Biology subjects

Dhotre, D.

Publications and source records attributed to Dhotre, D..

3 recordsLinked to original sources

bioRxiv2024

Evaluation of extraction solvents for untargeted metabolomics to decipher the DOM of Antarctic cryoconite holes

Cryoconite holes are biological hotspots with a high biogeochemical turnover rate, contributing significantly to the glacial ecosystems overall carbon cycles and net fluxes. Unfortunately, the information about the composition of low molecular weight molecules formed through the metabolic processes of cryoconite-dwelling microbes is scanty. These molecules constitute a substantial portion of the dissolved organic matter (DOM) within cryoconite holes. The present study investigated the composition of DOM in cryoconite holes using reverse-phase liquid chromatography (RP-LC) coupled with high-resolution tandem mass spectrometry. We evaluated various solvent combinations of water, methanol, and acetonitrile to extract chemically diverse polar and non-polar metabolites from the cryoconite holes. Among the single solvents, organic-rich MeOH: Water (70:30 v/v) and in parallel 2-single solvent combinations of MeOH: Water (70:30 v/v) and Acetonitrile: Methanol: Water (40:40:20 v/v) provided increased number and chemical diversity of extracted metabolites. Combining RP with the hydrophilic interaction liquid chromatography (HILIC) technique provided the highest number of unique metabolites. This dual-LC and ionization polarity combination increased the detection of metabolic features by 46.96% and 24.52% in single- and two-solvent combinations compared to RP alone. This study developed a simple untargeted metabolomics workflow that is highly sensitive and robust, detecting and potentially identifying a large number of chemically diverse molecules present in the DOM (extracellular) and microbes (intracellular) from the cryoconite holes environment. This method can better characterize DOMs chemical composition and, after integrating with other omics approaches, can be used to examine the link between metabolic pathways and microbial communities in global cryoconite holes or other similar ecosystems, revealing how these earthy systems and their microbial flora control carbon or nutrient storage or release in response to global climate change. Overall, the study presents a valuable methodology for studying the biogeochemistry of cryoconite holes.

microbiology↗

bioRxiv2022

Prolonged exposure to insulin causes epigenetic alteration leading to insulin resistance

Glucose homeostasis is maintained by insulin. It has been observed that hyperinsulinemia precedes insulin resistance and Type 2 diabetes. Insulin resistance is caused by multiple factors including genetic and diet. The molecular mechanism underlying insulin resistance (IR) is not completely understood. Using Glut4 and insulin receptor-expressing CHO cells we had previously shown that prolonged exposure of these cells to insulin in the absence of high levels of glucose led to insulin resistance in the cells. In the present study, we have shown that the underlying cause for the impaired GLUT4 trafficking is the defective PI3K/AKT pathway. This insulin resistance is likely due to epigenetic alterations as it is stable and can be maintained for several generations even when insulin is not provided, and epigenetic modifiers can reverse the insulin resistance. We extended these studies to liver cell line (BRL-3A) and show that these cells also develop impaired insulin signaling upon exposure to insulin in the absence of high levels of glucose. Transcriptomic analysis of the insulin-sensitive and -resistance cells uncover altered signaling networks involved in chromatin remodelling, Rho GTPases, and ubiquitination. Pathway analysis reveals the role of demethylase Kdm5b and lysine methyltransferase (Kmt2a and Kmt2e) in the development of insulin resistance. It is also observed that trimethylation of histone H3 at lysine 4 (H3K4me3) is increased in insulin resistance cellular models. We further showed that mice injected with low doses of insulin when fasting develop insulin resistance with impaired glucose tolerance and increased HOMA-IR index. Altogether, these findings suggest dysregulated synthesis of insulin in the absence of glucose stimulus could lead to epigenetic alterations that may lead to insulin resistance. Summary StatementInsulin stimulation in the absence of glucose leads to insulin resistance. We have developed a cell and mouse model of insulin resistance in this study to characterise the molecular signalling involved in insulin resistance and early onset of type 2 diabetes. The transcriptomic analysis provides new insights on epi-transcriptomic regulation in insulin resistance.

molecular biology↗

bioRxiv2018

Comparative Genome Analysis Reveals Important Genetic Factors Associated with Probiotic Property in Enterococcus faecium strains

Enterococcus faecium though commensals in human gut, few strains provide beneficial effect to humans as probiotics, few are responsible for nosocomial infection and few as non-pathogens. Comparative genomics of E. faecium will help to reveal the genomic differences responsible for the said properties. In this study, we compared E. faecium strain 17OM39 with a marketed probiotic, non-pathogenic non-probiotic (NPNP) and pathogenic strains. The core genome analysis revealed, 17OM39 was closely related with marketed probiotic strain T110. Strain 17OM39 was found to be devoid of known vancomycin, tetracycline resistance genes and functional virulence genes. Moreover, 17OM39 is \"less open\" due to absence of frequently found transposable elements. Genes imparting beneficial functional properties were observed to be present in marketed probiotic T110 and 17OM39 strains. Additional, genes associated with colonization within gastrointestinal tract were detected across all the strains. Beyond shared genetic features; this study particularly identified genes that are responsible to impart probiotic, non-pathogenic and pathogenic features to the strains of E. faecium. The study also provides insights into the acquired and intrinsic drug resistance genes, which will be helpful for better understanding of the physiology of antibiotic resistance in E. faecium strains. In addition, we could identify genes contributing to the intrinsic ability of 17OM39 E. faecium isolate to be a potential probiotic.\n\nThe study has comprehensively characterized genome sequence of each strain to find the genetic variation and understand effects of these on functionality, phenotypic complexity. Further the evolutionary relationship of species along with adaptation strategies have been including in this study.

bioinformatics↗