IGEM:Stanford/2009/Notebook/Marys iGEM Notebook/2009/07/31

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Entries
Um, this is copied from Leon's notebook... "
 * We created a model for how BLH and RalDHII convert B-carotene into retinoic acid. We started a model that shows how IPP is converted into B-carotene. The model is extremely complicated because of all the intermediates and there are likely a lot of side reactions which we have still yet to consider. We also did quite a bit of work with further modeling and analyzing how IDO will ultimately affect levels of Trp operon activity. Essentially, the problem we see from the models is that IDO reacts much more quickly with Trp than 5MT, which is problematic. If we have a high initial concentration of 5MT so that the system would see a large fluctuation of 5MT compared to Trp, time it takes for 5MT levels to drop are on the time scale of thousands of seconds because IDO reacts so slowly with 5MT. On the other hand, if we use lower levels of 5MT, we run into the problem that the levels of Trp fluctuate much more greatly than levels of 5MT. So yeah, basically the model just continues to confirm our troubles with the Trp Operon.

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 * For a more detailed look into our graphs and other stuff, Check out our PPT.

Daily Work
Goals

Project

Accomplishments

Problems

Alternative Solutions

Comments

 * The current model of B-carotene to RA is unrealistic. You guys should look into why its physiologically irrelevant and redesign the model. - Chris
 * Hmmm, b-carotene levels are insufficiently low. Could you increase it with additional IPP. Check out Martin et al. Nature Biotech 2003. - Chris
 * b-carotene levels are still too low? Maybe alter mRNA stability and RBS strengths for CRT genes. - Chris

Weekly Goals

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