associated with senescence. The mechanism by which overgrowth primes cells to exit the cell cycle remains unclear. We investigate this using CDK4/6 inhibitors that arrest cell cycle progression in G0/G1 and are used to treat ER+/HER2-metastatic breast cancer. We demonstrate that long-term CDK4/6 inhibition promotes cellular overgrowth during the G0/G1 arrest, causing widespread proteome remodeling and p38-p53-p21-dependent cell cycle exit. Cell cycle exit is triggered by two waves of p21 induction. First, overgrowth during a G0/G1 arrest induces an osmotic stress response, producing the first wave of p21 induction. Second, when CDK4/6 inhibitors are removed, a fraction of cells escape G0/G1 arrest and enter S-phase where overgrowth-driven replication stress results in a second wave of p21 induction that causes cell cycle withdrawal from G2, or the subsequent G1. This could explain why cellular hypertrophy is associated with senescence and why CDK4/6 inhibitors have long-lasting anti-proliferative effects in patients.

cell biology↗

bioRxiv2022

Water-Quality analysis and Fish diversity of Southern West Part of the West-Bengal

Marine fishes are one of the important factors to stabilize the local aquatic ecosystem and regulating socio-economy of local fishermen. In this study we emphasized upon finding out the interrelationship in the water quality, anthropogenic activity, and fish habitat through the 31km stretch of East Medinipur coast in West Bengal, India which is known for its tourist destinations. The study was conducted monthly on different trawler fish landing sites from Dec 2018 to Dec 2021. During this period, we took fish samples and identified them. We took water quality data such as SST, Concentration of Chl-a, Turbidity, and DO for further correlation between the water quality and species diversity. Total 154 numbers of commercially important marine fish species were documented. Among them, 12 species are from Elasmobranch and the rest is Actinopterygii. As per the IUCN database, 13% of the total fish species are under the red list category and 16% of the species showing decreasing population trend. After analyzing the water quality data, we found out that DO, SST, Turbidity, and Chlorophyll-A correlate with the species richness and it also differs during the seasons.

ecology↗

bioRxiv2022

mTORC2 Drives ZFX-mediated Ganglioside Biosynthesis to Promote Breast Cancer Progression.

Sphingolipid and ganglioside metabolic pathways are crucial components of cell signalling, having established roles in tumor cell proliferation, invasion, and migration. However, regulatory mechanisms controlling sphingolipid and ganglioside biosynthesis in mammalian cells is less known. Here, we show that RICTOR, the regulatory subunit of mTORC2, regulates the synthesis of sphingolipids and gangliosides in luminal breast cancer-specific MCF-7 and BT-474 cells through transcriptional and epigenetic mechanisms. RICTOR regulates glucosylceramide levels by modulating the expression of UDP-Glucose Ceramide Glucosyl transferase (UGCG). We identify Zinc Finger protein X-linked (ZFX) as a RICTOR-responsive transcription factor whose recruitment to the UGCG promoter is regulated by DNA methyltransferases and histone demethylase (KDM5A) that are known AKT substrates. We further demonstrate that RICTOR regulates the synthesis of GD3 gangliosides through ZFX and UGCG, and triggers the activation of EGFR signalling pathway, thereby promoting tumor growth. In line with our findings in cell culture and mice models, we observe an elevated expression of RICTOR, ZFX, and UGCG in Indian luminal breast cancer tissues, and in TCGA and METABRIC datasets. Together, we establish a key regulatory circuit, RICTOR-AKT-ZFX-UGCG-Ganglioside-EGFR-AKT, and elucidate its contribution to breast cancer progression.

cancer biology↗

bioRxiv2021

A single cell atlas of human and mouse white adipose tissue

White adipose tissue (WAT), once regarded as morphologically and functionally bland, is now recognized to be dynamic, plastic, heterogenous, and involved in a wide array of biological processes including energy homeostasis, glucose and lipid handling, blood pressure control, and host defense1. High fat feeding and other metabolic stressors cause dramatic changes in adipose morphology, physiology, and cellular composition1, and alterations in adiposity are associated with insulin resistance, dyslipidemia, and type 2 diabetes (T2D)2. Here, we provide detailed cellular atlases of human and murine subcutaneous and visceral white fat at single cell resolution across a range of body weight. We identify subpopulations of adipocytes, adipose stem and progenitor cells (ASPCs), vascular, and immune cells and demonstrate commonalities and differences across species and dietary conditions. We link specific cell types to increased risk of metabolic disease, and we provide an initial blueprint for a comprehensive set of interactions between individual cell types in the adipose niche in leanness and obesity. These data comprise an extensive resource for the exploration of genes, traits, and cell types in the function of WAT across species, depots, and nutritional conditions.

physiology↗

bioRxiv2021

Assessment of deep learning algorithms for 3D instance segmentation of confocal image datasets

Segmenting three dimensional microscopy images is essential for understanding phenomena like morphogenesis, cell division, cellular growth and genetic expression patterns. Recently, deep learning (DL) pipelines have been developed which claim to provide high accuracy segmentation of cellular images and are increasingly considered as the state-of-the-art for image segmentation problems. However, it remains difficult to define their relative performances as the concurrent diversity and lack of uniform evaluation strategies makes it difficult to know how their results compare. In this paper, we first made an inventory of the available DL methods for 3 dimensional (3D) cell segmentation. We next implemented and quantitatively compared a number of representative DL pipelines, alongside a highly efficient non-DL method named MARS. The DL methods were trained on a common dataset of 3D cellular confocal microscopy images. Their segmentation accuracies were also tested in the presence of different image artifacts. A specific method for segmentation quality evaluation was adopted which isolates segmentation errors due to under/over segmentation. This is complemented with a 3D visualization strategy for interactive exploration of segmentation quality. Our analysis shows that the DL pipelines have different levels of accuracy. Two of them, which are end to end 3D and were originally designed for cell boundary detection, show high performance, and offer clear advantages in terms of adaptability to new data. Author summaryIn recent years a number of deep learning (DL) algorithms based on computational neural networks have been developed which claim to achieve high accuracy and automatic segmentation of 3D microscopy images. Although these algorithms have received considerable attention in the literature, it is difficult to evaluate their relative performances, while it remains unclear whether they really perform better than other, more classical segmentation methods. To clarify these issues, we performed a detailed, quantitative analysis of a number of representative DL pipelines for cell instance segmentation from 3D confocal microscopy image datasets. We developed a protocol for benchmarking the performances of such DL based segmentation pipelines using common training and test datasets, evaluation metrics and visualizations. Using this protocol, we evaluated and compared four different DL pipelines to identify their strengths and limitations. A high performance non-DL method was also included in the evaluation. We show that DL pipelines may show significant differences in their performances depending on their model architecture and pipeline components but overall show excellent adaptability to unseen data. We also show that our benchmarking protocol could be extended to a variety of segmentation pipelines and datasets.

bioinformatics↗

bioRxiv2019

Inhibition of ATR Reverses a Mitochondrial Respiratory Insufficiency

Diseases that affect the mitochondrial electron transport chain (ETC) often manifest as threshold effect disorders, meaning patients only become symptomatic once a certain level of ETC dysfunction is reached. Multiple processes work to control proximity to the critical ETC threshold and as a consequence there can be significant variability in disease presentation among patients. Identification of such control processes remains an ongoing goal. Checkpoint signaling comprises a collection of alert mechanisms activated in cells in response to nuclear DNA damage. Well-defined hierarchies of proteins are involved in both sensing and signaling DNA damage, with ATM (ataxia telangiectasia mutated) and ATR (ATM and Rad3-related) acting as pivotal signaling kinases. In the nematode C. elegans, severe reduction of mitochondrial ETC activity shortens life, as in humans, but mild reduction extends life as a consequence of survival strategies that are invoked under these circumstances. Here we show that removal of ATL-1, the worm ortholog of ATR, unexpectedly lessens the severity of ETC dysfunction, but removal of ATM does not. Multiple genetic and biochemical tests show no evidence for increased mutation or DNA breakage in animals exposed to ETC disruption. Instead, we find that reduced ETC function alters nucleotide ratios within both the ribo- and deoxyribo-nucleotide pools, and causes stalling of RNA polymerase, which is also known to activate ATR. Unexpectedly, atl-1 mutants confronted with mitochondrial ETC disruption maintain normal levels of oxygen consumption and have an increased abundance of translating ribosomes. This suggests checkpoint signaling by ATL-1 normally dampens cytoplasmic translation. Taken together, our data suggests a model whereby ETC insufficiency in C. elegans results in nucleotide imbalances leading to stalling of RNA polymerase, activation of ATL-1, dampening of global translation and magnification of ETC dysfunction. Loss of ATL-1 effectively reverses the severity of ETC disruption so that animals become phenotypically closer to wild type.

pathology↗

bioRxiv2017

Whole exome sequencing reveals a mutation in ARMC9 as a cause of mental retardation, ptosis and polydactyly

Intellectual disability (ID) refers to deficits in mental abilities, social behaviour and motor skills to perform activities of daily living as compared to peers. Numerous genetic and environmental factors may be responsible for ID. We report on identification of a novel gene for syndromic ID, using homozygosity mapping followed by exome sequencing in a family with mental retardation, ptosis and polydactyly. The analysis revealed a synonymous mutation c.879G>A which leads to a splicing defect in ARMC9 gene. The variant is present in conserved region of ARM domain of ARMC9 protein which is predicted to form a platform for protein interaction. This domain is likely to be altered in patients due to splicing defect caused by this synonymous mutation. Our study was helpful in elucidation of molecular basis of mental retardation, ptosis and polydactyly phenotype and addition of ARMC9 to group of genes leading to syndromic ID.

genetics↗