Team:CIDEB-UANL Mexico/Test2

From 2012hs.igem.org

(Difference between revisions)

Latest revision as of 04:55, 17 June 2012

Team: UANL_Mty-Mexico

Team: CIDEB-UANL Mexico

Modelling

Overview

We decided to follow a deterministic approach for the mathematical representation of our genetic circuits. The simulations were made using MATLAB’s Simulink, according to the following general expressions for the genetic inhibition and activation elements present in the ODE systems. These expressions were adapted from Mendes, P, et al., (2003).

The effect of an inhibitor was modeled as follows:

Overview

References

iGEM High School Division, 2012 edition - CIDEB-UANL_Mexico team

@@ Line 1: / Line 1: @@
 {{:Team:CIDEB-UANL_Mexico/Templates/Header}}
 {{:Team:CIDEB-UANL_Mexico/Templates/Menu}}
+{{:Team:CIDEB-UANL_Mexico/Templates/Style}}
 <html>
@@ Line 19: / Line 20: @@
 <meta http-equiv="Content-Type" content="text/html; charset=UTF-8" />
-   <title>Team: UANL_Mty-Mexico</title>
+   <title>Team: CIDEB-UANL Mexico</title>
 <META NAME="keywords" CONTENT="">
@@ Line 27: / Line 28: @@
 <META NAME="robots" CONTENT="FOLLOW,INDEX">
-<link href="http://www.asebiogen.org/igemuanl/mainStyle.css" rel="stylesheet" type="text/css">
+<script type="text/javascript" src="http://www.asebiogen.org/igemuanl/Scripts/jquery-1.3.2.min.js"></script>
+<script type="text/javascript" src="http://www.asebiogen.org/igemuanl/Scripts/jquery-1.3.2.min.js"></script>
+<script type='text/javascript' src='http://www.asebiogen.org/igemuanl/jquery.easing.1.3.js'></script>
+<script type='text/javascript' src='http://www.asebiogen.org/igemuanl/jquery.slideup.menu.1.0.min.js'></script>
+<script type="text/javascript" src="http://www.asebiogen.org/igemuanl/Scripts/jquery.scroll-follow.js"></script>
+<script type="text/javascript" src="http://www.asebiogen.org/igemuanl/Scripts/slimbox2/js/slimbox2.js"></script>
@@ Line 46: / Line 58: @@
 </head>
@@ Line 64: / Line 79: @@
 <div class="br"></div><div class="br"></div>
 <div class="br"></div><div class="br"></div>
@@ Line 69: / Line 88: @@
 <div class="br2"></div><div class="br2"></div><div class="br2"></div>
             <a name="Overview"></a>Overview
-<div class="br2"></div><div class="br2"></div><div class="br2"></div>
+<div class="br2"></div><div class="br2"></div>
        </div>
+<div class="br"></div><div class="br"></div>
      <p>We decided to follow a deterministic approach for the mathematical representation of our genetic circuits. The simulations were made using MATLAB’s Simulink, according to the following general expressions for the genetic inhibition and activation elements present in the ODE systems. These expressions were adapted from Mendes, P, <i>et al</i>., (2003).</p>
 <p>The effect of an inhibitor was modeled as follows:</p>
@@ Line 76: / Line 97: @@
 <center>
 <div class = "img-holder" style="width:130px; font-size: 18px;">
-<a href="https://static.igem.org/mediawiki/2011/9/9d/1_Inhibitor_effect.gif" rel="lightbox">
+<a href="https://static.igem.org/mediawiki/2012hs/8/88/533285_4046679406517_1353833067_n.jpg" rel="lightbox">
-<img src="https://static.igem.org/mediawiki/2011/9/9d/1_Inhibitor_effect.gif"width="126px" height="44px" align="center">
+<img src="https://static.igem.org/mediawiki/2012hs/8/88/533285_4046679406517_1353833067_n.jpg"width="126px" height="44px" align="center">
 </a>
 <span class="img-holder-text"><b></b> </div><div class="br">
 </center>
-<p>where α is the maximum transcription rate of a gene, K is the dissociation constant of the inhibitor, I represents its concentration and n is its Hill coefficient.</p>
-<p>In the other hand, the effect of an activator was expressed as follows:</p>
-<center>
-<div class = "img-holder" style="width:135px; font-size: 18px;">
-<a href="https://static.igem.org/mediawiki/2011/4/41/2_Activator_effect.gif" rel="lightbox" >
-<img src="https://static.igem.org/mediawiki/2011/4/41/2_Activator_effect.gif"width="130px" height="44px" align="center">
-</a>
-<span class="img-holder-text"><b></b> </div><div class="br">
-</center>
-<p>where α is also the maximum transcription rate of a gene, K is the dissociation constant of the activator, A represents its concentration and n is its Hill coefficient.</p>
-<p>The maximum transcription rate is used instead of the basal transcription rate under the assumption that inducible promoters should not present significant basal activity and that repressible promoters are active at this maximum rate in the absence of an inhibitor. The maximum transcription rate was calculated according to the Team Beijing iGEM 2009 (<a href="https://2008.igem.org/Team:KULeuven/Model/Inverter">https://2009.igem.org/Team:PKU_Beijing/Modeling/Parameters</a>).</p>
-<p>The general form of the differential equations used to model the change of the mRNA concentration of a gene is as follows:</p>
-<center>
-<div class = "img-holder" style="width:490px; font-size: 18px;">
-<a href="https://static.igem.org/mediawiki/2011/a/ad/3_mRNA_concentration_change.gif" rel="lightbox" >
-<img src="https://static.igem.org/mediawiki/2011/a/ad/3_mRNA_concentration_change.gif"width="482px" height="44px" alt="" align="center">
-</a>
-<span class="img-holder-text"><b></b> </div><div class="br">
-</center>
-<p>This general form represents an hypothetical gene, whose transcription is affected by an inhibitor I and an activator A. Different Hill Coefficients (n1 and n2) are used for the inhibitor and activator. The equation includes also the degradation rate, µ, for which we used the same numerical value for all the genes included in our circuits, cell division rate (1/30 min) plus substance degradation rate (1/4.4 min), as suggested by the Team Beijing iGEM 2009.</p>
-<p>For the protein concentration differential equations we took into consideration the maximum translation rate, α<sub>T </sub>, (also calculated as suggested also by the Team Beijing iGEM), the degradation rate, µ<sub>T</sub> , and the rate of postranslational modifications, specifically, phosphorylations of some transcription factors.</p>
-<p>Because all the genes in our circuits have been modified with a LVA tag, unless it is otherwise stated, all the protein degradation rates were considered to be equal to the cell division rate (1/30 min) plus the substance degradation rate (1/40 min, as suggested by Team Leuven iGEM 2008, <a href="https://2008.igem.org/Team:KULeuven/Model/Inverter">https://2008.igem.org/Team:KULeuven/Model/Inverter</a>)</p>
-<p>The general form for the differential equation of protein concentration change the following:</p>
-<center>
-<div class = "img-holder" style="width:350px; font-size: 18px;">
-<a href="https://static.igem.org/mediawiki/2011/3/39/4_Protein_concentration_change.gif" rel="lightbox">
-<img src="https://static.igem.org/mediawiki/2011/3/39/4_Protein_concentration_change.gif"width="346px" height="39px" alt="" align="center">
-</a>
-<span class="img-holder-text"><b></b> </div><div class="br">
-</center>
-  <div id="header-project-column">
-<div class="br2"></div><div class="br2"></div><div class="br2"></div>
-           <a name="References"></a>References
-<div class="br2"></div><div class="br2"></div><div class="br2"></div>
-      </div>
-<ol>
-  <li>Mendes, P, et al., (2003), Artiﬁcial gene networks for objective comparison of analysis algorithms, BIOINFORMATICS, Vol. 19 Suppl. 2, pages ii122–ii129</li>
-  <li>Team Beijing iGEM 2009 (<a href="https://2008.igem.org/Team:KULeuven/Model/Inverter">https://2009.igem.org/Team:PKU_Beijing/Modeling/Parameters</a>).</li>
-  <li>Team Leuven iGEM 2008,<a href="https://2008.igem.org/Team:KULeuven/Model/Inverter">https://2008.igem.org/Team:KULeuven/Model/Inverter</a>)</li>
-</ol>
@@ Line 138: / Line 119: @@
 </div>
 <div id="rightColumn">
-<!--    	<div id="social-div">
-				<a href="http://twitter.com/iGEMUANL" class="twitter-follow-button" data-show-count="false" data-align="right">Follow @iGEMUANL</a>
-   				<script src="http://platform.twitter.com/widgets.js" type="text/javascript"></script>
-        <div class="br"></div>
-                <iframe src="http://www.facebook.com/plugins/like.php?app_id=134010103347967&amp;href=http%3A%2F%2Fwww.facebook.com%2Fpages%2FiGEM-UANL%2F257596767587618&amp;send=false&amp;layout=button_count&amp;width=200&amp;show_faces=false&amp;action=like&amp;colorscheme=light&amp;font&amp;height=21" scrolling="no" frameborder="0" style="border:none; overflow:hidden; width:80px; height:21px;" allowTransparency="true">
-            </iframe>
-		</div>-->
-     <a href="#top" title="Go back to top"><img src="https://static.igem.org/mediawiki/igem.org/0/09/OurSymbol.png" width="200" height="160" alt="OurSymbol"></a>
+     <a href="#top" title="Go back to top"><img src="https://static.igem.org/mediawiki/2012hs/1/1b/Khumus.jpg" width="150" height="300" alt="OurSymbol"></a>
   <div class="br"></div>
@@ Line 181: / Line 151: @@
    </div>
-  <p><img src="https://static.igem.org/mediawiki/igem.org/4/49/SymbolFooter.png" width="950" height="70" alt="OurSymbol"></p>
+<div id="footer1">
+       	<p class="footer-text"> iGEM High School Division, 2012 edition - CIDEB-UANL_Mexico team </p>
+      </div>
 </div>
@@ Line 187: / Line 161: @@
 </body>
 </html>
-{{:Team:UANL_Mty-Mexico/Templates/Footer-template}}