Team:UANL Mty-Mexico/MathModel

From 2014.igem.org

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<p align="justify"><b>Deterministic model</b><br>Our deterministic model represents the change in time of the concentrations of mRNAs and their corresponding proteins. It assumes that the variables behave continuously and obey kinetic rules that can be represented by constants. We are aware that, in practice, the components and variables in the model may not fall under the assumptions of a deterministic model and that there is always the chance that noise effects are being grossly underestimated; however, we propose this model as a general framework for thermoregulator modeling, upon which further work can be done.</p>
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<p align="justify"><b>INTRODUCTION TO MATH MODEL</b><br>The nature of our project, as a program embedded in a biological system, requires of a theoretical approach that describes its behavior, in order to predict how will function <i>in vivo</i> and therefore, understand how the scheme will work. </p>
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<center><img src="   https://static.igem.org/mediawiki/2013hs/thumb/f/f4/Circuit_function.png/800px-Circuit_function.png " height="300" width="740"></center>
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<p align="justify">While the deterministic approach of this program would explain its digital functioning, other characteristics have to be considered in order to have an accurate description of the system, considering factors as concentration, promoter strenght, volume of the system, temperature and others, which determine much of the behaviour of the system, to explain some features that might show.</p>
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<p align="justify">In our project, there are two principal components that will determine how the system will work.</p>
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<p align="justify"><b>The Protein Production</b><br>Since activity and responsiveness of the system are dependant on both concentration of TALEN, and since we measure it with production of GFP, it is necessary to predict when will this components be produced, using the promoter strength and degradation rate.
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<p align="justify">Our genetic system is composed by two parts, each one placed in different vectors: the first in the plasmid 2-4B C/C, consists of the transcription factor cI (c0051) under the regulation of a promoter with a riboswitch (<a href="http://partsregistry.org/wiki/index.php?title=Part:BBa_J23100" title="Part:BBa_J23100"><font color="blue"> J23100 </font></a> and <a href="http://partsregistry.org/wiki/index.php?title=Part:BBa_K115017" title="Part:BBa_K115017"><font color="blue"> k115017 </font></a>) that can be activated or repressed depending on the temperature; we call this our “thermosensor”. We found this piece in the <a href="https://2008.igem.org/Team:TUDelft" title="TUDelf 2008"> <font color="blue"> iGEM TUDelf-2008 Team </font></a> and saw we could use it because of its specific translation temperature at 32ºC. The second part located in the vector 2-6B K/K consist of two genes -the insecticide protein <a href="http://www.ncbi.nlm.nih.gov/nuccore/HQ876489" title=" Vip3Ca3"> <font color="blue"> Vip3Ca3 </font></a> and the green fluorescent protein, <a href="http://parts.igem.org/wiki/index.php?title=Part:BBa_E0240" title=Part:BBa_E0240 ><font color="blue">(GFP)</font></a>; both are under the regulation of cI(c0051).</p>
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<p align="justify"><b>The TALEN is the principal component of the system. Since its activity is not directly measurable, we have to predict when will it work, at which concentration, and how will it behave once the system is delivered, in order to know when will the reporter activity be measurable and most important, when will our system be effective once it is delivered.</p>
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<p align="justify">The thermosensor is repressed when the temperature is below 32°C, it does not translate because the mRNA takes a secondary structure just as the image below and cannot enter the ribosome for translation; when the temperatures reaches a range between 32°C and 37°C, the thermosensor is activated, the mRNA unfolds into a straight structure that now have access to the ribosome, start translation, be passed to aminoacids and form a protein . </p>
 
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<center><img src="https://static.igem.org/mediawiki/2013hs/9/9a/BBa_K115017_ss.png"></center>
 
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<p><a href="http://partsregistry.org/wiki/index.php?title=Part:BBa_C0051" title=Part:BBa_C0051 ><font color="blue"> cI (c0051)</font></a> is a gene that constitutively represses the promoter r0051. Once our promoter isn't affected by the cI(c0051), the promoter is activated once the production of Vip3Ac3 and GFP started. This means that a range below 32°C to 37°C enables the production of the Vip and GFP.</p>
 
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Revision as of 23:48, 17 October 2014

Math Model
Introduction

INTRODUCTION TO MATH MODEL
The nature of our project, as a program embedded in a biological system, requires of a theoretical approach that describes its behavior, in order to predict how will function in vivo and therefore, understand how the scheme will work.

While the deterministic approach of this program would explain its digital functioning, other characteristics have to be considered in order to have an accurate description of the system, considering factors as concentration, promoter strenght, volume of the system, temperature and others, which determine much of the behaviour of the system, to explain some features that might show.

In our project, there are two principal components that will determine how the system will work.

The Protein Production
Since activity and responsiveness of the system are dependant on both concentration of TALEN, and since we measure it with production of GFP, it is necessary to predict when will this components be produced, using the promoter strength and degradation rate.

The TALEN is the principal component of the system. Since its activity is not directly measurable, we have to predict when will it work, at which concentration, and how will it behave once the system is delivered, in order to know when will the reporter activity be measurable and most important, when will our system be effective once it is delivered.
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