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Team:IIT Delhi/Modelling
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<li><a href="https://2013.igem.org/Team:IIT_Delhi/Outreach" id="orientation">Orientation for Freshmen</a></li> | <li><a href="https://2013.igem.org/Team:IIT_Delhi/Outreach" id="orientation">Orientation for Freshmen</a></li> | ||
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<li><a href="https://2013.igem.org/Team:IIT_Delhi/BRAI" id="bill">BRAI Bill</a></li> | <li><a href="https://2013.igem.org/Team:IIT_Delhi/BRAI" id="bill">BRAI Bill</a></li> | ||
<li><a href="https://2013.igem.org/Team:IIT_Delhi/Biotoilet" id="biotoilets">Biotoilets</a></li> | <li><a href="https://2013.igem.org/Team:IIT_Delhi/Biotoilet" id="biotoilets">Biotoilets</a></li> | ||
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Our model involves both activation and repression systems. Activation of <b>asr</b> promoter in acidic medium results in production of <b>GFP</b> and <b>tetR</b> proteins. Increasing tetR in the system results in repression of <b>tet</b> promoter and hence reduction in the production of <b>RFP</b>. | Our model involves both activation and repression systems. Activation of <b>asr</b> promoter in acidic medium results in production of <b>GFP</b> and <b>tetR</b> proteins. Increasing tetR in the system results in repression of <b>tet</b> promoter and hence reduction in the production of <b>RFP</b>. | ||
</font> | </font> | ||
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| + | <table style="text-align: left; width: 100%;" border="0" | ||
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| + | <tbody> | ||
| + | <tr> | ||
| + | <td style="vertical-align: top; text-align: center;"><img | ||
| + | style="width: 480px; height: 320px;" alt="" | ||
| + | src="https://static.igem.org/mediawiki/2013/2/22/Iitd_1.jpg"></td> | ||
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| + | <td align="center" valign="top"><img | ||
| + | style="width: 480px; height: 320px;" alt="" | ||
| + | src="https://static.igem.org/mediawiki/2013/0/06/Iitd_2.jpg"></td> | ||
| + | </tr> | ||
| + | </tbody> | ||
| + | </table> | ||
| + | <br> <br> | ||
| + | <font color="#303030" > | ||
| + | Rates of formation of the above mentioned proteins can directly be related to the respective respressor/activator by using <b>Hill’s function</b>.<br> | ||
| + | Rate of production of protein Y = f(X*), where f is an input Hill function, and X* is the active form of activator/repressor X. | ||
| + | </font> | ||
| + | <br><br> | ||
| + | <table style="text-align: left; width: 100%;" border="0" | ||
| + | cellpadding="2" cellspacing="2"> | ||
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| + | <td style="vertical-align: top; text-align: center;"><img | ||
| + | style="width: 484px; height: 114px;" alt="" | ||
| + | src="https://static.igem.org/mediawiki/2013/a/a7/Iitd_3.jpg"></td> | ||
| + | </tr><tr> | ||
| + | <td align="center" valign="top"><img | ||
| + | style="width: 628px; height: 114px;" alt="" | ||
| + | src="https://static.igem.org/mediawiki/2013/f/fb/Iitd_4.jpg"></td> | ||
| + | </tr> | ||
| + | </tbody> | ||
| + | </table><br><br> | ||
| + | <font color="#303030" > | ||
| + | The <b>Hill parameters</b> are β, K and n. <br> | ||
| + | <b>β:</b> Maximal rate of expression of protein.<br> | ||
| + | <b>K (Activation coefficient):</b> Concentration of X* that is needed to significantly activate expression of Y.<br> | ||
| + | <b>n (Cooperativity coefficient):</b> Determined by the binding cooperativity of active for of repressor/activator to the binding site on promoter. | ||
| + | </font><br><br> | ||
| + | <b>For our model we simulated the acid inducible part by creating and simulating the following equations using MATLAB:</b><br> | ||
| + | <table style="text-align: left; width: 100%;" border="0" | ||
| + | cellpadding="2" cellspacing="2"> | ||
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| + | <td style="vertical-align: top; text-align: left;"><img | ||
| + | style="width: 349px; height: 63px;" alt="" | ||
| + | src="https://static.igem.org/mediawiki/2013/2/22/Iitd_5.jpg"></td> | ||
| + | </tr><br> | ||
| + | <tr> | ||
| + | <td align="left" valign="top"><img | ||
| + | style="width: 360px; height: 69px;" alt="" | ||
| + | src="https://static.igem.org/mediawiki/2013/1/1b/Iitd_d6.jpg"></td> | ||
| + | </tr><br> | ||
| + | <tr> | ||
| + | <td align="left" valign="top"><img | ||
| + | style="width: 360px; height: 65px;" alt="" | ||
| + | src="https://static.igem.org/mediawiki/2013/5/56/Iitd_7.jpg"></td> | ||
| + | </tr> | ||
| + | </tbody> | ||
| + | </table><br><br> | ||
| + | |||
| + | <font color="#303030" > | ||
| + | The input concentration of H+ and concentration of tetR are directly considered in the above equations. <br> | ||
| + | An <b>assumption</b> has been made here that all of the amount of activator/repressor is present in the active form. | ||
| + | </font><br><br> | ||
| + | The parameters for simulating the above equations were taken from team <a href="https://2011.igem.org/Team:ETH_Zurich">ETH Zurich</a>, iGEM 2011's work. Some of the parameters have been assumed due to their non-availability. | ||
| + | <br><br> | ||
| + | <img src="https://static.igem.org/mediawiki/2013/0/00/Model_parameters.png" height=600 width=450 align=middle> | ||
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| + | <br><br><br><br> | ||
| + | <b>SIMULATION RESULTS: </b><br> | ||
| + | <table style="text-align: left; width: 100%;" border="0" | ||
| + | cellpadding="2" cellspacing="2"> | ||
| + | <tbody> | ||
| + | <tr> | ||
| + | <td style="vertical-align: top; text-align: center;"><img | ||
| + | style="width: 480px; height: 320px;" alt="" | ||
| + | src="https://static.igem.org/mediawiki/2013/8/83/Iitd_8.jpg"></td> | ||
| + | </tr> | ||
| + | </tbody> | ||
| + | </table><br><br> | ||
| + | <b><u>GFP vs pH<b></u> | ||
| + | <table style="text-align: left; width: 100%;" border="0" | ||
| + | cellpadding="2" cellspacing="2"> | ||
| + | <tbody> | ||
| + | <tr> | ||
| + | <td style="vertical-align: top; text-align: center;"><img | ||
| + | style="width: 480px; height: 320px;" alt="" | ||
| + | src="https://static.igem.org/mediawiki/2013/1/14/Iitd_9.jpg"></td> | ||
| + | </tr> | ||
| + | </tbody> | ||
| + | </table><br><br> | ||
| + | <b><u>RFP vs pH<b></u> | ||
| + | <table style="text-align: left; width: 100%;" border="0" | ||
| + | cellpadding="2" cellspacing="2"> | ||
| + | <tbody> | ||
| + | <tr> | ||
| + | <td style="vertical-align: top; text-align: center;"><img | ||
| + | style="width: 480px; height: 320px;" alt="" | ||
| + | src="https://static.igem.org/mediawiki/2013/e/eb/Iitd_10.jpg"></td> | ||
| + | </tr> | ||
| + | </tbody> | ||
| + | </table><br><br> | ||
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Latest revision as of 03:19, 28 September 2013
 |
| Modelling and Simulation Our model involves both activation and repression systems. Activation of asr promoter in acidic medium results in production of GFP and tetR proteins. Increasing tetR in the system results in repression of tet promoter and hence reduction in the production of RFP.
Rates of formation of the above mentioned proteins can directly be related to the respective respressor/activator by using Hill’s function. Rate of production of protein Y = f(X*), where f is an input Hill function, and X* is the active form of activator/repressor X.
The Hill parameters are β, K and n. β: Maximal rate of expression of protein. K (Activation coefficient): Concentration of X* that is needed to significantly activate expression of Y. n (Cooperativity coefficient): Determined by the binding cooperativity of active for of repressor/activator to the binding site on promoter. For our model we simulated the acid inducible part by creating and simulating the following equations using MATLAB:
The input concentration of H+ and concentration of tetR are directly considered in the above equations. An assumption has been made here that all of the amount of activator/repressor is present in the active form. The parameters for simulating the above equations were taken from team ETH Zurich, iGEM 2011's work. Some of the parameters have been assumed due to their non-availability. 
SIMULATION RESULTS:
GFP vs pH
RFP vs pH
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Feel Free to contact us at igemiitdelhi2013 at gmail dot com if you have queries; requests; suggestions et cetera. Thanks to iGEM and IIT Delhi, we had an awesome summer! |
Our
Project was supported by and done by the students of IIT Delhi, India.  |
This
project was done as a part of iGEM: iGEM Main Website  |
