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| - | {{Team:UANL_Mty-Mexico/Templates/Banner-mathmodel}}
| + | <!-- *** What falls between these lines is the Alert Box! You can remove it from your pages once you have read and understood the alert *** --> |
| - | {{Team:UANL_Mty-Mexico/Templates/Menu-template}}
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| | <html> | | <html> |
| - | <head> | + | <div id="box" style="width: 700px; margin-left: 137px; padding: 5px; border: 3px solid #000; background-color: #fe2b33;"> |
| | + | <div id="template" style="text-align: center; font-weight: bold; font-size: large; color: #f6f6f6; padding: 5px;"> |
| | + | This is a template page. READ THESE INSTRUCTIONS. |
| | + | </div> |
| | + | <div id="instructions" style="text-align: center; font-weight: normal; font-size: small; color: #f6f6f6; padding: 5px;"> |
| | + | You are provided with this team page template with which to start the iGEM season. You may choose to personalize it to fit your team but keep the same "look." Or you may choose to take your team wiki to a different level and design your own wiki. We cannot give any examples because none have been created yet. So, use your imagination and strive for clarity. |
| | + | </div> |
| | + | <div id="warning" style="text-align: center; font-weight: bold; font-size: small; color: #f6f6f6; padding: 5px;"> |
| | + | You <strong>MUST</strong> have a team description page, a description of the problem you are solving/opportunity you are creating as well as your solution, an executive summary and 3 min elevator pitch video, description and links to any source and market data, and an attributions page. PLEASE keep all of your pages within your teams namespace. |
| | + | </div> |
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| | + | </html> |
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| - | <!--
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| - | ============================================================================================
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| - | *** Acknowledgments ***
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| | | | |
| - | >>>To TU_Delf Team | + | <!-- *** End of the alert box *** --> |
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| - | Thank you so much to TU_Delft iGEM2010 team for providing us with so many examples of html code and how to apply them.
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| - | If you like some of this code please check it out in their wiki: https://2010.igem.org/Team:TU_Delft#page=Modeling/wiki-tips-tricks
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| | + | {|align="justify" |
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| - | ============================================================================================
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| - | /-->
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| - | <meta http-equiv="Content-Type" content="text/html; charset=UTF-8" />
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| - | <title>Team: UANL_Mty-Mexico</title>
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| - | <META NAME="keywords" CONTENT="UANL,iGEM,Universidad,Autonoma,Nuevo,Leon,Biphasic,switch,Lambda,Genetic,Regulation,Quorum,Sensing,pRM,OL,Green Light,Red Light">
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| - | <META NAME="description" CONTENT="iGEM-UANL is the representative team from Universidad Autonoma de Nuevo León, at Monterrey, México. This team is composed of ten students who spent their summer in the lab, having fun with transformations, constructions and plasmidic DNA extractions. This">
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| - | <META NAME="abstract" CONTENT="Information processing through living things remains a challenge to science. Genetic logic-gates and">
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| - | <META NAME="author" CONTENT="iGEM-UANL">
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| - | <META NAME="robots" CONTENT="FOLLOW,INDEX">
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| - | <script type="text/javascript" src="http://www.asebiogen.org/igemuanl/Scripts/jquery-1.3.2.min.js"></script>
| + | |You can write a background of your team here. Give us a background of your team, the members, etc. Or tell us more about something of your choosing. |
| | + | |[[Image:UANLe_Mexico_logo.png|200px|right|frame]] |
| | + | |- |
| | + | | |
| | + | ''Tell us more about your project. Give us background. Use this as the abstract of your project. Be descriptive but concise (1-2 paragraphs)'' |
| | + | |[[Image:UANLe_Mexico_team.png|right|frame|Your team picture]] |
| | + | |- |
| | + | | |
| | + | |align="center"|[[Team:UANLe_Mexico | Team UANLe_Mexico]] |
| | + | |} |
| | | | |
| | + | <!--- The Mission, Experiments ---> |
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| - | <script type="text/javascript" src="http://www.asebiogen.org/igemuanl/Scripts/jquery-1.3.2.min.js"></script>
| + | {| style="color:#1b2c8a;background-color:#0c6;" cellpadding="3" cellspacing="1" border="1" bordercolor="#fff" width="62%" align="center" |
| | + | !align="center"|[[Team:UANLe_Mexico|Home]] |
| | + | !align="center"|[[Team:UANLe_Mexico/Team|Team]] |
| | + | !align="center"|[[Team:UANLe_Mexico/Opportunity|Problem,Opportunity and Solution]] |
| | + | !align="center"|[[Team:UANLe_Mexico/Summary|Executive Summary and Elevator Pitch]] |
| | + | !align="center"|[[Team:UANLe_Mexico/Source_Data|Source Data]] |
| | + | !align="center"|[[Team:UANLe_Mexico/Attributions|Attributions]] |
| | + | |} |
| | + | <forum_subtle /> |
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| - | var opts = {slideUpSpeed:500, slideDownSpeed: 200};
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| - | <div class="content">
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| - | <div class="main" style="width:930px">
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| - | <!--<div style="width:900px">-->
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| - | <div class="br2"></div><div class="br2"></div><div class="br2"></div>
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| - | <div id="leftColumn">
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| - | <div id="ColorHeader">
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| - | Modelling
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| - | </div>
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| - | <div class="br"></div><div class="br"></div>
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| - | <div class="br"></div><div class="br"></div>
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| - | <div id="header-project-column">
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| - | <div class="br2"></div><div class="br2"></div><div class="br2"></div>
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| - | <a name="Overview"></a>Overview
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| - | <div class="br2"></div><div class="br2"></div><div class="br2"></div>
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| - | </div>
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| - | <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>
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| - | <p>The effect of an inhibitor was modeled as follows:</p>
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| | + | <html> |
| | <center> | | <center> |
| - | <div class = "img-holder" style="width:130px; font-size: 18px;"> | + | <div id=" clustrmaps- widget" ></div><script type=" text/javascript"> var _clustrmaps = {'url' : 'https:// 2012e.igem.org/ wiki/ index.php/ Team:UANLe_Mexico', 'user' : 1031626, 'server' : '4', 'id' : 'clustrmaps-widget', 'version' : 1, 'date' : '2012-07-24', 'lang' : 'en', 'corners' : 'square' };(function (){ var s = document.createElement('script'); s.type = 'text/ javascript'; s.async = true; s.src = 'http:/ /www4. clustrmaps.com/counter/map.js'; var x = document.getElementsByTagName('script')[0]; x.parentNode.insertBefore(s, x);})();</script><noscript><a href=" http://www4.clustrmaps.com/user/49ffbdca"><img src=" http:// www4. clustrmaps. com/ stats/ maps-no_clusters/ 2012e.igem.org-wiki-index.php-Team-UANLe_Mexico-thumb. jpg" alt=" Locations of visitors to this page" /></a></ noscript> |
| - | <a href="https://static.igem.org/mediawiki/2011/9/9d/1_Inhibitor_effect.gif" rel="lightbox">
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| - | <img src="https://static.igem.org/mediawiki/2011/9/9d/1_Inhibitor_effect.gif"width="126px" height="44px" align="center"> | + | |
| - | </a> | + | |
| - | <span class="img-holder-text"><b></b> </div><div class="br">
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| | </center> | | </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>
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| - | <p>In the other hand, the effect of an activator was expressed as follows:</p>
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| - |
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| - | <center>
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| - | <div class = "img-holder" style="width:135px; font-size: 18px;">
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| - | <a href="https://static.igem.org/mediawiki/2011/4/41/2_Activator_effect.gif" rel="lightbox" >
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| - | <img src="https://static.igem.org/mediawiki/2011/4/41/2_Activator_effect.gif"width="130px" height="44px" align="center">
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| - | </a>
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| - | <span class="img-holder-text"><b></b> </div><div class="br">
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| - | </center>
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| - |
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| - | <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>
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| - | <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>
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| - | <p>The general form of the differential equations used to model the change of the mRNA concentration of a gene is as follows:</p>
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| - | <div class = "img-holder" style="width:490px; font-size: 18px;">
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| - | <a href="https://static.igem.org/mediawiki/2011/a/ad/3_mRNA_concentration_change.gif" rel="lightbox" >
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| - | <img src="https://static.igem.org/mediawiki/2011/a/ad/3_mRNA_concentration_change.gif"width="482px" height="44px" alt="" align="center">
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| - | </a>
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| - | <span class="img-holder-text"><b></b> </div><div class="br">
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| - | </center>
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| - | <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>
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| - | <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>
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| - | <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>
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| - | <p>The general form for the differential equation of protein concentration change the following:</p>
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| - | <div class = "img-holder" style="width:350px; font-size: 18px;">
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| - | <a href="https://static.igem.org/mediawiki/2011/3/39/4_Protein_concentration_change.gif" rel="lightbox">
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| - | <img src="https://static.igem.org/mediawiki/2011/3/39/4_Protein_concentration_change.gif"width="346px" height="39px" alt="" align="center">
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| - | </a>
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| - | <span class="img-holder-text"><b></b> </div><div class="br">
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| - | </center>
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| - | <div id="header-project-column">
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| - | <div class="br2"></div><div class="br2"></div><div class="br2"></div>
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| - | <a name="References"></a>References
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| - | <div class="br2"></div><div class="br2"></div><div class="br2"></div>
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| - | </div>
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| - | <ol>
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| - | <li>Mendes, P, et al., (2003), Artificial gene networks for objective comparison of analysis algorithms, BIOINFORMATICS, Vol. 19 Suppl. 2, pages ii122–ii129</li>
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| - | <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>
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| - | <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>
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| - | <div class="lateral-button"><a href="https://2011.igem.org/Team:UANL_Mty-Mexico/Modelling/Overview#Overview">Overview</a></div>
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