Systems & Synthetic Biology

The O’Malley group aspires to solve grand challenges in sustainability and medicine by deciphering how unwieldy microbes in the environment perform extraordinary tasks. They focus on anaerobic microbes, which have evolved to work together in complex communities that decompose and recycle carbon biomass throughout the Earth – from our guts to landfills and compost piles. Despite their importance, little information exists to parse the role of each microbial member within their dynamic community. By understanding natural systems and microbial “connection points” through advances in ‘omics’ technologies, engineers can build new, synthetic microbial partnerships to tailor the behavior of microbial consortia. Similarly, an understanding of how anaerobic microbes defend themselves from neighbors could translate into new antimicrobial compounds for therapeutic use.

The Mukherjee group engineers genetic tags for studying natural and engineered gene networks in anaerobic cells and living animals. The tools developed in their group have broad application in several emerging areas of synthetic biology including gene and cell-based therapy, bio-containment, microbiome engineering, and biomanufacturing.

The genome within all cell types of a multicellular organism is identical, yet different cell types display varied functions and properties due to differences in other regulatory factors, collectively termed as the epigenome. The Dey group focusses on understanding how the epigenome regulates gene expression, thereby influencing cellular functions. Regulation of the transcriptome (the genome-wide distribution of mRNA molecules) can be viewed as the output of a complex network of chemical and physical processes, and understanding how these processes interact to govern cellular behaviors is a major focus area of their research. Gaining mechanistic understanding of these processes will offer new insights into tissue development and cellular differentiation with important applications in regenerative medicine.