Difference between revisions of "Team:SPSingapore/Parts"

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<h2> Part Documentation</h2>
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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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<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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<h4>Note</h4>
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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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<h4>Adding parts to the registry</h4>
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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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<h4>What information do I need to start putting my parts on the Registry?</h4>
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<p>The information needed to initially create a part on the Registry is:</p>
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<ul>
 
<ul>
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<li>Part Name</li>
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<li class = 'active'><a href='https://2015.igem.org/Team:SPSingapore/'><span>Home</span></a></li>
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<li>Part type</li>
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<li><a href='https://2015.igem.org/Team:SPSingapore/Team'><span>Team</span></a>
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<li>Creator</li>
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<ul>
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<li>Sequence</li>
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<li><a href="https://2015.igem.org/Team:SPSingapore/Team">Overview</a></li>
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<li>Short Description (60 characters on what the DNA does)</li>
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<li><a href="https://igem.org/Team.cgi?id=1804">Official Profile</a></li>
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<li>Long Description (Longer description of what the DNA does)</li>
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        <li><a href="https://2015.igem.org/Team:SPSingapore/Team Bios">Team Bios</a></li>
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<li>Design considerations</li>
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        <li><a href="https://2015.igem.org/Team:SPSingapore/Mentors">Mentors</a></li>
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        <li><a href="https://2015.igem.org/Team:SPSingapore/Attributions">Attributions</a></li>
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</ul>
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</li>
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<li><a href='https://2015.igem.org/Team:SPSingapore/Project'><span>Project</span></a>
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<ul>
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<li><a href='https://2015.igem.org/Team:SPSingapore/Project'>Overview</a></li>
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        <li><a href="https://2015.igem.org/Team:SPSingapore/Invasin">Invasin + Listerolysin</a></li>
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        <li><a href="https://2015.igem.org/Team:SPSingapore/ESAQS">esa Quorum Sensing</a></li>
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        <li><a href="https://2015.igem.org/Team:SPSingapore/Anaerobic Promoter">Anaerobic Promoter</a></li>
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        <li><a href="https://2015.igem.org/Team:SPSingapore/Description">Parts</a></li>
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</ul>
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</li>
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<li><a href='https://2015.igem.org/Team:SPSingapore/Notebook'><span>Notebook</span></a>
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<ul>
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<li><a href="https://2015.igem.org/Team:SPSingapore/Protocol">Protocols</a></li>
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        <li><a href="https://2015.igem.org/Team:SPSingapore/Notebook">Entries</a></li>
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</ul>
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</li>
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<li><a href='https://2015.igem.org/Team:SPSingapore/Practices'><span>Human Practices</span></a>
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<ul>
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<li><a href="https://2015.igem.org/Team:SPSingapore/Practices">Overview</a></li>
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<li><a href="https://2015.igem.org/Team:SPSingapore/Workshop">Workshop</a></li>
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<li><a href="https://2015.igem.org/Team:SPSingapore/Workshop Materials">Workshop Materials</a></li>
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        <li><a href="https://2015.igem.org/Team:SPSingapore/Interview">Consultations</a></li>
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</ul>
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</li>
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<li><a href='https://2015.igem.org/Team:SPSingapore/Safety'><span>Safety</span></a></li>
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<li class='last'><a href='https://2015.igem.org/Team:SPSingapore/Medals'><span>Medals</span></a></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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<ul>
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  <li class = 'last'><a href = "https://2015.igem.org/Team:SPSingapore/Project"><span>PROJECT</span></a>
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<ul>
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        <li><a href = "https://2015.igem.org/Team:SPSingapore/ESAQS"><span>ESA Quorum Sensing</span></a></li>
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        <li><a href = "https://2015.igem.org/Team:SPSingapore/Invasin"><span>Invasin + Listerolysin</span></a></li>
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        <li><a href = "https://2015.igem.org/Team:SPSingapore/Anaerobic Promoter"><span>Anaerobic Promoter</span></a></li>
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        <li class = 'last'><a href = "https://2015.igem.org/Team:SPSingapore/Description"><span>Parts</span></a></li>
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<h4>Inspiration</h4>
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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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<td colspan=1 style = "box-shadow: 0 0 0; padding:0;border-top:5px white;font-size:15px"><h1>Contribution to Registry</h1></td>
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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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<center>
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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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<div style = "border-top: 5px solid blue; width:700px; text-align:justify;margin-bottom: 20px; line-height:normal;">
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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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</ul>
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<h4>Part Table </h4>
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<! ----------------------Start of Safety Text --------------------------------->
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<groupparts>iGEM015 Example</groupparts>
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The Invasin-Listerolysin system
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</b></a></td></tr>
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The Invasin protein from Yersinia is a outer surface protein that induces phagocytosis of the pathogenic Yersinia by mammalian cells in a beta integrin dependent manner(<a href = "#ref">Wiedemann et al., 2001</a>). Whereas the Listerolysin O cytolysin of Listeria moncytogenes is a well documented cytolysin, which allows for lysis of the endosome vacuole by the pathogen after entry into a mammalian cell (<a href = "#ref">Dramsi & Cossart, 2002</a>). This facilitates endosomal escape of the bacteria. When these two [proteins are coupled together, they can confer non-pathogenic bacteria with suitable features to serve as a drug delivery vector to the cytoplasm.
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Registry Update of BBa_299812
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In constructing our Anaerobic Response System, we chose Invasin and Listeriolysin as part of our drug delivery system, building upon a construct from the Warsaw 2010 team, BBa_K299812. BBa_K299812 is a useful intermediate part containing the Invasin and Listeriolysin with ribosome binding sites in front of the genes. Different promoter sequences could be prepended ahead of the part and modified for our use.
 +
<br><br>
 +
However, when sequencing the part we received from the repository, our team found that the part sequence had major mismatches with the documented sequence. This was particularly serious for the invasin gene, which had only 55% identity between the translated amino acid sequences from the part wiki and our sequencing results. Furthermore, even though BLAST results showed that the invasin gene was indeed present, the strain of origin seemed to be different from the documentation. Lastly, the part does not strictly adhere to BioBricks standard, because the suffix sequence had only the PstI site left. (Further details and updated sequence can be found <a href = "http://parts.igem.org/Part:BBa_K299812:Experience">here</a>.)
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<br><br>
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As our lab only has the resources to functionally characterise the effect of the expression of invasin through an invasion assay, invasin was our main focus for the construction of parts for our Anaerobic Response System. 
 
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References
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Dramsi, S. and Cossart, P. (2002) Listeriolysin O: a genuine cytolysin optimized for an intracellular parasite. J Cell Biol. 2002 Mar 18; 156(6): 943–946.
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<br><br>
 +
Wiedemann A1, Linder S, Grassl G, Albert M, Autenrieth I, Aepfelbacher M. (2001) Yersinia enterocolitica invasin triggers phagocytosis via beta1 integrins, CDC42Hs and WASp in macrophages. Cell Microbiol. 2001 Oct;3(10):693-702.
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<img src="https://static.igem.org/mediawiki/2015/7/72/SPSingapore_SPS-Logo.png" height="50px" style="margin-top:10px;margin-right:30px;">
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Latest revision as of 17:09, 14 November 2015


Contribution to Registry


The Invasin-Listerolysin system
The Invasin protein from Yersinia is a outer surface protein that induces phagocytosis of the pathogenic Yersinia by mammalian cells in a beta integrin dependent manner(Wiedemann et al., 2001). Whereas the Listerolysin O cytolysin of Listeria moncytogenes is a well documented cytolysin, which allows for lysis of the endosome vacuole by the pathogen after entry into a mammalian cell (Dramsi & Cossart, 2002). This facilitates endosomal escape of the bacteria. When these two [proteins are coupled together, they can confer non-pathogenic bacteria with suitable features to serve as a drug delivery vector to the cytoplasm.

Registry Update of BBa_299812
In constructing our Anaerobic Response System, we chose Invasin and Listeriolysin as part of our drug delivery system, building upon a construct from the Warsaw 2010 team, BBa_K299812. BBa_K299812 is a useful intermediate part containing the Invasin and Listeriolysin with ribosome binding sites in front of the genes. Different promoter sequences could be prepended ahead of the part and modified for our use.

However, when sequencing the part we received from the repository, our team found that the part sequence had major mismatches with the documented sequence. This was particularly serious for the invasin gene, which had only 55% identity between the translated amino acid sequences from the part wiki and our sequencing results. Furthermore, even though BLAST results showed that the invasin gene was indeed present, the strain of origin seemed to be different from the documentation. Lastly, the part does not strictly adhere to BioBricks standard, because the suffix sequence had only the PstI site left. (Further details and updated sequence can be found here.)

As our lab only has the resources to functionally characterise the effect of the expression of invasin through an invasion assay, invasin was our main focus for the construction of parts for our Anaerobic Response System.

References
Dramsi, S. and Cossart, P. (2002) Listeriolysin O: a genuine cytolysin optimized for an intracellular parasite. J Cell Biol. 2002 Mar 18; 156(6): 943–946.

Wiedemann A1, Linder S, Grassl G, Albert M, Autenrieth I, Aepfelbacher M. (2001) Yersinia enterocolitica invasin triggers phagocytosis via beta1 integrins, CDC42Hs and WASp in macrophages. Cell Microbiol. 2001 Oct;3(10):693-702.