Difference between revisions of "Team:Lambert GA"

 
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<a class="drplink" style="transition: color 0.5s ease-in-out;" href="https://2017.igem.org/Team:Lambert_GA/Notebook">Notebook</a>
 
<a class="drplink" style="transition: color 0.5s ease-in-out;" href="https://2017.igem.org/Team:Lambert_GA/Notebook">Notebook</a>
 
       <a class="drplink" style="transition: color 0.5s ease-in-out;" href="https://2017.igem.org/Team:Lambert_GA/InterLab">InterLab</a>
 
       <a class="drplink" style="transition: color 0.5s ease-in-out;" href="https://2017.igem.org/Team:Lambert_GA/InterLab">InterLab</a>
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<a class="drplink" style="transition: color 0.5s ease-in-out;" href="https://2017.igem.org/Team:Lambert_GA/Contribution">Contribution</a>
 
 
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<a class="drplink" style="transition: color 0.5s ease-in-out;" href="https://2017.igem.org/Team:Lambert_GA/Results">Results</a><a class="drplink" style="transition: color 0.5s ease-in-out;" href="https://2017.igem.org/Team:Lambert_GA/Demonstrate">Demonstrate</a>
 
<a class="drplink" style="transition: color 0.5s ease-in-out;" href="https://2017.igem.org/Team:Lambert_GA/Results">Results</a><a class="drplink" style="transition: color 0.5s ease-in-out;" href="https://2017.igem.org/Team:Lambert_GA/Demonstrate">Demonstrate</a>
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<a class="drplink" style="transition: color 0.5s ease-in-out;" href="https://2017.igem.org/Team:Lambert_GA/Attributions">Attributions</a>
 
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<center>  <h2> Characterization of Nonlysosomal Proteolysis </h2></center>
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<center>  <h2 class="maint"> Characterizing Non-Lysosomal Inducible Protein Degradation </h2></center>
  
  
  
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TinselPurple samples under varying levels of IPTG induction in the Chrome-Q base ready for imaging
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In the development of genetic circuits, researchers often face issues with the overlap of protein expression. As a result, the 2017 Lambert iGEM team aimed to develop a clean way to “switch” off protein expression by further characterizing a proteolytic mechanism known as ClpXP. An inducible genetic construct was made to express tsPurple (a chromoprotein) and degrade via ClpXP upon induction of varying levels of IPTG, resulting in correlating amounts of protein degradation. Data was collected on the team’s engineered Chrom-Q, a 3-D printed camera-device that supports a constant light source for centrifuged cells; in turn the data was analyzed using Lambert iGEM's self-constructed software app to determine HSL values. The purpose and goal for this technology was to promote scientific research under any financial circumstance to quantify data in standardized conditions. Measuring relative strengths of protein degradation using self-engineered products will allow an economic approach in characterizing non-lysosomal proteolysis.   
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Scientists around the world struggle with questions regarding chromoprotein expression, specifically in regards to their use in biosensors.  Biosensors are often seen as low-cost alternatives to expensive detection equipment for underfunded labs and field work.  Lambert iGEM was inspired to address the problem of quantifying chromoprotein expression through development of a 3-D printed original device: Chrome-Q, software app, and verification with a chromoprotein genetic circuit. Additionally, samples were prepared with the 3-D Fuge (which was modified from Prakash Lab’s Paperfuge) to investigate the viability of using a low-cost centrifuge to process cells for visualization.<br>
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<p style="font-size: 20px; color: white; text-indent: 50px;">
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Quantifying color relies on measures of Red, Green, Blue (RGB) values and evaluating them in a color space known as Hue, Saturation and Value (HSV). Another consideration for color quantification is standardization of environmental light.  To achieve this a device, the Chrome-Q, was developed to create a standardized environment for capturing images using Android and Apple mobile device cameras.  Self-developed android software evaluates the RGB images resulting in HSV values.  These HSV values can be normalized for cell density through subsequent serial dilutions of the cultures and plating to count Colony Forming Units (CFU).<br><br>
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<img src="https://static.igem.org/mediawiki/2017/c/cb/T--Lambert_GA--HSVModel.png" style="width:400px;">
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<img src="https://static.igem.org/mediawiki/2017/c/c6/T--Lambert_GA--ColonyCountHome.jpeg" style="height:300px;"><br>
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<br>
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<i style="font-size: 14px; color: white;">Left: The HSL (hue, saturation and value) that the Chrome-Q measures
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Right: Chromoproteins under four different levels of IPTG induction plated to determine CFU's
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Throughout the development of the Chrome-Q, engineering design principles were implemented.  Feedback and resulting changes were implemented into the next iteration.  Five different prototypes led to the final development of two designs optimized for both Android and Apple mobile devices.  The Android software was written in C#.  The Chrome-Q stl files and software are available on the hardware page are open source. <br>
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<p style="font-size: 20px; color: white; text-indent: 50px;">The device and software were then used to quantify data of ATUM’s Protein Paintbox proteins TinselPurple, ScroogeOrange and VirginiaViolet under varying levels of IPTG induction. An assembled genetic circuit of: Promoter- R0040, Ribosomal Binding Site B0034, and Tinsel purple (Tspurple)- (BBa_K1033906) (Uppsala 2013) was constructed to use in conjunction with a Protease mechanism of ClpXP. ClpXP is a protein complex comprised of two parts.  ClpX recognizes an SsrA tag sequence at the end of a protein linearizes the tagged protein and brings it to ClpP.  ClpP is an ATPase and cleaves the primary peptide bonds resulting in degradation of the original protein into individual amino acids.  This demonstrated the potential usefulness of the 3-D fuge and Chrome-Q system as a replacement for fluorescent plate readers and centrifuges.<br>
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<img src="https://static.igem.org/mediawiki/2017/5/5e/T--Lambert_GA--PrettyWellPlate3.jpeg" style="width:400px;">
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<i style="font-size: 14px; color: white;"> The full base of the Chrome-Q system with different dilutions of chromoproteins in the well plate
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<h2 style="margin=auto; margin-left=700px; color: black;"> Who We Are </h2><p style=" margin-left=300px; color: black;">  Lorem ipsum dolor sit amet, consectetur adipiscing elit. Duis sed dolor sit amet quam sodales bibendum at ut tellus. Ut quis congue turpis, a semper ex. Praesent laoreet condimentum odio vitae bibendum. Proin rutrum vulputate felis, vitae volutpat nisi scelerisque eget. Aliquam quis urna nisi. Curabitur id consectetur nulla, posuere malesuada orci
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<h2 style="margin-left: -300px; color: #7A7A79;"> Who We Are </h2><p style=" margin-left=300px; color: #7A7A79;">  We are comprised of 14 high school students from Suwanee, Georgia in the 10th, 11th, and 12th grades. We are an after-school/before-school club that meets simply for the love of synthetic biology.
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</p><a style="text-decoration: none;" href="https://2017.igem.org/Team:Lambert_GA/Team"><button class="button button1">Find Out More</button></a>
 
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<div align="right" style="color: white;"><h2> Who We Are </h2></div>
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<div align="right" ><h2 class="smallt" style="color: #FFFFFF; margin-left: -91px;"> Our Project</h2></div>
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<p style=" margin-left=300px;color: white;"> As an underfunded lab, our project aimed to reduce costs of lab work. While characterizing non-lysosomal inducible protein degradation, we developed the Chrome-Q to quantify the degradation of protein.
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</p><a style="text-decoration: none;" href="https://2017.igem.org/Team:Lambert_GA/Description"><button class="button button2">Find Out More</button></a><br><br><br><br><br></div>
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<h2 style="margin=auto; margin-left=700px; color: #7A7A79;"> Human Practices </h2><p style=" margin-left=300px; color: #7A7A79;">  This past year, we have performed a variety of human practices, to educate the public about synthetic biology, as well as our project, through multiple outreach events.
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</p><a style="text-decoration: none;" href="https://2017.igem.org/Team:Lambert_GA/HP/Silver"><button class="button button1">Find Out More</button></a>
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<h2 style="color:#F19B45;"> Bronze </h2>
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    <th width="20%">Requirements</th>
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    <td>Register and Attend</td>
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    <td><img src="https://static.igem.org/mediawiki/2017/c/c6/Lambertigemcheckmarkgray.png" style="width:45px;"></td>
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    <td>Yes</td>
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    <td>Deliverable</td>
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    <td><img src="https://static.igem.org/mediawiki/2017/b/bb/Lambertigemcheckmark.jpg" style="width:45px;"></td>
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    <td>Yes</td>
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    <td>Attributions</td>
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    <td><img src="https://static.igem.org/mediawiki/2017/c/c6/Lambertigemcheckmarkgray.png" style="width:45px;"></td>
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    <td>Yes, click <a href="https://2017.igem.org/Team:Lambert_GA/Attributions">HERE</a> for more information.</td>
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    <td>Interlab Study</td>
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    <td><img src="https://static.igem.org/mediawiki/2017/b/bb/Lambertigemcheckmark.jpg" style="width:45px;"></td>
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    <td>Yes, click <a href="https://2017.igem.org/Team:Lambert_GA/InterLab">HERE</a> for more information.</td>
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<h2 style="color:#c0c0c0;"> Silver </h2>
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    <th width="20%">Requirements</th>
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    <td>Validated Part</td>
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    <td><img src="https://static.igem.org/mediawiki/2017/c/c6/Lambertigemcheckmarkgray.png" style="width:45px;"></td>
 +
    <td>TsPurple and TsPurple with LAA degradation tag. <br> Click <a href="https://2017.igem.org/Team:Lambert_GA/Part_Collection">
 +
HERE</a> for more information regarding Lambert iGEM's parts.</td>
 +
  </tr>
 +
  <tr>
 +
    <td>Collaboration</td>
 +
    <td><img src="https://static.igem.org/mediawiki/2017/b/bb/Lambertigemcheckmark.jpg" style="width:45px;"></td>
 +
    <td>Emory iGEM, UGA iGEM and TAS Taipei iGEM. <br> Click <a href="https://2017.igem.org/Team:Lambert_GA/Collaborations">HERE</a>
 +
for more information regarding Lambert iGEM's collaborations with other teams.</td>
 +
  </tr>
 +
  <tr>
 +
    <td>Human Practices</td>
 +
    <td><img src="https://static.igem.org/mediawiki/2017/c/c6/Lambertigemcheckmarkgray.png" style="width:45px;"></td>
 +
    <td>Open House, Maker Faire, Survey, Ethics conferences. <br> Click <a href="https://2017.igem.org/Team:Lambert_GA/HP/Silver">HERE</a> for more information on Lambert iGEM's human practices.</td>
 +
  </tr>
 +
</table>
 +
</center>
 +
 
 +
<br><br>
 +
<h2 style="color:#FFD700;"> Gold </h2>
 +
<br>
 +
<center>
 +
<table>
 +
  <tr>
 +
    <th width="20%">Requirements</th>
 +
    <th width="20%">Checklist</th>
 +
    <th width="60%">Explanation</th>
 +
  </tr>
 +
  <tr>
 +
    <td>Integrated Human Practices</td>
 +
    <td><img src="https://static.igem.org/mediawiki/2017/c/c6/Lambertigemcheckmarkgray.png" style="width:45px;"></td>
 +
    <td><ul><li>Developed low cost solution for quantifying chromoprotein data </li>
 +
<li> Developed protocols to use a 3-D printed centrifuge for processing cells </li>
 +
<li> Gave feedback on 3-D fuge to Dr. Saad Bhamla of Georgia Institute of technology and Prakash Lab of Stanford. </li>
 +
<li> Donated blankets and supplies to impoverished families in Lambert iGEM's surrounding area. </li></ul>
 +
Click <a href="https://2017.igem.org/Team:Lambert_GA/HP/Gold_Integrated">HERE</a> for more information on Lambert iGEM's integrated human practices.
 +
</td>
 +
  </tr>
 +
  <tr>
 +
    <td>Improve BioBrick Part</td>
 +
    <td><img src="https://static.igem.org/mediawiki/2017/b/bb/Lambertigemcheckmark.jpg" style="width:45px;"></td>
 +
    <td>The part this year's team improved upon is: <a href="http://parts.igem.org/Part:BBa_K1911001">BBa_K1911001</a> created by last year's Lambert iGEM team. The updated part this year is: <a href="http://parts.igem.org/wiki/index.php/Part:BBa_K1911001" style="color:#D49AE6;"> BBa_KK1911001: pLac-ClpXP-CI</a>, as we improved the characterization of last year's part. <br>
 +
Click <a href="https://2017.igem.org/Team:Lambert_GA/Updated_Part">HERE</a> for more information on Lambert iGEM's BioBrick Improvement of their project.
 +
</td>
 +
  </tr>
 +
<tr>
 +
    <td>Model</td>
 +
    <td><img src="https://static.igem.org/mediawiki/2017/c/c6/Lambertigemcheckmarkgray.png" style="width:45px;"></td>
 +
    <td><ul><li>Developed a working Chrome-Q and software app to quantify chromoprotein data</li>
 +
<li> Used a 3-D printed centrifuge to process cells and demonstrate viability in field work and underfunded labs.</li>
 +
<li> Developed designs for printing Chrome-Q device for both Android and Apple mobile devices.</li>
 +
<li> Developed protocols for obtaining and normalizing data.</li>
 +
<li> Developed protocols for sterilizing the Chrome-Q, base and 3-D fuge.</li></ul>
 +
Click <a href="https://2017.igem.org/Team:Lambert_GA/Model">HERE</a> for more information on Lambert iGEM's model in their project.
 +
</td>
 +
  </tr>
 +
<tr>
 +
    <td>Demonstration of Work</td>
 +
    <td><img src="https://static.igem.org/mediawiki/2017/b/bb/Lambertigemcheckmark.jpg" style="width:45px;"></td>
 +
    <td><ul><li>Developed a working Chrome-Q to quantify chromoprotein data in inducible genetic circuits.</li>
 +
<li> Developed a protocol in order to test construct at varying levels of IPTG and quantify data. </li>
 +
<li> Developed a software app to accurately analyze chromoprotein data from Chrome-Q.
 +
</ul>
 +
Click <a href="https://2017.igem.org/Team:Lambert_GA/Demonstrate">HERE</a> for information on Lambert iGEM's demonstration of their project.
 +
 
 +
<h2 class="smallt" style="color: #FFFFFF;"> Medal Criteria</h2>
 +
 
 +
</td>
 +
  </tr>
 +
</table>
 +
</center>
 +
<br><br><br>
 +
<h2 class="smallt" style="color: #FFFFFF;"> Award</h2>
 +
<br><br>
 +
<center>
 +
<img src="https://static.igem.org/mediawiki/2017/f/f2/Bronze.png"style="width:10%">
 +
<br><br><br>
 +
<p style="color:white"> Bronze Medal</p>
 +
</center>
 +
</div>
  
  
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+
<div class="button_click" style="background-color: #7A7A79" onClick=" parent.location= 'https://2017.igem.org/Special:Upload '">
  
 
<!--<h2>2015 Lambert iGEM</h2>-->
 
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Latest revision as of 01:21, 14 December 2017



Characterizing Non-Lysosomal Inducible Protein Degradation




TinselPurple samples under varying levels of IPTG induction in the Chrome-Q base ready for imaging


Scientists around the world struggle with questions regarding chromoprotein expression, specifically in regards to their use in biosensors. Biosensors are often seen as low-cost alternatives to expensive detection equipment for underfunded labs and field work. Lambert iGEM was inspired to address the problem of quantifying chromoprotein expression through development of a 3-D printed original device: Chrome-Q, software app, and verification with a chromoprotein genetic circuit. Additionally, samples were prepared with the 3-D Fuge (which was modified from Prakash Lab’s Paperfuge) to investigate the viability of using a low-cost centrifuge to process cells for visualization.

Quantifying color relies on measures of Red, Green, Blue (RGB) values and evaluating them in a color space known as Hue, Saturation and Value (HSV). Another consideration for color quantification is standardization of environmental light. To achieve this a device, the Chrome-Q, was developed to create a standardized environment for capturing images using Android and Apple mobile device cameras. Self-developed android software evaluates the RGB images resulting in HSV values. These HSV values can be normalized for cell density through subsequent serial dilutions of the cultures and plating to count Colony Forming Units (CFU).



Left: The HSL (hue, saturation and value) that the Chrome-Q measures
Right: Chromoproteins under four different levels of IPTG induction plated to determine CFU's

Throughout the development of the Chrome-Q, engineering design principles were implemented. Feedback and resulting changes were implemented into the next iteration. Five different prototypes led to the final development of two designs optimized for both Android and Apple mobile devices. The Android software was written in C#. The Chrome-Q stl files and software are available on the hardware page are open source.

The device and software were then used to quantify data of ATUM’s Protein Paintbox proteins TinselPurple, ScroogeOrange and VirginiaViolet under varying levels of IPTG induction. An assembled genetic circuit of: Promoter- R0040, Ribosomal Binding Site B0034, and Tinsel purple (Tspurple)- (BBa_K1033906) (Uppsala 2013) was constructed to use in conjunction with a Protease mechanism of ClpXP. ClpXP is a protein complex comprised of two parts. ClpX recognizes an SsrA tag sequence at the end of a protein linearizes the tagged protein and brings it to ClpP. ClpP is an ATPase and cleaves the primary peptide bonds resulting in degradation of the original protein into individual amino acids. This demonstrated the potential usefulness of the 3-D fuge and Chrome-Q system as a replacement for fluorescent plate readers and centrifuges.


The full base of the Chrome-Q system with different dilutions of chromoproteins in the well plate





Who We Are

We are comprised of 14 high school students from Suwanee, Georgia in the 10th, 11th, and 12th grades. We are an after-school/before-school club that meets simply for the love of synthetic biology.






Our Project

As an underfunded lab, our project aimed to reduce costs of lab work. While characterizing non-lysosomal inducible protein degradation, we developed the Chrome-Q to quantify the degradation of protein.








Human Practices

This past year, we have performed a variety of human practices, to educate the public about synthetic biology, as well as our project, through multiple outreach events.








Bronze


Requirements Checklist Explanation
Register and Attend Yes
Deliverable Yes
Attributions Yes, click HERE for more information.
Interlab Study Yes, click HERE for more information.


Silver


Requirements Checklist Explanation
Validated Part TsPurple and TsPurple with LAA degradation tag.
Click HERE for more information regarding Lambert iGEM's parts.
Collaboration Emory iGEM, UGA iGEM and TAS Taipei iGEM.
Click HERE for more information regarding Lambert iGEM's collaborations with other teams.
Human Practices Open House, Maker Faire, Survey, Ethics conferences.
Click HERE for more information on Lambert iGEM's human practices.


Gold


Requirements Checklist Explanation
Integrated Human Practices
  • Developed low cost solution for quantifying chromoprotein data
  • Developed protocols to use a 3-D printed centrifuge for processing cells
  • Gave feedback on 3-D fuge to Dr. Saad Bhamla of Georgia Institute of technology and Prakash Lab of Stanford.
  • Donated blankets and supplies to impoverished families in Lambert iGEM's surrounding area.
Click HERE for more information on Lambert iGEM's integrated human practices.
Improve BioBrick Part The part this year's team improved upon is: BBa_K1911001 created by last year's Lambert iGEM team. The updated part this year is: BBa_KK1911001: pLac-ClpXP-CI, as we improved the characterization of last year's part.
Click HERE for more information on Lambert iGEM's BioBrick Improvement of their project.
Model
  • Developed a working Chrome-Q and software app to quantify chromoprotein data
  • Used a 3-D printed centrifuge to process cells and demonstrate viability in field work and underfunded labs.
  • Developed designs for printing Chrome-Q device for both Android and Apple mobile devices.
  • Developed protocols for obtaining and normalizing data.
  • Developed protocols for sterilizing the Chrome-Q, base and 3-D fuge.
Click HERE for more information on Lambert iGEM's model in their project.
Demonstration of Work
  • Developed a working Chrome-Q to quantify chromoprotein data in inducible genetic circuits.
  • Developed a protocol in order to test construct at varying levels of IPTG and quantify data.
  • Developed a software app to accurately analyze chromoprotein data from Chrome-Q.
Click HERE for information on Lambert iGEM's demonstration of their project.

Medal Criteria



Award






Bronze Medal