Team:METU Turkey modeling

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<a href="https://2014.igem.org/Team:METU_Turkey_modeling" style="text-decoration:none;color:#1C140D">MODELING </a> </td>
<a href="https://2014.igem.org/Team:METU_Turkey_modeling" style="text-decoration:none;color:#1C140D">MODELING </a> </td>
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<a href="https://2014.igem.org/Team:METU_Turkey_interlabstudy" style="text-decoration:none;color:#1C140D">INTERLAB STUDY </a></td>
<a href="https://2014.igem.org/Team:METU_Turkey_interlabstudy" style="text-decoration:none;color:#1C140D">INTERLAB STUDY </a></td>
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<a href="https://2014.igem.org/Team:METU_Turkey_attributions" style="text-decoration:none;color:#1C140D">ATTRIBUTIONS </a></td>
<a href="https://2014.igem.org/Team:METU_Turkey_attributions" style="text-decoration:none;color:#1C140D">ATTRIBUTIONS </a></td>
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<a href="https://2014.igem.org/Team:METU_Turkey_gallery" style="text-decoration:none;color:#1C140D">GALLERY </a></td>
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<a href="https://2014.igem.org/Team:METU_Turkey_protocols" style="text-decoration:none;color:#1C140D">PROTOCOLS </a></td>
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<a href="http://www.metuigem.com"color:#FFFFFF">
 
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<h3>Welcome!  <br> We are Team METU Turkey! </h3>
 
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<p>Scroll down to find more about our project! </p>
 
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<a class="twitter-timeline" href="https://twitter.com/iGEM_METU2014" data-widget-id="499378473245229057">@iGEM_METU2014 kullanıcısından Tweetler</a>
 
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<h3> Our Project's Model </h3>
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<h3>Degredo PETronum!</h3>
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<p> This graph shows us that E.coli during adding catechol to media, diffuses quickly because of the high diffusion rate. Therefore you can see catechol concentration inintiates with a high value. Then our bacteria degrade catechol to 2-hydoxymuconate semialdehyde then it degrades to 2-oxopent 4-enoate then continues to 4-hydroxy 2-oxopentoonate, finally we get our last degraded product of pyruvate. Our paramaeters of this cycle shows us that. While our bacteria diffuses catechol in its cytosol, its enzymes starts to degrade catechol fast to obtain pyruvate.     </p>
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<p> ABSTRACT</p>
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<p> The usage of polyethylene  terephthalate-PET (as like plastic bottles or textiles)  is one of the big problems of our era. Many plastic bottles are not reusable and are not safe for hot liquids or for use in dishwashers or microwaves. Some tougher, reusable plastic bottles may cause cancer. The main disadvantage of plastic bottles is that so many of them end up in landfills instead of being recycled. It takes thousands of years for plastic bottles to biodegrade, and the degrading process emits toxic chemicals into the air.
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We may alter the destiny of plastic in useful way.</p>
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<p> OUR MISSION</p>
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<p> Our project aims to clean enviroment with the degredation of PET to pyruvate by E.coli. With this project,while  the environment will be cleaned from PET, the E.coli would add pyruvate to the cell cycle and use it as a new source.
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We divide our project into two parts. At the first part we found gene design for converting the PET into 2-hydroxymuconate semialdehyde in iGEM database. The arrangement at the bottom explains the first part:</p>
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<p> At the second part, we wanted to go further and researched the gene parts for convertion of 2-hydroxymuconate semialdehyde into pyruvate. This part will give us the chance of adding new parts to iGEM database. In this arrangement, it can be observed in detail:</p>
 
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<img src="https://static.igem.org/mediawiki/2014/4/42/Maindenklem.PNG">
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<h3>SimBiology Results of our Kill-Switch Model:</h3>
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<h3>Interpretation of Kill-Switch:</h3>
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<h3> How does our project work?</h3>
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<p>Arabinose Promoter: (K808000) is activated when arabinose is present.</p>
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<p> Totally degradation of PET to pyruvate is done by E. coli. </p>
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<p>Antiholin: (K515004) is specific negative regulator of holin function.</p>
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<p>TetR+LVA: (C0040) tetracycline repressor modified with LVA tail for rapid degradation of the protein and faster fall time for the emission.</p>
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<p>TetR Promoter: (R0040) TetR repressible promoter.</p>
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<p>T4 Endolysin: (K112806) degrades peptiodoglycan layer.</p>
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<p>Holin: (K124014) protein causes pores in the inner membrane, which allows lysozyme to access and brakedown the peptidoglycan of the cell wall, causing lysis and death.</p>
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<h3>First Graph:</h3>
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<p>When arabinose is present TetR+LVA and Anti-Holin are produced, TetR+LVA suppress the production of Holin and Endolysin by binding with TetR Promoter.</p>
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<img src="https://static.igem.org/mediawiki/2014/e/ea/Grafik2.jpg">
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<h3>Second Graph:</h3>
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<p>When arabinose is absent, TetR+LVA is not produced so TetR Promoter does not suppress producing of Holin and T4 Endolysin. Therefore, Holin protein causes pores and T4 endolysin degrades peptidoglycan layer and cell dies. If the promoter and RBS are strengthened the kill-switch circuit will be more effective. </p>
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<h3> Who will our project help?</h3>
 
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<p> Our project will help the environment to become cleaner.</p>
 
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<h3>Why did we choose this project?</h3>
 
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<p> The biodegradation of plastic bottles took thousands of years, and the degrading process emits toxic chemicals into the air. Our project aims to clean enviroment with the degredation of PET to pyruvate by E.coli. With this project,while  the environment will be cleaned from PET, the E.coli would add pyruvate to the cell cycle and use it as a new source. </p>
 
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Latest revision as of 01:02, 18 October 2014

Team:METU Turkey/Templates/Navigationbar

HOME TEAM PROJECT PARTS MODELING INTERLAB STUDY
POLICY&PRACTICE CHARACTERIZATION SAFETY ATTRIBUTIONS GALLERY PROTOCOLS

Our Project's Model

This graph shows us that E.coli during adding catechol to media, diffuses quickly because of the high diffusion rate. Therefore you can see catechol concentration inintiates with a high value. Then our bacteria degrade catechol to 2-hydoxymuconate semialdehyde then it degrades to 2-oxopent 4-enoate then continues to 4-hydroxy 2-oxopentoonate, finally we get our last degraded product of pyruvate. Our paramaeters of this cycle shows us that. While our bacteria diffuses catechol in its cytosol, its enzymes starts to degrade catechol fast to obtain pyruvate.

SimBiology Results of our Kill-Switch Model:

Interpretation of Kill-Switch:

Arabinose Promoter: (K808000) is activated when arabinose is present.

Antiholin: (K515004) is specific negative regulator of holin function.

TetR+LVA: (C0040) tetracycline repressor modified with LVA tail for rapid degradation of the protein and faster fall time for the emission.

TetR Promoter: (R0040) TetR repressible promoter.

T4 Endolysin: (K112806) degrades peptiodoglycan layer.

Holin: (K124014) protein causes pores in the inner membrane, which allows lysozyme to access and brakedown the peptidoglycan of the cell wall, causing lysis and death.

First Graph:

When arabinose is present TetR+LVA and Anti-Holin are produced, TetR+LVA suppress the production of Holin and Endolysin by binding with TetR Promoter.

Second Graph:

When arabinose is absent, TetR+LVA is not produced so TetR Promoter does not suppress producing of Holin and T4 Endolysin. Therefore, Holin protein causes pores and T4 endolysin degrades peptidoglycan layer and cell dies. If the promoter and RBS are strengthened the kill-switch circuit will be more effective.

Our Supporter:

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