Team:Grenoble/Modeling/Amplification/ODE

From 2012.igem.org

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We can observe that until 100 minutes the bacterium is growing (the absorbance increases), and we don’t get any RFU signal. Then, the bacterium almost stops growing, and thus we begin to get a signal.
We can observe that until 100 minutes the bacterium is growing (the absorbance increases), and we don’t get any RFU signal. Then, the bacterium almost stops growing, and thus we begin to get a signal.
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<h1><img src="https://static.igem.org/mediawiki/2012/1/1e/2_mod.png" alt="" /> Sensitivity </h1>
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The first question was: what is the sensitivity of our system?
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Even if we don’t know the exact value of all the parameters, we have enough information on them to be able to have a good evaluation of the sensitivity of our system.
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To answer this question, we plot the evolution of the steady state of adenylate cyclase in function of 〖cAMP〗_out, the initial concentration of cAMP, which is assumed to be constant. Here are the scripts that enable us to plot the graphs. We solve the differential equations to get the steady state, because if we wanted to solve a set of equations we would have had to give an initial point. If we had given 0, matlab would have stayed at this point, and we couldn’t give another initial point without solving the equations.
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<center><img src="https://static.igem.org/mediawiki/2012/f/f3/Graphe3_ampli_grenoble.png" alt="" /></center>
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Revision as of 18:30, 20 September 2012

iGEM Grenoble 2012

iGEM Grenoble iGEM
iGEM 2012
main page
Project

Preliminary

We will use the quasi steady state approximation (QSSA) then. The idea is that there are quick reactions, such as enzymatic ones, complexations, etc… And there are slow reactions such as protein production. We assume that the evolution speed of an element that is created only by quick reaction is null.



Indeed, we have these types of evolution for the biological elements. The ones involved only in quick reactions are most of the time in a steady state, and there jump from one steady state to an other has an infinite speed, which doesn’t interest us.

Goal

In this part, we want to answer to three questions:

      What is the sensitivity of our system?
      What is the time response?
      What steady states will our system always reach?

The system

Here is the schema of the real system, in orange are the reactions which didn’t appear in the simplified system of the overview:


cAMP is the quorum sensing molecule. When we put some cAMP out of the system, it enters into the system. Then, it complexes with CRP to create (CRP-cAMP), which is the transcription factor of the gene arac. When some Arac is created, it will complex with arabinose to create Arac*. Arac* is the active form of Arac. Arac* with (CRP-cAMP) are the transcription factors of the gene cya. Then when some protein of adenylate cyclase is produced, it will catalyze the production of cAMP.

We first have the complexation of cAMP with CRP to get (CRP-CAMP). It is modeled by this biological reaction:



Thus, we get the evolution speed of (CRP-CAMP), r(CRP-cAMP):



Then, we have the conservation equations:



Thus, we get:



Eventually, we get:



where
We have

Eventually, we have to choose between the two solutions



These two solutions are positive, because:



To chose which solution is the good one, we know that:





Eventually, we get:



(CRP-cAMP) is the transcription factor of the gene arac. When it appears in the network, it activates the production of the protein Arac. This is modeled by a Hill function. In addition, there is some outflow linked to the promoter pAraBAD, which is the promoter regulating arac, thus there is a basal production of Arac. We take into account this basal production, because we need to know if because of them our system will always be turned on, thus useless. Arac is also naturally degraded by the bacterium. Thus, we get as the equation of evolution of Arac concentration:



Then, the protein Arac complexes with arabinose to create Arac active, written Arac*. It is modeled by the following chemical equation:



We get the evolution of Arac* rArac*:



With the qssa, we get:



In addition we have the conservation equation of Arac:



We assume that we have





Then, Arac* with (CRP-cAMP) are the transcription factors of of the gene ca. When they appear in the network the protein Ca is produced. The product of two hill functions models this. For the same reasons as for Arac we take into account the basal production of the adenylate cyclase. In addition it is degraded by the bacterium. Thus, we get the equation:



Eventually, Ca catalyzes the production of cAMP with ATP. We have the following enzymatic reaction:



We use the Michaelis Menten model for an enzymatic reaction, thus we get the evolution of cAMP rcAMP:



In addition, we assume that [ATP]>>KM. Eventually we get:



In addition, the bacterium naturally degrades cAMP. Finally there is a quorum sensing term. However, we are not modeling the quorum sensing here, thus we assume that [cAMPout] is constant. Thus, we get:



The QSSA enables us to have rcAMP=0. Then, we have:



Remark:

We don’t take into account in the equations the growth of the bacterium. Indeed, the bacterium grows as long as it has some glucose. However, as long as there is glucose the gene cya is not expressed. Cya begins to be expressed only when the bacterium doesn’t grow anymore. Indeed, the biologists in order to check the “AND gate” behavior, the biologists built, see protocol protocol "AND gate test" . Here we give the biological graphs of the absorbance and the graph of the RFU in function of the time for arabinose and cAMP maximum:







We can observe that until 100 minutes the bacterium is growing (the absorbance increases), and we don’t get any RFU signal. Then, the bacterium almost stops growing, and thus we begin to get a signal.

Sensitivity



The first question was: what is the sensitivity of our system?
Even if we don’t know the exact value of all the parameters, we have enough information on them to be able to have a good evaluation of the sensitivity of our system.
To answer this question, we plot the evolution of the steady state of adenylate cyclase in function of 〖cAMP〗_out, the initial concentration of cAMP, which is assumed to be constant. Here are the scripts that enable us to plot the graphs. We solve the differential equations to get the steady state, because if we wanted to solve a set of equations we would have had to give an initial point. If we had given 0, matlab would have stayed at this point, and we couldn’t give another initial point without solving the equations.



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