Team:Edinburgh/modelling(generegulatorynetwork)

Personal note

When I first heard about iGEM, I bored sitting in a computing lab doing uni work and thinking “Why am I doing this?” I had never heard of synthetic biology but always knew that I wanted to go down the biological/medical side of engineering so when I received the email I knew that is what I wanted to do this summer. When I first started I had no idea about biology, what a promoter was, what a repressor was, however over the course of the summer I have learnt this and a whole lot more. iGEM has shown me some of the advancements that synthetic biology can make to the world and it will be very interesting to see how all these weird and wonderful things are put into practise in the future.
Rachel

The systems were modelled in Cellucidate using a set of rules, and initial conditions shown in the appendix below. The rules are based on Ty Thomson’s framework for creating modular and reusable models of individual BioBrick parts. From the beginning of the project, it was thought that we would use pniR, a nitrite-sensitive promoter. Thus modelling of different setups was done with pniR first, but we did not get this to work in the wet lab whereas, another promoter we had, pYeaR did, so this was then modelled. The promoters are similar both being repressed by nsrR, but pniR is repressed by an nsrR that is not naturally expressed in E. coli, whereas pYeaR is. Therefore, nsrR had to be expressed in the pniR systems.

Here are the different setups modelled when using the pniR promoter:

Edinburgh University iGEM Team 2009