Focus
Hazardous Chemicals: Millions of chemicals have been used in huge amounts in our daily-life applications. We are getting exposed to some of them directly. On the other hand, many of them find their ways to the environment. Chemical pollution generated by unintended discharge of the chemicals into the environment pose a risk to natural life, ecosystems and human health. My research focuses on to evaluate the fate of extensively used organic chemicals (High Production Volume chemicals) in the environment, and their impact on ecosystems and human health. Understanding the role of microorganisms on the fate and impact of chemicals in the environment is the major motivation of the research @ BIOMIG.
Bioenergy, Biofuels, Biochemicals: Growing world population results in an increasing demand for energy and raw materials. Supplying this enormous demand from non-renewable resources causes degradation and pollution of the nature. The energy, fuels, and chemicals produced using biological processes are renewable, that is, they are either produced from wastes or biomass harvested using the sunlight, therefore do not contribute to, even decrease, environmental pollution. Although, the environmental biotechnology is proven for the treatment of many domestic and industrial waste streams, it cannot efficiently compete with the conventional non-renewable-resources dependent technologies for energy, fuel and chemical production. The major problem is the complexity of biological systems and the feedstocks used for the production. To overcome this problem, a balanced integrated knowledge on biological processes, analytical chemistry and molecular biology is crucial. Development of novel biological processes for production of energy, fuels and chemicals from biomass and organic waste streams is another motivation of the research @ BIOMIG.
Bioinformatics: Extraction the knowledge from the biological data is crucial to understand biological mechanisms and develop new technologies. Although there are huge amount of work done around the world, more than half of the genomic data in databases is basically unprocessed and most of the genes in bacterial genomes are unknown. For species living under extreme conditions, these unknowns are even greater. Our focus is to develop novel methodologies and find out novel mechanisms especially in bacteria that have been exposed to chemicals that are hazardous to the environment. Discovery of novel enzymes, mechanisms and strains are another motivation of the research @ BIOMIG.
Approach
Microbial Community Structure and Biodiversity: A microbial community capable of degrading the target chemical is developed. Structure and biodiversity of the microbial community are determined using cloning based on 16S rRNA isolated from the community. Metagenome of the community is also analyzed to get not only microbial but also metabolic diversity of the community.
Isolation and Identification of Target Microorganism:Microorganisms present in the microbial community are isolated after a sample is spreaded on a nutrient rich or a selective agar. Colonies grown on the plate are streak to multiple plates to get individual microbial isolates. Each isolate is tested for its biotransformation capability. Isolates capable of biotransforming the target compound is identified based on its 16S rRNA.
Genes and Enzymes: Enzyme(s) of the microbial strain responsible for biotransformation of the target chemical is identified using PAGE and purified using quantitative preparative native continuous PAGE (QPNC-PAGE). The activity of the enzyme on the target chemical is determined using biokinetic assays. The gene(s) responsible for the synthesis of the particular enzyme is determined using comparative genomics and transcriptome analysis. Right genes are identified following molecular cloning and comparing the recombinant protein with target enzyme obtained by QPNC-PAGE.