Team:UANL Mty-Mexico/Modeling/Biosensor

From 2012.igem.org

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<p><br><h2>Simulations</h2><br></p>
<p><br><h2>Simulations</h2><br></p>
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<p>For the constructed ODEs, we built a Simulink model. With the extracellular As set to zero and the initial conditions for all other variables set to zero, as well, we obtained the values for the variables ArsR and Fluc (both in protein and mRNA) at steady state and used them as initial conditions for further simulations:
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mRNAs: ArsR = 2.1058 nM; Fluc = 5 nM
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Proteins: ArsR = 887.7 nM; Fluc = 398.6 nM
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We also set all the numerical integrators to have lower saturation limits equal to zero, to be in concordance with the mass conservation law. Here are the results for simulations at extracellular As set to 0, 0.1, 1, 5 and 10 μM (0, 100, 1000, 5000, 10000 nM). </p>
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<table class="image" align="center">

Revision as of 03:09, 27 September 2012

iGEM UANL 2012


Biosensor


Our biosensor model is a continuation of the previously exposed transport and accumulation model with the addition of the production of luciferase as a function of ArsR|As concentration. In this way, we can relate the concentration of extracellular As to the production of luciferase.


ODEs



The ODEs that describe the kinetics of the biosensor modules include all the assumptions presented in the core model and the equations presented for the accumulation and transport module, along with their corresponding parameters.

Taking into account the equations from the accumulation and transport module, we introduce a generator for Luciferase:


Luciferase mRNA

\begin{equation} \large \frac{d[mRNA_{Luc}]}{dt} = \alpha _{mLuc}\cdot (pro_{ars})\cdot(\frac{k_{D1}^{h_{1}}}{k_{D1}^{h_{1}}+[ArsR]^{h_{1}}})- \delta _{mRNA_{Luc}}[mRNA_{Luc}] \end{equation}


Luciferase protein

\begin{equation} \large \frac{d[Luc]}{dt} = \alpha _{pLuc}\cdot[mRNA_{Luc}]- \delta _{Luc}[Luc] \end{equation}


Parameters




The parameters for the ODEs describing the production of luciferase mRNA and protein are shown in the next table.


Parameter table


Parameter

Description

Value

References

αmArsR

Maximal transcription rate of ArsR

3.74 nM/min

Assumptions

αmFluc

Maximal transcription rate of Fluc

1.40 nM/min

Assumptions

αpArsR

Maximal translation rate of ArsR

9.74 nM/min

Assumptions

αpFluc

Maximal translation rate of Fluc

2.06 nM/min

Assumptions

δmRNAArsR

Degradation rate of ArsR mRNA

2.16x10-1 min-1

Assumptions, Selinger, et al. (2003)

δmRNAFluc

Degradation rate of Fluc mRNA

3.37x10-2 min-1

Assumptions, Suter, et al. (2011), Karetnivok and Lehto (2006).

δArsR

Degradation rate of ArsR

2.31x10-2 min-1

Assumptions

δFluc

Degradation rate of Fluc

2.60x10-2 min-1

Assumptions, Auld, et al. (2008)

proars

Concentration of ars promoter

aprox. 1*plasmid copy (nM)

Assumptions


Simulations


For the constructed ODEs, we built a Simulink model. With the extracellular As set to zero and the initial conditions for all other variables set to zero, as well, we obtained the values for the variables ArsR and Fluc (both in protein and mRNA) at steady state and used them as initial conditions for further simulations: mRNAs: ArsR = 2.1058 nM; Fluc = 5 nM Proteins: ArsR = 887.7 nM; Fluc = 398.6 nM We also set all the numerical integrators to have lower saturation limits equal to zero, to be in concordance with the mass conservation law. Here are the results for simulations at extracellular As set to 0, 0.1, 1, 5 and 10 μM (0, 100, 1000, 5000, 10000 nM).

Figure 1. Time vs Luciferase production (nM)

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