Team:Evry/flush model

From 2013.igem.org

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<h1>Flush model overview</h1>
<h1>Flush model overview</h1>
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<h2>Introduction</h2>
<h2>Introduction</h2>
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<img src="https://static.igem.org/mediawiki/2013/9/91/Tube_digestif2.jpg" alt="Intestine" width="20%" style="float:right;"/>
<p>
<p>
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In the very beginning of the project, we focused on iron absorption by the duodenum. We first had to model the behaviour of the duodenum regarding iron absorption to determine if a flush treatment strategy was viable. Then we want to model the flush treatment by simulating a flush of iron-chelating bacteria.
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In the very beginning of the project, we focused on iron absorption by the duodenum. We first had to model the behaviour of the duodenum regarding iron absorption to determine if a flush treatment strategy was viable. Then we wanted to model the flush treatment by simulating a flush of iron-chelating bacteria.
</p>
</p>
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<br/>
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<h2>Disease model</h2>
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<p>
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We first modeled the iron absorption of a hemochromatosic patient using ODEs.
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</p>
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<p>
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<a href="https://2013.igem.org/Team:Evry/Modeltr1">Here is the link to the disease model</a>.
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</p>
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<h2>Treatment model</h2>
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<p>
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We then used the disease model as a base to develop our flush treatment model. It aims to answer the following question:<br/>
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<em>"Is it possible to chelate a significant amount of iron with a flush strategy?"</em>
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</p>
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<p>
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<a href="https://2013.igem.org/Team:Evry/Modeltr2">Here is the link to the treatment model</a>.
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</p>
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<br/><br/><br/><br/><br/><br/>
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<h2>Observations</h2>
<h2>Observations</h2>
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We know that 60% of iron is absorbed in the duodenum and 40% in the jejunum. The duodenum is located in the upper intestines, right after the stomach, and is usually 300mm long.
We know that 60% of iron is absorbed in the duodenum and 40% in the jejunum. The duodenum is located in the upper intestines, right after the stomach, and is usually 300mm long.
<br/>
<br/>
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A healthy person absorbs about 10% (2mg a day) of the daily iron uptake, while a hemochromatosic patient's absorption varies between 50% and 100% of the daily iron uptake<sup><a href="#Ref">[1]</a></sup>.
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A healthy person absorbs about 10% (2mg a day) of the daily iron uptake, while a hemochromatosic patient's absorption varies between 50% and 100% of the daily iron uptake.
<div align="center">
<div align="center">
<a id="Fig1"></a>
<a id="Fig1"></a>
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<h3>Assumptions</h3>
<h3>Assumptions</h3>
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<p>With use the same assumptions as in the previous model apply:
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<p>With use this same assumptions in our model:
<ul>
<ul>
<li>Our bacteria don't settle in the duodenum</li>
<li>Our bacteria don't settle in the duodenum</li>
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<h3>Model</h3>
<h3>Model</h3>
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<p>We use Ordinary Differential Equation to modelize the duodenum and the potentiel impact of our flush strategy treatment.
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<p>We use Ordinary Differential Equation to modelize the duodenum and the potentiel impact of our flush strategy treatment:
<p>
<p>
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<span style="float:right;"> <img src="https://static.igem.org/mediawiki/2013/1/1d/GrapheRaisonnementModele1.png" width=600px /> </span>
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<span style="float:right;"> <img src="https://static.igem.org/mediawiki/2013/1/1d/GrapheRaisonnementModele1.png" style="width:60%;" /> </span>
<b><span style="color:#0000FF;">A</span></b> : Total quantity of iron absorbed by the duodenum (mol)
<b><span style="color:#0000FF;">A</span></b> : Total quantity of iron absorbed by the duodenum (mol)
<br/>
<br/>
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<b><span style="color:#FF0000;">S</span></b> : Quantity of solved iron (mol)
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<b><span style="color:#FF0000;">S</span></b> : Quantity of solved iron in the duodenum lumen (mol)
<br/>
<br/>
<b>P</b> : Total quantity of enterobactin produced by our population of bacteria (mol)
<b>P</b> : Total quantity of enterobactin produced by our population of bacteria (mol)
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<b>N</b> : Number of bacteria
<b>N</b> : Number of bacteria
</p>
</p>
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<img src="https://static.igem.org/mediawiki/2013/1/1b/Duoeqcoul.png" width=300px /><br/>
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<img src="https://static.igem.org/mediawiki/2013/1/1b/Duoeqcoul.png" style="width:25%;" /><br/>
<p>
<p>
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The graph on the right explains the reasoning: for instance, the arrow with a + between N and P means that the variation of P has a positive linear term in N.
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<br/>
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<table border="1" style="border-collapse:collapse;">
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<tr>
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<td><b>S<sub>p</sub></b></td>
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<td>mol.s<sup>-1</sup></td>
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<td>Iron pulse</td>
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</tr>
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<tr>
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<td><b>v</b></td>
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<td>m.s<sup>-1</sup></td>
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<td>Chyme's flow average speed</td>
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</tr>
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<tr>
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<td><b>L</b></td>
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<td>m</td>
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<td>Duodenum length</td>
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</tr>
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<tr>
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<td><b>α</b></td>
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<td>s<sup>-1</sup></td>
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<td>Duodenum absorption rate</td>
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</tr>
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<tr>
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<td><b>K</b></td>
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<td>mol/s</td>
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<td>Activator Magnitude</td>
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</tr>
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<tr>
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<td><b>p</b></td>
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<td>mol.s<sup>-1</sup></td>
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<td>Value at zero of the activator</td>
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</tr>
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<tr>
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<td><b>h</b></td>
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<td>-</td>
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<td>Activator efficiency</td>
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</tr>
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<tr>
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<td><b>d</b></td>
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<td>mol</td>
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<td>Activator threshold</td>
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</tr>
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<tr>
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<td><b>δ</b></td>
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<td>mol<sup>-1</sup></td>
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<td>Dimensional parameter</td>
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</tr>
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</table>
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<br/><br/>
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</p>
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</p>
 
<h2>Results</h2>
<h2>Results</h2>
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<p>With our ODE system, we were able to answer to the questions presented at the begining of the page. The results are presented on the two following pages:
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</p>
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<ol>
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<li>Disease model on <a href="https://2013.igem.org/Team:Evry/Modeltr1">this</a> page.</li>
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<li>The potential effects of our treatment on <a href="https://2013.igem.org/Team:Evry/Modeltr2">this</a> page.</li>
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</ol>
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<h2>Conclusion</h2>
 
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<h2>Models and Scripts</h2>
 
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<table width="100%">
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<h2>Conclusion</h2>
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<tr>
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<p>Our model show that our <b><span style="color:#bb8900">Iron</span><span style="color:#7B0000"> Coli</span></b> with a flush strategy would be able to neutralize a significant quantity of iron before it is absorbed by the duodenum.
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<td align="center">img1</td>
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It would thus be possible to approximately divide the intestinal iron intake by 2 if the patient takes one pill during each meal. This means that the patient would endure a lighter treatment : less bloodletting for people suffering from hemochromatosis, and less iron chelator's side effects for the thalassemia. </p>
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<td align="center">img2</td>
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<td align="center">img3</td>
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</tr>
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<tr>
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<td align="center">txt1</td>
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<td align="center"></td>
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<td align="center">txt3</td>
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</tr>
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</table>
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<h2>Models and scripts</h2>
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<p>
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This model was made using the Python language. You can download the python script <a href="https://static.igem.org/mediawiki/2013/2/2e/Duodenum.zip"> here</a>.
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</p>
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<a id="Ref"></a>
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<div id="citation_box">
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<p id="references"><b>References:</b></p>
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<ul>
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<li>Physiol Rev 93: 1721–1741, 2013 doi:10.1152/physrev.00008.2013 - Tomas Ganz "SYSTEMIC IRON HOMEOSTASIS"</li>
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  <li>Calculated from : Computational Modeling and Simulation of the Human Duodenum - B. Hari, S. Bakalis, P. Fryer - 2012</li>
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  <li>Calculated from : Bacterial iron homeostasis - Simon C. Andrews, Andrea K. Robinson, Francisco Rodriguez-Quinones</li>
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  <li>Wikipedia</li>
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</ul>
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</div>
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{{:Team:Evry/foot}}
{{:Team:Evry/foot}}

Latest revision as of 02:58, 29 October 2013

Iron coli project

Flush model overview

Introduction

Intestine

In the very beginning of the project, we focused on iron absorption by the duodenum. We first had to model the behaviour of the duodenum regarding iron absorption to determine if a flush treatment strategy was viable. Then we wanted to model the flush treatment by simulating a flush of iron-chelating bacteria.


Disease model

We first modeled the iron absorption of a hemochromatosic patient using ODEs.

Here is the link to the disease model.

Treatment model

We then used the disease model as a base to develop our flush treatment model. It aims to answer the following question:
"Is it possible to chelate a significant amount of iron with a flush strategy?"

Here is the link to the treatment model.







Retrieved from "http://2013.igem.org/Team:Evry/flush_model"