Biology subjects

Dash, D.

Publications and source records attributed to Dash, D..

18 recordsLinked to original sources

bioRxiv2026

Scalp EEG detects motor sequence replay signatures during wakeful rest

Brief wakeful rest may support motor-memory processing through replay of recently practiced neural sequences, but human motor replay has been demonstrated mainly with invasive recordings or magnetoencephalography. Here we tested whether ordered motor-sequence replay can be detected from scalp EEG across wakeful rest during motor skill learning. During rest, participants received no cue, regular or accelerated auditory targeted-memory reactivation (TMR), or randomized tones. Neural states re-emerged in the practiced sequence order, revealing forward replay across conditions. Accelerated TMR enhanced total learning; within this condition, stronger forward replay showed the clearest exploratory relationship with micro-offline gains, while forward and reverse replay also covaried with gains across the cohort. The apparent replay timescale shifted systematically with decoder temporal resolution, showing that measured timing reflects both neural dynamics and the observation model. These findings support scalp EEG as a scalable approach for studying ordered motor-sequence reactivation during wakeful rest.

neuroscience↗

bioRxiv2026

Constricted pupil states index neural replay during wakeful rest in humans

Neural replay has been linked to skill consolidation during wakeful rest, yet its physiological context in humans remains poorly understood. In animals, hippocampal ripples and associated replay occur more frequently within intrinsically oriented brain states associated with constricted pupils, suggesting that pupil dynamics may index neural replay events in humans. We combined magnetoencephalography-derived sequence replay with pupillometry in 25 participants learning a motor sequence across alternating intervals of practice and rest. Replay was indexed by smaller-pupil states, and replay timing clustered on the constricting phase of slow pupil fluctuations. More frequent replay accompanied larger cumulative offline gains during early learning, while smaller rest pupil was associated with better performance when practice resumed. Multivariate pupil features predicted replay-associated states across and within individuals while preceding pupil dynamics showed modest predictive ability to identify the precise onset of individual replay events. Here, we show that constricted-pupil states index neural replay during wakeful rest in humans, linking replay-associated physiology with early motor learning.

neuroscience↗

bioRxiv2026

SPOUT: An open-source hardware and software platform to study decision making while manipulating and recording from neural activity

Recording and manipulating brain activity during behavior is critical to understanding the underlying mechanisms of decision-making. Linking neural activity to behavior requires behavioral hardware and software tightly integrated with recording and perturbation systems on a shared clock. We built SPOUT (State-machine Platform for Operant Uni/dual-spout Tasks), an open-source, Teensy-driven state-machine platform with a MATLAB interface that runs 10 unique decision-making tasks (with dozens of variations available through user-friendly settings) to study behavior in head-restrained mice. The platform is built on several custom hardware devices: a dual-lick detector, headplate designs for optogenetics and two-photon calcium imaging, a three-axis motorized spout manipulator, and an optogenetics power modulator. The firmware differentiates between one and two lick spout tasks and can be controlled by a user-friendly interface. Task settings can be selected through the interface or by loading predefined settings files. We validated the clock speed and lick detection against an independent, external acquisition system and identified highly precise, sub-millisecond detection of single licks. Using a pseudo-random synchronization pulse generated by SPOUT, we corrected for missing data due to glitches in the acquisition system and clock drift. We showcase the versatility of SPOUT by training mice on an uninstructed lick-left/lick-right task in which the rewarded side switches unexpectedly and found that mice use history-dependent action-outcome associations to guide future behavior. Transiently inhibiting the anterior lateral motor cortex (ALM) during cue presentation induced contralateral deficits, without affecting ipsilateral trials. Finally, two-photon imaging of ALM neurons revealed stronger population responses during contralateral choice licks compared to ipsilateral ones. Together, SPOUT offers an open-source, affordable platform to study decision-making in head-restrained mice while combining neural recordings and manipulations.

neuroscience↗

bioRxiv2026

Comparative Analysis of Ultrafine Particulate Matter, Black Carbon, and Polystyrene Nanoplastics Identifies Mitochondrial Stress Adaptation as a Conserved Mechanism of Immunotoxicity

Several studies have been conducted on human exposure to ultrafine particulate matter (UFPM), Black carbon (BC), and polystyrene nanoplastics (PS-NPs). However, it remains unclear whether different chemical types of environmental nanoparticles induce a similar mitochondrial stress response or a unique particle-specific response. In the present study, we examined the molecular mechanisms underlying nanoparticle-induced mitochondrial stress response and immunotoxicity using human peripheral blood mononuclear cells exposed to UFPM, BC, and PS-NPs under similar experimental conditions. Oxidative stress, mitochondrial adaptation, respiratory chain integrity, mitochondrial integrated stress response, inflammatory signaling, and systems-level interactions between molecules were analyzed through the evaluation of the expression of NRF2, HIF-1, PGC-1, TFAM, OMA1, DELE1, mitochondrial ND1, Complex I-V, NF-{kappa}B, TNF-, and NLRP3 and the use of principal component analysis, hierarchical clustering, and correlation networks. All three nanoparticles caused oxidative stress and mitochondrial dysfunction with different kinetics and mechanisms. UFPM mostly induced an acute antioxidant response and mitochondrial adaptation; BC led to chronic mitochondrial dysfunction, chronic activation of the OMA1-DELE1-mediated mitochondrial ISR pathway, and inflammation; while PS-NPs induced low but chronic mitochondrial adaptation along with mitochondrial biogenesis and stress responses. Our systems-level analysis showed that oxidative stress, mitochondrial adaptation, mitochondrial ISR, and inflammation represent a highly connected molecular network regardless of the physicochemical nature of the nanoparticles, with the OMA1- DELE1 axis being a key regulatory node connecting mitochondrial stress response and inflammation. Overall, we have found that mitochondrial stress response is a common mechanism underlying the toxicity of chemically different nanoparticles and have also revealed particle-specific stress-response dynamics responsible for the degree and persistence of cellular damage. The current work presents novel insights into the molecular mechanisms of nanoparticle-induced immunotoxicity and suggests OMA1, DELE1, NRF2, PGC-1, TFAM, ND1, and Complex I-V as potential biomarkers.

pharmacology and toxicology↗

bioRxiv2025

Methionine metabolism shapes immune response against Mycobacterium tuberculosis

The methionine metabolism is central to epigenetic reprogramming to produce pro-inflammatory cytokines. Disruptions in methionine metabolism contribute to complex disorders, providing an important target for nutrient interventions. Here, Mycobacterium tuberculosis (Mtb) H37Rv-infected C57BL/6 mice showed functional heterogeneity between alveolar and non-alveolar macrophage (AMs/Non-AMs) with major metabolic reprogramming in Non-AMs. Global metabolite and proteome analysis of Mtb-infected bone marrow-derived macrophages (BMDMs) showed a diversion of flux from methionine metabolism toward increased nucleotide salvage and glutathione (GSH) production. Carbon units of 13C5-methionine via isotopomer analysis contributed to polyamine synthesis, fuelling the nucleotide salvage node in Mtb-infected BMDMs. Methionine supplementation increased mycobacterial clearance in C57BL/6 mice and in BMDMs by promoting a pro-inflammatory response, as evident by increased IL-1{beta} and IFN-{gamma}. Increased IL-1{beta} production is mainly contributed to by increased H3K4 trimethylation in macrophages. These findings reveal an important strategy by which methionine supplementation in macrophages and mice remodels host metabolism to enhance acute pro-inflammatory responses and exploit dietary supplementation to improve nutritional immunity in TB. HighlightsO_LIMycobacterium tuberculosis (Mtb) infection decreases intracellular methionine levels and increases purine levels in primary macrophages. C_LIO_LIMethionine carbon units contribute to nucleotide salvage, and their restriction lowers IL-1 response and mycobacterial clearance. C_LIO_LIEx vivo methionine supplementation in Mtb-infected macrophages increases H3K4me3 at the Il-1b gene promoter and gene body, leading to an increased pro-inflammatory response and improved mycobacterial clearance. C_LIO_LIIn vivo methionine supplementation improved pro-inflammatory response in lungs, spleen and bone marrow, leading to accelerated mycobacterial clearance upon Mtb-H37Rv infection. C_LI Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=157 SRC="FIGDIR/small/680834v2_ufig1.gif" ALT="Figure 1"> View larger version (47K): org.highwire.dtl.DTLVardef@1bf5corg.highwire.dtl.DTLVardef@ba4dbdorg.highwire.dtl.DTLVardef@145f23dorg.highwire.dtl.DTLVardef@122b2a2_HPS_FORMAT_FIGEXP M_FIG C_FIG

immunology↗

bioRxiv2025

Silent Speech Recognition with Wearable Magnetometers

Next-generation human-computer interaction (HCI) is moving towards more seamless, intuitive, and personal modes of communication, redefining how we interact with technology and one another. Within this landscape, silent speech recognition (SSR) offers a powerful new interaction paradigm, enabling hands-free, private interaction while supporting individuals with speech impairments and enabling communication in noisy or sensitive environments. Recent advances in miniaturized sensors and artificial intelligence (AI) have accelerated the development of more sophisticated wearable SSR systems, driven by growing demand for effortless and accessible communication. Although electrophysiological (ExG) modalities, particularly electromyography (EMG), have dominated early efforts in developing wearable SSR, critical challenges remain. Limited generalizability across users, sensor-skin interface issues, and difficulties with the comfort of use are all current roadblocks to reliable, high-fidelity signals in a wearable form factor. We propose that magnetometers offer a promising alternative to ExG and have the potential to unlock more robust, generalizable, and user-friendly SSR systems. We demonstrate that magnetometers embedded in a headphone form factor achieve a per-user SSR accuracy of 86%, significantly outperforming previously reported state-of-the-art wearable headphones combining ExG and inertial measurement units (IMUs). In addition, we show that wearable magnetometry enables generalization across individuals for SSR. Extending beyond headphones, we also introduce a necklace form factor with magnetometers that is capable of decoding both silent and overt speech in ambient conditions, further showcasing the versatility of magnetometers across different wearable designs in real-world conditions.

neuroscience↗

bioRxiv2025

Laboratory adaptive evolution of thermotolerance is linked to the evolution of a robust proteostasis in S. cerevisiae

Thermophilic organisms have evolved a proteome that resists thermal denaturation. While the evolution of their complete proteome would require multiple generations, early on, organisms would need to develop strategies to survive at high temperatures despite their thermolabile proteome. We hypothesized that the organisms would do this by reinforcing their proteostasis capacity. We tested this hypothesis using adaptive laboratory evolution of thermotolerance in Saccharomyces cerevisiae and found that the cells reproducibly evolved better proteostasis capacity in short-term evolution experiments. However, rather than improving the global proteostasis capacity, most of the evolved strains demonstrated enhanced capacity to tackle misfolding in the Endoplasmic Reticulum (ER), specifically by increasing their capacity for ER-associated degradation (ERAD). Given the strong selective advantage of these strains, we posit that protein folding in the ER may be exquisitely sensitive to chronic thermal stress and may act as an early indicator for adaptation to higher temperatures.

evolutionary biology↗

bioRxiv2024

Cingulate and striatal hubs are linked to early skill learning

Early skill learning develops in the context of activity changes in distributed cortico-subcortical regions. Here, we investigated network hubs--centers of information integration and transmission--within the brain network supporting early skill learning. We recorded magnetoencephalographic (MEG) brain activity in healthy human subjects who learned a moderately difficult sequence skill with their non-dominant left hand. We then computed network hub strength by summing top 10% functional connectivity over 86 parcellated brain regions (AAL3 atlas) and five brain oscillatory frequency bands (alpha, low-, high-beta, low- and high-gamma). Virtually all skill gains developed during rest intervals of early learning (micro-offline gains). MEG hub strength in the alpha band (8-13Hz) in bilateral anterior cingulate (ACC) and caudate and in the low-beta band (13-16Hz) in bilateral caudate and right putamen correlated with micro-offline gains. These regions linked strongly with the hippocampus, parahippocampal cortex, and lingual and fusiform gyri. Thus, alpha and low-beta brain oscillatory activity in cingulate and striatal regions appear to contribute as hubs of information integration and transmission during early skill learning. Significance StatementEarly learning of moderately difficult skill sequences develops over periods of rest interspersed with practice (micro-offline gains). We demonstrate here a link between alpha and low-beta oscillatory activity in a cingulate-hippocampo-striato network hubs and rest intervals of early learning.

neuroscience↗

bioRxiv2024

Diabetes-Tuberculosis Comorbidity Characterized by Reduced Type-II Interferon and Elevated Th17 Responses.

Understanding the perturbed lung immune cells distribution and its functionality in tuberculosis (TB) is well documented; however, limited reports have covered their disruption, if any, in diabetes-tuberculosis (DM-TB) comorbid conditions. Here, we employed single-cell RNA-seq to investigate the molecular mechanisms that govern the heterogeneity in host immune response in DM-TB comorbid conditions. Diabetes is associated with chronic hyperinflammation and reduced lung-infiltrating immune cells, which delays the immune response to Mycobacterial infection. scRNA-seq of lung CD3 and CD11c cells revealed compromised adaptive and innate immunity, with decreased Th1 and M1 macrophage populations in DM-TB mice. A dampened immune response, marked by increased IL-16 signaling and reduced TNF and IFN-II responses, was observed in DM-TB. This study highlights chronic inflammation, hyperglycemia, and dyslipidemia associated with diabetes impairing anti-TB immunity. Selective inhibition of aberrant IL-16 secretion and Th17 cell activation might provide strategies for better managing DM-TB comorbidity.

immunology↗

bioRxiv2024

Generalizable gesture recognition usingmagnetomyography

The progression of human-computer interfaces into immersive and touchless realities requires new ways of interacting with machines that are correspondingly intuitive and seamless. Among these are gesture-based systems that use natural hand movements to interact with and control digital devices. Today, these systems are most commonly implemented through the use of cameras or inertial sensors, which have drawbacks in environments that are poorly lit, in conditions where the hands are obscured, or for applications that require fine motor control. More recent studies have advocated for the use of surface electromyography (sEMG) to capture gesture information by sensing electrical activity generated by muscle contraction. While promising demonstrations have been shown, studies have also outlined limitations in sEMG when it comes to generalization across a population, largely due to physiological differences between individuals. Magnetomyography (MMG) is an alternative modality for measuring the same motor signals at the muscle, but is impervious to distortions caused by tissue, hair, and moisture; this indicates potential for lower variability caused by physiological differences and changes in skin conductivity, making MMG a promising generalizable solution for gesture control. To test this theory, we developed wristbands with magnetic sensors and implemented a signal processing pipeline for gesture classification. Using this system, we measured MMG across 30 participants performing a gesture task consisting of nine discrete gestures. We demonstrate average single-participant classification accuracy of 95.4%, rivaling state-of-the-art accuracy with sEMG. In addition, we achieved higher cross-session and cross-participant accuracy compared to sEMG studies. Given that these results were obtained with a non-ideal recording system, we anticipate significantly better results with better sensors. Together, these findings suggest that MMG can provide higher performance for control systems based on gesture recognition by overcoming limitations of existing techniques.

neuroscience↗

bioRxiv2024

Sequence action representations contextualize during rapid skill learning

Activities of daily living rely on our ability to acquire new motor skills composed of precise action sequences. Here, we asked if the millisecond-level neural representation of an action performed at different contextual sequence locations within a skill differentiates or remains stable during early motor learning. We first optimized machine learning decoders predictive of sequence-embedded finger movements from magnetoencephalographic (MEG) activity. Using this approach, we found that the neural representation of the same action performed in different contextual sequence locations, progressively differentiated--primarily during rest intervals of early learning (offline)--correlating with skill gains. In contrast, representational differentiation during practice (online) did not reflect learning. The regions contributing to this representational differentiation evolved with learning, shifting from the contralateral pre- and post-central cortex during early learning (trials 1-11) to increased involvement of the superior and middle frontal cortex once skill performance plateaued (trials 12-36). Thus, the neural substrates supporting finger movements and their representational differentiation during early skill learning differ from those supporting stable performance during the subsequent skill plateau period. Representational contextualization extended to Day 2, exhibiting specificity for the practiced skill sequence. Altogether, our findings indicate that sequence action representations contextually differentiate during early skill learning, an issue relevant to brain-computer interface applications in neurorehabilitation.

neuroscience↗

bioRxiv2024

Magnetomyography: A novel modality for non-invasive muscle sensing

The measurement of magnetic fields generated by skeletal muscle activity, called magnetomyography (MMG), has seen renewed interest from the academic community in recent years. Although studies have demonstrated complex models of MMG and experiments classifying between different movements using MMG, there has yet to be time frequency analysis of MMG as well as concurrent recordings of MMG and its electrical counterpart, surface electromyography (sEMG). Here, we aim to better understand MMG in the context of sEMG by simultaneously recording both modalities during various muscle contraction tasks. We found that, similar to sEMG, MMG shows highly linearly correlated power to the degree of muscle contraction, has a unimodal distribution in spectral power, and can detect changes in muscle fatigue via changes in the spectral distribution. One main difference we found was that MMG typically has more high frequency content compared to sEMG, even when accounting for the filtering induced by the size of the sEMG electrodes. We additionally demonstrate empirically the decrease in MMG power due to distance from the arm and show MMG decreases slower than the inverse square law and can be measured up to 50 mm from the surface of the skin. Finally, we were able to capture MMG with non-OPM sensors showing that sensor technology has made great strides towards enabling MMG applications.

neuroscience↗

bioRxiv2023

Quality control and annotation of variant peptides identified through proteogenomics

Variant peptides resulting from translation of single nucleotide polymorphisms (SNPs) can lead to aberrant or altered protein functions and thus hold translational potential for disease diagnosis, therapeutics and personalized medicine. Variant peptides detected by proteogenomics are fraught with high number of false positives. Class-specific FDR along with ad-hoc post-search filters have been employed to tackle this issue, but there is no uniform and comprehensive approach to assess variant quality. These protocols are mostly manual or tedious, and not accessible across labs. We present a software tool, PgxSAVy, for the quality control of variant peptides. PgxSAVy provides a rigorous framework for quality control and annotations of variant peptides on the basis of (i) variant quality, (ii) isobaric masses, and (iii) disease annotation. PgxSAVy was able to segregate true and false variants with 98.43% accuracy on simulated data. We then used [~]2.8 million spectra (PXD004010 and PXD001468) and identified 12,705 variant PSMs, of which PgxSAVy evaluated 3028 (23.8%), 1409 (11.1%) and 8268 (65.1%) as confident, semi-confident and doubtful respectively. PgxSAVy also annotates the variants based on their pathogenicity and provides support for assisted manual validation. In these datasets, it identified previously found variants as well some novel variants not seen in original studies. The confident variants identified the importance of mutations in glycolysis and gluconeogenesis pathways in Alzheimers disease. The analysis of proteins carrying variants can provide fine granularity in discovering important pathways. PgxSAVy will advance personalized medicine by providing a comprehensive framework for quality control and prioritization of proteogenomics variants. AvailabilityPgxSAVy is freely available at https://github.com/anuragraj/PgxSAVy Key PointsO_LIVariant peptide in proteogenomics have high rates of false positives C_LIO_LIclass-specific FDR is not sufficiently effective, and tedious manual filtering is not scalable C_LIO_LIWe developed PgxSAVy for automated quality control and disease annotation of variant peptides from proteogenomics search results C_LIO_LIPgxSAVy was validated using simulation data and manually annotated variant PSMs C_LIO_LIIndependent application on large datasets on Alzheimers and HEK cell lines demonstrated that PgxSAVy discovered known and novel mutations with important biological roles. C_LI Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=161 HEIGHT=200 SRC="FIGDIR/small/542998v2_ufig1.gif" ALT="Figure 1"> View larger version (39K): org.highwire.dtl.DTLVardef@187a515org.highwire.dtl.DTLVardef@67471corg.highwire.dtl.DTLVardef@6d90e9org.highwire.dtl.DTLVardef@144c6c1_HPS_FORMAT_FIGEXP M_FIG C_FIG

bioinformatics↗

bioRxiv2022

Notch signaling functions in non-canonical juxtacrine manner in platelets to amplify thrombogenicity

BackgroundNotch signaling is an evolutionarily conserved pathway that dictates cell fate decisions in mammalian cells including megakaryocytes. Existence of functional Notch signaling in enucleate platelets that are generated as cytoplasmic buds from megakaryocytes still remains elusive. MethodsPlatelets were isolated from human blood by differential centrifugation under informed consent. Expression of transcripts as well as peptides of Notch1 and DLL-4 in platelets was studied by employing RT-qPCR, Western analysis and flow cytometry. Platelet activation responses that include aggregation, secretion of granule contents and platelet-leucocyte interaction were analyzed by Borns aggregometry, flow cytometry, Western analysis and lumi- aggregometry. Shedding of extracellular vesicles from platelets was documented with Nanoparticle Tracking Analyzer. Platelet adhesion and thrombus growth on immobilized matrix was quantified by employing microfluidics platform. Intracellular free calcium in Fura-2-loaded platelets was monitored from ratiometric fluorescence spectrophotometry. Coagulation parameters in whole blood were studied by thromboelastography. Ferric chloride-induced mesenteric arteriolar thrombosis in murine model was imaged by intravital microscopy. ResultsHere we demonstrate significant expression of Notch1 and its ligand, the Delta-like ligand (DLL)- 4, as well as their respective transcripts, in human platelets. Synthesis and surface translocation of Notch1 and DLL-4 were upregulated when cells were challenged with physiological agonists like thrombin. DLL-4, in turn, instigated neighbouring platelets to switch to activated phenotype, associated with cleavage of Notch receptor and generation of its intracellular domain (NICD). DLL-4-mediated pro-thrombotic attributes were averted by pharmacological inhibition of {gamma}-secretase and phosphatidylinositol 3-kinase. Inhibition of Notch signaling, too, restrained agonist-induced platelet activation, and significantly impaired arterial thrombosis in mice, suggestive of synergism between thrombin- and DLL-4-mediated pathways. Strikingly, prevention of DLL-4-Notch1 interaction by a blocking antibody abolished platelet aggregation and extracellular vesicle shedding induced by thrombin. ConclusionsOur study presents compelling evidence in support of non-canonical Notch signaling that propagates in juxtacrine manner within platelet aggregates and synergizes with physiological agonists to generate occlusive intramural thrombi. Thus, targeting Notch signaling can be investigated as a potential anti-platelet/anti-thrombotic therapeutic approach. FundingThis research was supported by J. C. Bose National Fellowship (JCB/2017/000029) and grants received by D. Dash from the Indian Council of Medical Research (ICMR) under CAR (71/4/2018-BMS/CAR), Department of Biotechnology (DBT) (BT/PR-20645/BRB/10/1541/2016) and Science and Engineering Research Board (SERB) (EMR/2015/000583), Government of India. S.N. Chaurasia is a recipient of financial assistance from the ICMR. M. Ekhlak is a recipient of CSIR-SRF and V. Singh is a recipient of UGC-SRF. D. Dash acknowledges assistance from the Humboldt Foundation, Germany. Funders have no role in the design, analysis and reporting of the study.

cell biology↗

bioRxiv2020

Integrated genomic view of SARS-CoV-2 in India

India first detected SARS-CoV-2, causal agent of COVID-19 in late January-2020, imported from Wuhan, China. March-2020 onwards; importation of cases from rest of the countries followed by seeding of local transmission triggered further outbreaks in India. We used ARTIC protocol based tiling amplicon sequencing of SARS-CoV-2 (n=104) from different states of India using a combination of MinION and MinIT from Oxford Nanopore Technology to understand introduction and local transmission. The analyses revealed multiple introductions of SARS-CoV-2 from Europe and Asia following local transmission. The most prevalent genomes with patterns of variance (confined in a cluster) remain unclassified, here, proposed as A4-clade based on its divergence within A-cluster. The viral haplotypes may link their persistence to geo-climatic conditions and host response. Despite the effectiveness of non-therapeutic interventions in India, multipronged strategies including molecular surveillance based on real-time viral genomic data is of paramount importance for a timely management of the pandemic.

microbiology↗

bioRxiv2020

Genetic differences between extreme and composite constitution types from whole exome sequences reveal actionable variations

Personalized medicine relies on successful identification of genome-wide variations that governs inter-individual differences in phenotypes and system level outcomes. In Ayurveda, assessment of composite constitution types "Prakriti" forms the basis for risk stratification, predicting health and disease trajectories and personalized recommendations. Here, we report a novel method for identifying pleiotropic genes and variants that associate with healthy individuals of three extreme and contrasting "Prakriti" constitutions through exome sequencing and state-of-the-art computational methods. Exome Seq of three extreme Prakriti types from 108 healthy individuals 54 each from genetically homogeneous populations of North India (NI, Discovery cohort) and Western India (VADU, Replication cohort) were evaluated. Fishers Exact Test was applied between Prakriti types in both cohorts and further permutation based p-value was used for selection of exonic variants. To investigate the effect of sample size per genetic association test, we performed power analysis. Functional impact of differentiating genes and variations were inferred using diverse resources -Toppfun, GTEx, GWAS, PheWAS, UK Biobank and mouse knockdown/knockout phenotype (MGI). We also applied supervised machine learning approach to evaluate the association of exonic variants with multisystem phenotypes of Prakriti. Our targeted investigation into exome sequencing from NI (discovery) and VADU (validation) cohorts datasets provide ~7,000 differentiating SNPs. Closer inspection further identified a subset of SNPs (2407 (NI) and 2393 (VADU)), that mapped to an overlapping set of 1181 genes. This set can robustly stratify the Prakriti groups into three distinct clusters with distinct gene ontological (GO) enrichments. Functional analysis further strengthens the potential pleiotropic effects of these differentiating genes/variants and multisystem phenotypic consequences. Replicated SNPs map to some very prominent genes like FIG4, EDNRA, ANKLE1, BCKDHA, ATP5SL, EXOCS5, IFIT5, ZNF502, PNPLA3 and IL6R. Lastly, multivariate analysis using random forest uncovered rs7244213 within urea transporter SLC14A2, that associate with an ensemble of features linked to distinct constitutions. Our results reinforce the concept of integration of Prakriti based deep phenotypes for risk stratification of healthy individuals and provides markers for early actionable interventions.

genomics↗

bioRxiv2019

Host cholesterol dependent activation of VapC12 toxin enriches persister population during Mycobacterium tuberculosis infection

A worldwide increase in the frequency of multidrug-resistant and extensively drug-resistant cases of tuberculosis is mainly due to therapeutic noncompliance associated with a lengthy treatment regimen. Depending on the drug susceptibility profile, the treatment duration can extend from 6 months to 2 years. This protracted regimen is attributed to a supposedly non-replicating and metabolically inert subset of the Mycobacterium tuberculosis (Mtb) population, called persisters. The mechanism underlying stochastic generation and enrichment of persisters is not fully known. We have previously reported that the utilization of host cholesterol is essential for mycobacterial persistence. In this study, we have demonstrated that cholesterol-induced activation of a ribonuclease toxin (VapC12) inhibits translation by targeting proT tRNA in Mtb. This results in cholesterol-specific growth modulation that increases the frequency of the generation of persisters in a heterogeneous Mtb population. Also, a null mutant strain of this toxin ({Delta}vapC12) failed to persist and demonstrated an enhanced growth phenotype in a guinea pig model of Mtb infection. Thus, we have identified a novel strategy through which cholesterol-specific activation of a toxin-antitoxin (TA) module in Mtb enhances persister formation during infection. In addition to identifying the mechanism, the study provides opportunity for targeting persisters, a new paradigm facilitating tuberculosis drug development.

microbiology↗

bioRxiv2017

Chaperone Network Based On Cellular Response Reveals The Non-Optimal Response To Perturbed Proteostasis

The proteostasis network (PN) comprises a plethora of proteins that are dedicated to aid in protein folding; some with over-lapping functions. Despite this, there are multiple pathophysiological states associated with depletion of chaperones. This is counter-intuitive assuming cells have the ability to re-program transcriptional outputs in accordance with its proteostasic limitations. To this effect, we have used S. cerevisiae to understand the route a cell takes as a response when challenged with different proteostasis impairments. Using 14 single deletion strains of genes of Protein Quality Control (PQC) system, we quantify their proteostasis impairment and the transcriptional response. In most cases cellular response was incapable of restoring proteostasis. The response did not activate proteostasis components or pathways that could complement the function of the missing PQC gene. Over-expression of alternate machineries, could restore part of the proteostasis defect in deletion strains. We posit that epistasis guided synthetic biology approaches may be helpful in realizing the true potential of the cellular chaperone machinery.

genetics↗