Seminar by Tirthankar

Aug 22, 2013 - 17:00

Aug 22, 2013 - 18:00

Creativity Hall Room No. 118

Seminars

Tirthankar Sengupta

Abstract: Metabolic engineering and synthetic biology are important emerging areas in biology. Metabolic engineering deals with performing genetic alterations to a wild type strain i.e. a strain as it exists in nature such that the mutant can overproduce some metabolite of commercial interest. Synthetic biology deals with the construction of artificial biological systems for the purpose of studying important biological processes or for the purpose of strain improvement. A common aim in both the disciplines is strain improvement which is the focus of this work. Strain improvement refers to the process of making alterations to a wild type strain such that the engineered strain has superior properties in comparison to the original strain in the context of some objective such as the production of a metabolite. Towards this end the work has three contributions. The first contribution is towards proposing an algorithm for identifying housekeeping genes i.e. genes performing important cellular functions from microarray gene expression data. We analyze the functions of a few genes obtained by applying the proposed algorithm to gene expression data of human lymphoblastoid cells and liver tissue and in each case we show that the genes indeed perform vital functions. The second contribution of this work is towards gaining insights into optimal ethanol production by the unicellular photosynthetic cyanobacterium Synechocystis species strain PCC 6803. Analysis suggests that combined gene deletions in ethanol and purine metabolism pathways result in optimal ethanol production along with the mutant producing the specified amount of biomass. The third contribution of the work provides an efficient alternate formulation for the Regulatory on off minimization (ROOM) algorithm. The ROOM algorithm is a popular metabolic modeling strategy for mutants and involves solving an integer programming problem. In the current work motivated by the emerging area of compressed sensing we propose a reformulation known as basis-pursuit of the original ROOM algorithm. Applying the original ROOM algorithm and the reformulation to various mutants of Synechocystis species strain PCC 6803 it is observed that the proposed algorithm performs better in most cases.About the Speaker: Tirthankar is currently a PhD student in the Department of Chemical Engineering at IIT Bombay. He is working under the guidance of Prof. Mani Bhushan and Prof. Pramod P Wangikar. He also holds a faculty position in the Department of Chemical Engineering of Heritage Institute of Technology Kolkata from where he is currently on leave. Tirthankar taught for two years before joining the PhD program at IIT Bombay. Prior to joining Heritage Institute of Technology Kolkata he worked as a software engineer in Infosys for two and half years. Tirthankar's Masters degree is in Chemical Engineering from IISc Bangalore. His bachelor's degree is also in Chemical Engineering from Jadavpur University Kolkata.