Latest revision as of 09:56, 26 October 2013

Iron coli project

Duodenum model

Overview

Once our genetically modified bacteria are released in the duodenum, they produce siderophores to chelate the solved iron, thus making it unavailable for intestinal absorption. Then, they eventually flush out of the duodenum. The main hypothesis in this model is that the bacteria don't colonize the duodenum : they only flow through.
The goal of this model is to measure how efficient could this form of treatment be. Because too much parameters remain unknown, it is a theoretical simulation which will not give any numerical results.

Assumptions

Our bacteria don't settle in the duodenum
No regulation in the patient's iron absorption
Constant iron flow
Homogeneous fluid
The bacterial quantity is constant
The bacterial natural absorption is insignificant compared to the chelation
The patient ingests 20mg of iron per day (Guideline Daily Amounts)

Model Description

A : Total quantity of iron absorbed by the duodenum (mol)
S : Quantity of solubilized iron (mol)
P : Total quantity of enterobactin produced by our population of bacteria (mol)
Q : Total quantity of chelated iron (mol)
N : Number of bacteria

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.

Where

is our logistic function (which we will here abusively call activator).

Results

Figure 1 : Iron Absorption in the duodenum with and without treatment.

Figure 1 represent the iron absorbed by the duodenum during a meal. We can see the reduction of iron absorption in the duodenum

Figure 2 : Iron in the duodenum during the simulation

Figure 2 represent iron disolved in the chyme. This graph point out the influence of bacteria on the middle. The blue curve decrease significantly under the bacteria flux. That underline the fact that the treatment don't affect the absorption directly.

Parameters:

The simulations was made with following parameters:

Name	Value	Unit	Description	Reference
alpha	0.03	s-1	Duodenum absorption rate	-
v	0.007	m/s	Chyme's flow average speed	[1]
L	0.3	m	Duodenum length	[3]
delta	2.65*10^-8	mol-1	Dimensional parameter	-
Sp	4.5*10^-9	mol/s	Iron pulse	[1]
K	100	mol/s	Activator Magnitude	-
p	0.005	mol/s	Value at zero of the activator	-
h	10^-5	-	Activator efficiency	-
d	10^-9	mol	Activator threshold	[2]

There is a slight difference between the two cases, which would possibly allow us to fit the treatment to the patient's characteristics.

Conclusion

It is possible to significantly reduce intestinal iron intake if the patient takes one pill before or 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.

References:

Calculated from : Computational Modeling and Simulation of the Human Duodenum - B. Hari, S. Bakalis, P. Fryer - 2012
http://onlinelibrary.wiley.com/doi/10.1016/S0168-6445%2803%2900055-X/pdf p.217
Wikipedia

Download the model

@@ Line 5: / Line 5: @@
 <div id="mainTextcontainer">
-<h1>Iron absorption</h1>
+<h1>Duodenum model</h1>
 <h2>Overview</h2>
 <p>
-The duodenum is the first part of the intestines. It is located right after the stomach, and is usually 300mm long.<br/>
+Once our genetically modified bacteria are released in the duodenum, they produce siderophores to chelate the solved iron, thus making it unavailable for intestinal absorption. Then, <b>they eventually flush out of the duodenum</b>. The main hypothesis in this model is that the bacteria don't colonize the duodenum : they only flow through. <br/>
-This model simulates the behaviour of a hemochromatosis suffering person's duodenum. We use it to compute the quantity of iron absorbed by the organism. Once our genetically modified bacteria are released in the duodenum, they produce siderophores to chelate the solved iron, thus making it unavailable for intestinal absorption. Then, <b>they eventually flush out of the duodenum</b>. The main hypothesis in this model is that the bacteria don't colonize the duodenum : they only flow through. <br/>
 The goal of this model is to measure how efficient could this form of treatment be. Because too much parameters remain unknown, it is a theoretical simulation which will <b>not</b> give any numerical results.
 </p>
+<a id="Assumptions"></a>
 <h2>Assumptions</h2>
@@ Line 23: / Line 23: @@
 <li>The bacterial quantity is constant</li>
 <li>The bacterial natural absorption is insignificant compared to the chelation</li>
+<li>The patient ingests 20mg of iron per day (Guideline Daily Amounts)</li>
 </ul>
@@ Line 30: / Line 31: @@
 <span style="color:#0000FF;">A</span> : Total quantity of iron absorbed by the duodenum (mol)
 <br/>
-<span style="color:#FF0000;">S</span> : Quantity of solved iron (mol)
+<span style="color:#FF0000;">S</span> : Quantity of solubilized iron (mol)
 <br/>
 P : Total quantity of enterobactin produced by our population of bacteria (mol)
@@ Line 42: / Line 43: @@
 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.
 </p>
-Where <img src="https://static.igem.org/mediawiki/2013/0/01/LogistiqueDuodenum.png" /> is our <a href="https://2013.igem.org/Team:Evry/LogisticFunctions">logistic function</a>.<br/>
+Where <img src="https://static.igem.org/mediawiki/2013/0/01/LogistiqueDuodenum.png" /> is our <a href="https://2013.igem.org/Team:Evry/LogisticFunctions">logistic function</a> (which we will here abusively call activator).<br/>
-<u>Parameters:</u><br/>
+<a id="Results"></a>
+<h2>Results</h2>
+<p>
+ <div class="captionedPicture" style="width:100%;">
+   <a title="Absorption" href="https://static.igem.org/mediawiki/2013/4/44/Model_absorption_treatment.png">
+    <img alt="Absorption" src="https://static.igem.org/mediawiki/2013/4/44/Model_absorption_treatment.png" class="Picture"/>
+   </a>
+   <div class="caption">
+     <b>Figure 1 : </b> Iron Absorption in the duodenum with and without treatment.
+   </div>
+ </div>
+<br/>
+Figure 1 represent the iron absorbed by the duodenum during a meal. We can see the reduction of iron absorption in the duodenum
+<br/>
+ <div class="captionedPicture" style="width:100%;">
+   <a title="Quantity" href="https://static.igem.org/mediawiki/2013/0/07/Model_iron_treatment.png">
+    <img alt="Quantity" src="https://static.igem.org/mediawiki/2013/0/07/Model_iron_treatment.png" class="Picture"/>
+   </a>
+   <div class="caption">
+     <b>Figure 2 : </b> Iron in the duodenum during the simulation
+   </div>
+ </div>
+<br/>
+Figure 2 represent iron disolved in the chyme. This graph point out the influence of bacteria on the middle. The blue curve decrease significantly under the bacteria flux. That underline the fact that the treatment don't affect the absorption directly.
+<br/><br/>
+<u>Parameters:</u><br/><br/>
+The simulations was made with following parameters:<br/>
 <table width="100%" border="1">
 <tr width="100%">
 <th>Name</th>
 <th>Value</th>
+<th>Unit</th>
 <th>Description</th>
 <th>Reference</th>
@@ Line 54: / Line 90: @@
 <td>alpha</td>
 <td>0.03</td>
-<td>-</td>
+<td>s-1</td>
+<td>Duodenum absorption rate</td>
 <td>-</td>
 </tr>
 <tr width="100%">
 <td>v</td>
-<td>0.007 m/s</td>
+<td>0.007</td>
+<td>m/s</td>
 <td>Chyme's flow average speed</td>
 <td>[1]</td>
@@ Line 65: / Line 103: @@
 <tr width="100%">
 <td>L</td>
-<td>0.3 m</td>
+<td>0.3</td>
+<td>m</td>
 <td>Duodenum length</td>
-<td>[2]</td>
+<td>[3]</td>
 </tr>
 <tr width="100%">
 <td>delta</td>
 <td>2.65*10^-8</td>
-<td>-</td>
+<td>mol-1</td>
+<td>Dimensional parameter</td>
 <td>-</td>
 </tr>
 <tr width="100%">
 <td>Sp</td>
-<td>4.5*10^-9 mol/s</td>
+<td>4.5*10^-9</td>
+<td>mol/s</td>
 <td>Iron pulse</td>
 <td>[1]</td>
@@ Line 84: / Line 125: @@
 <td>K</td>
 <td>100</td>
-<td>-</td>
+<td>mol/s</td>
+<td>Activator Magnitude</td>
 <td>-</td>
 </tr>
@@ Line 90: / Line 132: @@
 <td>p</td>
 <td>0.005</td>
-<td>-</td>
+<td>mol/s</td>
+<td>Value at zero of the activator</td>
 <td>-</td>
 </tr>
@@ Line 97: / Line 140: @@
 <td>10^-5</td>
 <td>-</td>
+<td>Activator efficiency</td>
 <td>-</td>
 </tr>
 <tr width="100%">
 <td>d</td>
-<td>5*10^-9</td>
+<td>10^-9</td>
-<td>-</td>
+<td>mol</td>
-<td>-</td>
+<td>Activator threshold</td>
+<td>[2]</td>
 </tr>
 </table>
-<h2>Results</h2>
-<p>
-The following graphs are simulations with different intake times. The purple line represents 50% of the total ingested iron, whereas the green line is set at 10%, which is the iron absorption of a sane individual.<br/>
-Note that the <b>black</b> curve represents the Blank simulation: a sick person's absorption without any bacterial intake.<br/>
-<div align="center"><img width="100%" src="https://static.igem.org/mediawiki/2013/5/52/ResultDuodenum2.png"/><br/><b>Bacterial intake before meal</b></div><br/><br/>
-<div align="center"><img width="100%" src="https://static.igem.org/mediawiki/2013/c/c5/ResultDuodenum3.png"/><br/><b>Bacterial intake during meal</b></div>
 </p><br/>
 <p>There is a slight difference between the two cases, which would possibly allow us to fit the treatment to the patient's characteristics.</p>
+<a id="Conclusion"></a>
 <h2>Conclusion</h2>
@@ Line 124: / Line 164: @@
   <p id="references">References:</p>
   <ol>
-   <li>Computational Modeling and Simulation of the Human Duodenum - B. Hari, S. Bakalis, P. Fryer - 2012</li>
+   <li>Calculated from : Computational Modeling and Simulation of the Human Duodenum - B. Hari, S. Bakalis, P. Fryer - 2012</li>
+  <li>http://onlinelibrary.wiley.com/doi/10.1016/S0168-6445%2803%2900055-X/pdf p.217 </li>
    <li>Wikipedia</li>
   </ol>
 </div>
+<a href="https://static.igem.org/mediawiki/2013/2/2e/Duodenum.zip"> Download the model</a>
 </div>

Team:Evry/Model1

From 2013.igem.org