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

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.

Extending the natural function spectrum and expression of new genes
In vitro evolution- biological regulation on a genetic and biochemical level
Genetic circuit construction for Quorum Sensing
Creating a quorum sensing system and chassis

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 flaw in their design process of the receivers. 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.

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:

Receiver Design Flowchart

Receiver Design Flowchart for Cloning

Receiver Design

Describe what each of the bio-bricks used during the design. In addition, tell the bio-brick parts of the senders use. Also the picture of the sender vector. Modular center vector on benchling.

Receiver Part Names	Part Number	Description
Inducible Promoter
Ribosomal binding site for GFP	RBS_BBa0032
Green Fluorescent Protein	BBa_E0040
Terminator for Green Fluorescent Protein	BBa_J61048
Promoter for Receiver Protein	BBa_J23100
Ribosomal Binding Site for Receiver Protein	BBa_B0034
Receiver Protein
Terminator for Receiver Protein	BBa_B0015

Sender Part Name	Part Number	Part Type
C12-HSL, N-(2-oxooxolan-3-yl)dodecanamide Sender-AubI	BBa_K2033000	Sender
Isovaleryl-HSL, 3-methyl-N-[(3S)-2-oxooxolan-3-yl]butanamide Sender-BjaI	BBa_K2033002	Sender
3-phenyl-HSL, (3S)-3-[(2-oxo-3-phenylpropyl)amino]oxolan-2-one Sender-BraI	BBa_K2033004	Sender
3OH-7-cis-C14-HSL, (Z)-3-hydroxy-N-[(3S)-2-oxooxolan-3-yl]tetradec-7-enamide Sender-CerI	BBa_K2033006	Sender
C8-HSL, N-[(3S)-2-oxooxolan-3-yl]octanamide Sender*-SinI	BBa_K2033008	Sender

References

[1] Endy, Drew. "Foundations for engineering biology." Nature 438.7067 (2005): 449

@@ Line 70: / Line 70: @@
    <tr>
      <td> Inducible Promoter </td>
-     <td> GFP_BBaE0040 </td>
+     <td>  </td>
      <td> </td>
    </tr>
@@ Line 80: / Line 80: @@
    <tr>
      <td> Green Fluorescent Protein </td>
-     <td>  </td>
+     <td> BBa_E0040  </td>
      <td> </td>
    </tr>
@@ Line 90: / Line 90: @@
    <tr>
      <td> Promoter for Receiver Protein </td>
-     <td>  </td>
+     <td> BBa_J23100 </td>
      <td> </td>
    </tr>
    <tr>
      <td> Ribosomal Binding Site for Receiver Protein </td>
-     <td>  </td>
+     <td> BBa_B0034 </td>
      <td> </td>
    </tr>
@@ Line 105: / Line 105: @@
    <tr>
      <td> Terminator for Receiver Protein </td>
-     <td>  </td>
+     <td> BBa_B0015 </td>
      <td> </td>
    </tr>