I am from Istanbul, TURKEY. I graduated with a bachelor degree in chemical engineering and master degree in bioengineering in Marmara University, Istanbul. I am studying for a bioengineering PhD at Yildiz Technical University in Istanbul, TURKEY.
During my PhD thesis, my aim is to develop iron selective electrodes and apply them on soil and water samples by using a computer-controlled multi channel potentiometric measurement system.
During my master thesis, I investigated a halophilic bacterium namely Halomonas smyrnensis AAD6 which is gram negative, aerobic, exopolysaccaride-producing and producing high levels of levan with many uses in foods, cosmetics, pharmaceutical and chemical industries. I constructed the first comprehensive genome-scale metabolic network of the microorganism in order to generate hypothesis on metabolic engineering strategies for levan overproduction with a systems biology approach. I reconstructed a stoichiometric model via the gene-enzyme-reaction associations of the metabolic pathways regarding to levan biosynthesis. I validated the model extensively against literature data on the use of sucrose as carbon source for both growth and levan synthesis using flux balance analysis. I obtained 488 different metabolic engineering strategies, pointing out gene knockout and overexpression targets as well as optimization of growth medium components. This work presents the first comprehensive genome-scale metabolic model of the levan-producing microorganism and strategies for enhanced levan biosynthesis. In further research, H. smyrnensis AAD6 was mutated to enhance levan production based on gene knockout strategies that I proposed. Thus, the halophilic bacteria resulted in levan overproduction. This research was funded by TUBITAK-MAG, 110M613, National (3501), “System Based Optimization of Microbial Biopolymer Production” and is going to be published soon.
For more details about the research conducted in the Borch group please click here.
Tugba Ozer, Busra Aydin, Ebru Toksoy Oner, and Kazim Yalcin Arga, “The genome-based metabolic systems engineering to boost levan production in a halophilic bacterial model” , OMICS: A Journal of Integrative Biology 2018 (in press).
Elif Diken, Tugba Ozer, Muzaffer Arikan, Zeliha Emrence, Ebru Toksoy Oner, Duran Ustek and Kazim Yalcin Arga (2015), “Genomic analysis reveals the biotechnological and industrial potential of levan producing halophilic extremophile, Halomonas smyrnensis AAD6T, Springerplus, 4: 393.
S. Yasar Yildiz, G. Anzelmo, T. Ozer, N. Radchenkova, S. Genc, P. Di Donato, B. Nicolaus,E. Toksoy Oner and M. Kambourova (2014), “Brevibacillus themoruber: a promising microbial cell.
For more publications in the Borch group please click here.
Name of collaborator, Institution, Link to their website.
Department of Chemical Engineering- Marmara University
Department of Bioengineering- Marmara University
Department of Bioengineering- Yildiz Technical University (Research and teaching assistant, 2013-present)