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Our research domains

CRISPR/Cas9 for Genome Engineering :
Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR) and CRISPR-associated (Cas) proteins were discovered in prokaryotes as an adaptive immune system against viral and plasmidal genome invasion. The type II CRISPR/Cas system uses a tracrRNA:crRNA hybrid to bind to Cas9 protein and guide it to create a site-specific double stranded break on target templates. Modification of the tracrRNA:crRNA hybrid to a single guide RNA that has a customizable recognition sequence to guide DNA cleavage has become a very popular technique in gene editing. CRISPR/Cas9 technique also allows a marker-less genome manipulation that enables several modifications on the same strain. Post-cleavage of DNA with CRISPR/Cas9, the DNA repair occurs via non-homologous end joining (NHEJ) or homologous recombination (HR).
An increasing global energy demand and environmental concerns associated with petroleum fuels have necessitated the need for alternative liquid fuels (biofuels). Microbes such as yeasts can utilize sugars (generally hexoses) to produce different compounds such as free fatty acids (FFA) and its derivatives such as fatty-acid ethyl ester (FAEE), fatty alcohols and alkane/alkene. These biomolecules have energy content comparable to diesel and petrol, making them an important candidate for biofuels. However, yeasts do not generally utilize hexose sugars such as xylose due to lack of intrinsic pathways and transporters. In our lab, we are utilizing CRISPR/Cas9 tool to engineer the metabolic pathways of different yeast strains for co-utilization of glucose and xylose and produce fatty acids (biofuels). We are also developing the CRISPR/Cas9 tool for certain industrially relevant yeasts.
Metabolic Flux Analysis and Metabolomics:
Metabolic Flux Analysis (MFA) is an important method for the quantitative estimation of intracellular metabolic flows through metabolic pathways in a variety of cellular metabolism of relevance to medicine and biotechnology. For more complete understanding of biochemical pathways along with a quantitative analysis, metabolic flux analysis is an important technique. Metabolic flux analysis is generally carried out with isotopic tracers (e.g., 13C) to elucidate the pathways followed by labeled metabolites. Mass spectrometry is absolutely instrumental to record the labeling patterns in metabolic intermediates and end products. Our current efforts aim at developing new approaches to identify the rate limiting steps in sugar utilization for biofuels production in the engineered yeast strains.
Molecular Dynamics Simulation :
Molecular Dynamics Simulation is a classical mechanics based computational approach that enables to investigate the behaviour of a microsystem consisting a large number of interacting particles and to predict the bulk properties of the macrosystem at molecular level. GPU accelerated high-performance computing has revolutionized the theoretical approached to study the structure and dynamics of biological macromolecules from a nanosecond (ns) to milliseconds (ms) timescale in recent years.
Our lab is particularly interested to explore the molecular mechanism of various biological processes in the domain of carbohydrates as well as protein chemistry using MD simulation. Currently, we are focussing to understand the dissolution of cellulose in Ionic liquid (1-Ethyl-3-methylimidazolium acetate) and water mixtures for designing a cost-effective and optimized lignocellulosic biomass pretreatment process using IL. We are also working to develop theoretical insights behind the IL tolerance of thermostable cellulolytic enzymes, which will guide the experimental biologists for engineering the existing cellulase with improved saccharification kinetics. Moreover, molecular simulations of proteins reveal multiple conformational states in a trajectory ensemble which can explain its in-vivo functionality. Steered Molecular Dynamics are also routinely carried out in our lab to study the force induced unfolding of proteins.

microcrystal solvated in an IL-Water solvent mixture

Systems Biology of Gut Microbiome :
Diverse environmental condition reinforce the growth of different microbial communities with specialized characteristic. Metagenomic study along with computational technique disclose the structural and functional complexity of microbial niche. Culture independent approach of metagenomics helps to conquer the hurdle of characterization of unculturable microbes, enhancing clarity of community based microbiology. Gut microbiota has been one of the most fascinating area of research during several decades because of enormous microbial diversity and their metabolic potential. We are interested to study the cumulative potential of different gut microbiota that effectively translate the lignocellusoic biomass to biofuel. A system level understanding of the microbial interdependency and cross communication will decrypt the natural system lignocellulose degradative system leading towards the designing of a successful invitro mechanism for effective biomass conversion for biofuel production. Systematic mathematical model development of inter species interaction will help to identify key-species (influencer) in microbial communities having powerful lignocellulolytic property.