"

From 2010.igem.org

Contents 1 In Silico 1.1 Modeling 1.1.1 Metabolic Flux Analysis 1.1.2 Hydrocarbon regulated expression system 1.2 Interaction mapping 1.3 Wiki Tips & Tricks

In Silico

Seeing as our team consists of a number of members who know their way around computers, quite some in silico work has been perfomed. More information on these projects can be found here.

Modeling

introduction to modeling Some stuff about what we modeled and why

Metabolic Flux Analysis

A metabolic flux analysis is an analysis to calculate the theoretical maximal yields for a proposed system of pathways in a micro-organism. With this analysis it is also possible to find whether a system is not viable because of a co-factor imbalance. Lastly, several product pathways were introduced to E. coli with hydrocarbon degradation to see what maximal theoretical yields on hydrocarbons are.

Find out more here

Hydrocarbon regulated expression system

P. putida has a regulation system that controls the expression of its hydrocarbon degradation pathway. This involves the protein crc, a global regulator. This regulator however is not present in E. coli and so a substitute was used. In our E. coli a crp dependent promoter was added to the gene. crp is a global regulator for E. coli. crc works on the mRNA and crp works on a promoter in the DNA. This simulation explores the difference between these two regulation mechanisms.

Find out more here

Interaction mapping

To give some clues about how our biobricks are working in their new E. coli proteome, an application has been developed that maps interactions from the native proteomes to the E. coli proteome. More info here

Wiki Tips & Tricks

As you might have noticed, we had some fun designing our wiki, want to know how we did it? You can find out here