Team:METU Turkey/human-practice.html

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<div class="clearfix colelem" id="u20714-4"><!-- content -->
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<p>• Antisense Kill Switch:</p>
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<img class="block" id="u20715_img" src="http://ghucuk.netii.net/12.png" alt="" width="544" height="408"/>
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<p>The aim of the Antisense Kill Switch model is to be able to predict the Mazf production according to IPTG concentration which is found in the environment. And with this theoretical data, we provided required data for our WetLab team about IPTG concentration and the choice of the promoters according to their strength. The model was created mainly by designing ODEs and enzyme kinetics equations.</p>
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<p>In our circuit, Mazf, B. subtilis specific toxic protein producing gene, and LacI genes are transcribed under Pveg, B. subtilis specific constitutive promoter. Antimazf, which produces complementary strand of Mazf mRNA as antisense RNA, is produced under Phyps, which is inhibited by LacI. LacI can form complex with IPTG molecule, in this way it won’t inhibit the&nbsp; Phyps&nbsp; promoter and the production of AntiMazf mrna.So, according to IPTG existence in the medium, LacI will form complex with IPTG and cannot inhibit the Phyps promoter and antiMazf mRNA production. If there is antimazf mRNA, the produced Mazf mRNA will form double stranded RNA with antimazf mRNA and will be degraded. Therefore, there won’t be Mazf mRNA to be translated and cells will remain alive with IPTG in the medium.</p>
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<div class="clearfix colelem" id="u20730-4"><!-- content -->
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<p>Mathematical Model:</p>
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<img class="block" id="u20731_img" src="http://ghucuk.netii.net/13.jpg" alt="" width="748" height="434"/>
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<div class="clearfix colelem" id="u20736-4"><!-- content -->
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<p>Differential Equations:</p>
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<img class="block" id="u20737_img" src="http://ghucuk.netii.net/eq4_1.png" alt="" width="692" height="502"/>
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</div>
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<div class="grpelem" id="u20742"><!-- image -->
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<img class="block" id="u20742_img" src="http://ghucuk.netii.net/eq4_2.png" alt="" width="674" height="379"/>
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<div class="clearfix colelem" id="u20747-8"><!-- content -->
 +
<p id="u20747-2">Simulation:</p>
 +
<p>After creating all equations, we expected that IPTG existence in the system will create a quick response to keep cells alive. Because once the production of AntiMazf mRNA will be higher than that of Mazf mRNA, there won’t be any chance of risk for cells according to IPTG concentration. For reverse situation, when there is decreasing amount of IPTG, once the AntiMazf mRNA falls under the concentration of Mazf mRNA, Mazf toxins production rate starts to increase.</p>
 +
<p>&nbsp;</p>
 +
<p>&nbsp;</p>
 +
</div>
 +
<div class="clearfix colelem" id="u21646-7"><!-- content -->
 +
<p>&nbsp;In these graphs ,it is seen that after certain concentration of IPTG , Mazf production drops to 0 very quickly. Because, after this IPTG concentration, antiMazf mRNA concentration won't permit any Mazf mRNA&nbsp; to be translated.</p>
 +
<p>&nbsp;</p>
 +
<p>In graphs, it is clearly seen that with increasing IPTG concentration,Mazf protein's production rate is decreasing, while the AntiMazf mRNA amount is increasing.</p>
 +
</div>
 +
<div class="clearfix colelem" id="pu21716-4"><!-- group -->
 +
<div class="clearfix grpelem" id="u21716-4"><!-- content -->
 +
<p>When IPTG=0</p>
 +
</div>
 +
<div class="clearfix grpelem" id="u21718-4"><!-- content -->
 +
<p>When IPTG=300</p>
 +
</div>
 +
</div>
 +
<div class="clearfix colelem" id="pu21649"><!-- group -->
 +
<div class="grpelem" id="u21649"><!-- image -->
 +
<img class="block" id="u21649_img" src="http://ghucuk.netii.net/0.jpg" alt="" width="357" height="327"/>
 +
</div>
 +
<div class="grpelem" id="u21659"><!-- image -->
 +
<img class="block" id="u21659_img" src="http://ghucuk.netii.net/300.jpg" alt="" width="333" height="327"/>
 +
</div>
 +
<div class="clearfix grpelem" id="u21757-4"><!-- content -->
 +
<p>MazF Protein</p>
 +
</div>
 +
<div class="clearfix grpelem" id="u21759-8"><!-- content -->
 +
<p>&#45;MazF mRNA</p>
 +
<p>&#45;AntiMazF<br/>mRNA</p>
 +
</div>
 +
</div>
 +
<div class="clearfix colelem" id="pu21720-4"><!-- group -->
 +
<div class="clearfix grpelem" id="u21720-4"><!-- content -->
 +
<p>When IPTG=600</p>
 +
</div>
 +
<div class="clearfix grpelem" id="u21724-4"><!-- content -->
 +
<p>When IPTG=1000</p>
 +
</div>
 +
</div>
 +
<div class="clearfix colelem" id="pu21662"><!-- group -->
 +
<div class="grpelem" id="u21662"><!-- image -->
 +
<img class="block" id="u21662_img" src="http://ghucuk.netii.net/600.jpg" alt="" width="365" height="351"/>
 +
</div>
 +
<div class="grpelem" id="u21670"><!-- image -->
 +
<img class="block" id="u21670_img" src="http://ghucuk.netii.net/1000.jpg" alt="" width="356" height="335"/>
 +
</div>
 +
</div>
 +
<div class="clearfix colelem" id="pu21726-4"><!-- group -->
 +
<div class="clearfix grpelem" id="u21726-4"><!-- content -->
 +
<p>When IPTG=1200</p>
 +
</div>
 +
<div class="clearfix grpelem" id="u21728-4"><!-- content -->
 +
<p>When IPTG=1270</p>
 +
</div>
 +
</div>
 +
<div class="clearfix colelem" id="pu21675"><!-- group -->
 +
<div class="grpelem" id="u21675"><!-- image -->
 +
<img class="block" id="u21675_img" src="http://ghucuk.netii.net/1200.jpg" alt="" width="339" height="310"/>
 +
</div>
 +
<div class="grpelem" id="u21680"><!-- image -->
 +
<img class="block" id="u21680_img" src="http://ghucuk.netii.net/1270.jpg" alt="" width="339" height="311"/>
 +
</div>
 +
</div>
 +
<div class="clearfix colelem" id="ppu21735-4"><!-- group -->
 +
<div class="clearfix grpelem" id="pu21735-4"><!-- column -->
 +
<div class="clearfix colelem" id="u21735-4"><!-- content -->
 +
<p>When IPTG=1275</p>
 +
</div>
 +
<div class="colelem" id="u21685"><!-- image -->
 +
<img class="block" id="u21685_img" src="http://ghucuk.netii.net/1275.jpg" alt="" width="343" height="306"/>
 +
</div>
 +
</div>
 +
<div class="grpelem" id="u21690"><!-- image -->
 +
<img class="block" id="u21690_img" src="http://ghucuk.netii.net/1290.jpg" alt="" width="370" height="324"/>
 +
</div>
 +
<div class="grpelem" id="u21730"><!-- simple frame --></div>
 +
<div class="clearfix grpelem" id="u21736-3"><!-- content -->
 +
<p>&nbsp;</p>
 +
</div>
 +
<div class="clearfix grpelem" id="u21737-3"><!-- content -->
 +
<p>&nbsp;</p>
 +
</div>
 +
<div class="clearfix grpelem" id="u21738-3"><!-- content -->
 +
<p>&nbsp;</p>
 +
</div>
 +
<div class="clearfix grpelem" id="u21739-3"><!-- content -->
 +
<p>&nbsp;</p>
 +
</div>
 +
<div class="clearfix grpelem" id="u21740-4"><!-- content -->
 +
<p>When IPTG=1290</p>
 +
</div>
 +
</div>
 +
<div class="clearfix colelem" id="pu21731"><!-- group -->
 +
<div class="clearfix grpelem" id="u21731"><!-- group -->
 +
<div class="clearfix grpelem" id="u21742-4"><!-- content -->
 +
<p>When IPTG=1295</p>
 +
</div>
 +
</div>
 +
<div class="clearfix grpelem" id="u21732"><!-- group -->
 +
<div class="clearfix grpelem" id="u21743-4"><!-- content -->
 +
<p>When IPTG=1300</p>
 +
</div>
 +
</div>
 +
</div>
 +
<div class="clearfix colelem" id="pu21695"><!-- group -->
 +
<div class="grpelem" id="u21695"><!-- image -->
 +
<img class="block" id="u21695_img" src="http://ghucuk.netii.net/1295.jpg" alt="" width="396" height="365"/>
 +
</div>
 +
<div class="grpelem" id="u21700"><!-- image -->
 +
<img class="block" id="u21700_img" src="http://ghucuk.netii.net/1300.jpg" alt="" width="370" height="348"/>
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</div>
 +
</div>
 +
<div class="clearfix colelem" id="pu21733"><!-- group -->
 +
<div class="clearfix grpelem" id="u21733"><!-- group -->
 +
<div class="clearfix grpelem" id="u21744-4"><!-- content -->
 +
<p>When IPTG=1305</p>
 +
</div>
 +
</div>
 +
<div class="clearfix grpelem" id="u21734"><!-- group -->
 +
<div class="clearfix grpelem" id="u21746-4"><!-- content -->
 +
<p>When IPTG=1325</p>
 +
</div>
 +
</div>
 +
</div>
 +
<div class="clearfix colelem" id="pu21705"><!-- group -->
 +
<div class="grpelem" id="u21705"><!-- image -->
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<img class="block" id="u21705_img" src="http://ghucuk.netii.net/1305.jpg" alt="" width="388" height="349"/>
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<div class="grpelem" id="u21710"><!-- image -->
 +
<img class="block" id="u21710_img" src="http://ghucuk.netii.net/1325.jpg" alt="" width="400" height="367"/>
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Revision as of 23:40, 4 October 2013

Kill Switch

• Antisense Kill Switch:

The aim of the Antisense Kill Switch model is to be able to predict the Mazf production according to IPTG concentration which is found in the environment. And with this theoretical data, we provided required data for our WetLab team about IPTG concentration and the choice of the promoters according to their strength. The model was created mainly by designing ODEs and enzyme kinetics equations.

In our circuit, Mazf, B. subtilis specific toxic protein producing gene, and LacI genes are transcribed under Pveg, B. subtilis specific constitutive promoter. Antimazf, which produces complementary strand of Mazf mRNA as antisense RNA, is produced under Phyps, which is inhibited by LacI. LacI can form complex with IPTG molecule, in this way it won’t inhibit the  Phyps  promoter and the production of AntiMazf mrna.So, according to IPTG existence in the medium, LacI will form complex with IPTG and cannot inhibit the Phyps promoter and antiMazf mRNA production. If there is antimazf mRNA, the produced Mazf mRNA will form double stranded RNA with antimazf mRNA and will be degraded. Therefore, there won’t be Mazf mRNA to be translated and cells will remain alive with IPTG in the medium.

Mathematical Model:

Differential Equations:

Simulation:

After creating all equations, we expected that IPTG existence in the system will create a quick response to keep cells alive. Because once the production of AntiMazf mRNA will be higher than that of Mazf mRNA, there won’t be any chance of risk for cells according to IPTG concentration. For reverse situation, when there is decreasing amount of IPTG, once the AntiMazf mRNA falls under the concentration of Mazf mRNA, Mazf toxins production rate starts to increase.

 

 

 In these graphs ,it is seen that after certain concentration of IPTG , Mazf production drops to 0 very quickly. Because, after this IPTG concentration, antiMazf mRNA concentration won't permit any Mazf mRNA  to be translated.

 

In graphs, it is clearly seen that with increasing IPTG concentration,Mazf protein's production rate is decreasing, while the AntiMazf mRNA amount is increasing.

When IPTG=0

When IPTG=300

MazF Protein

-MazF mRNA

-AntiMazF
mRNA

When IPTG=600

When IPTG=1000

When IPTG=1200

When IPTG=1270

When IPTG=1275

 

 

 

 

When IPTG=1290

When IPTG=1295

When IPTG=1300

When IPTG=1305

When IPTG=1325

Retrieved from "http://2013.igem.org/Team:METU_Turkey/human-practice.html"