Team:UPO-Sevilla/Project/Improving Flip Flop/Modeling/Introduction

From 2011.igem.org

(Difference between revisions)
(Created page with "{{:Team:UPO-Sevilla/headerTemplate}} <html> <div id="principal"> <div class="main"> <ul id="breadcrumbs" cl...")
 
(9 intermediate revisions not shown)
Line 2: Line 2:
<html>
<html>
 +
 +
<script type="text/javascript">
 +
            ddmenuactual = 1;
 +
            $("#menuPImproved").addClass("TopMenuSelected");
 +
</script>
                     <div id="principal">
                     <div id="principal">
                         <div class="main">
                         <div class="main">
Line 12: Line 17:
                                     <li><a href="/Team:UPO-Sevilla/Project/Overview" style="white-space: nowrap; float: left;">Project</a><ul></ul></li>
                                     <li><a href="/Team:UPO-Sevilla/Project/Overview" style="white-space: nowrap; float: left;">Project</a><ul></ul></li>
                                     <li><a href="/Team:UPO-Sevilla/Project/Improving_Flip_Flop/Overview" style="white-space: nowrap; float: left;">Improving Flip Flop</a><ul></ul></li>
                                     <li><a href="/Team:UPO-Sevilla/Project/Improving_Flip_Flop/Overview" style="white-space: nowrap; float: left;">Improving Flip Flop</a><ul></ul></li>
-
                                     <li class="current"><a href="/Team:UPO-Sevilla/Project/Improving_Flip_Flop/Modeling/Introduction" style="white-space: nowrap; float: left;">Modeling</a><ul></ul></li>
+
                                    <li><a href="/Team:UPO-Sevilla/Project/Improving_Flip_Flop/Modeling/Introduction" style="white-space: nowrap; float: left;">Modeling</a><ul></ul></li>
 +
                                     <li class="current"><a href="/Team:UPO-Sevilla/Project/Improving_Flip_Flop/Modeling/Introduction" style="white-space: nowrap; float: left;">Introduction</a><ul></ul></li>
                         </ul>
                         </ul>
                             <h1>Modeling</h1>
                             <h1>Modeling</h1>
-
                              
+
 
 +
                             <h2>Introduction</h2>
 +
 
 +
                            <p>We have also modeled the improved flip-flop. This models is an extension of the <a href="/Team:UPO-Sevilla/Project/Basic_Flip_Flop/Modeling/Basic_Bistable">Basic Flip-Flop model</a>. The main reactions at that model were:.</p>
 +
 
 +
                            <p><strong>TRANSCRIPTION:</strong> <i>RNAp + Promoter &rarr; RNAp + Promoter + mRNA</i></p>
 +
 
 +
                            <p>The mRNA production is described using Michaelis-Menten kinetics.</p>
 +
 
 +
                            <p><strong>TRANSLATION:</strong><i> mRNA + Ribosomes &rarr; mRNA + Ribosomes + Repressor</i></p>
 +
 
 +
                            <p>The Repressor production is also modeled using Michaelis-Menten kinetics.</p>
 +
 
 +
                            <p><strong>REPRESSION:</strong> <i>Promoter + n · Repressor &rarr; Promoter_Repressor<sub>n</sub></i></p>
 +
 
 +
                            <p>Finally we use a Hill kinetics model for the transcription inhibition, which offers an approximation to the cooperative action.</p>
 +
 
 +
                            <p>In the new model, we have to include the new reactions involved in the Improved Flip-Flop. These are:</p>
 +
 
 +
                            <p><strong>PROTEOLYSIS: </strong> <i>Protease + Repressor 1 &rarr; Protease</i></p>
 +
 
 +
                            <p>We will consider a mass action rate law, where the protein will be digested according to the protease concentration.</p>
 +
 
 +
                            <p><strong>INHIBITION of TRANSLATION: </strong><i> asRNA + mRNA &rarr; RNA complex</i></p>
 +
 
 +
                            <p>We assume a mass action rate law again.
 +
</p>
 +
 
                              
                              
 +
 +
                            <h2>Diagram</h2>
 +
 +
<p>These two new effects may enhance the robustness of the toggle switch. We will analyze their effects by implementing the model in Simbiology. The following diagram shows all the species and reactions of the model:</p>
 +
 +
                            <div class="center">
 +
                              <img src="https://static.igem.org/mediawiki/2011/f/f3/DiagramMB.png" alt="Diagram MB" />
 +
                            </div>
 +
 +
                            <p>Here we can see all the species involved in the new model for the bistable.</p>
 +
 +
<p>The model can be downloaded here:</p>
 +
 +
 +
<a href="https://static.igem.org/mediawiki/2011/a/a1/Improved_Bistable.sbproj.zip" title="Improving Flip-Flop"><img style="margin: 0em 0em 1em 0em" class="imgcenter" width="200px" src="https://static.igem.org/mediawiki/2011/9/97/UPOSevillaDownloadIcon.png" title="Download Improving Flip-Flop"></a>
 +
 +
<p>In the <a href="/Team:UPO-Sevilla/Project/Improving_Flip_Flop/Modeling/Equations">next section</a>, we describe in detail the equations of the model</p>
 +
 +
 +
                         </div>
                         </div>
                         <div class="left">
                         <div class="left">
-
                               </html>{{:Team:UPO-Sevilla/leftTemplateProject}}<html>
+
                               </html>{{:Team:UPO-Sevilla/leftTemplateProjectImproved}}<html>
 +
 
 +
                              <script type="text/javascript">
 +
                                          $("#menuVIMIntroduction").addClass("menuSelected");
 +
                              </script>
                         </div>
                         </div>
</html>
</html>
{{:Team:UPO-Sevilla/footTemplate}}
{{:Team:UPO-Sevilla/footTemplate}}

Latest revision as of 22:19, 27 October 2011

Grey iGEM Logo UPO icon

Modeling

Introduction

We have also modeled the improved flip-flop. This models is an extension of the Basic Flip-Flop model. The main reactions at that model were:.

TRANSCRIPTION: RNAp + Promoter → RNAp + Promoter + mRNA

The mRNA production is described using Michaelis-Menten kinetics.

TRANSLATION: mRNA + Ribosomes → mRNA + Ribosomes + Repressor

The Repressor production is also modeled using Michaelis-Menten kinetics.

REPRESSION: Promoter + n · Repressor → Promoter_Repressorn

Finally we use a Hill kinetics model for the transcription inhibition, which offers an approximation to the cooperative action.

In the new model, we have to include the new reactions involved in the Improved Flip-Flop. These are:

PROTEOLYSIS: Protease + Repressor 1 → Protease

We will consider a mass action rate law, where the protein will be digested according to the protease concentration.

INHIBITION of TRANSLATION: asRNA + mRNA → RNA complex

We assume a mass action rate law again.

Diagram

These two new effects may enhance the robustness of the toggle switch. We will analyze their effects by implementing the model in Simbiology. The following diagram shows all the species and reactions of the model:

Diagram MB

Here we can see all the species involved in the new model for the bistable.

The model can be downloaded here:

In the next section, we describe in detail the equations of the model

Retrieved from "http://2011.igem.org/Team:UPO-Sevilla/Project/Improving_Flip_Flop/Modeling/Introduction"