Publications

R&D Areas/Projects

• Genetic and metabolic networks of Cyanobacteria: Cyanobacteria are a group of photosynthetic prokaryotes that are widely distributed on planet earth and have potential applications in carbon dioxide capture and biofuel production. Our laboratory has been actively working to elucidate genetic regulatory networks of a model cyanobacterium Cyanothece sp. 51142 (Cyanothece 51142). Cyanothece 51142 is unicellular, diazotrophic cyanobacteria which is able to perform seemingly contrasting biological processes such as oxygenic photosynthesis and nitrogen fixation within a single cell. The organism temporally separates the oxygen evolving photosynthesis from oxygen sensitive nitrogen fixation. Cyanobacteria have evolved a circadian clock that enables continued oscillations even when the bacteria are switched to continuous light regime. It is now known that the mechanism of the clock is based on an intricate and as yet unknown relationship between a transcriptional / translational feedback loop (TTFL) and post translational oscillator (PTO). We use Dynamic Bayesian Network (DBN) to elucidate regulatory interactions between genes based on microarray gene expression data. Prior knowledge on genetic interactions available for other cyanobacterial species is transferred to Cyanothece by using bioinformatic tools and then incorporated into the construction of DBN. Design and prioritization of experiments is based on mathematical models and online monitoring of the exact time durations of oscillations in the culture. Detailed physiological, morphological, biochemical and molecular biological characterization typically precedes the microarray gene expression experiments. Our lab is well equipped with lab-scale photobioreactors, quantitative real time PCR, microarray scanner, GC-MS, etc., to carry out these experiments. We are also interested in genome scale metabolic models for cyanobacteria. A genome scale metabolic model is the essential prerequisite for analyzing the metabolism of an organism in quantitative terms. Such a model essentially consists of all metabolic and transport reactions occurring in an organism. In addition, the model would also consist of information about the association between genes, proteins and protein functions, referred to as Gene-Protein-Reaction associations or GPRs. Genetic changes would then be simulated in the model to predict genotypes that lead to overproduction of the metabolites of interest without compromising growth of the organism. In addition to the fundamental studies, we are also interested in applied research on cyanobacteria. To that end, model based optimization for high cell density cultivation of Cyanothece has been carried out.
• Modeling, optimization and monitoring of fermentation processes: Our lab has interests in developing and applying various optimization and monitoring techniques for fermentation processes. These have included optimization techniques that are based on a process model, statistical design of experiments and non-dominated sorting genetic algorithm (NSGA). In the past, we have worked on antibiotic producing strains of actinomycetes. Now, we are applying these techniques for cyanobacterial cultures.

PhD TA Topics