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So this will be like the modeling team's first ever notebook entry. Mary and I will be keeping the same notebook entries since we would basically end up writing the same thing anyway. So if you ever wonder why Mary has such a strange sense of humor...well...it's probably not her writing.
Anyway, I'll just give a quick rundown of what we've been up to these last couple of days.
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.
In addition, the team decided that it would be most productive to split all the non-modeling people into subgroups to allow them to study a particular component of the system. Basically, this would allow the modeling team to focus less on the biological details of a particular reaction and while allowing another team member to become the expert on a particular topic.
For a more detailed look into our graphs and other stuff, Check out our PPT.