Team:TP CC-SanDiego/Project.html

From 2014hs.igem.org

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           <a href="#linkheadertwo">Idea</a>
           <a href="#linkheadertwo">Idea</a>
         <a href="#linkheaderthree">How</a>
         <a href="#linkheaderthree">How</a>
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         <a href="#linkheaderfour">Attributions</a>
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         <a href="#linkheaderfour">Impact</a>
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        <a href="#linkheaderfive">Attributions</a>
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<div id="header-text">
         Background<br />
         Background<br />
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    <span style="font-family: 'Lato'; font-size: 18px;">The Project Background and Explanation</span>
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    <span style="font-family: 'Lato'; font-size: 20px;">The Project Background and Explanation</span>
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       <img src="https://static.igem.org/mediawiki/2014hs/3/36/C1.png" height="150px" /><br />
       <img src="https://static.igem.org/mediawiki/2014hs/3/36/C1.png" height="150px" /><br />
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            AflatoxinB1-Detoxifizyme is produced by <a style="text-decoration:underline; color:white; font-size: 18px; background: none; padding:0px;" href="http://www.ncbi.nlm.nih.gov/pubmed/21239152">Armillariella Tabescens</a> intracellularly. Its gene is analyzed to have no introns and has been recombined into a plasmid <a style="text-decoration:underline; color:white; font-size: 18px; background: none; padding:0px;" href="https://www.legionpatent.com/patents/7695751/">before</a>. Extraction is rather difficult and commercialization has not been able to be done yet.  
+
          <p align="left";>  AflatoxinB1-Detoxifizyme is produced by <a style="text-decoration:underline; color:white; font-size: 20px; background: none; padding:0px;" href="http://www.ncbi.nlm.nih.gov/pubmed/21239152">Armillariella Tabescens</a> intracellularly. Its gene is analyzed to have no introns and has been recombined into a plasmid <a style="text-decoration:underline; color:white; font-size: 20px; background: none; padding:0px;" href="https://www.legionpatent.com/patents/7695751/">before</a>. Extraction is rather difficult and commercialization has not been able to be done yet. </p>
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<div id="second-statistic">
<div id="second-statistic">
       <img src="https://static.igem.org/mediawiki/2014hs/a/a4/C2.png" height="150px" /><br />
       <img src="https://static.igem.org/mediawiki/2014hs/a/a4/C2.png" height="150px" /><br />
-
            Zearalenone Hydorlase is produced by Clonostachys Rosea. Its gene is also analyzed to have no introns and has been recombined into a plasmid <a style="text-decoration:underline; color:white; font-size: 18px; background: none; padding:0px;" href="http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1222652/">before</a>. Similar to ADTZ, commercialization has not been done yet.
+
            <p align="left";> Zearalenone Hydrolase is produced by Clonostachys Rosea. Its gene is also analyzed to have no introns and has been recombined into a plasmid <a style="text-decoration:underline; color:white; font-size: 20px; background: none; padding:0px;" href="http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1222652/">before</a>. Similar to ADTZ, commercialization has not been done yet. </p>
         <div id="third-phase-button"><br /></div>
         <div id="third-phase-button"><br /></div>
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     <div id="third-statistic">
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       <img src="https://static.igem.org/mediawiki/2014hs/5/54/C3.png" height="150px" /><br />
       <img src="https://static.igem.org/mediawiki/2014hs/5/54/C3.png" height="150px" /><br />
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            Natural E. coli secretes various proteins by signal peptides that recognize translocons. We focus on the SEC pathway that lets the protein fold in the periplasm first, as it usually results in more correct folding, correct formation of disulfide bridges, minimizes degradation, and is less likely to result in accumulation.
+
          <p align="left";> Natural E. coli secretes various proteins by signal peptides that recognize translocons. We focus on the SEC pathway that lets the protein fold in the periplasm first, as it usually results in a more accurate folding, correct formation of disulfide bridges, minimizes degradation, and is less likely to result in accumulation. </p>
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<div id="header-text">
<div id="header-text">
         Idea<br />
         Idea<br />
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    <span style="font-family: 'Lato'; font-size: 18px;">E. Coli Capable of Extracelluar Secretion of Mycotoxin Detoxifying Enzymes</span>
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    <span style="font-family: 'Lato'; font-size: 20px;">E. Coli Capable of Extracelluar Secretion of Mycotoxin Detoxifying Enzymes</span>
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<div id="phase-wrapper" style="background:url(https://static.igem.org/mediawiki/2014hs/1/10/3.png); background-size: 100%;">
<div id="phase-wrapper" style="background:url(https://static.igem.org/mediawiki/2014hs/1/10/3.png); background-size: 100%;">
   <div id="third-phase">
   <div id="third-phase">
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     <img src="https://static.igem.org/mediawiki/2014hs/c/c9/Cycle.png" width="800" height="300"/>
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     <img src="https://static.igem.org/mediawiki/2014hs/c/c9/Cycle.png" width="910" height="400"/>
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     <div id="third-text">  <p align="justify"> <br> Our idea is to attach signal peptides to the N-terminus of the detoxifying enzymes. We use <a style="text-decoration:underline; color:white; font-size: 18px; background: none; padding:0px;" href="http://www.signalpeptide.com/index.php?sess=&m=listspdb_bacteria&s=details&id=37&listname="> alpha amylase signal peptides</a> and  
+
     <div id="third-text">  <p align="justify"> Our idea is to attach signal peptides to the N-terminus of the detoxifying enzymes. We used <a style="text-decoration:underline; color:white; font-size: 20px; background: none; padding:0px;" href="http://www.signalpeptide.com/index.php?sess=&m=listspdb_bacteria&s=details&id=37&listname="> alpha amylase signal peptides</a> and  
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   <a style="text-decoration:underline; color:white; font-size: 18px; background: none; padding:0px;" href="http://www.signalpeptide.com/index.php?sess=&m=listspdb_bacteria&s=details&id=34&listname="> beta-lactamase signal peptides</a>. The original proteins for these signal peptides are <br><br><br><br> secreted out naturally by E. Coli, especially in strain K that we use for our project. They both follow sec-dependent pathways. In the case of beta-lactamase signal protein, cases have been shown of successful fusion proteins <br><br><br><br> <a style="text-decoration:underline; color:white; font-size: 18px; background: none; padding:0px;" href="http://www.ncbi.nlm.nih.gov/pubmed/6607473">secreted</a> by the beta-lactamase signal protein. Successful continual excretion of the mycotoxin degradation enzymes can be purified in mass amounts periodically, or the chimeric E. Coli can be placed directly on<br> <br><br><br>crops to prevent and combat mycotoxin exposure. Since there is no cure to mycotoxin exposure, enhanced prevention with successful secretion will be very influential. </p></div>   
+
   <a style="text-decoration:underline; color:white; font-size: 20px; background: none; padding:0px;" href="http://www.signalpeptide.com/index.php?sess=&m=listspdb_bacteria&s=details&id=34&listname="> beta-lactamase signal peptides</a>. The original proteins for these signal peptides are <br><br><br><br> secreted out naturally by E. Coli, especially in strain K that we used for our project. They both follow sec-dependent pathways. In the case of the beta-lactamase signal protein, cases of successful fusion proteins <a style="text-decoration:underline; color:white; font-size: 20px; background: none; padding:0px;" href="http://www.ncbi.nlm.nih.gov/pubmed/6607473">secreted</a> by the <br><br><br><br>beta-lactamase signal protein have been shown. Successful continual excretion of the mycotoxin degradation enzymes can be purified in mass amounts periodically, or the chimeric E. Coli can be placed directly on<br> <br><br><br>crops to prevent and combat mycotoxin exposure. Since there is no current cure to mycotoxin exposure, enhanced prevention with successful secretion will be very influential. </p></div>   
</div>
</div>
</div>
</div>
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<div id="header-text">
<div id="header-text">
         How<br />
         How<br />
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    <span style="font-family: 'Lato'; font-size: 18px;">The Process to Complete our Project</span>
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    <span style="font-family: 'Lato'; font-size: 20px;">The Process to Complete our Project</span>
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</div>
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<center>
<center>
         <iframe src="https://docs.google.com/document/d/1YebeCoK3eFT1LV-yTfUTqpbnhUsvMEaWs1kHNCbA5RA/pub?embedded=true"embedded=true" style="border-top: none; border-bottom: none; border-left: 1px solid black; border-right: 1px solid black; width: 800px; height: 300px; padding-top: 5px;"></iframe></center>
         <iframe src="https://docs.google.com/document/d/1YebeCoK3eFT1LV-yTfUTqpbnhUsvMEaWs1kHNCbA5RA/pub?embedded=true"embedded=true" style="border-top: none; border-bottom: none; border-left: 1px solid black; border-right: 1px solid black; width: 800px; height: 300px; padding-top: 5px;"></iframe></center>
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  <div id="third-text"><p align="justify">  
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  <div id="third-text"><p align="justify"> In order to achieve our goal, we modified our vector and synthesized genes with reverse PCR and primers with specific tails. After the parts were assembled by <a style="text-decoration:underline; color:white; font-size: 20px; background: none; padding:0px;" href="https://2014hs.igem.org/Team:TP_CC-SanDiego/Journal.html#linkheaderthree">Seamless Cloning</a>. The parts were transformed in an LB+Amp agar plate, and colony PCR was performed for an initial verification step. After the initial verification, the plasmids were purified from the colonies that were declared positive and compared to the theoretical sequences. The final colonies were then grown, and each culture was separated into two categories - IPTG induced, and non-induced. During the log-phase, induced and non-induced cultures were then separated into cell pellets and supernatant. SDS-PAGE gels were run for each induced pellet, non-induced pellet, induced supernatant, and non-induced supernatant for comparison. Induced and non-induced were compared to verify the functionality of the vector, and the pellets and supernatants were compared for excretion. The whole expression and secretion were verified by Western Blotting with anti-his antibodies. </p></div>
-
In order to achieve our goal, we modified our vector and synthesized genes with reverse PCR and primers with specific tails. After the parts were assembled by Seamless Cloning (Link to the Protocol page of our wiki). The parts were transformed in an LB+Amp agar plate, and colony PCR was performed for an initial verification step. After the initial verification, the plasmids were purified from the colonies that were declared positive and compared to the theoretical sequences. The final colonies were then grown, and each culture was separated into two - IPTG induced, and non-induced. The log-phase, induced and non-induced cultures were then separated into cell pellets and supernatant. SDS-PAGE gels were run for each induced pellet, non-induced pellet, induced supernatant, and non-induced supernatant for comparison. Induced and non-induced were compared to verify the functionality of the vector, and the pellets and supernatant were compared for excretion. The whole expression and secretion were verified by Western Blotting with anti-his antibodies. </p></div>
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     </div>
     </div>
</div>
</div>
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<div id="header-holder">
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<div id="header-text">
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        Impact<br />
 +
    <span style="font-family: 'Lato'; font-size: 20px;">The solution to mycotoxins.</span>
 +
    </div>
 +
</div>
 +
 +
<div id="phase-wrapper" style="background:url(https://static.igem.org/mediawiki/2014hs/1/10/3.png); background-size: 100%;">
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  <div id="third-phase">
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      <img src="https://static.igem.org/mediawiki/2014hs/3/34/Image.png" width="700px" height="350px" /><br />
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<span style="font-family: Lato; font-size: 20px; color: white;">
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<p align="justify">
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<br>
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Currently there is no cure for mycotoxin exposure and the symptoms that follow after, which is predominantly liver cancer. Nor is there an effective way of dealing with the amount of food that is affected annually. Improvements in the storage methods, for example, is ineffective in underprivileged communities and societies, and fungal infection of food is a persistent problem. <br> Therefore, with the improved secretion, there will be an estimated 15-20% gain of crops, industrial and financial gain especially in third world countries, up to 28% less cases of liver cancer due to mycotoxins, and in general, significantly less chronic exposure.
 +
 +
</p>
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</span>
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</div>
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<div id="header-holder">
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<div id="linkheaderfive"></div>
<div id="header-text">
<div id="header-text">
         Attributions<br />
         Attributions<br />
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    <span style="font-family: 'Lato'; font-size: 18px;">Teamwork, education, and assistance </span>
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    <span style="font-family: 'Lato'; font-size: 20px;">Teamwork, education, and assistance </span>
     </div>
     </div>
</div>
</div>
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 +
      
      
<div id="second-phase-wrapper"; style="background:url(https://static.igem.org/mediawiki/2014hs/1/10/3.png);background-size: 100%;">
<div id="second-phase-wrapper"; style="background:url(https://static.igem.org/mediawiki/2014hs/1/10/3.png);background-size: 100%;">
   <div id="second-phase">
   <div id="second-phase">
  <div id="first-statistic">
  <div id="first-statistic">
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       <img src="https://static.igem.org/mediawiki/2014hs/3/31/Tp_cc_sandiego_home_logo.png" width="190px" height="150px" /><br />
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       <img src="https://static.igem.org/mediawiki/2014hs/3/31/Tp_cc_sandiego_home_logo.png" width="170px" height="150px" /><br />
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            The TP_CC-SanDiego iGEM Team came up with the idea during its brainstorming meetings and performed the laboratory work. The team made group decisions about the direction of the project, troubleshooted, and put together the data and presentation.   
+
          <p align="left";>  The TP_CC-SanDiego iGEM Team came up with the idea during its brainstorming meetings and performed the laboratory work. The team made group decisions about the direction of the project, collaboratively troubleshooted, and as a group, put together the data and presentation.  </p>
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<div id="second-statistic">
<div id="second-statistic">
       <img src="https://static.igem.org/mediawiki/2014hs/9/9c/Ucsdlogo.png" width="250px" height="150px" /><br />
       <img src="https://static.igem.org/mediawiki/2014hs/9/9c/Ucsdlogo.png" width="250px" height="150px" /><br />
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             The Simpson Joseph Laboratory of UCSD provided the students with the lab space, equipments and various reagents that allowed the students to perform the web laboratory work. The members of the Joseph Lab gave the team many tips and protocols. The Jeff Hasty Laboratory of UCSD provided the team and others with lectures and past iGEM experiences that helped them greatly.
+
             <p align="left";>The Simpson Joseph Laboratory of UCSD provided the students with the lab space, equipments, and various reagents that allowed the students to perform the wet laboratory work. The members of the Joseph Lab gave the team many tips and protocols. The Jeff Hasty Laboratory of UCSD provided the team and others with lectures and past iGEM experiences that helped them greatly.</p>
         <div id="third-phase-button"><br /></div>
         <div id="third-phase-button"><br /></div>
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     <div id="third-statistic">
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       <img src="https://static.igem.org/mediawiki/2014hs/9/93/Thermo-fisher1.png" height="150px" /><br />
       <img src="https://static.igem.org/mediawiki/2014hs/9/93/Thermo-fisher1.png" height="150px" /><br />
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           Dr. Chang-Ho Baek from Thermo Fisher mentored the team throughout the project, gave them lectures, gave them advice for troubleshooting when there were obstacles. Thermo Fisher provided the team various reagent donations.
+
           <p align="left";>Dr. Chang-Ho Baek from Thermo Fisher mentored the team throughout the project, and gave them lectures and advices for troubleshooting when there were obstacles. Thermo Fisher provided the team with various reagent donations.</p>
    </div>
    </div>
     </div>
     </div>

Latest revision as of 01:49, 1 July 2014

iGEM San Diego - Project

Background
The Project Background and Explanation

AflatoxinB1-Detoxifizyme is produced by Armillariella Tabescens intracellularly. Its gene is analyzed to have no introns and has been recombined into a plasmid before. Extraction is rather difficult and commercialization has not been able to be done yet.


Zearalenone Hydrolase is produced by Clonostachys Rosea. Its gene is also analyzed to have no introns and has been recombined into a plasmid before. Similar to ADTZ, commercialization has not been done yet.



Natural E. coli secretes various proteins by signal peptides that recognize translocons. We focus on the SEC pathway that lets the protein fold in the periplasm first, as it usually results in a more accurate folding, correct formation of disulfide bridges, minimizes degradation, and is less likely to result in accumulation.

Idea
E. Coli Capable of Extracelluar Secretion of Mycotoxin Detoxifying Enzymes

Our idea is to attach signal peptides to the N-terminus of the detoxifying enzymes. We used alpha amylase signal peptides and beta-lactamase signal peptides. The original proteins for these signal peptides are



secreted out naturally by E. Coli, especially in strain K that we used for our project. They both follow sec-dependent pathways. In the case of the beta-lactamase signal protein, cases of successful fusion proteins secreted by the



beta-lactamase signal protein have been shown. Successful continual excretion of the mycotoxin degradation enzymes can be purified in mass amounts periodically, or the chimeric E. Coli can be placed directly on



crops to prevent and combat mycotoxin exposure. Since there is no current cure to mycotoxin exposure, enhanced prevention with successful secretion will be very influential.

How
The Process to Complete our Project

In order to achieve our goal, we modified our vector and synthesized genes with reverse PCR and primers with specific tails. After the parts were assembled by Seamless Cloning. The parts were transformed in an LB+Amp agar plate, and colony PCR was performed for an initial verification step. After the initial verification, the plasmids were purified from the colonies that were declared positive and compared to the theoretical sequences. The final colonies were then grown, and each culture was separated into two categories - IPTG induced, and non-induced. During the log-phase, induced and non-induced cultures were then separated into cell pellets and supernatant. SDS-PAGE gels were run for each induced pellet, non-induced pellet, induced supernatant, and non-induced supernatant for comparison. Induced and non-induced were compared to verify the functionality of the vector, and the pellets and supernatants were compared for excretion. The whole expression and secretion were verified by Western Blotting with anti-his antibodies.

Impact
The solution to mycotoxins.


Currently there is no cure for mycotoxin exposure and the symptoms that follow after, which is predominantly liver cancer. Nor is there an effective way of dealing with the amount of food that is affected annually. Improvements in the storage methods, for example, is ineffective in underprivileged communities and societies, and fungal infection of food is a persistent problem.
Therefore, with the improved secretion, there will be an estimated 15-20% gain of crops, industrial and financial gain especially in third world countries, up to 28% less cases of liver cancer due to mycotoxins, and in general, significantly less chronic exposure.

Attributions
Teamwork, education, and assistance

The TP_CC-SanDiego iGEM Team came up with the idea during its brainstorming meetings and performed the laboratory work. The team made group decisions about the direction of the project, collaboratively troubleshooted, and as a group, put together the data and presentation.


The Simpson Joseph Laboratory of UCSD provided the students with the lab space, equipments, and various reagents that allowed the students to perform the wet laboratory work. The members of the Joseph Lab gave the team many tips and protocols. The Jeff Hasty Laboratory of UCSD provided the team and others with lectures and past iGEM experiences that helped them greatly.



Dr. Chang-Ho Baek from Thermo Fisher mentored the team throughout the project, and gave them lectures and advices for troubleshooting when there were obstacles. Thermo Fisher provided the team with various reagent donations.