Team:Groningen/Brainstorm/Glucose Sensing

From 2009.igem.org

(Difference between revisions)
(Information on glucose sensing bacterium.)
(Modelling information.)
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* Product behind promoter as response.
* Product behind promoter as response.
* Degradation-tag(?) for product to increase response time.
* Degradation-tag(?) for product to increase response time.
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==Modelling==
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First of all we are trying to model the PTS system as is. We're looking at the following existing models:
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* A limited model consisting of only 9 substances and 7 reactions, as described in [[Team:Groningen/Literature#Neves1999|Neves1999]].
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* 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).
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Our attempts at using these models are available in [http://igemgroningen.googlecode.com/svn/trunk/glucose our SVN repository].

Revision as of 17:35, 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).

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

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