Biology subjects

Nandi, T.

Publications and source records attributed to Nandi, T..

11 recordsLinked to original sources

bioRxiv2026

ARCHER-LD: Rapid Long-Range Linkage Disequilibrium Calculations at Biobank Scale using GPU Acceleration

Linkage disequilibrium (LD) information from one's own dataset is considered optimal for downstream analyses such as statistical fine-mapping. However, the computational complexity ({approx}N2 / 2 computations for N variants) lead most studies to use external reference panels, such as from 1000 Genomes. To capture LD across all variant pairs in biobank-scale whole-genome sequencing (WGS) datasets with hundreds of millions of variants, new computational strategies are essential. We present a novel approach that uses multi-GPU distributed computing to compute R2 for every variant pair in a dataset. On chromosome 22 (1.8 million variants) of the 30x WGS 1000 Genomes dataset, our method using eight consumer-level 12GB GPUs (NVIDIA RTX 2080TIs) takes <10 minutes, while the same calculation with PLINK using a high-end 64-threaded CPU (Intel Xeon Gold 6338) takes >80 minutes, corresponding to a {approx}8x speedup. We further demonstrate true biobank-scale performance in the Penn Medicine Biobank (PMBB; 57,170 samples), computing chromosome 1 LD ({approx}1.38 million variants) in 49 minutes versus 22.7 hours for PLINK, a {approx}28x speedup. With this method, we successfully computed on the aforementioned 30x WGS 1000 Genomes dataset ({approx}120 million variants and {approx}2500 samples) the entire LD matrix (>1e16, or 10 quadrillion elements) in under 6 hours using 512 NVIDIA 40GB A100 GPUs on the Department of Energy Argonne Leadership Computing Facility Polaris Supercomputer. We make this tool, coded in Python using CuPy, publicly available. Using this tool, researchers can leverage the full extent of their genomic data without relying on external LD reference panels and acquire more accurate, population-specific findings, particularly for groups underrepresented in existing databases.

bioinformatics↗

bioRxiv2026

Inhibitors of HIV-1 maturation modulate conformational dynamics and heterogeneity of the immature Gag lattice

HIV-1 maturation requires the viral protease to cleave the Gag polyprotein into its constituent domains. Subsequent conformational and morphological changes result in a mature, infectious virion. Prior studies support a hypothesis in which Gag conformational dynamics and the heterogeneity of the immature Gag lattice enable proteolytic and morphological maturation. We developed a single-molecule Forster resonance energy transfer imaging approach to probe, in real time, the conformational dynamics of individual Gag molecules within immature HIV-1 virions. Our results capture Gag's conformational landscape and the spatial heterogeneity of the immature lattice. We evaluated inhibitors of maturation to identify immature lattice features that are modulated to disrupt maturation. Maturation inhibitors that act through diverse mechanisms, including lenacapavir and compounds that alter viral membrane composition, arrest Gag dynamics and reduce the spatial heterogeneity of the lattice. These observations support a model in which Gag dynamics and immature lattice organization regulate HIV-1 maturation.

biophysics↗

bioRxiv2025

Extracellular vesicles aid in the transfer of long-term associative memory between Caenorhabditis elegans

Memory formation is necessary for the survival of animals across phyla. Here, we elucidate the mechanism underlying the formation of long-term associative memory (LTAM) formed by treating Caenorhabditis elegans with a volatile chemoattractant and heat. Previous work has shown that training animals with a paradigm involving heat and isoamyl alcohol (IAA) simultaneously, causes C. elegans to lose their attraction to IAA. In this study, we elaborate on the mechanism behind this LTAM formation and suggest that during training with heat and IAA, C. elegans release extracellular vesicles (EVs) that upon being taken up by the same trained animals or their untrained counterparts causes the organism to lose attraction to IAA. Our data suggests that the vesicles are highly specific to the training paradigms used and differ with differing cues. Finally, we show that this mechanism of transfer of LTAM appears to be conserved between C. elegans and C. briggsae allowing for both intra and interspecies transfer of memory.

neuroscience↗

bioRxiv2024

Ultrasound system for precise neuromodulation of human deep brain circuits

Transcranial ultrasound stimulation (TUS) has emerged as a promising technique for non-invasive neuromodulation, but current systems lack the precision to target deep brain structures effectively. Here, we introduce an advanced TUS system that achieves unprecedented precision in deep brain neuromodulation. The system features a 256-element, helmet-shaped transducer array operating at 555 kHz, coupled with a stereotactic positioning system, individualised treatment planning, and real-time monitoring using functional MRI. In a series of experiments, we demonstrate the systems ability to selectively modulate the activity of the lateral geniculate nucleus (LGN) and its functionally connected regions in the visual cortex. Participants exhibited significantly increased visual cortex activity during concurrent TUS and visual stimulation, with high reproducibility across individuals. Moreover, a theta-burst TUS protocol induced robust neuromodulatory effects, with decreased visual cortex activity observed for at least 40 minutes post-stimulation. These neuromodulatory effects were specific to the targeted LGN, as confirmed by control experiments. Our findings highlight the potential of this advanced TUS system to non-invasively modulate deep brain circuits with high precision and specificity, offering new avenues for studying brain function and developing targeted therapies for neurological and psychiatric disorders. The unprecedented spatial resolution and prolonged neuromodulatory effects demonstrate the transformative potential of this technology for both research and clinical applications, paving the way for a new era of non-invasive deep brain neuromodulation.

neuroscience↗

bioRxiv2023

Auditory confounds can drive online effects of transcranial ultrasonic stimulation in humans

Transcranial ultrasonic stimulation (TUS) is rapidly emerging as a promising non-invasive neuromodulation technique. TUS is already well-established in animal models, providing foundations to now optimize neuromodulatory efficacy for human applications. Across multiple studies, one promising protocol, pulsed at 1000 Hz, has consistently resulted in motor cortical inhibition in humans (Fomenko et al., 2020). At the same time, a parallel research line has highlighted the potentially confounding influence of peripheral auditory stimulation arising from TUS pulsing at audible frequencies. In this study, we disentangle direct neuromodulatory and indirect auditory contributions to motor inhibitory effects of TUS. To this end, we include tightly matched control conditions across four experiments, one preregistered, conducted independently at three institutions. We employed a combined transcranial ultrasonic and magnetic stimulation paradigm, where TMS-elicited motor-evoked potentials (MEPs) served as an index of corticospinal excitability. First, we replicated motor inhibitory effects of TUS but showed through both tight controls and manipulation of stimulation intensity, duration, and auditory masking conditions that this inhibition was driven by peripheral auditory stimulation, not direct neuromodulation. Further, we consider neuromodulation beyond driving overall excitation/inhibition and show preliminary evidence of how TUS might interact with ongoing neural dynamics instead. Primarily, this study highlights the substantial shortcomings in accounting for the auditory confound in prior TUS-TMS work where only a flip-over sham and no active control was used. The field must critically reevaluate previous findings given the demonstrated impact of peripheral confounds. Further, rigorous experimental design via (in)active control conditions is required to make substantiated claims in future TUS studies. Only when direct effects are disentangled from those driven by peripheral confounds can TUS fully realize its potential for research and clinical applications.

neuroscience↗

bioRxiv2023

Ramped V1 transcranial ultrasonic stimulation modulates but does not evoke visual evoked potentials

Transcranial ultrasonic stimulation (TUS), has been shown to evoke visual evoked potential (VEP)-like potentials on EEG recordings, and also to modulate sensory evoked potentials. However, pulsed TUS is accompanied by an auditory confound, and it is possible that any observed effects were, in-part, evoked by this confound. Therefore, we used ramped TUS pulses, which are not as easily audible, to examine whether primary visual cortex (V1) TUS evokes VEP-like potentials, and modulates VEPs elicited using a checkerboard stimulus. MethodsWe tested 14 healthy participants (31 {+/-} 4.3 yrs, 4 F and 10 M). TUS was applied to the left V1 using a 270 kHz transducer (H115-2AA, Sonic Concepts). Ramped pulses (1 ms ramp, 3.25 ms total pulse duration) were repeated at 250 Hz, with a pulse train duration of 300 ms, an effective duty cycle of 50%, and Isppa without ramping of 16 W/cm2 in water. EEG was recorded from 16 channels using the g.USBamp amplifier (g.tec medical engineering GmbH). In two blocks (TUS-only), real and sham (100 each) TUS trials were repeated every 2 s. In another two blocks (TUS+checkerboard), a checkerboard stimulus was flipped every 0.5 s, and every fourth stimulus was associated with either a real or sham (100 each) TUS trial. The TUS trial started approx. 130 ms (0-5 ms jitter) before the checkerboard flip. All EEG data were analysed using Fieldtrip, and cluster-based permutation tests were used to test for differences between conditions. Results and discussionIn the TUS-only condition, in contrast to a previous study, we found no evoked potentials using ramped pulses which minimised the auditory artifact. In the TUS+checkerboard condition, we observed a modulation of the early-component of the VEP in real TUS, relative to no TUS trials. This suggests that, in line with in-vitro and animal data, there is a direct neuromodulatory effect of ultrasound, in addition to any confounding effects. Moving forward, ramping offers a relatively easy approach to minimise the auditory confound.

neuroscience↗

bioRxiv2022

tDCS induced GABA change is associated with the simulated electric field in M1, an effect mediated by grey matter volume in the MRS voxel

Background and ObjectiveTranscranial direct current stimulation (tDCS) has wide ranging applications in neuro-behavioural and physiological research, and in neurological rehabilitation. However, it is currently limited by substantial inter-subject variability in responses, which may be explained, at least in part, by anatomical differences that lead to variability in the electric field (E-field) induced in the cortex. Here, we tested whether the variability in the E-field in the stimulated cortex during tDCS, estimated using computational simulations, explains the variability in tDCS induced changes in GABA, a neurophysiological marker of stimulation effect. MethodsData from five previously conducted MRS studies were combined. The anode was placed over the left primary motor cortex (M1, 3 studies, N = 24) or right temporal cortex (2 studies, N = 32), with the cathode over the contralateral supraorbital ridge. Single voxel spectroscopy was performed in a 2x2x2cm voxel under the anode in all cases. MRS data were acquired before and either during or after 1mA tDCS using either a sLASER sequence (7T) or a MEGA-PRESS sequence (3T). sLASER MRS data were analysed using LCModel, and MEGA-PRESS using FID-A and Gannet. E-fields were simulated in a finite element model of the head, based on individual MPRAGE images, using SimNIBS. Separate linear mixed effects models were run for each E-field variable (mean and 95th percentile; magnitude, and components normal and tangential to grey matter surface, within the MRS voxel). The model included effects of time (pre or post tDCS), E-field, grey matter volume in the MRS voxel, and a 3-way interaction between time, E-field and grey matter volume. Additionally, we ran a permutation analysis using PALM to determine whether E-field anywhere in the brain, not just in the MRS voxel, correlated with GABA change. ResultsIn M1, higher mean E-field magnitude was associated with greater tDCS-induced decreases in GABA (t(24) = 3.24, p = 0.003). Further, the association between mean E-field magnitude and GABA change was moderated by the grey matter volume in the MRS voxel (t(24) = -3.55, p =0.002). These relationships were consistent across all E-field variables except the mean of the normal component. No significant relationship was found between tDCS-induced GABA decrease and E-field in the temporal voxel. No significant clusters were found in the whole brain analysis. ConclusionsOur data suggest that the electric field induced by tDCS within the brain is variable, and is significantly related to tDCS-induced decrease in GABA, a key neurophysiological marker of stimulation. These findings strongly support individualised dosing of tDCS, at least in M1. Further studies examining E-fields in relation to other outcome measures, including behaviour, will help determine the optimal E-fields required for any desired effects. HighlightsO_LIWe study the link between individually simulated electric field dose and tDCS-induced change in GABA in the cortex. C_LIO_LIThe electric field strength in the brain correlates with a decrease in GABA in the motor cortex. C_LIO_LIThe correlation between the electric field and GABA change is modulated by the amount of grey matter in the MRS voxel. C_LIO_LIWe find no association between the electric field and GABA in the temporal cortex. C_LI

neuroscience↗

bioRxiv2020

Rational design of protein-specific folding modifiers

Protein folding can go wrong in vivo and in vitro, with significant consequences for the living cell and the pharmaceutical industry, respectively. Here we propose a general design principle for constructing small peptide-based protein-specific folding modifiers. We construct a xenonucleus, which is a pre-folded peptide that resembles the folding nucleus of a protein, and demonstrate its activity on the folding of ubiquitin. Using stopped-flow kinetics, NMR spectroscopy, Forster Resonance Energy transfer, single-molecule force measurements, and molecular dynamics simulations, we show that the ubiquitin xenonucleus can act as an effective decoy for the native folding nucleus. It can make the refolding faster by 33 {+/-} 5% at 3 M GdnHCl. In principle, our approach provides a general method for constructing specific, genetically encodable, folding modifiers for any protein which has a well-defined contiguous folding nucleus.

biophysics↗

bioRxiv2018

Gut microbiome recovery after antibiotic usage is mediated by specific bacterial species

Dysbiosis in the gut microbiome due to antibiotic usage can persist for extended periods of time, impacting host health and increasing the risk for pathogen colonization. The specific factors associated with variability in gut microbiome recovery remain unknown. Using data from 4 different cohorts in 3 continents comprising >500 microbiome profiles from 117 subjects, we identified 20 bacterial species exhibiting robust association with gut microbiome recovery post antibiotic therapy. Functional and growth analysis showed that microbiome recovery is supported by enrichment in carbohydrate degradation and energy production capabilities. Association rule mining on 782 microbiome profiles from the MEDUSA database enabled reconstruction of the gut microbial food-web, identifying many recovery-associated bacteria (RABs) as primary colonizing species, with the ability to use both host and diet-derived energy sources, and to break down complex carbohydrates to support the growth of other bacteria. Experiments in a mouse model recapitulated the ability of RABs (Bacteroides thetaiotamicron and Bifidobacterium adolescentis) to promote microbiome recovery with synergistic effects, providing a two orders of magnitude boost to microbial abundance in early time-points and faster maturation of microbial diversity. The identification of specific microbial factors promoting microbiome recovery opens up opportunities for rationally fine-tuning pre- and probiotic formulations that prevent pathogen colonization and promote gut health.

genomics↗

bioRxiv2017

Pan-cancer study of heterogeneous RNA aberrations

We present the most comprehensive catalogue of cancer-associated gene alterations through characterization of tumor transcriptomes from 1,188 donors of the Pan-Cancer Analysis of Whole Genomes project. Using matched whole-genome sequencing data, we attributed RNA alterations to germline and somatic DNA alterations, revealing likely genetic mechanisms. We identified 444 associations of gene expression with somatic non-coding single-nucleotide variants. We found 1,872 splicing alterations associated with somatic mutation in intronic regions, including novel exonization events associated with Alu elements. Somatic copy number alterations were the major driver of total gene and allele-specific expression (ASE) variation. Additionally, 82% of gene fusions had structural variant support, including 75 of a novel class called \"bridged\" fusions, in which a third genomic location bridged two different genes. Globally, we observe transcriptomic alteration signatures that differ between cancer types and have associations with DNA mutational signatures. Given this unique dataset of RNA alterations, we also identified 1,012 genes significantly altered through both DNA and RNA mechanisms. Our study represents an extensive catalog of RNA alterations and reveals new insights into the heterogeneous molecular mechanisms of cancer gene alterations.

genomics↗

bioRxiv2017

A pan cancer analysis of promoter activity highlights the regulatory role of alternative transcription start sites and their association with noncoding mutations

Most human protein-coding genes are regulated by multiple, distinct promoters, suggesting that the choice of promoter is as important as its level of transcriptional activity. While the role of promoters as driver elements in cancer has been recognized, the contribution of alternative promoters to regulation of the cancer transcriptome remains largely unexplored. Here we infer active promoters using RNA-Seq data from 1,188 cancer samples with matched whole genome sequencing data. We find that alternative promoters are a major contributor to context-specific regulation of isoform expression and that alternative promoters are frequently deregulated in cancer, affecting known cancer-genes and novel candidates. Our study suggests that a highly dynamic landscape of active promoters shapes the cancer transcriptome, opening many opportunities to further explore the interplay of regulatory mechanism and noncoding somatic mutations with transcriptional aberrations in cancer.

genomics↗