Team:Uppsala/Parts

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<p><b>All the parts the Uppsala iGEM Team 2014 provide for the iGEM Part Registry:</b></p>
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document.getElementById("tab1").innerHTML = '<h1 class="project_header">Background</h1><p class="project_text">When creating a biological machine that efficiently can kill off specific pathogens without disturbing other cells in its environment, an adhesion system could play a vital role. Getting our probiotic to attach to its target, like Yersinia enterocolitica in our case, could give important advantages in target specificity and delivering medicine in a way that ensures it reaches Y. enterocolitica in a concentration as high as possible. The idea is to manipulate Lactobacillus expression of membrane proteins to create a somewhat stable bonding to any of Yersina’s surface structures, preventing the pathogen from even entering the gut wall. This could be done with a DNA construct coding for a membrane protein that either resembles the bonding that Yersinia makes to our cells or one that itself binds to Yersinia. <br><br> We studied the ways of infection of Yersinia Enterocolitica and could determine that the main strategies of entering through the gut wall is by using it’s diverse membrane proteins YadA, Invasin and Ail. YadA and Invasin work together to bind to our cell membranes. While YadA binds to collagen on our cells, Invasin structurally resembles fibronectin , that is present in the extracellular matrix, which is recognized by the fibronectin binding membrane protein Integrin alpha-5-beta-1 in our cell mambranes. [1] Yersinia uses our own cell-to-cell binding mechanism to find a target cell and fooling it to get inside by binding to the Integrin and to the collagen outside and in between cells. [2] <br> At first glance we thought of manipulating our probiotics to also use the same bioorganic systems. That could be done by expressing collagen like proteins by fusing them with an anchor protein that could transport the whole construct to the outer membrane and keep the collagen part attached to the probiotic surface. YadA binds strongly to some parts of collagen which could be expressed individually. [3] <br><br> But by experimenting with collagen, and especially putting it on the surface of a bacterial outer membrane that is meant to enter the human body, is an extremely risky procedure. “As anti-bodies would be produced to target the collagen and anchor protein complex this could lead to an auto immune reaction as they would also react on the collagen naturally present in our body” says Lars Hellman, a professor in immunology in Uppsala University. More about Problems with Yersinia adhesion and developing auto immune disease can be read in this text:TEXT link. <br><br> Instead we took inspiration from the killing system we are using which secrets a bacteriocin, CFY, which specifically binds to and ruptures the outer cell membrane of Yersinia.[4] The main focus of the adhesion system drastically changed from expressing human like proteins to expressing the bacteriocine fused with the anchor protein. This process is less studied, as the bacteriocin was first discovered and characterized as early as 2012.[5] If the bacteriocin would survive degradation in stomach like environments and later on find Y. enterocolitica, the bacteriocine, while attaching to the membrane, would somewhat fix the probiotic to its target. Even thou this connection would be much weaker than a system with collagen it is safe and still an advantage to the pathogen killer.</p><ul class="reference"><li>[1]http://edoc.rki.de/oa/articles/reeQGIo7WUhm/PDF/247mpj5mInEcs.pdf</li><li>[2]http://edoc.rki.de/oa/articles/reeQGIo7WUhm/PDF/247mpj5mInEcs.pdf </li></ul></p>';
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<table id=partsT style="width:100%">
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<tr><th>Fav.</th><th>BioBrick code</th><th>Type</th><th>Construct</th><th>Description</th><th>Designers</th></tr>
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<tr><td><img src="https://static.igem.org/mediawiki/2014/e/ef/GoodGuy.png" Style="width: 20px"></img></td><td><a href="http://parts.igem.org/Part:BBa_K1381000">BBa_K1381000</a></td><td>Regulatory</td><td>yenbox_WT</td><td>The Yen systems recognition region fused with a wildtype promoter</td><td>Sensing Group</td></tr>
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<tr><td></td><td><a href="http://parts.igem.org/Part:BBa_K1381001">BBa_K1381001</a></td><td>Regulatory</td><td>yenbox_J23113</td><td>The Yen systems recognition region fused with the promoter J23113</td><td>Sensing Group</td></tr>
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<tr><td></td><td><a href="http://parts.igem.org/Part:BBa_K1381002">BBa_K1381002</a></td><td>Regulatory</td><td>yenbox_J23101</td><td>The Yen systems recognition region fused with the promoter J23101</td><td>Sensing Group</td></tr>
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<tr><td><img src="https://static.igem.org/mediawiki/2014/e/ef/GoodGuy.png" Style="width: 20px"></img></td><td><a href="http://parts.igem.org/Part:BBa_K1381004">BBa_K1381004</a></td><td>Coding</td><td>B0034-YenR</td><td>YenR, the activator in the Yen system</td><td>Sensing Group</td></tr>
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<tr><td></td><td><a href="http://parts.igem.org/Part:BBa_K1381005">BBa_K1381005</a></td><td>Regulatory</td><td>J23110-B0034-YenR</td><td>The activator YenR coupled to the promoter J23110</td><td>Sensing Group</td></tr>
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<tr><td></td><td><a href="http://parts.igem.org/Part:BBa_K1381006">BBa_K1381006</a></td><td>Regulatory</td><td>J23102-B0034-YenR</td><td>The activator YenR coupled to the promoter J23102</td><td>Sensing Group</td></tr>
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<tr><td></td><td><a href="http://parts.igem.org/Part:BBa_K1381007">BBa_K1381007</a></td><td>Regulatory</td><td>J23101-B0034-YenR</td><td>The activator YenR coupled to the promoter J23101</td><td>Sensing Group</td></tr>
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<tr><td></td><td><a href="http://parts.igem.org/Part:BBa_K1381008">BBa_K1381008</a></td><td>Measurement</td><td>yenbox_WT-B0032-GFP</td><td>A characterisation construct for the yenbox with the wildtype promoter</td><td>Sensing Group</td></tr>
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<tr><td></td><td><a href="http://parts.igem.org/Part:BBa_K1381009">BBa_K1381009</a></td><td>Measurement</td><td>yenbox_J23113-B0032-GFP</td><td>A characterisation construct for the yenbox with the promoter J23113</td><td>Sensing Group</td></tr>
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<tr><td></td><td><a href="http://parts.igem.org/Part:BBa_K1381010">BBa_K1381010</a></td><td>Measurement</td><td>yenbox_J23101-B0032-GFP</td><td>A characterisation construct for the yenbox with the promoter J23101</td><td>Sensing Group</td></tr>
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<tr><td></td><td><a href="http://parts.igem.org/Part:BBa_K1381011">BBa_K1381011</a></td><td>Generator</td><td>J23113-B0034-CheZ</td><td>The chemotaxis controlling gene CheZ with the promoter J23113</td><td>Targeting Group</td></tr>
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<tr><td></td><td><a href="http://parts.igem.org/Part:BBa_K1381012">BBa_K1381012</a></td><td>Generator</td><td>J23114-B0034-CheZ</td><td>The chemotaxis controlling gene CheZ with the promoter J23114</td><td>Targeting Group</td></tr>
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<tr><td></td><td><a href="http://parts.igem.org/Part:BBa_K1381013">BBa_K1381013</a></td><td>Generator</td><td>J23100-B0034-CheZ</td><td>The chemotaxis controlling gene CheZ with the promoter J23100</td><td>Targeting Group</td></tr>
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<tr><td></td><td><a href="http://parts.igem.org/Part:BBa_K1381014">BBa_K1381014</a></td><td>Regulatory</td><td>J23101-spot42_USP45_10bp</td><td>Silencing sRNA with affinity to USP45</td><td>Killing Group</td></tr>
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<tr><td></td><td><a href="http://parts.igem.org/Part:BBa_K1381015">BBa_K1381015</a></td><td>Regulatory</td><td>J23101-spot42_USP45_15bp</td><td>Silencing sRNA with affinity to USP45</td><td>Killing Group</td></tr>
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<tr><td></td><td><a href="http://parts.igem.org/Part:BBa_K1381016">BBa_K1381016</a></td><td>Regulatory</td><td>J23101-spot42_USP45_20bp</td><td>Silencing sRNA with affinity to USP45</td><td>Killing Group</td></tr>
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<tr><td><img src="https://static.igem.org/mediawiki/2014/e/ef/GoodGuy.png" Style="width: 20px"></img></td><td><a href="http://parts.igem.org/Part:BBa_K1381017">BBa_K1381017</a></td><td>Coding</td><td>CFY-X6 his</td><td>The gene coding for the bacteriocin colicin Fy</td><td>Killing Group</td></tr>
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<tr><td></td><td><a href="http://parts.igem.org/Part:BBa_K1381018">BBa_K1381018</a></td><td>Tag</td><td>B0034-USP45</td><td>The secretion tag USP45 with the RBS B0034</td><td>Killing Group</td></tr>
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<tr><td></td><td><a href="http://parts.igem.org/Part:BBa_K1381019">BBa_K1381019</a></td><td>Device</td><td>B0034-pelB-CFY-X6 his</td><td>The bacteriocin colicin Fy coupled to the the secretion tag pelB</td><td>Killing Group</td></tr>
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<tr><td></td><td><a href="http://parts.igem.org/Part:BBa_K1381020">BBa_K1381020</a></td><td>Generator</td><td>J23106-B0034-pelB-CFY-X6 his</td><td>Colicin Fy coupled to the the secretion tag pelB with the promoter J23106</td><td>Killing Group</td></tr>
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<tr><td></td><td><a href="http://parts.igem.org/Part:BBa_K1381021">BBa_K1381021</a></td><td>Generator</td><td>J23116-B0034-pelB-CFY-X6 his</td><td>Colicin Fy coupled to the the secretion tag pelB with the promoter J23116</td><td>Killing Group</td></tr>
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<tr><td></td><td><a href="http://parts.igem.org/Part:BBa_K1381022">BBa_K1381022</a></td><td>Device</td><td>B0034-USP45-CFY-X6 his</td><td>The bacteriocin colicin Fy coupled to the the secretion tag USP45</td><td>Killing Group</td></tr>
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<tr><td></td><td><a href="http://parts.igem.org/Part:BBa_K1381023">BBa_K1381023</a></td><td>Generator</td><td>J23106-B0034-CFY-X6 his</td><td>Colicin Fy coupled with the promoter J23106</td><td>Killing Group</td></tr>
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<tr><td></td><td><a href="http://parts.igem.org/Part:BBa_K1381024">BBa_K1381024</a></td><td>Tag</td><td>B0034-pgsA-(EAAAR)x4</td><td>The anchor tag pgsA with the RBS B0034 and a linker</td><td>Adhesion Group</td></tr>
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<tr><td></td><td><a href="http://parts.igem.org/Part:BBa_K1381025">BBa_K1381025</a></td><td>Reporter</td><td>B0034-BFP (RFC25)</td><td>A mutagenised version of B0034-BFP, compatible with RFC25</td><td>Adhesion Group</td></tr>
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</table>
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document.getElementById("tab2").innerHTML = '<h1 class="project_header">Methods</h1><p class="project_text"> ---> SKRIV TEXT HÄR!  <---</p><ul class="reference"><li>Reference 1</li><li>Reference 2</li></ul>';
 
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document.getElementById("tab4").innerHTML = '<p>Excepteur sint occaecat cupidatat non proident, sunt in culpa qui officia deserunt mollit anim id est laborum.Lorem ipsum dolor sit amet, consectetur adipisicing elit, sed do eiusmod tempor incididunt ut labore et dolore magna aliqua. Ut enim ad minim veniam, quis nostrud exercitation ullamco laboris nisi ut aliquip ex ea commodo consequat. Duis aute irure dolor in reprehenderit in voluptate velit esse cillum dolore eu fugiat nulla pariatur. Excepteur sint occaecat cupidatat non id est laborum.Lorem ipsum dolor sit amet, consectetur adipisicing elit, sed do eiusmod tempor incididunt ut labore et dolore magna aliqua. Ut enim ad minim veniam, quis nostrud exercitation ullamco labproident, sunt in culpa qui officia deserunt mollit anim id est laborum.Lorem ipsum dolor sit amet, consectetur adipisicing elit, sed do eiusmod tempor incididunt ut labore et dolore magna aliqua. Ut enim ad minim veniam, quis nostrud exercitation ullamco laboris nisi ut aliquip ex ea commodo consequat. Duis aute irure dolor in reprehenderit in voluptate velit esse cillum dolore eu fugiat nulla pasit amet, consectetur adipisicing elit, sed do eiusmod tempor incididunt ut labore et dolore magna aliqua. Ut enim ad minim veniam, quis nostrud exercitation ullamco laboris nisi ut aliquip ex ea commodo consequat. Duis aute irure dolor in reprehenderit in voluptate velit esse cillum dolore eu fugiat nut ut labore et dolore magna aliqua. Ut enim ad minim veniam, quis nostrud exercitation ullamco laboris nisi ut aliquip ex ea commodo consequat. Duis aute irure dolor in reprehenderit in voluptate velit esse cillum dolore eu fugiat nulla pariatur. Excepteur sint occaecat cupidatat non proident, sunt in culpa qui officia deserunt mollit anim id est laborum.Lorem ipsum dolor sit amet, consectetur adipisicing elit, sed do eiusmod tempor incididunt ut labore et dolore magna aliqua. Ut enim ad minim veniam, quis nostrud exercitation ullamcdolor sit amet, consectetur adipisicing elit, sed do eiusmod tempor incididunt ut labore et dolore magna aliqua. Ut enim ad minim veniam, quis nostrud exercitation ullamco laboris nisi ut aliquip ex ea commodo consequat. Duis aute irure dolor in reprehenderit in voluptate velit esse cillum dolore eu fugiat nulla pariatur. Excepteur sint occaecat cupidatat non proident, sunt in culpa qui officia deserunt mollit anim id est laborum.Lorem ipsum dolor sit amet, consectetur adipisicing elit, sed do eiusmod tempor incididunt ut labore et dolore magna aliqua. Ut enim ad minim veniam, quis nostrud exercitation ullamco laboris nisi ut aliquip ex ea commodo consequat. Duis aute irure dolor in reprehenderit in voluptate velit esse cillum dolore eu fugiat nulla pasit amet, consectetur adipisicing elit, sed do eiusmod tempor incididunt ut labore et dolore magna aliqua. Ut enim ad minim veniam, quis nostrud exercitation ullamco laboris nisi ut aliquioris nisi ut aliquip ex ea commodo consequat.</p>';
 
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Latest revision as of 20:06, 17 October 2014

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All the parts the Uppsala iGEM Team 2014 provide for the iGEM Part Registry:

Fav.BioBrick codeTypeConstructDescriptionDesigners
BBa_K1381000Regulatoryyenbox_WTThe Yen systems recognition region fused with a wildtype promoterSensing Group
BBa_K1381001Regulatoryyenbox_J23113The Yen systems recognition region fused with the promoter J23113Sensing Group
BBa_K1381002Regulatoryyenbox_J23101The Yen systems recognition region fused with the promoter J23101Sensing Group
BBa_K1381004CodingB0034-YenRYenR, the activator in the Yen systemSensing Group
BBa_K1381005RegulatoryJ23110-B0034-YenRThe activator YenR coupled to the promoter J23110Sensing Group
BBa_K1381006RegulatoryJ23102-B0034-YenRThe activator YenR coupled to the promoter J23102Sensing Group
BBa_K1381007RegulatoryJ23101-B0034-YenRThe activator YenR coupled to the promoter J23101Sensing Group
BBa_K1381008Measurementyenbox_WT-B0032-GFPA characterisation construct for the yenbox with the wildtype promoterSensing Group
BBa_K1381009Measurementyenbox_J23113-B0032-GFPA characterisation construct for the yenbox with the promoter J23113Sensing Group
BBa_K1381010Measurementyenbox_J23101-B0032-GFPA characterisation construct for the yenbox with the promoter J23101Sensing Group
BBa_K1381011GeneratorJ23113-B0034-CheZThe chemotaxis controlling gene CheZ with the promoter J23113Targeting Group
BBa_K1381012GeneratorJ23114-B0034-CheZThe chemotaxis controlling gene CheZ with the promoter J23114Targeting Group
BBa_K1381013GeneratorJ23100-B0034-CheZThe chemotaxis controlling gene CheZ with the promoter J23100Targeting Group
BBa_K1381014RegulatoryJ23101-spot42_USP45_10bpSilencing sRNA with affinity to USP45Killing Group
BBa_K1381015RegulatoryJ23101-spot42_USP45_15bpSilencing sRNA with affinity to USP45Killing Group
BBa_K1381016RegulatoryJ23101-spot42_USP45_20bpSilencing sRNA with affinity to USP45Killing Group
BBa_K1381017CodingCFY-X6 hisThe gene coding for the bacteriocin colicin FyKilling Group
BBa_K1381018TagB0034-USP45The secretion tag USP45 with the RBS B0034Killing Group
BBa_K1381019DeviceB0034-pelB-CFY-X6 hisThe bacteriocin colicin Fy coupled to the the secretion tag pelBKilling Group
BBa_K1381020GeneratorJ23106-B0034-pelB-CFY-X6 hisColicin Fy coupled to the the secretion tag pelB with the promoter J23106Killing Group
BBa_K1381021GeneratorJ23116-B0034-pelB-CFY-X6 hisColicin Fy coupled to the the secretion tag pelB with the promoter J23116Killing Group
BBa_K1381022DeviceB0034-USP45-CFY-X6 hisThe bacteriocin colicin Fy coupled to the the secretion tag USP45Killing Group
BBa_K1381023GeneratorJ23106-B0034-CFY-X6 hisColicin Fy coupled with the promoter J23106Killing Group
BBa_K1381024TagB0034-pgsA-(EAAAR)x4The anchor tag pgsA with the RBS B0034 and a linkerAdhesion Group
BBa_K1381025ReporterB0034-BFP (RFC25)A mutagenised version of B0034-BFP, compatible with RFC25Adhesion Group