Difference between revisions of "Team:Wageningen UR/Basic Part"

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<h4><a href="#header">BioBricks</a></h4>
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<h1><b>BioBricks overview</b></h1>
  
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<p>Below, you can find all the biobricks we created!</p>
  
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<table>
 +
  <tr>
 +
    <th>BioBrick number</th>
 +
    <th>BioBrick name</th>     
 +
    <th>Designer</th>
 +
  </tr>
 +
  <tr>
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    <td><a href="http://parts.igem.org/Part:BBa_K1913000">BBa_K1913000</a></td>
 +
    <td>chiA for Varroa destructor</td>
 +
    <td>Lisa</td>
 +
  </tr>
 +
  <tr>
 +
    <td><a href="http://parts.igem.org/Part:BBa_K1913001">BBa_K1913001</a></td>
 +
    <td>chiB for Varroa destructor</td>
 +
    <td>Lisa</td>
 +
  </tr>
 +
  <tr>
 +
    <td><a href="http://parts.igem.org/Part:BBa_K1913002">BBa_K1913002</a></td>
 +
    <td>chiA device regulated by pBAD</td>
 +
    <td>Lisa</td>
 +
  </tr>
 +
  <tr>
 +
    <td><a href="http://parts.igem.org/Part:BBa_K1913003">BBa_K1913003</a></td>
 +
    <td>chiB device regulated by pBAD</td>
 +
    <td>Lisa</td>
 +
  </tr>
 +
  <tr>
 +
    <td><a href="http://parts.igem.org/Part:BBa_K1913005">BBa_K1913005</a></td>
 +
    <td>lux quorum sensing system + GFP reporter</td>
 +
    <td>Thomas</td>
 +
  </tr>
 +
  <tr>
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    <td><a href="http://parts.igem.org/Part:BBa_K1913006">BBa_K1913006</a></td>
 +
    <td>434- and lambda cI balance operon + mRFP reporter</td>
 +
    <td>Thomas</td>
 +
  </tr>
 +
  <tr>
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    <td><a href="http://parts.igem.org/Part:BBa_K1913007">BBa_K1913007</a></td>
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    <td>434- and lambda cI operon for tuning protein balance</td>
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    <td>Thomas</td>
 +
  </tr>
 +
  <tr>
 +
    <td><a href="http://parts.igem.org/Part:BBa_K19130014">BBa_K19130014</a></td>
 +
    <td>3-oxo-hexanoyl-HSL GFP reporter</td>
 +
    <td>Thomas</td>
 +
  </tr>
 +
  <tr>
 +
    <td><a href="http://parts.igem.org/Part:BBa_K19130016">BBa_K19130016</a></td>
 +
    <td>434- and lambda cI balance RFP reporter</td>
 +
    <td>Thomas</td>
 +
  </tr>
 +
  <tr>
 +
    <td><a href="http://parts.igem.org/Part:BBa_K1913008">BBa_K1913008</a></td>
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    <td>vitamin b12 riboswitch</td>
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    <td>Carina</td>
 +
  </tr>
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  <tr>
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    <td><a href="http://parts.igem.org/Part:BBa_K1913009">BBa_K1913009</a></td>
 +
    <td>Guanine riboswitch</td>
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    <td>Carina</td>
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  </tr>
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  <tr>
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    <td><a href="http://parts.igem.org/Part:BBa_K19130010">BBa_K19130010</a></td>
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    <td>tetR QPI + mRFP</td>
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    <td>Carina</td>
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  </tr>
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  <tr>
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    <td><a href="http://parts.igem.org/Part:BBa_K19130011">BBa_K19130011</a></td>
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    <td>Vitamin b12 riboswitch + mRFP</td>
 +
    <td>Carina</td>
 +
  </tr>
 +
  <tr>
 +
    <td><a href="http://parts.igem.org/Part:BBa_K19130012">BBa_K19130012</a></td>
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    <td>Guanine riboswitch + guanine riboswitch</td>
 +
    <td>Carina</td>
 +
  </tr>
 +
  <tr>
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    <td><a href="http://parts.igem.org/Part:BBa_K19130019">BBa_K19130019</a></td>
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    <td>Guanine riboswitch BS-yxjA</td>
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    <td>Tianhe</td>
 +
  </tr>
 +
  <tr>
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    <td><a href="http://parts.igem.org/Part:BBa_K19130020">BBa_K19130020</a></td>
 +
    <td>mRFP with degredation tag</td>
 +
    <td>Tianhe</td>
 +
  </tr>
 +
  <tr>
 +
    <td><a href="http://parts.igem.org/Part:BBa_K19130021">BBa_K19130021</a></td>
 +
    <td>sGFP with defredation tag</td>
 +
    <td>Tianhe</td>
 +
  </tr>
 +
  <tr>
 +
    <td><a href="http://parts.igem.org/Part:BBa_K19130022">BBa_K19130022</a></td>
 +
    <td>Artificial FixK2 promoter with lac operon O1, O3 consitutive promoter </td>
 +
    <td>Tianhe</td>
 +
  </tr>
 +
  <tr>
 +
    <td><a href="http://parts.igem.org/Part:BBa_K19130023">BBa_K19130023</a></td>
 +
    <td>Artificial FixK2 promoter with lac operon O1, O3 ompR</td>
 +
    <td>Tianhe</td>
 +
  </tr>
 +
  <tr>
 +
    <td><a href="http://parts.igem.org/Part:BBa_K19130024">BBa_K19130024</a></td>
 +
    <td>Artificial FixK2 promoter with two tetO operons</td>
 +
    <td>Tianhe</td>
 +
  </tr>
 +
  <tr>
 +
    <td><a href="http://parts.igem.org/Part:BBa_K19130025">BBa_K19130025</a></td>
 +
    <td>Natural FixK2 promoter with lac operons O1, O3</td>
 +
    <td>Tianhe</td>
 +
  </tr>
 +
  <tr>
 +
    <td><a href="http://parts.igem.org/Part:BBa_K19130026">BBa_K19130026</a></td>
 +
    <td>Natural FixK2 promoter with two tetO operons</td>
 +
    <td>Tianhe</td>
 +
  </tr>
 +
  <tr>
 +
    <td><a href="http://parts.igem.org/Part:BBa_K19130027">BBa_K19130027</a></td>
 +
    <td>Wild type plac-FixK2 hybrid promoter with mRFP</td>
 +
    <td>Tianhe</td>
 +
  </tr>
 +
  <tr>
 +
    <td><a href="http://parts.igem.org/Part:BBa_K19130028">BBa_K19130028</a></td>
 +
    <td>Wild type ptet-FixK2 hybrid promoter with mRFP</td>
 +
    <td>Tianhe</td>
 +
  </tr>
 +
  <tr>
 +
    <td><a href="http://parts.igem.org/Part:BBa_K19130029">BBa_K19130029</a></td>
 +
    <td>Synthetic plac-FixK2 hybrid promoter +RBS with mRFP</td>
 +
    <td>Tianhe</td>
 +
  </tr>
 +
  <tr>
 +
    <td><a href="http://parts.igem.org/Part:BBa_K19130030">BBa_K19130030</a></td>
 +
    <td>Synthetic plac-FixK2 hybrid promoter+RBS with mRFP</td>
 +
    <td>Tianhe</td>
 +
  </tr>
 +
  <tr>
 +
    <td><a href="http://parts.igem.org/Part:BBa_K19130031">BBa_K19130031</a></td>
 +
    <td>Syntheitc ptet-FixK2 hybrid promoter+RBS with mRFP</td>
 +
    <td>Tianhe</td>
 +
  </tr>
 +
  <tr>
 +
    <td><a href="http://parts.igem.org/Part:BBa_K19130032">BBa_K19130032</a></td>
 +
    <td>Toggle Switch device</td>
 +
    <td>Tianhe</td>
 +
  </tr>
 +
  <tr>
 +
    <td><a href="http://parts.igem.org/Part:BBa_K19130033">BBa_K19130033</a></td>
 +
    <td>Toggle Switch device</td>
 +
    <td>Tianhe</td>
 +
  </tr>
 +
  <tr>
 +
    <td><a href="http://parts.igem.org/Part:BBa_K19130013">BBa_K19130013</a></td>
 +
    <td>Cry3Aa + RBS + TEV + His-tag</td>
 +
    <td>Jaccoline/Linea</td>
 +
  </tr>
 +
</table>
  
 +
<p>
 +
Besides, we submitted one part that cannot be classified as a biobrick because it has some illegal restriction sites:</p>
  
 +
<table> 
 +
  <tr>
 +
    <th>BioBrick number</th>
 +
    <th>BioBrick name</th>     
 +
    <th>Designer</th>
 +
  </tr>
 +
<tr>
 +
    <td><a href="http://parts.igem.org/Part:BBa_K19130015">BBa_K19130015</a></td>
 +
    <td>Cry3Aa with araC/pBAD</td>
 +
    <td>Jaccoline/Linea</td>
 +
  </tr>
 +
</table>
  
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<p>
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Initally, part BBa_K19130015 was made only to for testing the <a href="https://2016.igem.org/Team:Wageningen_UR/Description/Specificity#Assay"><i>in vitro</i> assay</a>, <b>jacco, please put the rest of your excuse here ;)</b>.
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<p>
 
<p>
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A <b>basic part</b> is a functional unit of DNA that cannot be subdivided into smaller component parts. <a href="http://parts.igem.org/wiki/index.php/Part:BBa_R0051">BBa_R0051</a> is an example of a basic part, a promoter regulated by lambda cl.
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<b>No Cas9 biobrick?!</b><br>
 +
When we started making the constructs for the <a href="https://2016.igem.org/Team:Wageningen_UR/Description/Biocontainment#SAA">Cas9 kill switch</a>, two approaches were taken: one was taking the Cas9 that is available in the iGEM registry (BBa_K1218011) as a starting point for making mutations and expressing Cas9. The other approach was starting with pdCas9 (Addgene plasmid # 46569). While cloning, it proved to be difficult to transfer BBa_K1218011 to another backbone (see also the <a href="https://2016.igem.org/Team:Wageningen_UR/Notebook/Cas9">notebook</a>). Furthermore, when cultures transformed with BBa_K1218011 were checked for Cas9 expression with SDS-PAGE, no convincing Cas9 band could be observed. Because of time limitations we decided to continue working with the Addgene construct for making the mutations, and chose an established system for protein expression. For that reason, no Cas9-biobricks were submitted. Furthermore, the pEVOL construct containing an aminoacyl-synthetase and a tRNA for introducing BipA in response to the TAG stopcodon were isolated from a strain kindly received from George Church (described in <a href="http://www.nature.com/nature/journal/v518/n7537/full/nature14121.html">Mandel <i>et al.</i>, 2015</a>). The MTA that was signed to receive the strain does not allow for redistribution.
 
</p>
 
</p>
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<p>Most genetically-encoded functions have not yet been converted to BioBrick parts. Thus, there are <b>many</b> opportunities to find new, cool, and important genetically encoded functions, and refine and convert the DNA encoding these functions into BioBrick standard biological parts. </p>
 
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<div class="highlight">
 
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<h4>Note</h4>
 
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<p>This page should list all the basic parts your team has made during your project. You must add all characterization information for your parts on the Registry. You should not put characterization information on this page.</p>
 
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</div>
 
  
  
 
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{{Wageningen_UR/footer}}

Revision as of 14:23, 16 October 2016

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Wageningen UR iGEM 2016

 

 

 

BioBricks

BioBricks overview

Below, you can find all the biobricks we created!

BioBrick number BioBrick name Designer
BBa_K1913000 chiA for Varroa destructor Lisa
BBa_K1913001 chiB for Varroa destructor Lisa
BBa_K1913002 chiA device regulated by pBAD Lisa
BBa_K1913003 chiB device regulated by pBAD Lisa
BBa_K1913005 lux quorum sensing system + GFP reporter Thomas
BBa_K1913006 434- and lambda cI balance operon + mRFP reporter Thomas
BBa_K1913007 434- and lambda cI operon for tuning protein balance Thomas
BBa_K19130014 3-oxo-hexanoyl-HSL GFP reporter Thomas
BBa_K19130016 434- and lambda cI balance RFP reporter Thomas
BBa_K1913008 vitamin b12 riboswitch Carina
BBa_K1913009 Guanine riboswitch Carina
BBa_K19130010 tetR QPI + mRFP Carina
BBa_K19130011 Vitamin b12 riboswitch + mRFP Carina
BBa_K19130012 Guanine riboswitch + guanine riboswitch Carina
BBa_K19130019 Guanine riboswitch BS-yxjA Tianhe
BBa_K19130020 mRFP with degredation tag Tianhe
BBa_K19130021 sGFP with defredation tag Tianhe
BBa_K19130022 Artificial FixK2 promoter with lac operon O1, O3 consitutive promoter Tianhe
BBa_K19130023 Artificial FixK2 promoter with lac operon O1, O3 ompR Tianhe
BBa_K19130024 Artificial FixK2 promoter with two tetO operons Tianhe
BBa_K19130025 Natural FixK2 promoter with lac operons O1, O3 Tianhe
BBa_K19130026 Natural FixK2 promoter with two tetO operons Tianhe
BBa_K19130027 Wild type plac-FixK2 hybrid promoter with mRFP Tianhe
BBa_K19130028 Wild type ptet-FixK2 hybrid promoter with mRFP Tianhe
BBa_K19130029 Synthetic plac-FixK2 hybrid promoter +RBS with mRFP Tianhe
BBa_K19130030 Synthetic plac-FixK2 hybrid promoter+RBS with mRFP Tianhe
BBa_K19130031 Syntheitc ptet-FixK2 hybrid promoter+RBS with mRFP Tianhe
BBa_K19130032 Toggle Switch device Tianhe
BBa_K19130033 Toggle Switch device Tianhe
BBa_K19130013 Cry3Aa + RBS + TEV + His-tag Jaccoline/Linea

Besides, we submitted one part that cannot be classified as a biobrick because it has some illegal restriction sites:

BioBrick number BioBrick name Designer
BBa_K19130015 Cry3Aa with araC/pBAD Jaccoline/Linea

Initally, part BBa_K19130015 was made only to for testing the in vitro assay, jacco, please put the rest of your excuse here ;).

No Cas9 biobrick?!
When we started making the constructs for the Cas9 kill switch, two approaches were taken: one was taking the Cas9 that is available in the iGEM registry (BBa_K1218011) as a starting point for making mutations and expressing Cas9. The other approach was starting with pdCas9 (Addgene plasmid # 46569). While cloning, it proved to be difficult to transfer BBa_K1218011 to another backbone (see also the notebook). Furthermore, when cultures transformed with BBa_K1218011 were checked for Cas9 expression with SDS-PAGE, no convincing Cas9 band could be observed. Because of time limitations we decided to continue working with the Addgene construct for making the mutations, and chose an established system for protein expression. For that reason, no Cas9-biobricks were submitted. Furthermore, the pEVOL construct containing an aminoacyl-synthetase and a tRNA for introducing BipA in response to the TAG stopcodon were isolated from a strain kindly received from George Church (described in Mandel et al., 2015). The MTA that was signed to receive the strain does not allow for redistribution.