Biology subjects

Dasgupta, R.

Publications and source records attributed to Dasgupta, R..

14 recordsLinked to original sources

bioRxiv2026

Neuropixels 1536 Channel Quad Base probe reveals brain-wide communication underlying flexible sensorimotor sequences

The brain orchestrates billions of neurons spanning hundreds of regions to drive behavior. High-density electrophysiology has provided insights into this process, but monitoring brain-wide patterns of spiking activity demands new tools. Here we present Neuropixels 2.0 Quad Base, a 1536-channel probe with four times the simultaneous recording capacity of state-of-art Neuropixels 2.0. Using two Quad Base probes, we performed 3072-channel recordings in mice trained to produce complex sequences of goal-directed licks. We decoded behavioral kinematics from neural populations across more than 20 brain regions and identified the spatiotemporal emergence of motor decision signals. The probes high channel count further revealed expanded inter-neuronal functional subnetworks and latent dynamics across multiple areas--features significantly undersampled when channels were subsampled to mimic standard Neuropixels 2.0. Neuropixels 2.0 Quad Base offers a powerful tool to explore neural encoding of cognition and behavior at grand scale.

neuroscience↗

bioRxiv2026

HLiCA: An integrated cell atlas of the healthy human liver

The human liver is composed of a heterogeneous mix of cell types. How these distinct populations contribute individually and collectively to liver function remains poorly understood. Although single-cell technologies have advanced our understanding of liver biology, individual studies have often been limited by small donor cohorts and inconsistent cell type annotations. Integrating multiple datasets can overcome these challenges and better capture biological variability. We present the Human Liver Cell Atlas (HLiCA), an integrated reference of non-disease liver cells assembled from eight datasets across six research centers, encompassing more than 525,000 cells from 110 donors. Developed in collaboration with the Human Cell Atlas Liver Bionetwork, the HLiCA incorporates expert-curated cell annotations refined through community feedback and dedicated cell type annotation meetings. The HLiCA classifies cells into six lineages and expands the cell type resolution to include 47 distinct cell types. Starting from raw sequencing reads, we realigned all data and performed rigorous benchmarking to ensure robust integration across technical and biological variables. Genetic ancestry was inferred for all samples to evaluate the range of ancestral backgrounds represented in the atlas. The expanded cell type annotation enabled identification of previously unrecognized liver cell types, including NRXN1+ stromal cells. Their presence was validated using spatial transcriptomics, which localized NRXN1+ stromal cells to periportal regions. With the number of donors included in the HLiCA we were able to examine cell type specific associations with demographic covariates. In hepatocytes, drug metabolism genes showed differential expression between sexes, and in cholangiocytes, mucus-production genes varied with age. As the largest and most genetically diverse human liver cell atlas to date, the HLiCA provides a comprehensive, well-annotated reference for the field, annotated by expert consensus. This resource will enable deeper interrogation of liver cellular diversity, architecture, and function in the healthy human liver and serve as a reference to understand changes that occur with disease.

genomics↗

bioRxiv2025

1H R1{rho} Relaxation Identifies a Hidden Intermediate in DNA Base-Pairing

1H R1{rho} Relaxation dispersion (RD) NMR experiments provide valuable atomic-level insights into transient, high-energy conformational states of biomolecules. However, cross-relaxation artifacts can hamper its interpretation and therefore limiting broader adoption. This study explicitly quantifies cross-relaxation effects on 1H R1{rho} relaxation rates, extending the general applicability of 1H R1{rho} to probe dynamics at natural abundance. Artifacts were found to be negligible for neighbouring dipolar-coupled protons, >3 [A] apart, and a concept for identification for protons less than 3[A] is provided. This approach revealed a previously hidden, second excited state (ES2) in DNA base-pairing that extends the well-established Watson-Crick-Franklin (WCF) ground state (GS) - Hoogsteen (HG) equilibrium. A structural model for ES2 is proposed based on evidence from 1H R1{rho} RD, trapping via DNA modifications, metadynamics simulations, and DFT-based chemical shift calculations. ES2 was stabilised by the anticancer drug Actinomycin D, providing direct experimental evidence that small molecule can remodel conformational landscape of DNA. Together, these results demonstrate both a methodological advance by establishing reliable conditions for 1H R1{rho} studies, and a mechanistic discovery of a drug-stabilized intermediate in DNA base-pairing dynamics.

biophysics↗

bioRxiv2025

Single-Cell Integration of Chromatin Accessibility and Transcriptomics Reveals Regulatory Networks in Ovarian Tumor-Infiltrating Adaptive NK Cells

Natural killer (NK) cells are traditionally recognized for their rapid, non-specific responses against virus-infected or malignantly transformed cells, functioning as key effectors of innate immunity. However, a distinct subset known as adaptive NK (aNK) cells has been shown to acquire memory-like properties following viral infections, indicating their capacity for antigen-specific immune recall. Intriguingly, aNK cells have also been identified within the tumor microenvironment, where they can mediate tumor-specific recall responses. Yet, the regulatory mechanisms governing their function in tumor-infiltrating aNK cells remain largely undefined. In this study, we integrated publicly available multiomics datasets from ovarian cancer, including single-cell chromatin accessibility (scATAC-seq) and single-cell RNA sequencing (scRNA-seq), to identify chromatin-accessible regions and construct transcription factors (TF)-gene regulatory networks. To validate and extend these findings, we performed Smart-seq3 on NK cells isolated from ovarian tumors and applied SCENIC analysis to identify TF-driven gene regulation. By integrating results from both analyses, we identified PRDM1 and STAT2 as key TFs, along with their downstream targets CRCP and MTFP1, specifically enriched in tumor-infiltrating aNK cells. The expression levels of CRCP and MTFP1 positively correlated with NK cell infiltration in ovarian cancer tissues, suggesting their potential functions in supporting tumor-specific NK cell memory responses. In addition, external validation using data from the PROMIX clinical trial demonstrated that PRDM1 and STAT2 expression levels are positively associated with both overall survival and aNK cell-associated transcriptional features. Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=111 SRC="FIGDIR/small/676040v1_ufig1.gif" ALT="Figure 1"> View larger version (37K): org.highwire.dtl.DTLVardef@6df026org.highwire.dtl.DTLVardef@1b16dc8org.highwire.dtl.DTLVardef@19e916borg.highwire.dtl.DTLVardef@15d431a_HPS_FORMAT_FIGEXP M_FIG C_FIG

immunology↗

bioRxiv2025

BioImageSuiteLite: An Interactive Open-Source Platform for Automated Detection and Analysis of Transient Events in Time-Lapse Microscopy

The quantitative analysis of dynamic cellular events from time-lapse microscopy is critical for understanding biological processes but is often hindered by low signal-to-signal ratios and subjective manual parameter 1,2.To address these limitations, TransiScope was developed as an open-source tool built on Python and the napari viewer, offering a seamless workflow within a single graphical user interface2-4. Its key innovation is a data driven, interactive approach to parameter optimization, where the software analyzes user defined regions of interest (ROIs) to propose optimal settings for algorithms like the Difference of Gaussians (DoG) filter5,6, ensuring consistency by averaging signals from multiple ROIs. The platforms performance, validated using open-resource .avi files from published studies, demonstrates high specificity and a low false-positive rate, accurately quantifying events in signal-positive regions while correctly identifying zero events in background areas7-11. By replacing manual trial-and-error with a guided workflow, TransiScope enhances the objectivity, speed, and reproducibility of transient event analysis, providing an accessible solution for robust quantitative imaging12.

bioinformatics↗

bioRxiv2025

Flexible sensitivity to inputs during skilled tongue movements

A hallmark of complex goal-directed movement sequences is the ability to rapidly switch motor programs by integrating incoming sensations with action context1,2, yet the underlying neural implementation remains elusive. Here, we demonstrate a network mechanism for flexibly adjusting the sensitivity of ongoing motor execution to external inputs in different sensorimotor contexts. We trained mice to make sequences of licks directed at a moving target. In a random subset of trials, they made "backtracking" licks by abruptly switching motor programs based on tactile feedback. We divided sessions into alternating cued blocks of trials; sensory-driven backtracking was required during one block-type, but not in the other. Targeted optogenetic stimulation of tongue/jaw somatosensory cortical inputs to the tongue premotor (anterolateral motor, or ALM) cortex that were precisely timed to arrive near the motor switching point reliably induced licking movements resembling those in backtracking trials. This effect was more readily induced during blocks with sensory-driven backtracking and was accompanied by larger optically-evoked deviations in neural activity. Population activity patterns could be separated along a latent axis that discriminated between block-types. On single trials, the location of population activity along this axis correlated with the impact of optogenetic stimulation and influenced the speed of sensory-driven motor switching. Our findings provide causal evidence for how external inputs are integrated with internal context signals to achieve flexible motor control.

neuroscience↗

bioRxiv2024

Modelling oxaliplatin resistance in colorectal cancer reveals a SERPINE1-based gene signature (RESIST-M) and therapeutic strategies for pro-metastatic CMS4 subtype

Drug resistance and distant metastases are major contributors to mortality in colorectal cancer (CRC). Here we investigate mechanisms underlying acquired resistance to oxaliplatin, a first-line, standard-of-care CRC treatment. We generated oxaliplatin-resistant CRC tumor cells with clinically relevant dosing regimen, which displayed enhanced metastatic potential. Transcriptomic and phenotypic analyses revealed a critical function for cholesterol biogenesis in modulating TGF-{beta} signaling activity, which in turn regulates SERPINE1 expression, a gene we identified as a key player in promoting drug resistance and metastasis. Additionally, we uncovered a SERPINE1-associated nine-gene expression signature, RESIST-M, that can predict overall and relapse-free survival (RFS) in clinical cohorts and is able to stratify patients into CMS4/iCMS3-fibrotic CRC-subtypes, underscoring its clinical utility. Using mouse tumor models, we provide further evidence that targeting SERPINE1 and cholesterol biogenesis can be viable approaches to re-sensitize the resistant pro-metastatic CRC cells to oxaliplatin. This study not only elucidates the molecular underpinnings of drug resistance and metastasis in primary CRC, but also offers prognostic and therapeutic strategies to guide clinical management of the disease. SignificanceThis study reveals critical resources and insights on oxaliplatin resistance and metastasis in CRC via a novel TGF-{beta} cholesterol axis. We generated improved oxaliplatin-resistant models that enabled identification of a prognostic SERPINE1-based gene signature to predict oxaliplatin resistance-induced metastasis in CRC. This gene signature derived from our models showed that the models can mimic CMS-4/iCMS-fibrotic-like metastatic CRC patients. We validated therapeutic candidates targeting CMS-4/iCMS-fibrotic-like metastatic CRC cells which can reverse drug resistance and metastasis.

cancer biology↗

bioRxiv2024

Mechanics of E. coli cell width homeostasis and bulging dynamics from MreB and septum inhibition

The mechanobiology of cytoskeleton and cell envelope play a vital role in cell shape homeostasis. In the gram-negative model rod-shaped bacterium Escherichia coli antibiotics that weaken the cell envelope are seen to result in bulges that eventually lead to lysis. Here, we quantify the shape dynamics of E. coli treated with cephalexin, a PBP3 inhibitor and A22, an MreB polymerization inhibitor from single cell microscopy. We find low concentrations of both inhibitors result in bulge formation with multiple cell shapes observed: rugby, large bacilli and rods with two and three bulges. We quantify the parameters of cell envelope rigidity, pressure and fluidity obtained from fitting a computational model of shell-mechanics to length and width dynamics from experiment. Using this optimized model we estimate the turgor and growth pressures of untreated growing cells as {approx}0.15 MPa and {approx}0.4 MPa. The bulge expansion dynamics correlate most prominently with a change in bending rigidity of the cell wall and cytoskeleton. Simulations predict a threshold behavior in response to envelope bending rigidity that is validated by comparison with experiments of E. coli treated with A22 either in isolation or in combination, resulting in loss of width control and cell shape change.

cell biology↗

bioRxiv2024

Elucidating microRNA-34a organisation within Human Argonaute-2 by NMR

Understanding mRNA regulation by microRNA (miR) relies on the structural understanding of the RNA-induced silencing complex (RISC). Here, we elucidate the structural organisation of miR-34a, deregulated in various cancers, in hAgo2, effector protein in RISC, using guanosine-specific isotopic labelling and dynamic nuclear polarisation (DNP)-enhanced solid-state NMR. Homonuclear correlation experiments revealed that the non-A-form helical conformation of miR-34a increases when incorporated into hAgo2 and then bound to SIRT1 mRNA compared to the free hairpin or the free duplex formed with mRNA. Nucleotide-specific information of the of C2- and C3-endo sugar puckering can be obtained from the C8 - C1 correlation with varying distributions, revealing a trapping of different confirmations upon freezing. C3-endo puckering was predominantly observed for the seed, while C2-endo for the central region and a mixture of both elsewhere. These observations provide insights into the molecular dynamic basis of miR-based mRNA regulation, while also providing a proof-of-concept that experiments under cryogenic conditions, e.g. at 90K, can trap and with that reveal frozen dynamic states, using methods such as (DNP-enhanced) solid-state NMR or Cryo-EM

biochemistry↗

bioRxiv2023

The HIV-1 capsid serves as a nanoscale reaction vessel for reverse transcription

The viral capsid performs critical functions during HIV-1 infection and is a validated target for antiviral therapy. Previous studies have established that the proper structure and stability of the capsid are required for efficient HIV-1 reverse transcription in target cells. Moreover, it has recently been demonstrated that permeabilized virions and purified HIV-1 cores undergo efficient reverse transcription in vitro when the capsid is stabilized by addition of the host cell metabolite inositol hexakisphosphate (IP6). However, the molecular mechanism by which the capsid promotes reverse transcription is undefined. Here we show that wild type HIV-1 particles can undergo efficient reverse transcription in vitro in the absence of a membrane-permeabilizing agent. This activity, originally termed "natural endogenous reverse transcription" (NERT), depends on expression of the viral envelope glycoprotein during virus assembly and its incorporation into virions. Truncation of the gp41 cytoplasmic tail markedly reduced NERT activity, indicating that gp41 permits the entry of nucleotides into virions. Protease treatment of virions markedly reduced NERT suggesting the presence of a proteinaceous membrane channel. By contrast to reverse transcription in permeabilized virions, NERT required neither the addition of IP6 nor a mature capsid, indicating that an intact viral membrane can substitute for the function of the viral capsid during reverse transcription in vitro. Collectively, these results demonstrate that the viral capsid functions as a nanoscale container for reverse transcription during HIV-1 infection.

microbiology↗

bioRxiv2023

Fiberbots: Robotic fibers for high-precision minimally invasive surgery

Technologies that rely on the fundamental principle of thermal expansion have demonstrated high-precision, a growing demand in fields driven by miniaturization. However, scalable production of high aspect ratio devices that harness this capability while facilitating flexibility in design and functionality remains a challenge. We employed the high-throughput fiber thermal drawing technique to readily fabricate multimaterial fiberbots that can precisely and omnidirectionally move by asymmetric thermal expansion. These millimeter-scale fibers (< 2 mm) show excellent repeatability and linearity, negligible hysteresis, and can achieve micron-level resolution over four orders of magnitude motion range. By integrating these robotic fibers with medical devices that can perform cellular-level tissue imaging, diagnosis, and manipulation, we showcase their versatility through benchtop and preclinical animal studies and their overall potential impact on medicine, biomedical engineering, robotics, and beyond. One Sentence SummaryScalable manufacturing and integration of robotic fibers that deliver high-precision motion when heated.

bioengineering↗

bioRxiv2020

First report of an insilico study of Luciferase in Mycobacterium sp. EPa45

Mycobacterium are a genus of Actinobacteria known to be responsible for several deadly diseases in both humans and animals, including tuberculosis. Luciferase is the primary protein in Mycobacteria that plays a role in bioluminescence. It also plays a role in some bacteria of being a source of energy transference, such as in the case of lumazine proteins. Although studies have been conducted in different luciferase in bacteria, there has been hardly any structural studies on luciferase expressed in Mycobacterium sp. EPa45. Therefore, in this paper we have studied luciferase expressed in Mycobacterium sp. EPa45 by insilico analysis of its structure from its protein sequence. We report the observed differences within luciferase reported from other strains of mycobacterium and pathogenic and non-pathogenic forms of bacteria in terms of their (i) physiochemical characteristics, (ii) protein structure, (iii) multiple sequence alignment and (iv) phylogenetic relationships. We report for the first time the relation of this specific strain of Luciferase in mycobacterium and bacterium at large. HighlightsO_LIMycobacterium sp. EPa45 shows similar characteristics to pathogenic mycobacterium C_LIO_LIAnalysis of Luciferase sequence and protein qualities provides insight to pathogenicity C_LIO_LIThe deadly nature of infectious mycobacterium, especially with luciferase sequences similar to Mycobacterium sp. EPa45, is analyzed C_LI

bioinformatics↗

bioRxiv2020

Comparative analysis of the molecular mechanism of heat shock proteins from pathogenic and non-pathogenic E.coli

Cells can withstand the effects of temperature stress by activating small heat shock proteins IbpA and IbpB. Lon protease employing Ser679 - Lys722 catalytic dyad proteolyze IbpA and IbpB in their free forms, at physiological temperature i.e. without any temperature stress. However, the proteolytic activity of IbpA and IbpB is affected when the catalytic dyad residue of Lon protease is mutated. The mutation S679A in Lon protease brings about some changes so that the proteolytic interactions between the small heat shock proteins with that of the mutant Lon protease are lost which makes a difference in the interaction pattern of mutant Lon protease with their substrates. In the present study, we made an attempt through in-silico approach to figure out the underlying aspects of the interactions between the small heat shock proteins IbpA and IbpB with mutant Lon protease in Escherichia coli. We have tried to decipher the molecular details of the mechanism of interaction of proteolytic machinery of small heat shock proteins and mutant Lon protease with S679A mutation at physiological temperature in absence cellular temperature stress. Our study may therefore be helpful to decode the mechanistic details of the correlation with IbpA, IbpB and S679A mutant Lon protease in E. coli.

bioinformatics↗

bioRxiv2018

Synaptic release of acetylcholine rapidly suppresses cortical activity by recruiting muscarinic receptors in layer 4

Basal forebrain (BF) cholinergic projections to neocortex dynamically regulate information processing. However, the underlying synaptic and cellular mechanisms remain poorly understood. While synaptically released acetylcholine (ACh) can recruit nicotinic ACh receptors (nAChRs) expressed in distinct types of interneurons, previous work has not defined a clear role for muscarinic ACh receptors (mAChRs) in the fast cholinergic control of cortical activity. To address this question, we employed a slice model of cortical activity and used optogenetics to selectively activate cholinergic afferents. We found that transient ACh increases led to a rapid and persistent suppression of cortical activity, mediated by mAChRs in layer 4 and by nAChRs in layer 2/3. Furthermore, mAChR-dependent cholinergic control was mediated at least in part by a short-latency and long-lasting inhibition of layer 4 excitatory neurons. Thus, the activation of postsynaptic mAChRs is central to the flexible cholinergic control of cortical activity.

neuroscience↗