Team:ULB-Brussels/Project/Mathematical

From 2009.igem.org

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==Introduction==
==Introduction==
-
Synthetic biology is a recent development in biology which aims at producing useful material via biological agents. In this context, a biological system can be seen as a complex network composed of different functional parts (\cite{uri}). Mathematical tools allow one to make prediction on the dynamical behaviour of a given bio-system. We aim at studying ft
+
 
-
the system which has been built in the second section of this report. We already know from our experiment that our system is able to produce glue in the presence of IPTG inductor. We now address the following question: what is the influence of the different parameters on the global dynamics (degradation rate, production rate, level of initial quantity for the C$2$P$22$ repressor,...) with and without IPTG. In order to achieve this task, we will consider three different models: the first one shows the basal property we are looking for: a system able to produce glue. The two next models can be seen as two different steps of improvement. The purpose of these models is to improve the experimental control of the glue production. Parameters values result from the literature and previous iGEM team wiki's. We know these remain qualitative and that lab work should be carried out to specify them more precisely.
+
Synthetic biology is a recent development in biology which aims at producing useful material
 +
via biological agents. In this context, a biological system can be seen as a complex network
 +
composed of different functional parts ( [14]). Mathematical tools allow one to make prediction
 +
on the dynamical behaviour of a given bio-system. We aim at studying ft the system which has
 +
been built in the second section of this report. We already know from our experiment that our
 +
system is able to produce glue in the presence of IPTG inductor. We now address the following
 +
question: what is the influence of the different parameters on the global dynamics (degradation
 +
rate, production rate, level of initial quantity for the C2P22 repressor,...) with and without
 +
IPTG. In order to achieve this task, we will consider three different models: the first one shows
 +
the basal property we are looking for: a system able to produce glue. The two next models can
 +
be seen as two different steps of improvement. The purpose of these models is to improve the experimental control of the glue production. Parameters values result from the literature and
 +
previous iGEM team wiki’s. We know these remain qualitative and that lab work should be
 +
carried out to specify them more precisely.
 +
 
 +
*Hill function for activator
 +
EQUATION1
 +
*Hill function for repressor
 +
EQUATION2
 +
 
 +
In these expressions, [x] is the concentration of activated genes, p is called the Hill coefficient,
 +
k is the activation coefficient and \alpha is the maximum expression level of the promotor.
 +
 
 +
For each block of the system, we can obtain a dynamical equation by considering its interactions
 +
with the other blocks of the system. For each block we can build an equation of the following
 +
form:
 +
 
 +
EQUATION3
 +
 
 +
Where, [x]-i is the concentration of the gene i, R(Ha([x]);Hp([x])) is the regulating function
 +
which is a combination of Hill functions. The second term of the right side is the destruction
 +
term, where °i is the maximum destruction rate of the gene i.

Revision as of 23:49, 21 October 2009

iGEM Team:ULB-Brussels Wiki

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Introduction

Synthetic biology is a recent development in biology which aims at producing useful material via biological agents. In this context, a biological system can be seen as a complex network composed of different functional parts ( [14]). Mathematical tools allow one to make prediction on the dynamical behaviour of a given bio-system. We aim at studying ft the system which has been built in the second section of this report. We already know from our experiment that our system is able to produce glue in the presence of IPTG inductor. We now address the following question: what is the influence of the different parameters on the global dynamics (degradation rate, production rate, level of initial quantity for the C2P22 repressor,...) with and without IPTG. In order to achieve this task, we will consider three different models: the first one shows the basal property we are looking for: a system able to produce glue. The two next models can be seen as two different steps of improvement. The purpose of these models is to improve the experimental control of the glue production. Parameters values result from the literature and previous iGEM team wiki’s. We know these remain qualitative and that lab work should be carried out to specify them more precisely.

  • Hill function for activator

EQUATION1

  • Hill function for repressor

EQUATION2

In these expressions, [x] is the concentration of activated genes, p is called the Hill coefficient, k is the activation coefficient and \alpha is the maximum expression level of the promotor.

For each block of the system, we can obtain a dynamical equation by considering its interactions with the other blocks of the system. For each block we can build an equation of the following form:

EQUATION3

Where, [x]-i is the concentration of the gene i, R(Ha([x]);Hp([x])) is the regulating function which is a combination of Hill functions. The second term of the right side is the destruction term, where °i is the maximum destruction rate of the gene i.