Difference between revisions of "Team:Arizona State/Design"

 
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<h1>Design for New Receivers</h1>
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<h2>Engineering Aims for ASU iGEM 2017 </h2>
  
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During the first steps of the design process, our iGEM team discussed what engineering aims our project wanted to achieve. It was an important first step in determining the goals for our research. We based our engineering aims on Endy's "Foundations for engineering biology," from 2005.
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<li>Extending the natural function spectrum and expression of new genes</li>
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<li>In vitro evolution- biological regulation on a genetic and biochemical level</li>
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<li> Genetic circuit construction for Quorum Sensing</li>
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<li> Creating a quorum sensing system and chassis</li>
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<h1>Design</h1>
 
 
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Design is the first step in the design-build-test cycle in engineering and synthetic biology. Use this page to describe the process that you used in the design of your parts. You should clearly explain the engineering principles used to design your project.
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After determining our engineering goals and aims for this year's competition. Our team needed to do background research into quorum sensing to familiarize ourselves with the terminology going to be used for this competition. In addition to this, our team needed to reaffirm the 2016 ASU iGEM team's data collected from last year before going any further with designing our project. While confirming last year's team data, we discovered a major flaws while running their protocols. These receivers were showed poor expression and only a select few were good enough to characterize. In addition to this, the system these receivers were cloned into did not show a good cloning ratio. In fact, it was very difficult to clone these receivers. After this, we realized we need to re-evaluate these receivers to determine whether it was the system we were cloning them in was bad, or the receivers themselves that needed to be redesigned.  
 
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This page is different to the "Applied Design Award" page. Please see the <a href="https://2017.igem.org/Team:Arizona_State/Applied_Design">Applied Design</a> page for more information on how to compete for that award.
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From this, it was determined that the receivers themselves were bad and needed to be redesigned this year. From this realization, our design process was re-evaluated and is represented in the flow chart below:  
 
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<h2>Receiver Design Flowchart</h2>
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<center><img src="https://static.igem.org/mediawiki/2017/8/87/R_flowchart.PNG" alt="Design Flowchart" style="max-width: 800px; width: 100%"></center>
  
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<h5>What should this page contain?</h5>
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<li>Explanation of the engineering principles your team used in your design</li>
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<li>Discussion of the design iterations your team went through</li>
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<li>Experimental plan to test your designs</li>
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<h2>Receiver Design Flowchart for Cloning</h2>
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<center><img src="https://static.igem.org/mediawiki/2017/e/e4/Gblock_flowchart.PNG" alt="Design Flowchart 2" style="max-width: 900px; width: 100%"></center>
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<center><img src="https://static.igem.org/mediawiki/2017/4/4a/Cloning_process_design.PNG" alt="Design Flowchart 3" style="max-width:900px; width: 100%"></center>
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<h2>Receiver Design</h2>
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<center><img src="https://static.igem.org/mediawiki/2017/9/92/Receiver_design_with_sbol.PNG" alt="Design Flowchart 2" style="max-width: 900px; width: 100%"></center>
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<p> In our receiver design, there a multitude of parts attained that are already Bio-Brick verified. The table below shows the various parts from the BioBrick database used in our design. Promoters, ribosomal binding sites, terminators and green fluorescent protein were chosen. In addition to this information, the reason and description of how each works in our system is described.
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    <th>Receiver Part Names</th>
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    <th>Part Number</th>
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    <th>Description</th>
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    <td> Ribosomal binding site for GFP </td>
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    <td><a href="http://parts.igem.org/Part:BBa_B0032">BBa_B0032</a> </td>
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    <td> Stronger relative strength compared to other Ribosomal Binding Sites</td>
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    <td> Green Fluorescent Protein </td>
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    <td> <a href="http://parts.igem.org/Part:BBa_E0040">BBa_E0040</a>  </td>
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    <td> Green fluorescent protein derived from jellyfish Aequeora victoria wild-type GFP </td>
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    <td> Terminator for Green Fluorescent Protein </td>
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    <td> <a href="http://parts.igem.org/Part:BBa_J61048:Design">BBa_J61048</a> </td>
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    <td> Terminates the expression of GFP</td>
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    <td> Promoter for Receiver Protein </td>
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    <td> <a href="http://parts.igem.org/Part:BBa_J23100">BBa_J23100</a> </td>
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    <td> Stronger promoter relative to the GFP promoter for stronger transcription </td>
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    <td> Ribosomal Binding Site for Receiver Protein </td>
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    <td> <a href="http://parts.igem.org/Part:BBa_B0034">BBa_B0034</a> </td>
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    <td>Ribosomal binding site for receiver protein </td>
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    <td> Terminator for Receiver Protein </td>
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    <td> <a href="http://parts.igem.org/Part:BBa_B0015">BBa_B0015</a> </td>
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    <td> Strong terminator to end transcription of receiver promoter; A combination of RBS BBa_B0010 and BBa_B0012</td>
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  </tr>
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</table>
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<h2>Senders Used in Our System</h2>
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    <th>Sender Part Name</th>
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    <th>Part Number</th>
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    <th>Part Type</th>
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    <td>C12-HSL, N-(2-oxooxolan-3-yl)dodecanamide Sender-AubI </td>
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    <td><a href="http://parts.igem.org/Part:BBa_K2033000">BBa_K2033000</a></td>
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    <td>Sender</td>
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    <td>Isovaleryl-HSL, 3-methyl-N-[(3S)-2-oxooxolan-3-yl]butanamide Sender-BjaI </td>
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    <td><a href="http://parts.igem.org/Part:BBa_K2033002">BBa_K2033002</a></td>
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    <td>Sender</td>
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    <td>3-phenyl-HSL, (3S)-3-[(2-oxo-3-phenylpropyl)amino]oxolan-2-one Sender-BraI </td>
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    <td><a href="http://parts.igem.org/Part:BBa_K2033004">BBa_K2033004</a></td>
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    <td>Sender</td>
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    <td>3OH-7-cis-C14-HSL, (Z)-3-hydroxy-N-[(3S)-2-oxooxolan-3-yl]tetradec-7-enamide Sender-CerI</td>
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    <td><a href="http://parts.igem.org/Part:BBa_K2033006">BBa_K2033006</a></td>
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    <td>Sender</td>
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    <td>C8-HSL, N-[(3S)-2-oxooxolan-3-yl]octanamide Sender*-SinI</td>
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    <td><a href="http://parts.igem.org/Part:BBa_K2033008">BBa_K2033008</a></td>
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    <td>Sender</td>
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</table>
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<h2>2017 New Receiver Systems </h2>
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    <th>Part Name</th>
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    <th>Part Number</th>
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    <th>Part Type</th>
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    <td> TraR </td>
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    <td> <a href="http://parts.igem.org/Part:BBa_K2357028">BBa_K2357028</a> </td>
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    <td>Reciever</td>
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    <td> LasR </td>
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    <td> <a href="http://parts.igem.org/wiki/index.php?title=Part:BBa_K2357000">BBa_K2357000</a> </td>
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    <td>Receiver</td>
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<h5>Inspiration</h5>
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<h2> iGEM F2620 Improvement  </h2>
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<li><a href="https://2016.igem.org/Team:MIT/Experiments/Promoters">2016 MIT</a></li>
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<li><a href="https://2016.igem.org/Team:BostonU/Proof">2016 BostonU</a></li>
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    <th>Part Name</th>
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<li><a href="https://2016.igem.org/Team:NCTU_Formosa/Design">2016 NCTU Formosa</a></li>
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    <th>Part Number</th>
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    <th>Improvement</th>
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    <td> F2620 </td>
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    <td> <a href=" http://parts.igem.org/Part:BBa_F2620:Experience">BBa_F2620</a> </td>
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    <td>Reciever that our team further characterized and improved by running induction plates and various sender AHL experiments. In addition, safety for degrading and disposing. </td>
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<h2>References</h2>
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[1] Endy, Drew. "Foundations for engineering biology." Nature 438.7067 (2005): 449
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<p> [2] “PCR Cycling Parameters—Six Key Considerations for Success.” Thermo Fisher Scientific, Thermo Fisher Scientific. Web. 20 Oct. 2017. </p>
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Latest revision as of 02:44, 2 November 2017

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