PhD student
Vo Tri Nam

Title of the talk: Studying on gene optimization for Bacillus subtilis and Escherichia coli

Abstract

Gene optimization technique which will alter the natural gene sequences to make them more compatible with expression systems is applied to raise gene expression levels while maintaining target protein sequences. Some gene optimization programs have been constructed for scientists to optimize gene sequences for each particular expression system. Escherichia coli and Bacillus subtilis are engaging hosts for expression of recombinant proteins because of model organisms for basic research and industrial organisms for protein production. However, in certain cases, using optimized genes could not express or improve gene expression in these bacteria. Additionally, there is no existing gene optimization program which could optimize or dis-optimized a single gene sequence for two organisms at the same time. Here, we will present bioinformatics methods to create tools for gene optimization or dis-optimization for both organisms. In this context, our research group has studied on highly expressed gene prediction, gene optimization algorithms, scoring functions and finally construction of a gene optimization program. This tool has three main features: i) optimizing for each expression system, E. coli or B. subtilis; ii) optimize simultaneously for both E. coli and B. subtilis; iii) optimize for increasing expression level in B. subtilis while reducing in E. coli. Existing algorithms along with new potential algorithms such as k-mean clustering, radius clustering or Ant colony optimization were applied and compared to each other. After that, the optimized results from tool were compared to those from some existing gene optimization programs. In the end, some practical experiments at Center for Bioscience and Biotechnology, VNUHCM-University of Science will evaluate the in silico results. Our study has given a full view about gene optimization and also proved new useful algorithms that can be applied in gene optimization for a practical study.

 Biography

 Nam Tri Vo is a PhD student of University of Science, Vietnam National University-Hochiminh City from 2014. He has studied on Bioinformatics for 10 years while doing his bachelor and master theses along with teaching Bioinformatics subject in University. His bioinformatics group has focused on genomics, especially on Gene Optimization. This group, one of a few Bioinformatics group in Vietnam has been formed based on researchers and students from Biotechnology, Mathematics and Information Technology. Nam Tri Vo and his group members contribute to the establishment of Bioinformatics research of HCMC in individual and of Vietnam in general.

Publications: Researchgate.