Premkumar Jayaraman

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School of Chemical and Biomedical Engineering, Nanyang Technological University
Jayaraman, Prekumar

Premkumar Jayaraman received his Bachelor’s degree in Industrial Biotechnology, 2006 from Anna University, Chennai, India. He completed his Master’s degree in Biomedical Engineering with the Certificate of Excellence 2008 for MAE MSc Top Graduates award, at Nanyang Technological University (NTU), Singapore after which he went on to complete his PhD from Biomedical and Engineering Research Centre in 2012 at NTU, Singapore.

He joined the School of Chemical and Biomedical Engineering, NTU as a postdoctoral researcher in 2012. His current research is focused in modeling a virtual cell to evaluate the protein synthesis and host effects by different topology synthetic gene circuits.

Tue July 9 | 2:00 - 4:00
ABSTRACT: Bottom-up coarse-grained modelling approach to build an E. coli virtual cell for synthetic gene circuits engineering

Given an unprecedented ability to manipulate cells through synthetic biology to address problems in areas such as energy, health and environment, currently we still face challenges in perfecting an engineered system to our desire. The daunting challenges confronted by the biological circuit engineers are, complexity, unpredictability and variable behavior of the host system that contains the engineered designs. In addition, the practice of trial-and-error synthetic circuit designs and in vitro evaluation are laborious and time-consuming. Currently, models able to predict host-dependent circuit functions and burden on the host-cell environment accounting energy consumption, resource uptake and cellular processes are lacking. The insights from those models could be used to engineer and fine-tune the synthetic gene circuit’s components and parameters for optimal protein production and reduced host-burden effects. To this end, we propose a novel E. coli virtual cell for predicting the behavior of different synthetic biological devices in silico. The model incorporates three key ‘cellular processes’ and its components: (i) ‘nutrient uptake’ to evaluate energy compensation, (ii) ‘growth’ to determine macromolecular composition, pools of cellular machinery and monomer synthesis, and (iii) ‘replication’ of its components under regulation. Our preliminary results demonstrate that our model is able to reproduce the number and concentration of proteins, RNAs and cellular machineries of the host system at varying growth rates. We will present the development of this model considering how glucose as the sole energy source under regulation, a single virtual cell allocates energy and resources in synthesizing RNAs, proteins including machineries and monomers, initiation until completion of replication (doubling time) by monitoring growth rate and timing cellular processes. Looking forward, the work described here is a step towards predicting synthetic circuits behavior and its host-effects.