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

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<p>The part Bba_F2620 (found <a href="http://parts.igem.org/Part:BBa_F2620">here</a>), designed by Barry Canton and Anna Labno from MIT, is a device designed to output PoPs when LuxR is activated. This was used to test interactions between inducers from other quorum sensing systems. The Aub, Bja, Bra, Cer, and Sin systems stem from various organisms and their inducers were submitted as parts to the registry with the purpose of completing this induction test. </p>
 
<p>The part Bba_F2620 (found <a href="http://parts.igem.org/Part:BBa_F2620">here</a>), designed by Barry Canton and Anna Labno from MIT, is a device designed to output PoPs when LuxR is activated. This was used to test interactions between inducers from other quorum sensing systems. The Aub, Bja, Bra, Cer, and Sin systems stem from various organisms and their inducers were submitted as parts to the registry with the purpose of completing this induction test. </p>
 
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<h2>N-Acyl Homoserine Lactones</h2>
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<p>AHL quorum sensing has a myriad of different systems. A total of 10 systems were investigated in this project </p>
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<table style="width:100%">
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  <tr>
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    <th>AHL System</th>
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    <th>Bacteria of Origin</th>
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    <th>AHL Name</th>
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    <th>3D-Model</th>
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  </tr>
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  <tr>
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    <td>Aub</td>
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    <td>Unknown</td>
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    <td>N-(2-oxooxolan-3-yl)dodecanamide</td>
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<td><img src="https://static.igem.org/mediawiki/2016/3/38/T--Arizona_State--aubhsl3d.png" height=150px></td>
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  </tr>
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  <tr>
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    <td>Bja</td>
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    <td>Bradyrhizobium japonicum</td>
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    <td>3-methyl-N-[(3S)-2-oxooxolan-3-yl]butanamide</td>
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<td><img src="https://static.igem.org/mediawiki/2016/b/b0/T--Arizona_State--bjahsl3d.png" height=150px></td>
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  </tr>
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  <tr>
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    <td>Bra</td>
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    <td>Paraburkholderia kururiensis</td>
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    <td>(3S)-3-[(2-oxo-3-phenylpropyl)amino]oxolan-2-one</td>
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<td><img src="https://static.igem.org/mediawiki/2016/4/42/T--Arizona_State--brahsl3d.png" height=150px></td>
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  </tr>
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  <tr>
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    <td>Cer</td>
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    <td>Rhodobacter sphaeroides</td>
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    <td>(Z)-3-hydroxy-N-[(3S)-2-oxooxolan-3-yl]tetradec-7-enamide</td>
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<td><img src="https://static.igem.org/mediawiki/2016/6/6d/T--Arizona_State--cerhsl3d.png" height=150px></td>
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  </tr>
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  <tr>
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    <td>Esa</td>
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    <td>Erwinia stewartii</td>
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    <td>3-oxo-N-[(3S)-2-oxooxolan-3-yl]hexanamide</td>
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<td><img src="https://static.igem.org/mediawiki/2016/c/c5/T--Arizona_State--esahsl3d.png" height=150px></td>
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  </tr>
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  <tr>
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    <td>Las</td>
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    <td>Pseudomonas aeruginosa</td>
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    <td>3-oxo-N-(2-oxooxolan-3-yl)dodecanamide</td>
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<td><img src="https://static.igem.org/mediawiki/2016/e/ef/T--Arizona_State--lashsl3d.png" height=150px></td>
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  </tr>
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  <tr>
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    <td>Lux</td>
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    <td>Vibrio fischeri</td>
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    <td>3-oxo-N-(2-oxooxolan-3-yl)hexanamide</td>
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<td><img src="https://static.igem.org/mediawiki/2016/2/28/T--Arizona_State--rhlhsl3d.png" height=150px></td>
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  </tr>
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  <tr>
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    <td>Rhl</td>
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    <td>Rhizobium leguminosarum</td>
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    <td>N-(2-oxooxolan-3-yl)butanamide</td>
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<td><img src="https://static.igem.org/mediawiki/2016/2/28/T--Arizona_State--rhlhsl3d.png" height=150px></td>
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  </tr>
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  <tr>
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    <td>Rpa</td>
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    <td>Rhodopseudomonas palustris</td>
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    <td>(S)-(−)α-amino-γ-butyrolactone</td>
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<td><img src="https://static.igem.org/mediawiki/2016/0/08/T--Arizona_State--rpahsl3d.png" height=150px></td>
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  </tr>
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  <tr>
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    <td>Sin</td>
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    <td>Sinorhizobium meliloti</td>
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    <td>N-[(3S)-2-oxooxolan-3-yl]octanamide*</td>
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<td><img src="https://static.igem.org/mediawiki/2016/6/6d/T--Arizona_State--sin2hsl3d.png" height=150px></td>
 +
  </tr>
 +
</table> 
 +
<p>*Sin system produces 6 different variants of AHL. The 3D structures of all the Sin compounds can be found <a href="https://www.dropbox.com/sh/cfo744xq81t6iu4/AAAAG8yiFkHfnUojBZE7bWKla?dl=0">here</a>.</p>
 +
<p>All systems were investigated in an inductions investigation. The part BBa_F2620 was used to induce production in the Lux AHL system and test induction in any other AHL systems. Should induction occur, then possible interference between systems are conceivable, which may have implications towards any use of that system. The resulting part collection allows direct comparison in AHL induction between multiple systems. </p>
 
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<h5>Note</h5>
 
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<p>Note that parts must be documented on the <a href="http://parts.igem.org/Main_Page"> Registry</a>. This page serves to <i>showcase</i> the parts you have made. Future teams and other users and are much more likely to find parts by looking in the Registry than by looking at your team wiki.</p>
 
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<h5>Adding parts to the registry</h5>
 
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<p>You can add parts to the Registry at our <a href="http://parts.igem.org/Add_a_Part_to_the_Registry">Add a Part to the Registry</a> link.</p>
 
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<p>We encourage teams to start completing documentation for their parts on the Registry as soon as you have it available. The sooner you put up your parts, the better you will remember all the details about your parts. Remember, you don't need to send us the DNA sample before you create an entry for a part on the Registry. (However, you <b>do</b> need to send us the DNA sample before the Jamboree. If you don't send us a DNA sample of a part, that part will not be eligible for awards and medal criteria.)</p>
 
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<h5>What information do I need to start putting my parts on the Registry?</h5>
 
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<p>The information needed to initially create a part on the Registry is:</p>
 
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<li>Creator</li>
 
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<li>Sequence</li>
 
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<li>Short Description (60 characters on what the DNA does)</li>
 
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<li>Design considerations</li>
 
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We encourage you to put up <em>much more</em> information as you gather it over the summer. If you have images, plots, characterization data and other information, please also put it up on the part page. </p>
 
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<p>We have a created  a <a href="http://parts.igem.org/Well_Documented_Parts">collection of well documented parts</a> that can help you get started.</p>
 
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<p> You can also take a look at how other teams have documented their parts in their wiki:</p>
 
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<li><a href="https://2014.igem.org/Team:MIT/Parts"> 2014 MIT </a></li>
 
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<li><a href="https://2014.igem.org/Team:Heidelberg/Parts"> 2014 Heidelberg</a></li>
 
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<li><a href="https://2014.igem.org/Team:Tokyo_Tech/Parts">2014 Tokyo Tech</a></li>
 
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<groupparts>iGEM2016 Example</groupparts>
 
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Revision as of 07:31, 14 October 2016

Parts

Overview of Parts

Our team submitted a total of 6 parts to the iGEM registry. The parts that were submitted were all components to AHL quorum sensing systems. The parts are all RFC21 compatible with other parts possessing other compatibilities. There are 5 basic parts that are part of the part collection and 1 composite part. The senders for the Aub, Bja, Bra, Cer, and Sin systems were submitted as part of the inductance test with the F2620 part, and compose a submitted part collection. The 1 composite part is the modular vector for the inducer.

Quorum Sensing-F2620 Inductions

The part Bba_F2620 (found here), designed by Barry Canton and Anna Labno from MIT, is a device designed to output PoPs when LuxR is activated. This was used to test interactions between inducers from other quorum sensing systems. The Aub, Bja, Bra, Cer, and Sin systems stem from various organisms and their inducers were submitted as parts to the registry with the purpose of completing this induction test.

N-Acyl Homoserine Lactones

AHL quorum sensing has a myriad of different systems. A total of 10 systems were investigated in this project

AHL System Bacteria of Origin AHL Name 3D-Model
Aub Unknown N-(2-oxooxolan-3-yl)dodecanamide
Bja Bradyrhizobium japonicum 3-methyl-N-[(3S)-2-oxooxolan-3-yl]butanamide
Bra Paraburkholderia kururiensis (3S)-3-[(2-oxo-3-phenylpropyl)amino]oxolan-2-one
Cer Rhodobacter sphaeroides (Z)-3-hydroxy-N-[(3S)-2-oxooxolan-3-yl]tetradec-7-enamide
Esa Erwinia stewartii 3-oxo-N-[(3S)-2-oxooxolan-3-yl]hexanamide
Las Pseudomonas aeruginosa 3-oxo-N-(2-oxooxolan-3-yl)dodecanamide
Lux Vibrio fischeri 3-oxo-N-(2-oxooxolan-3-yl)hexanamide
Rhl Rhizobium leguminosarum N-(2-oxooxolan-3-yl)butanamide
Rpa Rhodopseudomonas palustris (S)-(−)α-amino-γ-butyrolactone
Sin Sinorhizobium meliloti N-[(3S)-2-oxooxolan-3-yl]octanamide*

*Sin system produces 6 different variants of AHL. The 3D structures of all the Sin compounds can be found here.

All systems were investigated in an inductions investigation. The part BBa_F2620 was used to induce production in the Lux AHL system and test induction in any other AHL systems. Should induction occur, then possible interference between systems are conceivable, which may have implications towards any use of that system. The resulting part collection allows direct comparison in AHL induction between multiple systems.

Each team will make new parts during iGEM and will submit them to the Registry of Standard Biological Parts. The iGEM software provides an easy way to present the parts your team has created. The <groupparts> tag (see below) will generate a table with all of the parts that your team adds to your team sandbox.

Remember that the goal of proper part documentation is to describe and define a part, so that it can be used without needing to refer to the primary literature. Registry users in future years should be able to read your documentation and be able to use the part successfully. Also, you should provide proper references to acknowledge previous authors and to provide for users who wish to know more.

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