Team:Imperial College London/Modelling

From 2010.igem.org

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|Diagram showing 1 step amplification. TEV enzyme is being simply produced to activate pre-produced inactive dioxygenase.
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|Diagram illustrating 2 step amplification. Enzyme is activating enzyme which activates dioxygenase. Both pre-products have same TEV-site, so simply produced TEV is allowed to act directly on dioxygenase too.
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Revision as of 12:51, 11 October 2010

Introduction to modelling
In the process of designing our construct two major questions arose which could be answered by computer modelling:
  1. Output Amplification Model
    We came up with an idea of using amplification of colour output to make it show within minutes after stimulus. The question that arose concerned whether amplification will actually perform better than simple production in the cellular environment. Furthermore, we had trouble deciding whether we should design the amplification module to be consisting of 1,2 or even more amplification steps. It appeared that the problem was recognised to be difficult enough to employ modelling.
  2. Protein Display Model
    We came up with novel idea of detecting organisms that we do not have a specific receptor for. In the particular example that we have been considering, Schistosoma's protease was meant to cleave designed by us protein displayed on bacteria's cell wall. The cleaved peptide was supposed to be recognised by the receptor which would act to activate the colour expression. That solution raised questions about the risk of false positive or whether in there are any chances for ComD receptors to get activated in the diluted environment. Modelling was recognised as suitable to answer those questions.
Quick overview of models
Output Amplification Model


Diagram of simple production of Dioxygenase Diagram of simple production of Dioxygenase Diagram of simple production of Dioxygenase
Diagram illustrating simple production of dioxygenase. Diagram showing 1 step amplification. TEV enzyme is being simply produced to activate pre-produced inactive dioxygenase. Diagram illustrating 2 step amplification. Enzyme is activating enzyme which activates dioxygenase. Both pre-products have same TEV-site, so simply produced TEV is allowed to act directly on dioxygenase too.

Protein Display Model

Results
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