Biology subjects

Bhaskar, A.

Publications and source records attributed to Bhaskar, A..

7 recordsLinked to original sources

bioRxiv2024

A screen of mutants generated and imaged by the International Mouse Phenotyping Consortium identifies 39 novel genes regulating the development of the secondary palate.

The International Mouse Phenotyping Consortium (IMPC) has generated thousands of knockout mouse lines, many of which exhibit embryonic or perinatal lethality. Using micro-computed tomography (micro-CT), the IMPC has created and publicly released 3D image datasets of embryos from these lethal and subviable lines. In this study, we leveraged this dataset to screen homozygous null mutants for anomalies in secondary palate development. We analyzed optical sections from 2,987 embryos at embryonic days E15.5 and E18.5, representing 484 homozygous mutant lines. Our analysis identified 45 novel genes implicated in palatogenesis. Gene set enrichment analysis highlighted biological processes and pathways relevant to palate development and uncovered 18 genes jointly regulating the development of the eye and the palate. These findings present a valuable resource for further research, offer novel insights into the molecular mechanisms underlying palatogenesis, and provide important context for understanding the etiology of rare human congenital disorders involving simultaneous malformations of the palate and other organs, including the eyes, ears, kidneys, and lungs.

developmental biology↗

bioRxiv2023

DIGEST: An online tool for designing of multiple reaction monitoring assays

Targeted proteomics using multiple reaction monitoring (MRM) assays enables fast and sensitive detection of a preselected set of target peptides. This technique utilizes the specificity of precursors to product transitions for quantitative analysis of multiple proteins in a single sample. The success of an MRM experiment depends on the selection of transitions however, given the existing resources, accurately predicting signal intensity of peptides and their fragmentation patterns ab initio is challenging task. We present an alternative for rapid design of MRM transitions for proteomics research: DIGEST. Our method predicts the b and y ions with +1 and +2 charge produced in a collision cell of a mass spectrometer from peptides of multiple proteotypically digested proteins. Additionally, by using the existing knowledge of the fundamental rules for designing transitions, the tool provides optimal MRM transitions, negating the need to undertake prior "discovery" MS studies. We demonstrate that our algorithm is directed toward the selection of MRM precursor and product-ions pairs, and can avoid the pitfalls of interference due to cross-contamination of samples by selecting ion combinations that uniquely map to target peptides. Comparison with SRMAtlas showed that DIGEST successfully predicted the peptide and production pairs in the majority of cases. We believe that DIGEST will facilitate rapid design of MRM assays with increased specificity, reducing the overall time required to design an MRM assay for routine mass-spectrometry. DIGEST is available as a web-based tool at https://digest.raylab.iiitd.edu.in/

bioinformatics↗

bioRxiv2023

Rhythm generating mechanisms in rat sino-atrial node and ventricle

The major membrane currents responsible for sinoatrial and idioventricular rhythm-generation were studied in isolated rat heart preparations, perfused in Langendorff mode. The rates of whole isolated hearts beating with sinoatrial rhythm decreased with cesium and ivabradine, both blockers of the funny current, and were not affected by nickel, at a dose which blocks T-type calcium current. The sinoatrial rhythm was completely abolished by reduction or removal of sodium from the perfusate (interventions that inhibit calcium-extrusive mode of the sodium/calcium exchanger), or by nifedipine, an L-type calcium channel blocker. Idioventricular rhythm, however, was arrested only by reduction of sodium in the perfusate. Ivabradine reduced the idioventricular rate, nickel did not cause any change, while nifedipine in some cases increased it. The inferences made based on these observations are that INCX and ICaL are obligatory rhythm-generating currents in the sinoatrial node, while INCX is the only obligatory mechanism for an idioventricular rhythm. The funny current is not an obligatory requirement for sinoatrial as well as idioventricular rhythm-generation. However, it enhances the frequency of LCRs. Our results in the isolated whole heart are in corroboration with results from isolated cells.

physiology↗

bioRxiv2021

Pseudohypoxic HIF pathway activation dysregulates collagen structure-function in human lung fibrosis

Extracellular matrix (ECM) stiffening with downstream activation of mechanosensitive pathways is strongly implicated in fibrosis. We previously reported that altered collagen nanoarchitecture is a key determinant of pathogenetic ECM structure-function in human fibrosis (Jones et al., 2018). Here, through human tissue, bioinformatic and ex vivo studies we show that hypoxia-inducible factor (HIF) pathway activation is a critical pathway for this process regardless of oxygen status (pseudohypoxia). Whilst TGF{beta} increased rate of fibrillar collagen synthesis, HIF pathway activation was required to dysregulate post-translational modification of fibrillar collagen, promoting bone-type cross-linking, altering collagen nanostructure, and increasing tissue stiffness. In vitro, knock down of Factor Inhibiting HIF (FIH) or oxidative stress caused pseudohypoxic HIF activation in normal fibroblasts. In contrast, endogenous FIH activity was reduced in fibroblasts from patients with lung fibrosis in association with significantly increased normoxic HIF pathway activation. In human lung fibrosis tissue, HIF mediated signalling was increased at sites of active fibrogenesis whilst subpopulations of IPF lung mesenchymal cells had increases in both HIF and oxidative stress scores. Our data demonstrate that oxidative stress can drive pseudohypoxic HIF pathway activation which is a critical regulator of pathogenetic collagen structure-function in fibrosis.

cell biology↗

bioRxiv2017

Geometry of the sample frequency spectrum and the perils of demographic inference

The sample frequency spectrum (SFS), which describes the distribution of mutant alleles in a sample of DNA sequences, is a widely used summary statistic in population genetics. The expected SFS has a strong dependence on the historical population demography and this property is exploited by popular statistical methods to infer complex demographic histories from DNA sequence data. Most, if not all, of these inference methods exhibit pathological behavior, however. Specifically, they often display runaway behavior in optimization, where the inferred population sizes and epoch durations can degenerate to 0 or diverge to infinity, and show undesirable sensitivity of the inferred demography to perturbations in the data. The goal of this paper is to provide theoretical insights into why such problems arise. To this end, we characterize the geometry of the expected SFS for piecewise-constant demographic histories and use our results to show that the aforementioned pathological behavior of popular inference methods is intrinsic to the geometry of the expected SFS. We provide explicit descriptions and visualizations for a toy model with sample size 4, and generalize our intuition to arbitrary sample sizes n using tools from convex and algebraic geometry. We also develop a universal characterization result which shows that the expected SFS of a sample of size n under an arbitrary population history can be recapitulated by a piecewise-constant demography with only{kappa} n epochs, where{kappa} n is between n/2 and 2n - 1. The set of expected SFS for piecewise-constant demographies with fewer than{kappa} n epochs is open and non-convex, which causes the above phenomena for inference from data.

evolutionary biology↗

bioRxiv2017

Inferring Relevant Cell Types For Complex Traits Using Single-Cell Gene Expression

Previous studies have prioritized trait-relevant cell types by looking for an enrichment of GWAS signal within functional regions. However, these studies are limited in cell resolution by the lack of functional annotations from difficult-to-characterize or rare cell populations. Measurement of single-cell gene expression has become a popular method for characterizing novel cell types, and yet, hardly any work exists linking single-cell RNA-seq to phenotypes of interest. To address this deficiency, we present RolyPoly, a regression-based polygenic model that can prioritize trait-relevant cell types and genes from GWAS summary statistics and single-cell RNA-seq. We demonstrate RolyPolys accuracy through simulation and validate previously known tissue-trait associations. We discover a significant association between microglia and late-onset Alzheimers disease, and an association between oligodendrocytes and replicating fetal cortical cells with schizophrenia. Additionally, RolyPoly computes a trait-relevance score for each gene which reflects the importance of expression specific to a cell type. We found that differentially expressed genes in the prefrontal cortex of Alzheimers patients were significantly enriched for highly ranked genes by RolyPoly gene scores. Overall, our method represents a powerful framework for understanding the effect of common variants on cell types contributing to complex traits.

genomics↗

bioRxiv2017

Efficacy of the β-lactam\β-lactamase inhibitor combination is linked to WhiB4 mediated changes in redox physiology of Mycobacterium tuberculosis

AimsInhibition of {beta}-lactamase by clavulanate (Clav) sensitizes multi-and extensively drug-resistant Mycobacterium tuberculosis (Mtb) strains towards {beta}-lactams such as amoxicillin (Amox). However, the underlying mechanism of how Mtb responds to Amox-Clav combination (Augmentin; AG) is not characterized.\n\nResultsWe integrated global expression profiling with the protein-protein interaction landscape and generated a genome-scale network of Mtb in response to AG. In addition to specific targets (e.g., peptidoglycan biosynthesis and {beta}-lactamase), the response to AG was also centered on redox-balance, central carbon metabolism (CCM), and respiration in Mtb. We discovered that AG modulates superoxide levels, NADH/NAD+ balance and mycothiol redox potential (EMSH) of Mtb. Higher intra-mycobacterial EMSH potentiates mycobactericidal efficacy of AG, whereas lower EMSH induces tolerance. Further, Mtb responds to AG via a redox-sensitive transcription factor, WhiB4. Mtb{Delta}whiB4 displayed higher expression of genes involved in {beta}-lactam resistance along with those mediating respiration, CCM and redox balance. Moreimportantly, WhiB4 binds to the promoter regions and represses transcription of genes involved in {beta}-lactamase expression in a redox-dependent manner. Lastly, while Mtb{Delta}whiB4 maintained internal EMSH, exhibited greater {beta}-lactamase activity and displayed AG-tolerance, overexpression of WhiB4 induced oxidative shift in EMSH and repressed {beta}-lactamase activity to aggravate AG-mediated killing of drug-sensitive and -resistant strains of Mtb.\n\nInnovation and ConclusionsThis work demonstrate that efficacy of {beta}-lactam\\{beta}-lactamase inhibitor combination can be attenuated by elevating mycobacterial antioxidant capabilities and potentiated by impairing redox buffering capacity of Mtb. The functional linkage between {beta}-lactams, redox balance, and WhiB4 can be exploited to potentiate AG action against drug-resistant Mtb.

microbiology↗