http://2013.igem.org/wiki/index.php?title=Special:Contributions/Hyunsoo_kim&feed=atom&limit=50&target=Hyunsoo_kim&year=&month=2013.igem.org - User contributions [en]2024-03-29T15:44:29ZFrom 2013.igem.orgMediaWiki 1.16.5http://2013.igem.org/Team:Duke/PartsTeam:Duke/Parts2013-09-28T01:03:24Z<p>Hyunsoo kim: /* Biological Parts Submitted */</p>
<hr />
<div>{{Template:Team:Duke}}<br />
<div class="right_box"><br />
='''Biological Parts Submitted'''=<br />
<br />
<br><br />
[[File:LibraryConstructs.png|700px|center]] <br><br />
<div align="center"> Figure 2.1.1. Our Library of Gene Constructs</div> <br> <br />
<br><br />
<br />
From our library of gene constructs shown above, we have selected twelve parts to submit to the Registry of Standard Biological Parts. The twelve that were submitted are tabulated below, and are also labelled on the diagram above. These parts all contain a TEF1 promoter, YFP gene downstream, and a variable number of repressor binding sites (x1, x3) in the 5' UTR region. There are six difference repressor binding site sequences--three that are 16 nucleotides long, and three that are 20 nucleotides long--which can be targeted with our library of repressor constructs (TALEs and sgRNA-dCas9) shown in the diagram. These repressor constructs were not submitted. Summary of the six different binding site sequences and where they are found in our gene constructs are also tabulated at the bottom of this page in Table 2.1.2. Click on the links below to see the '''documentation on the Registry'''.<br />
<br><br />
<br><br><br />
'''Data For Our "Best New BioBrick Part (Engineered)"'''<br />
*[http://parts.igem.org/wiki/index.php?title=Part:BBa_K1204021 Main Page] - Reporter with 3x16C Repressor Binding Sequence, BBa_K1204021 : TEF1pr-BS3x-16C<br />
<br><br />
'''Data For Our "Most Improved Registry Part"'''<br />
*[http://parts.igem.org/wiki/index.php?title=Part:BBa_K1204013 Main Page] - Reporter with 1x16A Repressor Binding Sequence, BBa_K1204013 : TEF1pr-BS1x-16A<br />
<br><br />
'''Data For Our "Best Part Collection"'''<br />
*[http://parts.igem.org/wiki/index.php?title=Part:BBa_K1204013 Main Page] - A collection of reporters with different types/number of repressor binding sequences<br />
**BBa_K1204013 ~ BBa_K1204024<br />
<br />
<br><br><br />
<br />
<groupparts>iGEM013 Duke</groupparts><br />
<div align="center"> Table 2.1.1. Biological Parts Submitted by Team Duke, iGEM 2013 <br>(Disregard the last row entry)</div> <br> <br />
<br />
<br />
<br><br />
[[File:BindingSiteSequence.png|700px|center]] <br><br />
<div align="center"> Table 2.1.2. Our Library of Gene Constructs</div> <br> <br />
<br><br />
<br><br><br><br />
<br />
</div></div>Hyunsoo kimhttp://2013.igem.org/Team:Duke/PartsTeam:Duke/Parts2013-09-28T01:03:05Z<p>Hyunsoo kim: /* Biological Parts Submitted */</p>
<hr />
<div>{{Template:Team:Duke}}<br />
<div class="right_box"><br />
='''Biological Parts Submitted'''=<br />
<br />
<br><br />
[[File:LibraryConstructs.png|700px|center]] <br><br />
<div align="center"> Figure 2.1.1. Our Library of Gene Constructs</div> <br> <br />
<br><br />
<br />
From our library of gene constructs shown above, we have selected twelve parts to submit to the Registry of Standard Biological Parts. The twelve that were submitted are tabulated below, and are also labelled on the diagram above. These parts all contain a TEF1 promoter, YFP gene downstream, and a variable number of repressor binding sites (x1, x3) in the 5' UTR region. There are six difference repressor binding site sequences--three that are 16 nucleotides long, and three that are 20 nucleotides long--which can be targeted with our library of repressor constructs (TALEs and sgRNA-dCas9) shown in the diagram. These repressor constructs were not submitted. Summary of the six different binding site sequences and where they are found in our gene constructs are also tabulated at the bottom of this page in Table 2.1.2. Click on the links below to see the '''documentation on the Registry'''.<br />
<br><br />
<br><br><br />
'''Data For Our "Best New BioBrick Part (Engineered)"'''<br />
*[http://parts.igem.org/wiki/index.php?title=Part:BBa_K1204021 Main Page] - Reporter with 3x16C Repressor Binding Sequence, BBa_K1204021 : TEF1pr-BS3x-16C<br />
<br><br />
'''Data For Our "Most Improved Registry Part"'''<br />
*[http://parts.igem.org/wiki/index.php?title=Part:BBa_K1204013 Main Page] - Reporter with 1x16A Repressor Binding Sequence, BBa_K1204013 : TEF1pr-BS1x-16A<br />
<br><br />
'''Data For Our "Best Part Collection"'''<br />
*[http://parts.igem.org/wiki/index.php?title=Part:BBa_K1204013 Main Page] - A collection of reporters with different types/number of repressor binding sequences, BBa_K1204013 ~ BBa_K1204024<br />
<br />
<br><br><br />
<br />
<groupparts>iGEM013 Duke</groupparts><br />
<div align="center"> Table 2.1.1. Biological Parts Submitted by Team Duke, iGEM 2013 <br>(Disregard the last row entry)</div> <br> <br />
<br />
<br />
<br><br />
[[File:BindingSiteSequence.png|700px|center]] <br><br />
<div align="center"> Table 2.1.2. Our Library of Gene Constructs</div> <br> <br />
<br><br />
<br><br><br><br />
<br />
</div></div>Hyunsoo kimhttp://2013.igem.org/File:BindingSiteSequence.pngFile:BindingSiteSequence.png2013-09-28T00:57:36Z<p>Hyunsoo kim: uploaded a new version of &quot;File:BindingSiteSequence.png&quot;</p>
<hr />
<div></div>Hyunsoo kimhttp://2013.igem.org/Team:Duke/PartsTeam:Duke/Parts2013-09-28T00:56:19Z<p>Hyunsoo kim: /* Biological Parts Submitted */</p>
<hr />
<div>{{Template:Team:Duke}}<br />
<div class="right_box"><br />
='''Biological Parts Submitted'''=<br />
<br />
<br><br />
[[File:LibraryConstructs.png|700px|center]] <br><br />
<div align="center"> Figure 2.1.1. Our Library of Gene Constructs</div> <br> <br />
<br><br />
<br />
From our library of gene constructs shown above, we have selected twelve parts to submit to the Registry of Standard Biological Parts. The twelve that were submitted are tabulated below, and are also labelled on the diagram above. These parts all contain a TEF1 promoter, YFP gene downstream, and a variable number of repressor binding sites (x1, x3) in the 5' UTR region. There are six difference repressor binding site sequences--three that are 16 nucleotides long, and three that are 20 nucleotides long--which can be targeted with our library of repressor constructs (TALEs and sgRNA-dCas9) shown in the diagram. These repressor constructs were not submitted. Summary of the six different binding site sequences and where they are found in our gene constructs are also tabulated at the bottom of this page in Table 2.1.2. Click on the links below to see the '''documentation on the Registry'''.<br />
<br><br />
<br><br><br />
'''Data For Our "Best New BioBrick Part (Engineered)"'''<br />
*[http://parts.igem.org/wiki/index.php?title=Part:BBa_K1204021 Main Page] - Reporter with 3x16C Repressor Binding Sequence, BBa_K1204021 : short description<br />
<br><br />
'''Data For Our "Most Improved Registry Part"'''<br />
*[http://parts.igem.org/wiki/index.php?title=Part:BBa_K1204013 Main Page] - Reporter with 1x16A Repressor Binding Sequence, BBa_K1204013 : short description<br />
*[http://parts.igem.org/wiki/index.php?title=Part:BBa_K1204025 Main Page] - Reporter with 3x16A Repressor Binding Sequence, BBa_K1204025('''<-fix this''') : short description<br />
<br><br />
'''Data For Our "Best Part Collection"'''<br />
*[http://parts.igem.org/wiki/index.php?title=Part:BBa_K1204013 Main Page] - Reporter with 1x20A Repressor Binding Sequence, BBa_K1204013 ~ BBa_K1204024 : short description<br />
<br />
<br><br><br />
<br />
<groupparts>iGEM013 Duke</groupparts><br />
<div align="center"> Table 2.1.1. Biological Parts Submitted by Team Duke, iGEM 2013 <br>(Disregard the last row entry)</div> <br> <br />
<br />
<br />
<br><br />
[[File:BindingSiteSequence.png|700px|center]] <br><br />
<div align="center"> Table 2.1.2. Our Library of Gene Constructs</div> <br> <br />
<br><br />
<br><br><br><br />
<br />
</div></div>Hyunsoo kimhttp://2013.igem.org/Team:Duke/PartsTeam:Duke/Parts2013-09-28T00:50:56Z<p>Hyunsoo kim: /* Biological Parts Submitted */</p>
<hr />
<div>{{Template:Team:Duke}}<br />
<div class="right_box"><br />
='''Biological Parts Submitted'''=<br />
<br />
<br><br />
[[File:LibraryConstructs.png|700px|center]] <br><br />
<div align="center"> Figure 2.1.1. Our Library of Gene Constructs</div> <br> <br />
<br><br />
<br />
From our library of gene constructs shown above, we have selected twelve parts to submit to the Registry of Standard Biological Parts. The twelve that were submitted are tabulated below, and are also labelled on the diagram above. These parts all contain a TEF1 promoter, YFP gene downstream, and a variable number of repressor binding sites (x1, x3) in the 5' UTR region. There are six difference repressor binding site sequences--three that are 16 nucleotides long, and three that are 20 nucleotides long--which can be targeted with our library of repressor constructs (TALEs and sgRNA-dCas9) shown in the diagram. These repressor constructs were not submitted. Summary of the six different binding site sequences and where they are found in our gene constructs are also tabulated at the bottom of this page in Table 2.1.2. Click on the links below to see the '''documentation on the Registry'''.<br />
<br><br />
<br><br><br />
'''Data For Our "Best New BioBrick Part (Engineered)"'''<br />
*[http://parts.igem.org/wiki/index.php?title=Part:BBa_K1204021 Main Page] - Reporter with 1x16A Repressor Binding Sequence, BBa_K1204021 : short description<br />
<br><br />
'''Data For Our "Most Improved Registry Part"'''<br />
*[http://parts.igem.org/wiki/index.php?title=Part:BBa_K1204013 Main Page] - Reporter with 3x16A Repressor Binding Sequence, BBa_K1204013 : short description<br />
*[http://parts.igem.org/wiki/index.php?title=Part:BBa_K1204025 Main Page] - Reporter with 3x16A Repressor Binding Sequence, BBa_K1204025 : short description<br />
<br><br />
'''Data For Our "Best Part Collection"'''<br />
*[http://parts.igem.org/wiki/index.php?title=Part:BBa_K1204013 Main Page] - Reporter with 1x20A Repressor Binding Sequence, BBa_K1204013 ~ BBa_K1204024 : short description<br />
<br />
<br><br><br />
<br />
<groupparts>iGEM013 Duke</groupparts><br />
<div align="center"> Table 2.1.1. Biological Parts Submitted by Team Duke, iGEM 2013 <br>(Disregard the last row entry)</div> <br> <br />
<br />
<br />
<br><br />
[[File:BindingSiteSequence.png|700px|center]] <br><br />
<div align="center"> Table 2.1.2. Our Library of Gene Constructs</div> <br> <br />
<br><br />
<br><br><br><br />
<br />
</div></div>Hyunsoo kimhttp://2013.igem.org/Team:Duke/PartsTeam:Duke/Parts2013-09-28T00:50:32Z<p>Hyunsoo kim: /* Biological Parts Submitted */</p>
<hr />
<div>{{Template:Team:Duke}}<br />
<div class="right_box"><br />
='''Biological Parts Submitted'''=<br />
<br />
<br><br />
[[File:LibraryConstructs.png|700px|center]] <br><br />
<div align="center"> Figure 2.1.1. Our Library of Gene Constructs</div> <br> <br />
<br><br />
<br />
From our library of gene constructs shown above, we have selected twelve parts to submit to the Registry of Standard Biological Parts. The twelve that were submitted are tabulated below, and are also labelled on the diagram above. These parts all contain a TEF1 promoter, YFP gene downstream, and a variable number of repressor binding sites (x1, x3) in the 5' UTR region. There are six difference repressor binding site sequences--three that are 16 nucleotides long, and three that are 20 nucleotides long--which can be targeted with our library of repressor constructs (TALEs and sgRNA-dCas9) shown in the diagram. These repressor constructs were not submitted. Summary of the six different binding site sequences and where they are found in our gene constructs are also tabulated at the bottom of this page in Table 2.1.2. Click on the links below to see the '''documentation on the Registry'''.<br />
<br><br />
<br><br><br />
'''Data For Our "Best New BioBrick Part (Engineered)"'''<br />
*[http://parts.igem.org/wiki/index.php?title=Part:BBa_K1204021 Main Page] - Reporter with 1x16A Repressor Binding Sequence, BBa_K1204021 : short description<br />
<br><br />
'''Data For Our "Most Improved Registry Part"'''<br />
*[http://parts.igem.org/wiki/index.php?title=Part:BBa_K1204013 Main Page] - Reporter with 3x16A Repressor Binding Sequence, BBa_K1204013 : short description<br />
*[http://parts.igem.org/wiki/index.php?title=Part:BBa_K1204025 Main Page] - Reporter with 3x16A Repressor Binding Sequence, BBa_K1204025 : short description<br />
<br><br />
'''Data For Our "Best Part Collection"'''<br />
*[http://parts.igem.org/wiki/index.php?title=Part:BBa_K1204013 Main Page] - Reporter with 1x20A Repressor Binding Sequence, BBa_K1204013 ~ ?? : short description<br />
<br />
<br><br><br />
<br />
<groupparts>iGEM013 Duke</groupparts><br />
<div align="center"> Table 2.1.1. Biological Parts Submitted by Team Duke, iGEM 2013 <br>(Disregard the last row entry)</div> <br> <br />
<br />
<br />
<br><br />
[[File:BindingSiteSequence.png|700px|center]] <br><br />
<div align="center"> Table 2.1.2. Our Library of Gene Constructs</div> <br> <br />
<br><br />
<br><br><br><br />
<br />
</div></div>Hyunsoo kimhttp://2013.igem.org/Team:Duke/PartsTeam:Duke/Parts2013-09-28T00:50:15Z<p>Hyunsoo kim: /* Biological Parts Submitted */</p>
<hr />
<div>{{Template:Team:Duke}}<br />
<div class="right_box"><br />
='''Biological Parts Submitted'''=<br />
<br />
<br><br />
[[File:LibraryConstructs.png|700px|center]] <br><br />
<div align="center"> Figure 2.1.1. Our Library of Gene Constructs</div> <br> <br />
<br><br />
<br />
From our library of gene constructs shown above, we have selected twelve parts to submit to the Registry of Standard Biological Parts. The twelve that were submitted are tabulated below, and are also labelled on the diagram above. These parts all contain a TEF1 promoter, YFP gene downstream, and a variable number of repressor binding sites (x1, x3) in the 5' UTR region. There are six difference repressor binding site sequences--three that are 16 nucleotides long, and three that are 20 nucleotides long--which can be targeted with our library of repressor constructs (TALEs and sgRNA-dCas9) shown in the diagram. These repressor constructs were not submitted. Summary of the six different binding site sequences and where they are found in our gene constructs are also tabulated at the bottom of this page in Table 2.1.2. Click on the links below to see the '''documentation on the Registry'''.<br />
<br><br />
<br><br><br />
'''Data For Our "Best New BioBrick Part (Engineered)"'''<br />
*[http://parts.igem.org/wiki/index.php?title=Part:BBa_K1204021 Main Page] - Reporter with 1x16A Repressor Binding Sequence, BBa_K1204021 : short description<br />
<br><br><br />
'''Data For Our "Most Improved Registry Part"'''<br />
*[http://parts.igem.org/wiki/index.php?title=Part:BBa_K1204013 Main Page] - Reporter with 3x16A Repressor Binding Sequence, BBa_K1204013 : short description<br />
*[http://parts.igem.org/wiki/index.php?title=Part:BBa_K1204025 Main Page] - Reporter with 3x16A Repressor Binding Sequence, BBa_K1204025 : short description<br />
<br><br><br />
'''Data For Our "Best Part Collection"'''<br />
*[http://parts.igem.org/wiki/index.php?title=Part:BBa_K1204013 Main Page] - Reporter with 1x20A Repressor Binding Sequence, BBa_K1204013 ~ ?? : short description<br />
<br />
<br><br><br />
<br />
<groupparts>iGEM013 Duke</groupparts><br />
<div align="center"> Table 2.1.1. Biological Parts Submitted by Team Duke, iGEM 2013 <br>(Disregard the last row entry)</div> <br> <br />
<br />
<br />
<br><br />
[[File:BindingSiteSequence.png|700px|center]] <br><br />
<div align="center"> Table 2.1.2. Our Library of Gene Constructs</div> <br> <br />
<br><br />
<br><br><br><br />
<br />
</div></div>Hyunsoo kimhttp://2013.igem.org/Team:Duke/PartsTeam:Duke/Parts2013-09-28T00:49:30Z<p>Hyunsoo kim: /* Biological Parts Submitted */</p>
<hr />
<div>{{Template:Team:Duke}}<br />
<div class="right_box"><br />
='''Biological Parts Submitted'''=<br />
<br />
<br><br />
[[File:LibraryConstructs.png|700px|center]] <br><br />
<div align="center"> Figure 2.1.1. Our Library of Gene Constructs</div> <br> <br />
<br><br />
<br />
From our library of gene constructs shown above, we have selected twelve parts to submit to the Registry of Standard Biological Parts. The twelve that were submitted are tabulated below, and are also labelled on the diagram above. These parts all contain a TEF1 promoter, YFP gene downstream, and a variable number of repressor binding sites (x1, x3) in the 5' UTR region. There are six difference repressor binding site sequences--three that are 16 nucleotides long, and three that are 20 nucleotides long--which can be targeted with our library of repressor constructs (TALEs and sgRNA-dCas9) shown in the diagram. These repressor constructs were not submitted. Summary of the six different binding site sequences and where they are found in our gene constructs are also tabulated at the bottom of this page in Table 2.1.2. Click on the links below to see the '''documentation on the Registry'''.<br />
<br><br />
<br><br><br />
'''Data For Our "Best New BioBrick Part (Engineered)"'''<br />
*[http://parts.igem.org/wiki/index.php?title=Part:BBa_K1204021 Main Page] - Reporter with 1x16A Repressor Binding Sequence, BBa_K1204021 : short description<br />
'''Data For Our "Most Improved Registry Part"'''<br />
*[http://parts.igem.org/wiki/index.php?title=Part:BBa_K1204013 Main Page] - Reporter with 3x16A Repressor Binding <br />
Sequence, BBa_K1204013 : short description<br />
*[http://parts.igem.org/wiki/index.php?title=Part:BBa_K1204025 Main Page] - Reporter with 3x16A Repressor Binding <br />
Sequence, BBa_K1204025 : short description<br />
'''Data For Our "Best Part Collection"'''<br />
*[http://parts.igem.org/wiki/index.php?title=Part:BBa_K1204013 Main Page] - Reporter with 1x20A Repressor Binding Sequence, BBa_K1204013 ~ ?? : short description<br />
<br />
<br><br><br />
<br />
<groupparts>iGEM013 Duke</groupparts><br />
<div align="center"> Table 2.1.1. Biological Parts Submitted by Team Duke, iGEM 2013 <br>(Disregard the last row entry)</div> <br> <br />
<br />
<br />
<br><br />
[[File:BindingSiteSequence.png|700px|center]] <br><br />
<div align="center"> Table 2.1.2. Our Library of Gene Constructs</div> <br> <br />
<br><br />
<br><br><br><br />
<br />
</div></div>Hyunsoo kimhttp://2013.igem.org/Template:Team:DukeTemplate:Team:Duke2013-09-28T00:46:13Z<p>Hyunsoo kim: </p>
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<div><a href="https://2013.igem.org/Team:Duke">Home</a></div><br />
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<li><a href="https://2013.igem.org/Team:Duke/Project/Problem">The Project</a></li><br />
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<li><a href="https://2013.igem.org/Team:Duke/Project/Design">Experimental Design</a></li> <br />
<li><a href="https://2013.igem.org/Team:Duke/Project/Results/Part1">Results:<br>Library of DNA Parts</a></li><br />
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<!-- <li><a href="https://2013.igem.org/Team:Duke/Project/CRISPR_Results">Results: CRISPR</a></li> --><br />
<br />
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<div><a href="https://2013.igem.org/Team:Duke/Parts">Biological Parts Submitted</a></div><br />
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<li><a href="https://2013.igem.org/Team:Duke/Modeling/Thermodynamic_Model_Application">Thermodynamic Model : Cooperative Repression</a></li><br />
<li><a href="https://2013.igem.org/Team:Duke/Modeling/Kinetic_Model">Kinetic Model : <br>Bifurcation and Bistability</a></li><br />
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<!-- <li><a href="https://2013.igem.org/Team:Duke/Notebook/Prezi">Project Outline (Prezi) </a></li> --><br />
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<li><a href="https://2013.igem.org/Team:Duke/Safety/Xanthomonas"><i>Xanthomonas</i> Bacteria</a></li><br />
</ul> <br />
<div><a href="https://2013.igem.org/Team:Duke/Attributions">Attributions</a></div><br />
<!--ul><br />
<li><a href="#">1</a></li><br />
<li><a href="#">2</a></li><br />
<li><a href="#">3</a></li><br />
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<!-- <div><a href="https://2013.igem.org/Team:Duke/Gallery">Gallery</a></div> --><br />
<br />
<!-- <div class="menuheaders"><a>University & Jamboree</a></div> --><br />
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<!--<br />
<div><a href="https://2013.igem.org/Team:Duke/Sponsors">Our Sponsors</a></div><br />
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<li><a href="#">Military Press</a></li><br />
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<br />
<div><a href="https://2013.igem.org/">iGEM 2013</a></div><br />
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<!-- *** COLOMBIA 2012 HEADER USED/EDITED *** --></div>Hyunsoo kimhttp://2013.igem.org/File:Banner_transparent_small_2.pngFile:Banner transparent small 2.png2013-09-28T00:44:35Z<p>Hyunsoo kim: uploaded a new version of &quot;File:Banner transparent small 2.png&quot;</p>
<hr />
<div></div>Hyunsoo kimhttp://2013.igem.org/File:Banner_transparent_small_2.pngFile:Banner transparent small 2.png2013-09-28T00:43:41Z<p>Hyunsoo kim: uploaded a new version of &quot;File:Banner transparent small 2.png&quot;</p>
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<div></div>Hyunsoo kimhttp://2013.igem.org/Template:Team:DukeTemplate:Team:Duke2013-09-28T00:42:17Z<p>Hyunsoo kim: </p>
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<!-- *** COLOMBIA 2012 HEADER USED/EDITED *** --></div>Hyunsoo kimhttp://2013.igem.org/Template:Team:DukeTemplate:Team:Duke2013-09-28T00:40:26Z<p>Hyunsoo kim: </p>
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<!-- <li><a href="https://2013.igem.org/Team:Duke/Project/CRISPR_Results">Results: CRISPR</a></li> --><br />
<br />
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<div><a href="https://2013.igem.org/Team:Duke/Parts">Biological Parts Submitted</a></div><br />
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<li><a href="https://2013.igem.org/Team:Duke/Safety/Xanthomonas"><i>Xanthomonas</i> Bacteria</a></li><br />
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<div><a href="https://2013.igem.org/Team:Duke/Attributions">Attributions</a></div><br />
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<!-- *** COLOMBIA 2012 HEADER USED/EDITED *** --></div>Hyunsoo kimhttp://2013.igem.org/File:Banner_transparent_small_2.pngFile:Banner transparent small 2.png2013-09-28T00:39:46Z<p>Hyunsoo kim: </p>
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<div></div>Hyunsoo kimhttp://2013.igem.org/Template:Team:DukeTemplate:Team:Duke2013-09-28T00:37:57Z<p>Hyunsoo kim: </p>
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<div><a href="https://2013.igem.org/Team:Duke">Home</a></div><br />
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<div class="menuheaders"><a href="https://2013.igem.org/Team:Duke/Team">Team Duke 2013</a></div><br />
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<li><a href="https://2013.igem.org/Team:Duke/Team#The_Team">The Team</a></li><br />
<li><a href="https://2013.igem.org/Team:Duke/Team#Undergrads">Undergrads</a></li><br />
<li><a href="https://2013.igem.org/Team:Duke/Team#Grad_Students">Grad Students</a></li><br />
<li><a href="https://2013.igem.org/Team:Duke/Team#Instructors">Instructors</a></li><br />
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<div class="menuheaders"><a>Genetic Toggle Switch</a></div><br />
<ul class="menucontents"><br />
<li><a href="https://2013.igem.org/Team:Duke/Project/Problem">The Project</a></li><br />
<li><a href="https://2013.igem.org/Team:Duke/Project/Basics">Background Information</a></li> <br />
<li><a href="https://2013.igem.org/Team:Duke/Project/Design">Experimental Design</a></li> <br />
<li><a href="https://2013.igem.org/Team:Duke/Project/Results/Part1">Results:<br>Library of DNA Parts</a></li><br />
<li><a href="https://2013.igem.org/Team:Duke/Project/Results/Part2">Results:<br>Parts Characterization</a></li><br />
<!-- <li><a href="https://2013.igem.org/Team:Duke/Project/CRISPR_Results">Results: CRISPR</a></li> --><br />
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<div><a href="https://2013.igem.org/Team:Duke/Parts">Biological Parts Submitted</a></div><br />
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<br />
<div><a href="https://2013.igem.org/">iGEM 2013</a></div><br />
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<div></div>Hyunsoo kimhttp://2013.igem.org/File:Title_Gene.jpgFile:Title Gene.jpg2013-09-28T00:31:28Z<p>Hyunsoo kim: </p>
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<div></div>Hyunsoo kimhttp://2013.igem.org/Template:Team:DukeTemplate:Team:Duke2013-09-28T00:28:52Z<p>Hyunsoo kim: </p>
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<div><a href="https://2013.igem.org/Team:Duke">Home</a></div><br />
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<div class="menuheaders"><a href="https://2013.igem.org/Team:Duke/Team">Team Duke 2013</a></div><br />
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<li><a href="https://2013.igem.org/Team:Duke/Team#The_Team">The Team</a></li><br />
<li><a href="https://2013.igem.org/Team:Duke/Team#Undergrads">Undergrads</a></li><br />
<li><a href="https://2013.igem.org/Team:Duke/Team#Grad_Students">Grad Students</a></li><br />
<li><a href="https://2013.igem.org/Team:Duke/Team#Instructors">Instructors</a></li><br />
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<br />
<div class="menuheaders"><a>Genetic Toggle Switch</a></div><br />
<ul class="menucontents"><br />
<li><a href="https://2013.igem.org/Team:Duke/Project/Problem">The Project</a></li><br />
<li><a href="https://2013.igem.org/Team:Duke/Project/Basics">Background Information</a></li> <br />
<li><a href="https://2013.igem.org/Team:Duke/Project/Design">Experimental Design</a></li> <br />
<li><a href="https://2013.igem.org/Team:Duke/Project/Results/Part1">Results:<br>Library of DNA Parts</a></li><br />
<li><a href="https://2013.igem.org/Team:Duke/Project/Results/Part2">Results:<br>Parts Characterization</a></li><br />
<!-- <li><a href="https://2013.igem.org/Team:Duke/Project/CRISPR_Results">Results: CRISPR</a></li> --><br />
<br />
</ul> <br />
<div><a href="https://2013.igem.org/Team:Duke/Parts">Biological Parts Submitted</a></div><br />
<!--ul><br />
<li><a href="#">Via Email</a></li><br />
<li><a href="#">Stalk Us Elsewhere</a></li><br />
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<div class="menuheaders"><a>Mathematical Modeling</a></div><br />
<ul class="menucontents"><br />
<li><a href="https://2013.igem.org/Team:Duke/Modeling/Cooperativity">Cooperativity and Hill Equation</a></li><br />
<li><a href="https://2013.igem.org/Team:Duke/Modeling/Thermodynamic_Model_Intro">Thermodynamic Model : Introduction</a></li><br />
<li><a href="https://2013.igem.org/Team:Duke/Modeling/Thermodynamic_Model_Application">Thermodynamic Model : Cooperative Repression</a></li><br />
<li><a href="https://2013.igem.org/Team:Duke/Modeling/Kinetic_Model">Kinetic Model : <br>Bifurcation and Bistability</a></li><br />
</ul> <br />
<!-- <div><a href="https://2013.igem.org/Team:Duke/Notebook">Results</a></div> --><br />
<div class="menuheaders"><a href="https://2013.igem.org/Team:Duke/Human/">Human Practices</a></div><br />
<ul class="menucontents"><br />
<li><a href="https://2013.igem.org/Team:Duke/Human/FromBenchToBiotech">From Bench to Biotech</a></li><br />
<!--<li><a href="https://2013.igem.org/Team:Duke/Human/2">BBBB</a></li>--><br />
</ul><br />
<br />
<div class="menuheaders"><a>Lab Notebook</a></div><br />
<ul class="menucontents"><br />
<li><a href="https://2013.igem.org/Team:Duke/Notebook/Lab_Notebook">Overview</a></li><br />
<li><a href="https://2013.igem.org/Team:Duke/Notebook/Protocols">Protocols</a></li><br />
<li><a href="https://2013.igem.org/Team:Duke/Notebook/Strain List">Strain List</a></li><br />
<!-- <li><a href="https://2013.igem.org/Team:Duke/Notebook/Prezi">Project Outline (Prezi) </a></li> --><br />
</ul> <br />
<div class="menuheaders"><a href="https://2013.igem.org/Team:Duke/Safety">Safety</a></div><br />
<ul class="menucontents"><br />
<li><a href="https://2013.igem.org/Team:Duke/Safety/Ecoli_and_Scerevisiae"><i>E.coli</i> and <i>S.cerevisiae</i></a></li><br />
<li><a href="https://2013.igem.org/Team:Duke/Safety/Xanthomonas"><i>Xanthomonas</i> Bacteria</a></li><br />
</ul> <br />
<div><a href="https://2013.igem.org/Team:Duke/Attributions">Attributions</a></div><br />
<!--ul><br />
<li><a href="#">1</a></li><br />
<li><a href="#">2</a></li><br />
<li><a href="#">3</a></li><br />
</ul--> <br />
<!-- <div><a href="https://2013.igem.org/Team:Duke/Gallery">Gallery</a></div> --><br />
<br />
<!-- <div class="menuheaders"><a>University & Jamboree</a></div> --><br />
<!--ul class="menucontents"><br />
<li><a href="http://www.uniandes.edu.co">DUKE? </a></li><br />
<li><a href="https://2012.igem.org/Regions/Latin_America/Jamboree">North American Jamboree 2013</a></li><br />
</ul--> <br />
<!--<br />
<div><a href="https://2013.igem.org/Team:Duke/Sponsors">Our Sponsors</a></div><br />
<!--ul><br />
<li><a href="#">Bench Press</a></li><br />
<li><a href="#">Military Press</a></li><br />
<li><a href="#">Press n Seal</a></li><br />
</ul--> <br />
<br />
<div><a href="https://2013.igem.org/">iGEM 2013</a></div><br />
<br />
</div><br />
<br />
<br />
<br />
<br />
</div><br />
<br />
</body><br />
</html><br />
<br />
<!-- *** COLOMBIA 2012 HEADER USED/EDITED *** --></div>Hyunsoo kimhttp://2013.igem.org/File:Banner_transparent.pngFile:Banner transparent.png2013-09-28T00:16:55Z<p>Hyunsoo kim: </p>
<hr />
<div></div>Hyunsoo kimhttp://2013.igem.org/Team:Duke/Project/Results/Part2Team:Duke/Project/Results/Part22013-09-28T00:06:08Z<p>Hyunsoo kim: /* TEF1 reporters */</p>
<hr />
<div>{{Template:Team:Duke}}<br />
<div class="right_box"><br />
<br />
='''Results: Part Characterization using Flow Cytometry'''=<br />
<br />
After being integrated into the yeast genome, parts were characterized individually by flow cytometry.<br />
<br><br><br />
==TALEs==<br />
<br />
*Initial characterization: TALE-mCherry constructs are present and expression is inducible by &beta;-estradiol. Cells were grown with and without &beta;-estradiol and fluorescence was compared to background levels using a control strain. Our flow cytometry data shows ~4 fold increase in fluorescence with &beta;-estradiol, indicating TALE transcription with operating mCherry tag.<br />
<br />
<br />
<br />
[[File:TaleInduction.png|450px|center]] <br><br />
<div align="center"> Figure 1.5.1. Change in Fluorescence with &beta;-estradiol Induction</div><br />
<br><br />
<br><br />
*Relationship between beta-estradiol concentration and TALE-mCherry expression: Cells were grown in varied &beta;-estradiol concentrations and fluorescence was compared to background levels using a control strain. The induction curves are shown for four strains of yeast that produced different TALEs (16B, 16C, 20B, and 20C) with &beta;-ED concentrations of 0.1nM through 1000nM<br />
<br />
<br />
[[File:TaleInduction2.png|730px|center]] <br><br />
<div align="center"> Figure 1.5.2. Induction Curves for TALEs with Varying &beta;-estradiol Concentrations</div><br />
<br><br />
<br><br />
<br />
==ACT1 reporters==<br />
<br />
*Initial characterization: ACT1-yEVenus constructs with no operators showed distinct constitutive gene expression (green). However, presence of operator sites in the 5' UTR knocked down constitutive expression almost to background levels. In lieu of these results, we decided to construct TEF1-promoter reporter constructs. TEF1 is a stronger constitutive promoter that we hoped would counteract the effects of the operator sequence on constitutive expression levels. <br />
<br />
<br />
<br />
[[File:ActReporter.png|450px|center]] <br><br />
<div align="center"> Figure 1.5.3. Reduced ACT1 Promoter Activity with Binding Sites in 5' UTR </div><br />
<br><br />
<br><br />
<br />
==TEF1 reporters==<br />
<br />
*Initial characterization: TEF1-yEVenus constructs with operator sites in the 5' UTR showed expression levels significantly higher than background levels, and comparatively higher than the ACT1-yEVenus constructs. <br />
<br><br />
<br><br />
<br />
<br />
[[File:TefReporter.png|450px|center]] <br><br />
<div align="center"> Figure 1.5.3. Strong TEF1 Promoter Activity </div><br />
<br><br />
<br><br />
<br><br />
<br><br />
<br><br />
<br />
</div></div>Hyunsoo kimhttp://2013.igem.org/Team:Duke/Project/Results/Part2Team:Duke/Project/Results/Part22013-09-28T00:05:30Z<p>Hyunsoo kim: /* Results: Part Characterization using Flow Cytometry */</p>
<hr />
<div>{{Template:Team:Duke}}<br />
<div class="right_box"><br />
<br />
='''Results: Part Characterization using Flow Cytometry'''=<br />
<br />
After being integrated into the yeast genome, parts were characterized individually by flow cytometry.<br />
<br><br><br />
==TALEs==<br />
<br />
*Initial characterization: TALE-mCherry constructs are present and expression is inducible by &beta;-estradiol. Cells were grown with and without &beta;-estradiol and fluorescence was compared to background levels using a control strain. Our flow cytometry data shows ~4 fold increase in fluorescence with &beta;-estradiol, indicating TALE transcription with operating mCherry tag.<br />
<br />
<br />
<br />
[[File:TaleInduction.png|450px|center]] <br><br />
<div align="center"> Figure 1.5.1. Change in Fluorescence with &beta;-estradiol Induction</div><br />
<br><br />
<br><br />
*Relationship between beta-estradiol concentration and TALE-mCherry expression: Cells were grown in varied &beta;-estradiol concentrations and fluorescence was compared to background levels using a control strain. The induction curves are shown for four strains of yeast that produced different TALEs (16B, 16C, 20B, and 20C) with &beta;-ED concentrations of 0.1nM through 1000nM<br />
<br />
<br />
[[File:TaleInduction2.png|730px|center]] <br><br />
<div align="center"> Figure 1.5.2. Induction Curves for TALEs with Varying &beta;-estradiol Concentrations</div><br />
<br><br />
<br><br />
<br />
==ACT1 reporters==<br />
<br />
*Initial characterization: ACT1-yEVenus constructs with no operators showed distinct constitutive gene expression (green). However, presence of operator sites in the 5' UTR knocked down constitutive expression almost to background levels. In lieu of these results, we decided to construct TEF1-promoter reporter constructs. TEF1 is a stronger constitutive promoter that we hoped would counteract the effects of the operator sequence on constitutive expression levels. <br />
<br />
<br />
<br />
[[File:ActReporter.png|450px|center]] <br><br />
<div align="center"> Figure 1.5.3. Reduced ACT1 Promoter Activity with Binding Sites in 5' UTR </div><br />
<br><br />
<br><br />
<br />
==TEF1 reporters==<br />
<br />
*Initial characterization: TEF1-yEVenus constructs with operator sites in the 5' UTR showed expression levels significantly higher than background levels, and comparatively higher than the ACT1-yEVenus constructs. <br />
<br><br />
<br><br />
<br />
<br />
[[File:TefReporter.png|450px|center]] <br><br />
<div align="center"> Figure 1.5.3. Reduced ACT1 Promoter Activity with Binding Sites in 5' UTR </div><br />
<br><br />
<br><br />
<br><br />
<br><br />
<br><br />
<br />
</div></div>Hyunsoo kimhttp://2013.igem.org/File:TefReporter.pngFile:TefReporter.png2013-09-28T00:05:10Z<p>Hyunsoo kim: </p>
<hr />
<div></div>Hyunsoo kimhttp://2013.igem.org/Team:Duke/PartsTeam:Duke/Parts2013-09-27T23:53:13Z<p>Hyunsoo kim: /* Biological Parts Submitted */</p>
<hr />
<div>{{Template:Team:Duke}}<br />
<div class="right_box"><br />
='''Biological Parts Submitted'''=<br />
<br />
<br><br />
[[File:LibraryConstructs.png|700px|center]] <br><br />
<div align="center"> Figure 2.1.1. Our Library of Gene Constructs</div> <br> <br />
<br><br />
<br />
From our library of gene constructs shown above, we have selected twelve parts to submit to the Registry of Standard Biological Parts. The twelve that were submitted are tabulated below, and are also labelled on the diagram above. These parts all contain a TEF1 promoter, YFP gene downstream, and a variable number of repressor binding sites (x1, x3) in the 5' UTR region. There are six difference repressor binding site sequences--three that are 16 nucleotides long, and three that are 20 nucleotides long--which can be targeted with our library of repressor constructs (TALEs and sgRNA-dCas9) shown in the diagram. These repressor constructs were not submitted. Summary of the six different binding site sequences and where they are found in our gene constructs are also tabulated at the bottom of this page in Table 2.1.2. Click on the links below to see the '''documentation on the Registry'''.<br />
<br><br />
<br><br><br />
'''Data For Our Favorite New Parts'''<br />
#[http://parts.igem.org/wiki/index.php?title=Part:BBa_K1204013 Main Page] - Reporter with 1x16A Repressor Binding Sequence, BBa_K1204013 : short description<br />
#[http://parts.igem.org/wiki/index.php?title=Part:BBa_K1204014 Main Page] - Reporter with 3x16A Repressor Binding Sequence, BBa_K1204014 ?? : short description<br />
#[http://parts.igem.org/wiki/index.php?title=Part:BBa_K1204016 Main Page] - Reporter with 1x20A Repressor Binding Sequence, BBa_K1204016 ?? : short description<br />
<br />
<br><br><br />
<br />
<groupparts>iGEM013 Duke</groupparts><br />
<div align="center"> Table 2.1.1. Biological Parts Submitted by Team Duke, iGEM 2013 <br>(Disregard the last row entry)</div> <br> <br />
<br />
<br />
<br><br />
[[File:BindingSiteSequence.png|700px|center]] <br><br />
<div align="center"> Table 2.1.2. Our Library of Gene Constructs</div> <br> <br />
<br><br />
<br><br><br><br />
<br />
</div></div>Hyunsoo kimhttp://2013.igem.org/Team:Duke/PartsTeam:Duke/Parts2013-09-27T23:48:34Z<p>Hyunsoo kim: /* Biological Parts Submitted */</p>
<hr />
<div>{{Template:Team:Duke}}<br />
<div class="right_box"><br />
='''Biological Parts Submitted'''=<br />
<br />
<br><br />
[[File:LibraryConstructs.png|700px|center]] <br><br />
<div align="center"> Figure 2.1.1. Our Library of Gene Constructs</div> <br> <br />
<br><br />
<br />
From our library of gene constructs shown above, we have selected twelve parts to submit to the Registry of Standard Biological Parts. The twelve that were submitted are tabulated below, and are also labelled on the diagram above. These parts all contain a TEF1 promoter, YFP gene downstream, and a variable number of repressor binding sites (x1, x3) in the 5' UTR region. There are six difference repressor binding site sequences--three that are 16 nucleotides long, and three that are 20 nucleotides long--which can be targeted with our library of repressor constructs (TALEs and sgRNA-dCas9) shown in the diagram. These repressor constructs were not submitted. Summary of the six different binding site sequences and where they are found in our gene constructs are also tabulated at the bottom of this page in Table 2.1.2. Click on the links below to see the '''documentation on the Registry'''.<br />
<br><br />
<br><br><br />
'''Data For Our Favorite New Parts'''<br />
#[http://parts.igem.org/wiki/index.php?title=Part:BBa_K1204013 Main Page] - Reporter with 1x16A Repressor Binding Sequence, BBa_K1204013 : short description<br />
<br />
#[http://parts.igem.org/wiki/index.php?title=Part:BBa_K1204014 Main Page] - Reporter with 3x16A Repressor Binding Sequence, BBa_K1204014 ?? : short description<br />
<br />
#[http://parts.igem.org/wiki/index.php?title=Part:BBa_K1204016 Main Page] - Reporter with 1x20A Repressor Binding Sequence, BBa_K1204016 ?? : short description<br />
<br />
<br><br><br />
<br />
<groupparts>iGEM013 Duke</groupparts><br />
<div align="center"> Table 2.1.1. Biological Parts Submitted by Team Duke, iGEM 2013 <br>(Disregard the last row entry)</div> <br> <br />
<br />
<br />
<br><br />
[[File:BindingSiteSequence.png|700px|center]] <br><br />
<div align="center"> Table 2.1.2. Our Library of Gene Constructs</div> <br> <br />
<br><br />
<br><br><br><br />
<br />
</div></div>Hyunsoo kimhttp://2013.igem.org/Team:Duke/PartsTeam:Duke/Parts2013-09-27T23:47:56Z<p>Hyunsoo kim: /* Biological Parts Submitted */</p>
<hr />
<div>{{Template:Team:Duke}}<br />
<div class="right_box"><br />
='''Biological Parts Submitted'''=<br />
<br />
<br><br />
[[File:LibraryConstructs.png|700px|center]] <br><br />
<div align="center"> Figure 2.1.1. Our Library of Gene Constructs</div> <br> <br />
<br><br />
<br />
From our library of gene constructs shown above, we have selected twelve parts to submit to the Registry of Standard Biological Parts. The twelve that were submitted are tabulated below, and are also labelled on the diagram above. These parts all contain a TEF1 promoter, YFP gene downstream, and a variable number of repressor binding sites (x1, x3) in the 5' UTR region. There are six difference repressor binding site sequences--three that are 16 nucleotides long, and three that are 20 nucleotides long--which can be targeted with our library of repressor constructs (TALEs and sgRNA-dCas9) shown in the diagram. These repressor constructs were not submitted. Summary of the six different binding site sequences and where they are found in our gene constructs are also tabulated at the bottom of this page in Table 2.1.2. Click on the links below to see the '''documentation on the Registry'''.<br />
<br><br />
<br><br><br />
'''Data For Our Favorite New Parts'''<br />
#[http://parts.igem.org/wiki/index.php?title=Part:BBa_K1204013 Main Page] - <br />
Reporter with 1x16A Repressor Binding Sequence, BBa_K1204013 : short description<br />
<br />
#[http://parts.igem.org/wiki/index.php?title=Part:BBa_K1204014 Main Page] - <br />
Reporter with 3x16A Repressor Binding Sequence, BBa_K1204014 ?? : short description<br />
<br />
#[http://parts.igem.org/wiki/index.php?title=Part:BBa_K1204016 Main Page] - <br />
Reporter with 1x20A Repressor Binding Sequence, BBa_K1204016 ?? : short description<br />
<br />
<br><br><br />
<br />
<groupparts>iGEM013 Duke</groupparts><br />
<div align="center"> Table 2.1.1. Biological Parts Submitted by Team Duke, iGEM 2013 <br>(Disregard the last row entry)</div> <br> <br />
<br />
<br />
<br><br />
[[File:BindingSiteSequence.png|700px|center]] <br><br />
<div align="center"> Table 2.1.2. Our Library of Gene Constructs</div> <br> <br />
<br><br />
<br><br><br><br />
<br />
</div></div>Hyunsoo kimhttp://2013.igem.org/Team:Duke/PartsTeam:Duke/Parts2013-09-27T23:45:03Z<p>Hyunsoo kim: /* Biological Parts Submitted */</p>
<hr />
<div>{{Template:Team:Duke}}<br />
<div class="right_box"><br />
='''Biological Parts Submitted'''=<br />
<br />
<br><br />
[[File:LibraryConstructs.png|700px|center]] <br><br />
<div align="center"> Figure 2.1.1. Our Library of Gene Constructs</div> <br> <br />
<br><br />
<br />
From our library of gene constructs shown above, we have selected twelve parts to submit to the Registry of Standard Biological Parts. The twelve that were submitted are tabulated below, and are also labelled on the diagram above. These parts all contain a TEF1 promoter, YFP gene downstream, and a variable number of repressor binding sites (x1, x3) in the 5' UTR region. There are six difference repressor binding site sequences--three that are 16 nucleotides long, and three that are 20 nucleotides long--which can be targeted with our library of repressor constructs (TALEs and sgRNA-dCas9) shown in the diagram. These repressor constructs were not submitted. Click on the links below to see the '''documentation on the Registry'''.<br />
<br><br />
<br><br><br />
'''Data For Our Favorite New Parts'''<br />
#[http://parts.igem.org/wiki/index.php?title=Part:BBa_K1204013 Main Page] - <br />
Reporter with 1x16A Repressor Binding Sequence, BBa_K1204013 : short description<br />
<br />
#[http://parts.igem.org/wiki/index.php?title=Part:BBa_K1204014 Main Page] - <br />
Reporter with 3x16A Repressor Binding Sequence, BBa_K1204014 ?? : short description<br />
<br />
#[http://parts.igem.org/wiki/index.php?title=Part:BBa_K1204016 Main Page] - <br />
Reporter with 1x20A Repressor Binding Sequence, BBa_K1204016 ?? : short description<br />
<br />
<br><br><br />
<br />
<groupparts>iGEM013 Duke</groupparts><br />
<div align="center"> Table 2.1.1. Biological Parts Submitted by Team Duke, iGEM 2013 <br>(Disregard the last row entry)</div> <br> <br />
<br />
<br />
<br><br />
[[File:BindingSiteSequence.png|700px|center]] <br><br />
<div align="center"> Table 2.1.2. Our Library of Gene Constructs</div> <br> <br />
<br><br />
<br><br><br><br />
<br />
</div></div>Hyunsoo kimhttp://2013.igem.org/Team:Duke/PartsTeam:Duke/Parts2013-09-27T23:44:40Z<p>Hyunsoo kim: /* Biological Parts Submitted */</p>
<hr />
<div>{{Template:Team:Duke}}<br />
<div class="right_box"><br />
='''Biological Parts Submitted'''=<br />
<br />
<br><br />
[[File:LibraryConstructs.png|700px|center]] <br><br />
<div align="center"> Figure 2.1.1. Our Library of Gene Constructs</div> <br> <br />
<br><br />
<br />
From our library of gene constructs shown above, we have selected twelve parts to submit to the Registry of Standard Biological Parts. The twelve that were submitted are tabulated below, and are also labelled on the diagram above. These parts all contain a TEF1 promoter, YFP gene downstream, and a variable number of repressor binding sites (x1, x3) in the 5' UTR region. There are six difference repressor binding site sequences--three that are 16 nucleotides long, and three that are 20 nucleotides long--which can be targeted with our library of repressor constructs (TALEs and sgRNA-dCas9) shown in the diagram. These repressor constructs were not submitted. Click on the links below to see the '''documentation on the Registry'''.<br />
<br><br />
<br><br><br />
'''Data For Our Favorite New Parts'''<br />
#[http://parts.igem.org/wiki/index.php?title=Part:BBa_K1204013 Main Page] - <br />
Reporter with 1x16A Repressor Binding Sequence, BBa_K1204013 : short description<br />
<br />
#[http://parts.igem.org/wiki/index.php?title=Part:BBa_K1204014 Main Page] - <br />
Reporter with 3x16A Repressor Binding Sequence, BBa_K1204014 ?? : short description<br />
<br />
#[http://parts.igem.org/wiki/index.php?title=Part:BBa_K1204016 Main Page] - <br />
Reporter with 1x20A Repressor Binding Sequence, BBa_K1204016 ?? : short description<br />
<br />
<br><br><br />
<br />
<groupparts>iGEM013 Duke</groupparts><br />
<div align="center"> Table 2.1.1. Biological Parts Submitted by Team Duke, iGEM 2013 <br>(Disregard the last row entry)</div> <br> <br />
<br />
<br />
<br><br />
[[File:BindingSiteSequence.png|700px|center]] <br><br />
<div align="center"> Table 2.1.2. Our Library of Gene Constructs</div> <br> <br />
<br><br />
<br />
<br />
<br />
<br />
[https://igem.org/Sample_Data_Page Sample Data Page]<br />
<br />
<br />
An important aspect of the iGEM competition is the use and creation of standard biological parts. Each team will make new parts during iGEM and will place them in the [http://partsregistry.org Registry of Standard Biological Parts]. The iGEM software provides an easy way to present the parts your team has created . The "groupparts" tag will generate a table with all of the parts that your team adds to your team sandbox. Note that if you want to document a part you need to document it on the [http://partsregistry.org Registry], not on your team wiki.<br />
<br />
Remember that the goal of proper part documentation is to describe and define a part such that it can be used without a need to refer to the primary literature. The next iGEM team 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.<br />
<br />
<br />
<br />
<br />
<br />
</div></div>Hyunsoo kimhttp://2013.igem.org/File:LibraryConstructs.pngFile:LibraryConstructs.png2013-09-27T23:43:48Z<p>Hyunsoo kim: uploaded a new version of &quot;File:LibraryConstructs.png&quot;</p>
<hr />
<div></div>Hyunsoo kimhttp://2013.igem.org/Team:Duke/PartsTeam:Duke/Parts2013-09-27T23:41:51Z<p>Hyunsoo kim: /* Biological Parts Submitted */</p>
<hr />
<div>{{Template:Team:Duke}}<br />
<div class="right_box"><br />
='''Biological Parts Submitted'''=<br />
<br />
<br><br />
[[File:LibraryConstructs.png|700px|center]] <br><br />
<div align="center"> Figure 2.1.1. Our Library of Gene Constructs</div> <br> <br />
<br><br />
<br />
From our library of gene constructs shown above, we have selected twelve parts to submit to the Registry of Standard Biological Parts. The twelve that were submitted are tabulated below, and are also labelled on the diagram above. These parts all contain a TEF1 promoter, YFP gene downstream, and a variable number of repressor binding sites (x1, x3) in the 5' UTR region. There are six difference repressor binding site sequences--three that are 16 nucleotides long, and three that are 20 nucleotides long--which can be targeted with our library of repressor constructs (TALEs and sgRNA-dCas9) shown in the diagram. These repressor constructs were not submitted. Click on the part number below to see the '''documentation on the Registry'''.<br />
<br><br />
<br><br><br />
'''Data For Our Favorite New Parts'''<br />
#[http://parts.igem.org/wiki/index.php?title=Part:BBa_K1204013 Main Page] - <br />
Reporter with 1x16A Repressor Binding Sequence, BBa_K1204013 : short description<br />
<br />
#[http://parts.igem.org/wiki/index.php?title=Part:BBa_K1204014 Main Page] - <br />
Reporter with 3x16A Repressor Binding Sequence, BBa_K1204014 ?? : short description<br />
<br />
#[http://parts.igem.org/wiki/index.php?title=Part:BBa_K1204016 Main Page] - <br />
Reporter with 1x20A Repressor Binding Sequence, BBa_K1204016 ?? : short description<br />
<br />
<br><br><br />
<br />
<groupparts>iGEM013 Duke</groupparts><br />
<div align="center"> Table 2.1.1. Biological Parts Submitted by Team Duke, iGEM 2013 <br>(Disregard the last row entry)</div> <br> <br />
<br />
<br />
<br><br />
[[File:BindingSiteSequence.png|700px|center]] <br><br />
<div align="center"> Table 2.1.2. Our Library of Gene Constructs</div> <br> <br />
<br><br />
<br />
<br />
<br />
<br />
[https://igem.org/Sample_Data_Page Sample Data Page]<br />
<br />
<br />
An important aspect of the iGEM competition is the use and creation of standard biological parts. Each team will make new parts during iGEM and will place them in the [http://partsregistry.org Registry of Standard Biological Parts]. The iGEM software provides an easy way to present the parts your team has created . The "groupparts" tag will generate a table with all of the parts that your team adds to your team sandbox. Note that if you want to document a part you need to document it on the [http://partsregistry.org Registry], not on your team wiki.<br />
<br />
Remember that the goal of proper part documentation is to describe and define a part such that it can be used without a need to refer to the primary literature. The next iGEM team 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.<br />
<br />
<br />
<br />
<br />
<br />
</div></div>Hyunsoo kimhttp://2013.igem.org/Team:Duke/PartsTeam:Duke/Parts2013-09-27T23:41:34Z<p>Hyunsoo kim: /* Biological Parts Submitted */</p>
<hr />
<div>{{Template:Team:Duke}}<br />
<div class="right_box"><br />
='''Biological Parts Submitted'''=<br />
<br />
<br><br />
[[File:LibraryConstructs.png|700px|center]] <br><br />
<div align="center"> Figure 2.1.1. Our Library of Gene Constructs</div> <br> <br />
<br><br />
<br />
From our library of gene constructs shown above, we have selected twelve parts to submit to the Registry of Standard Biological Parts. The twelve that were submitted are tabulated below, and are also labelled on the diagram above. These parts all contain a TEF1 promoter, YFP gene downstream, and a variable number of repressor binding sites (x1, x3) in the 5' UTR region. There are six difference repressor binding site sequences--three that are 16 nucleotides long, and three that are 20 nucleotides long--which can be targeted with our library of repressor constructs (TALEs and sgRNA-dCas9) shown in the diagram. These repressor constructs were not submitted. Click on the part number below to see the '''documentation on the Registry'''.<br />
<br><br />
<br />
'''Data For Our Favorite New Parts'''<br />
#[http://parts.igem.org/wiki/index.php?title=Part:BBa_K1204013 Main Page] - <br />
Reporter with 1x16A Repressor Binding Sequence, BBa_K1204013 : short description<br />
<br />
#[http://parts.igem.org/wiki/index.php?title=Part:BBa_K1204014 Main Page] - <br />
Reporter with 3x16A Repressor Binding Sequence, BBa_K1204014 ?? : short description<br />
<br />
#[http://parts.igem.org/wiki/index.php?title=Part:BBa_K1204016 Main Page] - <br />
Reporter with 1x20A Repressor Binding Sequence, BBa_K1204016 ?? : short description<br />
<br />
<br><br><br />
<br />
<groupparts>iGEM013 Duke</groupparts><br />
<div align="center"> Table 2.1.1. Biological Parts Submitted by Team Duke, iGEM 2013 <br>(Disregard the last row entry)</div> <br> <br />
<br />
<br />
<br><br />
[[File:BindingSiteSequence.png|700px|center]] <br><br />
<div align="center"> Table 2.1.2. Our Library of Gene Constructs</div> <br> <br />
<br><br />
<br />
<br />
<br />
<br />
[https://igem.org/Sample_Data_Page Sample Data Page]<br />
<br />
<br />
An important aspect of the iGEM competition is the use and creation of standard biological parts. Each team will make new parts during iGEM and will place them in the [http://partsregistry.org Registry of Standard Biological Parts]. The iGEM software provides an easy way to present the parts your team has created . The "groupparts" tag will generate a table with all of the parts that your team adds to your team sandbox. Note that if you want to document a part you need to document it on the [http://partsregistry.org Registry], not on your team wiki.<br />
<br />
Remember that the goal of proper part documentation is to describe and define a part such that it can be used without a need to refer to the primary literature. The next iGEM team 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.<br />
<br />
<br />
<br />
<br />
<br />
</div></div>Hyunsoo kimhttp://2013.igem.org/Team:Duke/PartsTeam:Duke/Parts2013-09-27T23:27:37Z<p>Hyunsoo kim: /* Biological Parts Submitted */</p>
<hr />
<div>{{Template:Team:Duke}}<br />
<div class="right_box"><br />
='''Biological Parts Submitted'''=<br />
<br />
<br><br />
[[File:LibraryConstructs.png|700px|center]] <br><br />
<div align="center"> Figure 2.1.1. Our Library of Gene Constructs</div> <br> <br />
<br><br />
<br />
From our library of gene constructs shown above, we have selected twelve parts to submit to the Registry of Standard Biological Parts. The twelve that were submitted are tabulated below, and are also labelled on the diagram above. These parts all contain a TEF1 promoter, YFP gene downstream, and a variable number of repressor binding sites (x1, x3) in the 5' UTR region. There are six difference repressor binding site sequences--three that are 16 nucleotides long, and three that are 20 nucleotides long--which can be targeted with our library of repressor constructs (TALEs and sgRNA-dCas9) shown in the diagram. These repressor constructs were not submitted. Click on the part number below to see the '''documentation on the Registry'''.<br />
<br><br />
<br><br><br />
<br />
<groupparts>iGEM013 Duke</groupparts><br />
<div align="center"> Table 2.1.1. Biological Parts Submitted by Team Duke, iGEM 2013 <br>(Disregard the last row entry)</div> <br> <br />
<br />
<br />
<br><br />
[[File:BindingSiteSequence.png|700px|center]] <br><br />
<div align="center"> Table 2.1.2. Our Library of Gene Constructs</div> <br> <br />
<br><br />
<br />
<br />
<br />
<br />
[https://igem.org/Sample_Data_Page Sample Data Page]<br />
<br />
<br />
An important aspect of the iGEM competition is the use and creation of standard biological parts. Each team will make new parts during iGEM and will place them in the [http://partsregistry.org Registry of Standard Biological Parts]. The iGEM software provides an easy way to present the parts your team has created . The "groupparts" tag will generate a table with all of the parts that your team adds to your team sandbox. Note that if you want to document a part you need to document it on the [http://partsregistry.org Registry], not on your team wiki.<br />
<br />
Remember that the goal of proper part documentation is to describe and define a part such that it can be used without a need to refer to the primary literature. The next iGEM team 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.<br />
<br />
<br />
<br />
<br />
<br />
</div></div>Hyunsoo kimhttp://2013.igem.org/Team:Duke/Project/Results/Part1Team:Duke/Project/Results/Part12013-09-27T23:24:13Z<p>Hyunsoo kim: /* Results: Library of DNA Parts for Gene Circuit Construction */</p>
<hr />
<div>{{Template:Team:Duke}}<br />
<div class="right_box"><br />
<br />
='''Results: Library of DNA Parts for Gene Circuit Construction'''=<br />
<br />
<br />
<br />
<div>As plasmids were constructed, they were confirmed by restriction digest and sequencing. </div><br />
<br><br />
<br />
==TALEs==<br />
#All 6 TALEs with mCherry tags were built and sequence confirmed<br />
<br />
[[File:TaleConstructs.png|300px|center]] <br><br />
<div align="center"> Figure 1.4.1. TALE Parts Constructed</div> <br><br />
<br />
==CRISPR==<br />
#6 sgRNAs were built and sequence confirmed.<br />
#dCas9-mCherry fusion protein was not cloned successfully, despite many attempts at various cloning protocols. We suspect problems with the source plasmid, or possibly effects of the large insert size. We obtained a dCas9 plasmid without an mCherry fusion that is not yet yeast-integrable. We then cloned a dCas9 plasmid without the fused mCherry gene; this plasmid was sequence confirmed but is yet to be integrated into yeast.<br />
<br />
<br />
[[File:SgRNA_cas9.png|350px|center]] <br><br />
<div align="center"> Figure 1.4.2. sgRNA-CRISPR Parts Constructed</div> <br><br />
<br />
==Reporters==<br />
#ACT1pr+yEVenus with no operator was built and sequence confirmed<br />
#ACT1pr+operator+yEVenus was built and sequence confirmed with 1 and 3 copies of each operator sequence<br />
#ACT1pr+operator+yEVenus with 5 copies of an operator sequence caused more difficulties, because the operator insert was too repetitive to be synthesized by standard means. We split each sequence into six small oligonucleotides for PCR amplification, but the product was messy and not useful. We then designed two large oligonucleotides for each sequence and were able to PCR amplify and clone the resulting inserts. In this way we obtained and confirmed constructs with 5 copies of certain operator sequences, but not all sequences have been completed. <br />
#After initial testing, we decided to build reporters with TEF1 promoters replacing the ACT1 promoter. TEF1pr+operator+yEVenus with 1 and 3 copies of each operator were built and sequence confirmed.<br />
<br />
<br><br />
[[File:ReporterLibrary.png|370px|center]] <br><br />
<div align="center"> Figure 1.4.3. Reporter Parts Constructed</div> <br> <br />
<br><br />
<br><br><br />
</div></div>Hyunsoo kimhttp://2013.igem.org/Team:Duke/Project/Results/Part1Team:Duke/Project/Results/Part12013-09-27T23:23:08Z<p>Hyunsoo kim: /* Results: A Library of DNA Parts for Gene Circuit Construction */</p>
<hr />
<div>{{Template:Team:Duke}}<br />
<div class="right_box"><br />
<br />
='''Results: Library of DNA Parts for Gene Circuit Construction'''=<br />
<br />
<br><br />
<br />
<div>As plasmids were constructed, they were confirmed by restriction digest and sequencing. </div><br />
<br><br />
<br />
==TALEs==<br />
#All 6 TALEs with mCherry tags were built and sequence confirmed<br />
<br />
[[File:TaleConstructs.png|300px|center]] <br><br />
<div align="center"> Figure 1.4.1. TALE Parts Constructed</div> <br><br />
<br />
==CRISPR==<br />
#6 sgRNAs were built and sequence confirmed.<br />
#dCas9-mCherry fusion protein was not cloned successfully, despite many attempts at various cloning protocols. We suspect problems with the source plasmid, or possibly effects of the large insert size. We obtained a dCas9 plasmid without an mCherry fusion that is not yet yeast-integrable. We then cloned a dCas9 plasmid without the fused mCherry gene; this plasmid was sequence confirmed but is yet to be integrated into yeast.<br />
<br />
<br />
[[File:SgRNA_cas9.png|350px|center]] <br><br />
<div align="center"> Figure 1.4.2. sgRNA-CRISPR Parts Constructed</div> <br><br />
<br />
==Reporters==<br />
#ACT1pr+yEVenus with no operator was built and sequence confirmed<br />
#ACT1pr+operator+yEVenus was built and sequence confirmed with 1 and 3 copies of each operator sequence<br />
#ACT1pr+operator+yEVenus with 5 copies of an operator sequence caused more difficulties, because the operator insert was too repetitive to be synthesized by standard means. We split each sequence into six small oligonucleotides for PCR amplification, but the product was messy and not useful. We then designed two large oligonucleotides for each sequence and were able to PCR amplify and clone the resulting inserts. In this way we obtained and confirmed constructs with 5 copies of certain operator sequences, but not all sequences have been completed. <br />
#After initial testing, we decided to build reporters with TEF1 promoters replacing the ACT1 promoter. TEF1pr+operator+yEVenus with 1 and 3 copies of each operator were built and sequence confirmed.<br />
<br />
<br><br />
[[File:ReporterLibrary.png|370px|center]] <br><br />
<div align="center"> Figure 1.4.3. Reporter Parts Constructed</div> <br> <br />
<br><br />
<br><br><br><br><br />
</div></div>Hyunsoo kimhttp://2013.igem.org/Team:Duke/Project/Results/Part1Team:Duke/Project/Results/Part12013-09-27T23:22:11Z<p>Hyunsoo kim: /* Reporters */</p>
<hr />
<div>{{Template:Team:Duke}}<br />
<div class="right_box"><br />
<br />
='''Results:<br> <br>A Library of DNA Parts for Gene Circuit Construction'''=<br />
<br />
<br><br />
<br />
<div>As plasmids were constructed, they were confirmed by restriction digest and sequencing. </div><br />
<br><br />
<br />
==TALEs==<br />
#All 6 TALEs with mCherry tags were built and sequence confirmed<br />
<br />
[[File:TaleConstructs.png|300px|center]] <br><br />
<div align="center"> Figure 1.4.1. TALE Parts Constructed</div> <br><br />
<br />
==CRISPR==<br />
#6 sgRNAs were built and sequence confirmed.<br />
#dCas9-mCherry fusion protein was not cloned successfully, despite many attempts at various cloning protocols. We suspect problems with the source plasmid, or possibly effects of the large insert size. We obtained a dCas9 plasmid without an mCherry fusion that is not yet yeast-integrable. We then cloned a dCas9 plasmid without the fused mCherry gene; this plasmid was sequence confirmed but is yet to be integrated into yeast.<br />
<br />
<br />
[[File:SgRNA_cas9.png|350px|center]] <br><br />
<div align="center"> Figure 1.4.2. sgRNA-CRISPR Parts Constructed</div> <br><br />
<br />
==Reporters==<br />
#ACT1pr+yEVenus with no operator was built and sequence confirmed<br />
#ACT1pr+operator+yEVenus was built and sequence confirmed with 1 and 3 copies of each operator sequence<br />
#ACT1pr+operator+yEVenus with 5 copies of an operator sequence caused more difficulties, because the operator insert was too repetitive to be synthesized by standard means. We split each sequence into six small oligonucleotides for PCR amplification, but the product was messy and not useful. We then designed two large oligonucleotides for each sequence and were able to PCR amplify and clone the resulting inserts. In this way we obtained and confirmed constructs with 5 copies of certain operator sequences, but not all sequences have been completed. <br />
#After initial testing, we decided to build reporters with TEF1 promoters replacing the ACT1 promoter. TEF1pr+operator+yEVenus with 1 and 3 copies of each operator were built and sequence confirmed.<br />
<br />
<br><br />
[[File:ReporterLibrary.png|370px|center]] <br><br />
<div align="center"> Figure 1.4.3. Reporter Parts Constructed</div> <br> <br />
<br><br />
<br><br><br><br><br />
</div></div>Hyunsoo kimhttp://2013.igem.org/Team:Duke/Project/Results/Part1Team:Duke/Project/Results/Part12013-09-27T23:21:36Z<p>Hyunsoo kim: /* CRISPR */</p>
<hr />
<div>{{Template:Team:Duke}}<br />
<div class="right_box"><br />
<br />
='''Results:<br> <br>A Library of DNA Parts for Gene Circuit Construction'''=<br />
<br />
<br><br />
<br />
<div>As plasmids were constructed, they were confirmed by restriction digest and sequencing. </div><br />
<br><br />
<br />
==TALEs==<br />
#All 6 TALEs with mCherry tags were built and sequence confirmed<br />
<br />
[[File:TaleConstructs.png|300px|center]] <br><br />
<div align="center"> Figure 1.4.1. TALE Parts Constructed</div> <br><br />
<br />
==CRISPR==<br />
#6 sgRNAs were built and sequence confirmed.<br />
#dCas9-mCherry fusion protein was not cloned successfully, despite many attempts at various cloning protocols. We suspect problems with the source plasmid, or possibly effects of the large insert size. We obtained a dCas9 plasmid without an mCherry fusion that is not yet yeast-integrable. We then cloned a dCas9 plasmid without the fused mCherry gene; this plasmid was sequence confirmed but is yet to be integrated into yeast.<br />
<br />
<br />
[[File:SgRNA_cas9.png|350px|center]] <br><br />
<div align="center"> Figure 1.4.2. sgRNA-CRISPR Parts Constructed</div> <br><br />
<br />
==Reporters==<br />
#ACT1pr+yEVenus with no operator was built and sequence confirmed<br />
#ACT1pr+operator+yEVenus was built and sequence confirmed with 1 and 3 copies of each operator sequence<br />
#ACT1pr+operator+yEVenus with 5 copies of an operator sequence caused more difficulties, because the operator insert was too repetitive to be synthesized by standard means. We split each sequence into six small oligonucleotides for PCR amplification, but the product was messy and not useful. We then designed two large oligonucleotides for each sequence and were able to PCR amplify and clone the resulting inserts. In this way we obtained and confirmed constructs with 5 copies of certain operator sequences, but not all sequences have been completed. <br />
#After initial testing, we decided to build reporters with TEF1 promoters replacing the ACT1 promoter. TEF1pr+operator+yEVenus with 1 and 3 copies of each operator were built and sequence confirmed.<br />
<br />
<br><br />
[[File:ReporterLibrary.png|400px|center]] <br><br />
<div align="center"> Figure 1.4.3. Reporter Parts Constructed</div> <br> <br />
<br><br />
<br><br><br><br><br />
</div></div>Hyunsoo kimhttp://2013.igem.org/Team:Duke/Project/Results/Part1Team:Duke/Project/Results/Part12013-09-27T23:21:18Z<p>Hyunsoo kim: /* CRISPR */</p>
<hr />
<div>{{Template:Team:Duke}}<br />
<div class="right_box"><br />
<br />
='''Results:<br> <br>A Library of DNA Parts for Gene Circuit Construction'''=<br />
<br />
<br><br />
<br />
<div>As plasmids were constructed, they were confirmed by restriction digest and sequencing. </div><br />
<br><br />
<br />
==TALEs==<br />
#All 6 TALEs with mCherry tags were built and sequence confirmed<br />
<br />
[[File:TaleConstructs.png|300px|center]] <br><br />
<div align="center"> Figure 1.4.1. TALE Parts Constructed</div> <br><br />
<br />
==CRISPR==<br />
#6 sgRNAs were built and sequence confirmed.<br />
#dCas9-mCherry fusion protein was not cloned successfully, despite many attempts at various cloning protocols. We suspect problems with the source plasmid, or possibly effects of the large insert size. We obtained a dCas9 plasmid without an mCherry fusion that is not yet yeast-integrable. We then cloned a dCas9 plasmid without the fused mCherry gene; this plasmid was sequence confirmed but is yet to be integrated into yeast.<br />
<br />
<br />
[[File:SgRNA_cas9.png|300px|center]] <br><br />
<div align="center"> Figure 1.4.2. sgRNA-CRISPR Parts Constructed</div> <br><br />
<br />
==Reporters==<br />
#ACT1pr+yEVenus with no operator was built and sequence confirmed<br />
#ACT1pr+operator+yEVenus was built and sequence confirmed with 1 and 3 copies of each operator sequence<br />
#ACT1pr+operator+yEVenus with 5 copies of an operator sequence caused more difficulties, because the operator insert was too repetitive to be synthesized by standard means. We split each sequence into six small oligonucleotides for PCR amplification, but the product was messy and not useful. We then designed two large oligonucleotides for each sequence and were able to PCR amplify and clone the resulting inserts. In this way we obtained and confirmed constructs with 5 copies of certain operator sequences, but not all sequences have been completed. <br />
#After initial testing, we decided to build reporters with TEF1 promoters replacing the ACT1 promoter. TEF1pr+operator+yEVenus with 1 and 3 copies of each operator were built and sequence confirmed.<br />
<br />
<br><br />
[[File:ReporterLibrary.png|400px|center]] <br><br />
<div align="center"> Figure 1.4.3. Reporter Parts Constructed</div> <br> <br />
<br><br />
<br><br><br><br><br />
</div></div>Hyunsoo kimhttp://2013.igem.org/Team:Duke/Project/Results/Part1Team:Duke/Project/Results/Part12013-09-27T23:21:10Z<p>Hyunsoo kim: /* TALEs */</p>
<hr />
<div>{{Template:Team:Duke}}<br />
<div class="right_box"><br />
<br />
='''Results:<br> <br>A Library of DNA Parts for Gene Circuit Construction'''=<br />
<br />
<br><br />
<br />
<div>As plasmids were constructed, they were confirmed by restriction digest and sequencing. </div><br />
<br><br />
<br />
==TALEs==<br />
#All 6 TALEs with mCherry tags were built and sequence confirmed<br />
<br />
[[File:TaleConstructs.png|300px|center]] <br><br />
<div align="center"> Figure 1.4.1. TALE Parts Constructed</div> <br><br />
<br />
==CRISPR==<br />
#6 sgRNAs were built and sequence confirmed.<br />
#dCas9-mCherry fusion protein was not cloned successfully, despite many attempts at various cloning protocols. We suspect problems with the source plasmid, or possibly effects of the large insert size. We obtained a dCas9 plasmid without an mCherry fusion that is not yet yeast-integrable. We then cloned a dCas9 plasmid without the fused mCherry gene; this plasmid was sequence confirmed but is yet to be integrated into yeast.<br />
<br />
<br />
[[File:SgRNA_cas9.png|400px|center]] <br><br />
<div align="center"> Figure 1.4.2. sgRNA-CRISPR Parts Constructed</div> <br><br />
<br />
==Reporters==<br />
#ACT1pr+yEVenus with no operator was built and sequence confirmed<br />
#ACT1pr+operator+yEVenus was built and sequence confirmed with 1 and 3 copies of each operator sequence<br />
#ACT1pr+operator+yEVenus with 5 copies of an operator sequence caused more difficulties, because the operator insert was too repetitive to be synthesized by standard means. We split each sequence into six small oligonucleotides for PCR amplification, but the product was messy and not useful. We then designed two large oligonucleotides for each sequence and were able to PCR amplify and clone the resulting inserts. In this way we obtained and confirmed constructs with 5 copies of certain operator sequences, but not all sequences have been completed. <br />
#After initial testing, we decided to build reporters with TEF1 promoters replacing the ACT1 promoter. TEF1pr+operator+yEVenus with 1 and 3 copies of each operator were built and sequence confirmed.<br />
<br />
<br><br />
[[File:ReporterLibrary.png|400px|center]] <br><br />
<div align="center"> Figure 1.4.3. Reporter Parts Constructed</div> <br> <br />
<br><br />
<br><br><br><br><br />
</div></div>Hyunsoo kimhttp://2013.igem.org/File:LibraryConstructs.pngFile:LibraryConstructs.png2013-09-27T23:09:32Z<p>Hyunsoo kim: uploaded a new version of &quot;File:LibraryConstructs.png&quot;</p>
<hr />
<div></div>Hyunsoo kimhttp://2013.igem.org/Team:Duke/PartsTeam:Duke/Parts2013-09-27T23:07:56Z<p>Hyunsoo kim: /* Biological Parts Submitted */</p>
<hr />
<div>{{Template:Team:Duke}}<br />
<div class="right_box"><br />
='''Biological Parts Submitted'''=<br />
<br />
<br><br />
[[File:LibraryConstructs.png|700px|center]] <br><br />
<div align="center"> Figure 2.1.1. Our Library of Gene Constructs</div> <br> <br />
<br><br />
<br />
From our library of gene constructs shown above, we have selected twelve parts to submit to the Registry of Standard Biological Parts. The twelve that were submitted are tabulated below, and are also labelled on the diagram above. These parts all contain a TEF1 promoter, YFP gene downstream, and a variable number of repressor binding sites (x1, x3) in the 5' UTR region. There are six difference repressor binding site sequences--three that are 16 nucleotides long, and three that are 20 nucleotides long--which can be targeted with our library of repressor constructs (TALEs and sgRNA-dCas9) shown in the diagram. These repressor constructs were not submitted. <br />
<br><br />
<br><br><br />
<br />
<groupparts>iGEM013 Duke</groupparts><br />
<div align="center"> Table 2.1.1. Biological Parts Submitted by Team Duke, iGEM 2013 <br>(Disregard the last row entry)</div> <br> <br />
<br />
<br />
<br><br />
[[File:BindingSiteSequence.png|700px|center]] <br><br />
<div align="center"> Table 2.1.2. Our Library of Gene Constructs</div> <br> <br />
<br><br />
<br />
<br />
<br />
<br />
[https://igem.org/Sample_Data_Page Sample Data Page]<br />
<br />
<br />
An important aspect of the iGEM competition is the use and creation of standard biological parts. Each team will make new parts during iGEM and will place them in the [http://partsregistry.org Registry of Standard Biological Parts]. The iGEM software provides an easy way to present the parts your team has created . The "groupparts" tag will generate a table with all of the parts that your team adds to your team sandbox. Note that if you want to document a part you need to document it on the [http://partsregistry.org Registry], not on your team wiki.<br />
<br />
Remember that the goal of proper part documentation is to describe and define a part such that it can be used without a need to refer to the primary literature. The next iGEM team 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.<br />
<br />
<br />
<br />
<br />
<br />
</div></div>Hyunsoo kimhttp://2013.igem.org/Team:Duke/PartsTeam:Duke/Parts2013-09-27T23:06:41Z<p>Hyunsoo kim: /* Biological Parts Submitted */</p>
<hr />
<div>{{Template:Team:Duke}}<br />
<div class="right_box"><br />
='''Biological Parts Submitted'''=<br />
<br />
<br><br />
[[File:LibraryConstructs.png|700px|center]] <br><br />
<div align="center"> Figure 2.1.1. Our Library of Gene Constructs</div> <br> <br />
<br><br />
<br />
From our library of gene constructs shown above, we have selected twelve parts to submit to the Registry of Standard Biological Parts. The twelve that were submitted are tabulated below, and are also labelled on the diagram above. These parts all contain a TEF1 promoter, YFP gene downstream, and a variable number of repressor binding sites (x1, x3) in the 5' UTR region. There are six difference repressor binding site sequences--three that are 16 nucleotides long, and three that are 20 nucleotides long--which can be targeted with our library of repressor constructs (TALEs and sgRNA-dCas9) shown in the diagram. These repressor constructs were not submitted. <br />
<br><br />
<br><br><br />
<br />
<groupparts>iGEM013 Duke</groupparts><br />
<div align="center"> Table 2.1.1. Biological Parts Submitted by Team Duke, iGEM 2013 <br>(Disregard the last row entry)</div> <br> <br />
<br />
<br />
<br><br />
[[File:BindingSiteSequence.png|700px|center]] <br><br />
<div align="center"> Figure 2.1.2. Our Library of Gene Constructs</div> <br> <br />
<br><br />
<br />
<br />
<br />
<br />
[https://igem.org/Sample_Data_Page Sample Data Page]<br />
<br />
<br />
An important aspect of the iGEM competition is the use and creation of standard biological parts. Each team will make new parts during iGEM and will place them in the [http://partsregistry.org Registry of Standard Biological Parts]. The iGEM software provides an easy way to present the parts your team has created . The "groupparts" tag will generate a table with all of the parts that your team adds to your team sandbox. Note that if you want to document a part you need to document it on the [http://partsregistry.org Registry], not on your team wiki.<br />
<br />
Remember that the goal of proper part documentation is to describe and define a part such that it can be used without a need to refer to the primary literature. The next iGEM team 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.<br />
<br />
<br />
<br />
<br />
<br />
</div></div>Hyunsoo kimhttp://2013.igem.org/Team:Duke/PartsTeam:Duke/Parts2013-09-27T23:06:28Z<p>Hyunsoo kim: /* Biological Parts Submitted */</p>
<hr />
<div>{{Template:Team:Duke}}<br />
<div class="right_box"><br />
='''Biological Parts Submitted'''=<br />
<br />
<br><br />
[[File:LibraryConstructs.png|700px|center]] <br><br />
<div align="center"> Figure 2.1.1. Our Library of Gene Constructs</div> <br> <br />
<br><br />
<br />
From our library of gene constructs shown above, we have selected twelve parts to submit to the Registry of Standard Biological Parts. The twelve that were submitted are tabulated below, and are also labelled on the diagram above. These parts all contain a TEF1 promoter, YFP gene downstream, and a variable number of repressor binding sites (x1, x3) in the 5' UTR region. There are six difference repressor binding site sequences--three that are 16 nucleotides long, and three that are 20 nucleotides long--which can be targeted with our library of repressor constructs (TALEs and sgRNA-dCas9) shown in the diagram. These repressor constructs were not submitted. <br />
<br><br />
<br><br />
<br />
<groupparts>iGEM013 Duke</groupparts><br />
<div align="center"> Table 2.1.1. Biological Parts Submitted by Team Duke, iGEM 2013 <br>(Disregard the last row entry)</div> <br> <br />
<br />
<br />
<br><br />
[[File:BindingSiteSequence.png|700px|center]] <br><br />
<div align="center"> Figure 2.1.2. Our Library of Gene Constructs</div> <br> <br />
<br><br />
<br />
<br />
<br />
<br />
[https://igem.org/Sample_Data_Page Sample Data Page]<br />
<br />
<br />
An important aspect of the iGEM competition is the use and creation of standard biological parts. Each team will make new parts during iGEM and will place them in the [http://partsregistry.org Registry of Standard Biological Parts]. The iGEM software provides an easy way to present the parts your team has created . The "groupparts" tag will generate a table with all of the parts that your team adds to your team sandbox. Note that if you want to document a part you need to document it on the [http://partsregistry.org Registry], not on your team wiki.<br />
<br />
Remember that the goal of proper part documentation is to describe and define a part such that it can be used without a need to refer to the primary literature. The next iGEM team 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.<br />
<br />
<br />
<br />
<br />
<br />
</div></div>Hyunsoo kimhttp://2013.igem.org/Team:Duke/PartsTeam:Duke/Parts2013-09-27T23:06:00Z<p>Hyunsoo kim: /* Biological Parts Submitted */</p>
<hr />
<div>{{Template:Team:Duke}}<br />
<div class="right_box"><br />
='''Biological Parts Submitted'''=<br />
<br />
<br><br />
[[File:LibraryConstructs.png|700px|center]] <br><br />
<div align="center"> Figure 2.1.1. Our Library of Gene Constructs</div> <br> <br />
<br><br />
<br />
From our library of gene constructs shown above, we have selected twelve parts to submit to the Registry of Standard Biological Parts. The twelve that were submitted are tabulated below, and are also labelled on the diagram above. These parts all contain a TEF1 promoter, YFP gene downstream, and a variable number of repressor binding sites (x1, x3) in the 5' UTR region. There are six difference repressor binding site sequences--three that are 16 nucleotides long, and three that are 20 nucleotides long--which can be targeted with our library of repressor constructs (TALEs and sgRNA-dCas9) shown in the diagram. These repressor constructs were not submitted. <br />
<br><br />
<br />
<br />
<groupparts>iGEM013 Duke</groupparts><br />
<div align="center"> Table 2.1.1. Biological Parts Submitted by Team Duke, iGEM 2013 <br>(Disregard the last row entry)</div> <br> <br />
<br />
<br />
<br><br />
[[File:BindingSiteSequence.png|700px|center]] <br><br />
<div align="center"> Figure 2.1.2. Our Library of Gene Constructs</div> <br> <br />
<br><br />
<br />
<br />
<br />
<br />
[https://igem.org/Sample_Data_Page Sample Data Page]<br />
<br />
<br />
An important aspect of the iGEM competition is the use and creation of standard biological parts. Each team will make new parts during iGEM and will place them in the [http://partsregistry.org Registry of Standard Biological Parts]. The iGEM software provides an easy way to present the parts your team has created . The "groupparts" tag will generate a table with all of the parts that your team adds to your team sandbox. Note that if you want to document a part you need to document it on the [http://partsregistry.org Registry], not on your team wiki.<br />
<br />
Remember that the goal of proper part documentation is to describe and define a part such that it can be used without a need to refer to the primary literature. The next iGEM team 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.<br />
<br />
<br />
<br />
<br />
<br />
</div></div>Hyunsoo kimhttp://2013.igem.org/Team:Duke/PartsTeam:Duke/Parts2013-09-27T23:05:32Z<p>Hyunsoo kim: /* Biological Parts Submitted */</p>
<hr />
<div>{{Template:Team:Duke}}<br />
<div class="right_box"><br />
='''Biological Parts Submitted'''=<br />
<br />
<br><br />
[[File:LibraryConstructs.png|700px|center]] <br><br />
<div align="center"> Figure 2.1.1. Our Library of Gene Constructs</div> <br> <br />
<br><br />
<br />
From our library of gene constructs shown above, we have selected twelve parts to submit to the Registry of Standard Biological Parts. The twelve that were submitted are tabulated below, and are also labelled on the diagram above. These parts all contain a TEF1 promoter, YFP gene downstream, and a variable number of repressor binding sites (x1, x3) in the 5' UTR region. There are six difference repressor binding site sequences--three that are 16 nucleotides long, and three that are 20 nucleotides long--which can be targeted with our library of repressor constructs (TALEs and sgRNA-dCas9) shown in the diagram. These repressor constructs were not submitted. <br />
<br><br />
<br />
<br />
<groupparts>iGEM013 Duke</groupparts><br />
<div align="center"> Table 2.1.1. Biological Parts Submitted by Team Duke, iGEM 2013 <br>(Disregard the last row entry)</div> <br> <br />
<br />
<br />
<br><br />
[[File:BindingSiteSequence2.png|700px|center]] <br><br />
<div align="center"> Figure 2.1.2. Our Library of Gene Constructs</div> <br> <br />
<br><br />
<br />
<br />
<br />
<br />
[https://igem.org/Sample_Data_Page Sample Data Page]<br />
<br />
<br />
An important aspect of the iGEM competition is the use and creation of standard biological parts. Each team will make new parts during iGEM and will place them in the [http://partsregistry.org Registry of Standard Biological Parts]. The iGEM software provides an easy way to present the parts your team has created . The "groupparts" tag will generate a table with all of the parts that your team adds to your team sandbox. Note that if you want to document a part you need to document it on the [http://partsregistry.org Registry], not on your team wiki.<br />
<br />
Remember that the goal of proper part documentation is to describe and define a part such that it can be used without a need to refer to the primary literature. The next iGEM team 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.<br />
<br />
<br />
<br />
<br />
<br />
</div></div>Hyunsoo kimhttp://2013.igem.org/Team:Duke/Project/Results/Part1Team:Duke/Project/Results/Part12013-09-27T23:03:37Z<p>Hyunsoo kim: /* CRISPR */</p>
<hr />
<div>{{Template:Team:Duke}}<br />
<div class="right_box"><br />
<br />
='''Results:<br> <br>A Library of DNA Parts for Gene Circuit Construction'''=<br />
<br />
<br><br />
<br />
<div>As plasmids were constructed, they were confirmed by restriction digest and sequencing. </div><br />
<br><br />
<br />
==TALEs==<br />
#All 6 TALEs with mCherry tags were built and sequence confirmed<br />
<br />
[[File:TaleConstructs.png|400px|center]] <br><br />
<div align="center"> Figure 1.4.1. TALE Parts Constructed</div> <br><br />
<br />
==CRISPR==<br />
#6 sgRNAs were built and sequence confirmed.<br />
#dCas9-mCherry fusion protein was not cloned successfully, despite many attempts at various cloning protocols. We suspect problems with the source plasmid, or possibly effects of the large insert size. We obtained a dCas9 plasmid without an mCherry fusion that is not yet yeast-integrable. We then cloned a dCas9 plasmid without the fused mCherry gene; this plasmid was sequence confirmed but is yet to be integrated into yeast.<br />
<br />
<br />
[[File:SgRNA_cas9.png|400px|center]] <br><br />
<div align="center"> Figure 1.4.2. sgRNA-CRISPR Parts Constructed</div> <br><br />
<br />
==Reporters==<br />
#ACT1pr+yEVenus with no operator was built and sequence confirmed<br />
#ACT1pr+operator+yEVenus was built and sequence confirmed with 1 and 3 copies of each operator sequence<br />
#ACT1pr+operator+yEVenus with 5 copies of an operator sequence caused more difficulties, because the operator insert was too repetitive to be synthesized by standard means. We split each sequence into six small oligonucleotides for PCR amplification, but the product was messy and not useful. We then designed two large oligonucleotides for each sequence and were able to PCR amplify and clone the resulting inserts. In this way we obtained and confirmed constructs with 5 copies of certain operator sequences, but not all sequences have been completed. <br />
#After initial testing, we decided to build reporters with TEF1 promoters replacing the ACT1 promoter. TEF1pr+operator+yEVenus with 1 and 3 copies of each operator were built and sequence confirmed.<br />
<br />
<br><br />
[[File:ReporterLibrary.png|400px|center]] <br><br />
<div align="center"> Figure 1.4.3. Reporter Parts Constructed</div> <br> <br />
<br><br />
<br><br><br><br><br />
</div></div>Hyunsoo kim