Talk:IGEM:Cambridge/2008/Turing Pattern Formation

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Here's a copy of the email I sent on the 20th, with some early thoughts:

Here's an interesting one: http://www.pnas.org/content/96/4/1218.abstract

Did you know that there are four different AIPs (and associated machinery) in different strains of S. aureus, and that they are mutually exclusive? In other words, if you use one strain's AIP in another's receptor histidine kinase, it inhibits phosphorylation and stops the cascade? This could have some interesting potential applications in our project, and would be cool to model.

All of that is discussed in the following paper, which I have yet to read through thoroughly: http://pubs.acs.org/cgi-bin/abstract.cgi/bichaw/2002/41/i31/abs/bi026049u.html

The following is also a great paper, and but think you probably both have seen it: http://arjournals.annualreviews.org/doi/full/10.1146/annurev.cellbio.21.012704.131001?cookieSet=1

It goes over quorum sensing in both gram-neg and gram-pos bacteria, and describes exhaustively all the well-known systems and examples. I think you probably know this already James, but there is a well-characterized exporter that pumps out LasI, thus mitigating its toxicity. My guess is you had trouble expressing/folding/localizing the exporter to the membrane in E. coli. It might work better in Bacillus?

I know I mentioned this before, but working with as many different signalling systems as possible will give us more options when it comes to putting the whole system together. I know it's rather ambitious, but once we get transformation working this week (and possibly next), and assuming we get more people to work in parallel on this, we could examine transplanting multiple different QS systems into B. subtilis so we can do different combinations if need be. Maybe I'm getting ahead of myself.

In any case, I'd like to know why we're going with the AIP/lux combo specifically - what do we know about these systems so that we're confident that they will yield the right parameters for pattern formation? The idea of using one peptide and one AHL seems intuitive, as one will diffuse faster than the other, but if lux is 100s of times faster, instead of just 10-15x faster, won't lateral inhibition totally quash any activation at all?

I'm also concerned that, if we use a subtilin-based expression system like SURE, we will get some weird effects, as subtilin is responsible for modulating sporulation/competence in B. subtilis. I think this expression system works great if you're just trying to overexpress something, but I'm worried we could get medium- to long-term feedback effects that we're not currently anticipating. I will try to read more into this.

I'll keep reading for now, let me know your thoughts.

Cheers, Daniel

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