Team:Aberdeen Scotland/modeling/combined model

From 2009.igem.org

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=Introduction=
=Introduction=
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In order to examine how the system as a whole behaves it is necessary to combine the results of modelling the gene regulatory network with a macroscopic model of interacting <i>E. Coli</i> cells. This was done by estimating that quorum sensing becomes activated when the density of bacteria around the source of chemoattractant goes above a critical value, and then saying that after a given time calculated from the stochastic model the cells will then lyse.
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==Results==
==Results==
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A schematic diagram of the model as it works in SimBiology is displayed below:
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The graph below shows the effective radius in which the bacteria have activated quorum sensing:
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The dashed lines represent an enzymatic reaction, and the arrows represent the direction of chemical reaction. As stated before all mRNA productions must be modelled by an enzymatic production from DNA, and all protein productions must be modelled as enzymatic production from mRNA. This is useful as the repression and activation of gene networks can be modelled by mass action reactions between the unbound and bound form of the DNA or mRNA.
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As you can see, the radius increases from point 1 to a stable
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Our SimBiology model can be downloaded on the download page if you want to see how we modelled it exactly, and if you want to see the set of parameters we used. Below is a graph of the system turning on in response to input signals of quorum sensing and IPTG, and below that is one of the system reaching steady state without inputs:
 
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finish this liam!!!!!!!!!!!
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Revision as of 18:18, 21 October 2009

University of Aberdeen iGEM 2009

Contents

Combined Chemotaxis and Lysis Model

Introduction

In order to examine how the system as a whole behaves it is necessary to combine the results of modelling the gene regulatory network with a macroscopic model of interacting E. Coli cells. This was done by estimating that quorum sensing becomes activated when the density of bacteria around the source of chemoattractant goes above a critical value, and then saying that after a given time calculated from the stochastic model the cells will then lyse.


Results

The graph below shows the effective radius in which the bacteria have activated quorum sensing:

As you can see, the radius increases from point 1 to a stable




finish this liam!!!!!!!!!!!

Conclusions and Results

blah blah

  Back to Stochastic Model Continue to Parameters  


References

[1] A.B. Goryachev, D.J. Toh, T. Lee. “Systems analysis of a quorum sensing network: Design constraints imposed by the functional requirements, network topology and kinetic constants”. BioSystems 83 (2006) 178–187

[2] Michail Stamatakis and Nikos V. Manttaris. “Comparison of Deterministic and Stochastic Models of the lac Operon Genetic Network” Biophysical Journal Volume 96 February 2009 887-906 887




  Back to Quorum Sensing Activation Point Continue to Downloads Page  

 

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