Team:Groningen/Brainstorm/Glucose Sensing

From 2009.igem.org

(Difference between revisions)

Revision as of 17:51, 20 May 2009

Originally the Rainbow bacteria we now no longer plan to use the Cre/Lox system, but rather focus on glucose sensing. This choice was made because we have no good way to control the cre/lox recombination the way we would need for glucose sensing.

The idea now is to create a bacterium that senses the outside glucose concentration and produces an inversely proportional response.

Requirements

We use the [http://en.wikipedia.org/wiki/MoSCoW_Method MoSCoW prioritization method]:

Must have this:
- Response should be inversely proportional to the outside glucose concentration.
- It should be measurable on-line (visually for example).
Should have this if at all possible:
- Response should be a gradient (not just on/off).
- Delay in the response should not exceed roughly 5-10 minutes.
- (Model) parameters should be known or obtainable.
Could have this if it does not affect anything else:
- Response should reasonably accurately follow the concentration (after a delay).
Won't have this now but would like in the future:
- Expand to other metabolisms.
- Produce something more useful than a colour.

Design

Our bacterium would have the following components:

The PTS system, which is already present in ... Which organisms?
A promoter that hooks into the PTS system. Can be either:
- Constitutively active, but repressed by ccpa(?).
- Activated by ccpa(?).
Product behind promoter as response.
Degradation-tag(?) for product to increase response time.

Modelling

First of all we are trying to model the PTS system as is. We're looking at the following existing models:

A limited model consisting of only 9 substances and 7 reactions, as described in Neves1999.
A more complete model [http://jjj.biochem.sun.ac.za/cgi-bin/processModelSelection.py?organism=Lactococcus+lactis&category=metabolism by M.H.N. Hoefnagel, J. Hugenholtz and J.L. Snoep] (hoefnagel2), discussed in Hoefnagel2004.

Our attempts at using these models are available in [http://igemgroningen.googlecode.com/svn/trunk/glucose our SVN repository].

@@ Line 33: / Line 33: @@
 * A limited model consisting of only 9 substances and 7 reactions, as described in [[Team:Groningen/Literature#Neves1999|Neves1999]].
-* A more complete model [http://jjj.biochem.sun.ac.za/cgi-bin/processModelSelection.py?organism=Lactococcus+lactis&category=metabolism by M.H.N. Hoefnagel, J. Hugenholtz and J.L. Snoep] (hoefnagel2).
+* A more complete model [http://jjj.biochem.sun.ac.za/cgi-bin/processModelSelection.py?organism=Lactococcus+lactis&category=metabolism by M.H.N. Hoefnagel, J. Hugenholtz and J.L. Snoep] (hoefnagel2), discussed in [[Team:Groningen/Literature#Hoefnagel2004|Hoefnagel2004]].
 Our attempts at using these models are available in [http://igemgroningen.googlecode.com/svn/trunk/glucose our SVN repository].