Difference between revisions of "Team:Sorbonne U Paris/Parts"

 
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        <meta name="description" content="Sugar is the main source of energy in synthetic biology. To bring a solution to the dramatical environmental impacts of its massive production this year iGEM Sorbonne U Paris wants to engineer green microalgae, Chlamydomonas Reinhardtti, to allow an ecofriendly sugar production within marin water. In order to spread the use of microalgae we will create a toolkit for C. reinhardtti with a synthetic retrotransposon to generate in vivo continuous directed evolution ">
 
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    <article class="col-md-10">
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<h1>Parts</h1>
  
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<h2>New parts submitted to the registry</h2>
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<br><br>
  
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<h1>Parts</h1>
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<p>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 <code>&lt;groupparts&gt;</code> tag (see below) will generate a table with all of the parts that your team adds to your team sandbox.</p>
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      <thead>   
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<p>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.</p>
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  <tr>
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  <th class="th-notebook">Parts name</th>
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  <th class="th-notebook">Type</th>
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      <th class="th-notebook">Part number</th>
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  </tr>
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</thead>   
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  <tbody>     
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  <tr>
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  <td class="td-notebook"><a class="link-inside-page" href="http://parts.igem.org/Part:BBa_K2703000">RBCS2i1</a></td>
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  <td class="td-notebook">Protein domain </td>
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  <td class="td-notebook">BBa_K2703000 </td> 
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  </tr>
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  <tr>
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  <td class="td-notebook"><a class="link-inside-page" href="http://parts.igem.org/Part:BBa_K2703002">pSAD</a></td>
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  <td class="td-notebook">Regulatory</td>
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  <td class="td-notebook">BBa_K2703002 </td> 
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  </tr>
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        <tr>
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  <td class="td-notebook"><a class="link-inside-page" href="http://parts.igem.org/Part:BBa_K2703003">3'LTR_Cr</a></td>
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  <td class="td-notebook">Regulatory</td>
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  <td class="td-notebook">BBa_K2703003</td> 
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  </tr>
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        <tr>
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  <td class="td-notebook"><a class="link-inside-page" href="http://parts.igem.org/Part:BBa_K2703004">5'LTR</a></td>
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  <td class="td-notebook">Regulatory</td>
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  <td class="td-notebook">BBa_K2703004</td> 
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  </tr>
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        <tr>
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  <td class="td-notebook"><a class="link-inside-page" href="http://parts.igem.org/Part:BBa_K2703008">paromycin resistance gene</a></td>
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  <td class="td-notebook">Coding</td>
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  <td class="td-notebook">BBa_K2703008 </td> 
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  </tr>
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  </tbody>
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</table>
 
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<br><br>
  
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<h2 class="title-h2">pSAD</h2>
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<div class="highlight decoration_background">
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<br>
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<h3>Note</h3>
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<p>pSAD is a constitutive promoter in Chlamydomonas reinhardtii. It is is a high  expression constitutive promoter that controls the expression of the gene encoding for a ferrodoxin-binding protein of photosystem I. This pSAD promoter was submitted in 2014 by the Concordia team (BBa_K1547005). To be compatible with the PhytoBrick standard (RFC1000), an illegal BpiI restriction site was removed (A289T). We cloned pSAD by PCR amplification in A2-A3 fusion site to use it for our retrotransposon design. The acceptor plasmid is the MoClo Universal Level 0 plasmid (pL0): pAGM9121. We sequenced again the sequence to be sure there are no unwanted mutations. <br><br>
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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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<h6>Role in our project </h6>
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</div>
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Our part is compatible with the PhytoBrick MoClo standard. This PhytoBrick was intented to be used as a constitutive promoter for the transcription unit of paromomycine in the CARGO of our synthetic retrotransposons for directed evolution in the <i>Chlamydomonas</i>. It is part of our reporter system to characterize the activity and transposition rates.</p>
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<h2 class="title-h2">paromycin resistance gene</h2>
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<p> The sequence of the paromomycine-resistance marker is an aminoglycoside antibiotic. The aphVIII gene from Streptomyces rimosus encodes an aminoglycoside 3’-phosphotransferase gene (aph). From the aphVIII gene sequence of the BioBrick BBa_K1884013 (iGEM16_SZU-China) BpiI estriction sites were removed ( G551C) by PCR point mutation. We cloned aphVIII by PCR amplification in B4-B5 position of the MoClo standard2 to use it in our retrotransposon design. Acceptor plasmid is the MoClo Universal pL0 acceptor plasmid pAGM91212. We sequenced again the sequence to be sure there is no unwanted mutations.
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<br><br>
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<h6>Role in our project </h6>
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Our part is compatible with the PhytoBrick MoClo standard. This PhytoBrick was intended to be used as a reporter gene in the CARGO to test the functionality of our synthetic retrotransposons for directed evolution in C. reinhardtii.</p>
  
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<h2 class="title-h2">RBCS2i1</h2>
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<br>
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<p>This is the second intron of the rubisco protein from Chlamydomonas reinhardtii. </P>
  
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<h2 class="title-h2">3'LTR_Cr</h2>
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<br>
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<p>Long-Terminal-Repeat in the 3'end of a retrotransposon (or retrovirus). It contains the information necessary to start the reverse transcription. <p>
  
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<h2 class="title-h2">5'LTR</h2>
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<br>
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<p>Long-Terminal-repeat in the 5'end of a retrotransposon (or retrovirus). It contains the regulatory elements to start the transcription of the retrotransposon. </p>
  
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<h2>Parts used in our project but not submitted to the registry</h2>
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<br><br>
  
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<h3>Adding parts to the registry</h3>
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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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  <th class="th-notebook">Parts name</th>
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  <th class="th-notebook">Type</th>
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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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      <th class="th-notebook">Part number</th>
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ADD PARTS
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  <tr>
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  <td class="td-notebook"><a class="link-inside-page" href="http://parts.igem.org/Part:BBa_K2703001">otsA</a></td>
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  <td class="td-notebook">Coding </td>
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  <td class="td-notebook">Bba_K2703001 </td> 
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  </tr>
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  <tr>
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  <td class="td-notebook"><a class="link-inside-page" href="http://parts.igem.org/Part:BBa_K2703005">pL0-pSAD_A2-B1</a></td>
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  <td class="td-notebook">Regulatory</td>
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  <td class="td-notebook">Bba_K2703005 </td> 
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  </tr>
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        <tr>
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  <td class="td-notebook"><a class="link-inside-page" href="http://parts.igem.org/Part:BBa_K2703006">otsB</a></td>
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  <td class="td-notebook">Coding</td>
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  <td class="td-notebook">Bba_K2703006</td> 
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  </tr>
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        <tr>
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  <td class="td-notebook"><a class="link-inside-page" href="http://parts.igem.org/Part:BBa_K2703007">Bba_K2703006</a></td>
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  <td class="td-notebook">Regulatory</td>
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  <td class="td-notebook">Bba_K2703007</td> 
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  </tr>
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        <tr>
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  <td class="td-notebook"><a  class="link-inside-page" href="http://parts.igem.org/Part:BBa_K2703009">5' UTR pSAD</a></td>
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  <td class="td-notebook">Regulatory</td>
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  <td class="td-notebook">Bba_K2703009 </td> 
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  </tr>
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            <tr>
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  <td class="td-notebook"><a class="link-inside-page"  href="http://parts.igem.org/Part:BBa_K2703010">Gag Pol</a></td>
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  <td class="td-notebook">Coding</td>
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  <td class="td-notebook">Bba_K2703010 </td> 
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  </tr>
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                <tr>
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  <td class="td-notebook"><a class="link-inside-page" href="http://parts.igem.org/Part:BBa_K2703011">pAGM9121</a></td>
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  <td class="td-notebook">backbone</td>
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  <td class="td-notebook">Bba_K2703011 </td> 
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  </tr>s
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<h3>Inspiration</h3>
 
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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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<ul>
 
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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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<h3>What information do I need to start putting my parts on the Registry?</h3>
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<p>The information needed to initially create a part on the Registry is:</p>
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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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<h3>Part Table </h3>
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<p>Please include a table of all the parts your team has made during your project on this page. Remember part characterization and measurement data must go on your team part pages on the Registry. </p>
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<groupparts>iGEM18 Sorbonne_U_Paris</groupparts>
 
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Latest revision as of 01:29, 18 October 2018

Parts

New parts submitted to the registry



Parts name Type Part number
RBCS2i1 Protein domain BBa_K2703000
pSAD Regulatory BBa_K2703002
3'LTR_Cr Regulatory BBa_K2703003
5'LTR Regulatory BBa_K2703004
paromycin resistance gene Coding BBa_K2703008


pSAD


pSAD is a constitutive promoter in Chlamydomonas reinhardtii. It is is a high expression constitutive promoter that controls the expression of the gene encoding for a ferrodoxin-binding protein of photosystem I. This pSAD promoter was submitted in 2014 by the Concordia team (BBa_K1547005). To be compatible with the PhytoBrick standard (RFC1000), an illegal BpiI restriction site was removed (A289T). We cloned pSAD by PCR amplification in A2-A3 fusion site to use it for our retrotransposon design. The acceptor plasmid is the MoClo Universal Level 0 plasmid (pL0): pAGM9121. We sequenced again the sequence to be sure there are no unwanted mutations.

Role in our project
Our part is compatible with the PhytoBrick MoClo standard. This PhytoBrick was intented to be used as a constitutive promoter for the transcription unit of paromomycine in the CARGO of our synthetic retrotransposons for directed evolution in the Chlamydomonas. It is part of our reporter system to characterize the activity and transposition rates.

paromycin resistance gene


The sequence of the paromomycine-resistance marker is an aminoglycoside antibiotic. The aphVIII gene from Streptomyces rimosus encodes an aminoglycoside 3’-phosphotransferase gene (aph). From the aphVIII gene sequence of the BioBrick BBa_K1884013 (iGEM16_SZU-China) BpiI estriction sites were removed ( G551C) by PCR point mutation. We cloned aphVIII by PCR amplification in B4-B5 position of the MoClo standard2 to use it in our retrotransposon design. Acceptor plasmid is the MoClo Universal pL0 acceptor plasmid pAGM91212. We sequenced again the sequence to be sure there is no unwanted mutations.

Role in our project
Our part is compatible with the PhytoBrick MoClo standard. This PhytoBrick was intended to be used as a reporter gene in the CARGO to test the functionality of our synthetic retrotransposons for directed evolution in C. reinhardtii.

RBCS2i1


This is the second intron of the rubisco protein from Chlamydomonas reinhardtii.

3'LTR_Cr


Long-Terminal-Repeat in the 3'end of a retrotransposon (or retrovirus). It contains the information necessary to start the reverse transcription.

5'LTR


Long-Terminal-repeat in the 5'end of a retrotransposon (or retrovirus). It contains the regulatory elements to start the transcription of the retrotransposon.

Parts used in our project but not submitted to the registry



s
Parts name Type Part number
otsA Coding Bba_K2703001
pL0-pSAD_A2-B1 Regulatory Bba_K2703005
otsB Coding Bba_K2703006
Bba_K2703006 Regulatory Bba_K2703007
5' UTR pSAD Regulatory Bba_K2703009
Gag Pol Coding Bba_K2703010
pAGM9121 backbone Bba_K2703011

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