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<!--{{IGEM_TopBar}}--> | <!--{{IGEM_TopBar}}--> | ||
{{IISER-Tirupati India}} | {{IISER-Tirupati India}} | ||
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− | <div class="wrapper"> | + | <div class="wrapper" style="background-color: #FDF8D7;"> |
<header> | <header> | ||
<section class="container-fluid" style="background-color: #8D1063;"> | <section class="container-fluid" style="background-color: #8D1063;"> | ||
− | <img class="img img-fluid" src="https://static.igem.org/mediawiki/2021/ | + | <img class="img img-fluid" src="https://static.igem.org/mediawiki/2021/8/8b/T--IISER-Tirupati_India--safety.svg" style="width: 100%;"> |
− | <div class=" row justify-content-center | + | <div class=" row justify-content-center d-none d-lg-flex" style="width: 100% !important;"> |
− | + | <div class="down-arrow" style="color: hsl(320, 80%, 31%);"><strong>SCROLL</strong> | |
− | + | <svg width="16" height="16" fill="#8D1063" class="bi bi-chevron-double-down" viewBox="0 0 16 16"> | |
− | + | <path fill-rule="evenodd" d="M1.646 6.646a.5.5 0 0 1 .708 0L8 12.293l5.646-5.647a.5.5 0 0 1 .708.708l-6 6a.5.5 0 0 1-.708 0l-6-6a.5.5 0 0 1 0-.708z"/> | |
− | + | <path fill-rule="evenodd" d="M1.646 2.646a.5.5 0 0 1 .708 0L8 8.293l5.646-5.647a.5.5 0 0 1 .708.708l-6 6a.5.5 0 0 1-.708 0l-6-6a.5.5 0 0 1 0-.708z"/> | |
+ | </svg> | ||
+ | </div> | ||
</div> | </div> | ||
</section> | </section> | ||
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<li><a class="dropdown-item" href="https://2021.igem.org/Team:IISER-Tirupati_India/Description">DESCRIPTION</a></li> | <li><a class="dropdown-item" href="https://2021.igem.org/Team:IISER-Tirupati_India/Description">DESCRIPTION</a></li> | ||
<li><a class="dropdown-item" href="https://2021.igem.org/Team:IISER-Tirupati_India/Blueprint">BLUEPRINT</a></li> | <li><a class="dropdown-item" href="https://2021.igem.org/Team:IISER-Tirupati_India/Blueprint">BLUEPRINT</a></li> | ||
− | <li><a class="dropdown-item" href="https://2021.igem.org/Team:IISER-Tirupati_India/Engineering">ENGINEERING SUCCESS</a></li> | + | <li><a class="dropdown-item" href="https://2021.igem.org/Team:IISER-Tirupati_India/Engineering">ENGINEERING SUCCESS </a></li> |
<li><a class="dropdown-item" href="https://2021.igem.org/Team:IISER-Tirupati_India/Background">BACKGROUND</a></li> | <li><a class="dropdown-item" href="https://2021.igem.org/Team:IISER-Tirupati_India/Background">BACKGROUND</a></li> | ||
<li><a class="dropdown-item" href="https://2021.igem.org/Team:IISER-Tirupati_India/Implementation">IMPLEMENTATION</a></li> | <li><a class="dropdown-item" href="https://2021.igem.org/Team:IISER-Tirupati_India/Implementation">IMPLEMENTATION</a></li> | ||
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</a> | </a> | ||
<ul class="dropdown-menu fade-down" aria-labelledby="navbarDropdown"> | <ul class="dropdown-menu fade-down" aria-labelledby="navbarDropdown"> | ||
− | <li><a class="dropdown-item" href="https://2021.igem.org/Team:IISER-Tirupati_India/ | + | <li><a class="dropdown-item" href="https://2021.igem.org/Team:IISER-Tirupati_India/Proof_Of_Concept">PROOF OF CONCEPT </a></li> |
<li><a class="dropdown-item" href="https://2021.igem.org/Team:IISER-Tirupati_India/Design">DESIGN</a></li> | <li><a class="dropdown-item" href="https://2021.igem.org/Team:IISER-Tirupati_India/Design">DESIGN</a></li> | ||
<li><a class="dropdown-item" href="https://2021.igem.org/Team:IISER-Tirupati_India/Parts">PARTS</a></li> | <li><a class="dropdown-item" href="https://2021.igem.org/Team:IISER-Tirupati_India/Parts">PARTS</a></li> | ||
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<li><a class="dropdown-item" href="https://2021.igem.org/Team:IISER-Tirupati_India/Communication">COMMUNICATION</a></li> | <li><a class="dropdown-item" href="https://2021.igem.org/Team:IISER-Tirupati_India/Communication">COMMUNICATION</a></li> | ||
<li><a class="dropdown-item" href="https://2021.igem.org/Team:IISER-Tirupati_India/Inclusivity">INCLUSIVITY</a></li> | <li><a class="dropdown-item" href="https://2021.igem.org/Team:IISER-Tirupati_India/Inclusivity">INCLUSIVITY</a></li> | ||
− | <li><a class="dropdown-item" href="https://2021.igem.org/Team:IISER-Tirupati_India/Sustainable">SUSTAINABLE DEVELOPMENT</a></li> | + | <li><a class="dropdown-item" href="https://2021.igem.org/Team:IISER-Tirupati_India/Sustainable">SUSTAINABLE DEVELOPMENT </a></li> |
</ul> | </ul> | ||
</li> | </li> | ||
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TEAM | TEAM | ||
</a> | </a> | ||
− | <ul class="dropdown-menu fade-down" aria-labelledby="navbarDropdown"> | + | <ul class="dropdown-menu dropdown-menu-end fade-down" aria-labelledby="navbarDropdown"> |
<li><a class="dropdown-item" href="https://2021.igem.org/Team:IISER-Tirupati_India/Team">MEMBERS</a></li> | <li><a class="dropdown-item" href="https://2021.igem.org/Team:IISER-Tirupati_India/Team">MEMBERS</a></li> | ||
<li><a class="dropdown-item" href="https://2021.igem.org/Team:IISER-Tirupati_India/Attributions">ATTRIBUTION</a></li> | <li><a class="dropdown-item" href="https://2021.igem.org/Team:IISER-Tirupati_India/Attributions">ATTRIBUTION</a></li> | ||
− | <li><a class="dropdown-item" href="https://2021.igem.org/Team:IISER-Tirupati_India/Collaborations">COLLABORATIONS</a></li> | + | <li><a class="dropdown-item" href="https://2021.igem.org/Team:IISER-Tirupati_India/Collaborations">COLLABORATIONS </a></li> |
<li><a class="dropdown-item" href="https://2021.igem.org/Team:IISER-Tirupati_India/Partnership">PARTNERSHIP</a></li> | <li><a class="dropdown-item" href="https://2021.igem.org/Team:IISER-Tirupati_India/Partnership">PARTNERSHIP</a></li> | ||
</ul> | </ul> | ||
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<main> | <main> | ||
− | <div class="container"> | + | <div class="container-fluid"> |
− | <div class="row | + | <div class="row"> |
− | <div class="col-md- | + | |
− | < | + | <div class="col-md-4 col-lg-3 p-2 d-none d-md-block" style="background-color: #FFBD59 !important; color: #8D1063;"> |
− | + | <div class="card" style=" max-width: 15.5rem; border: none !important;background-color:#FFBD59;" id="index"> | |
− | + | <div class="card-body"> | |
− | + | <h3 class="card-title text-center mb-3">INDEX</h3> | |
− | + | <section id="Index1"> | |
− | + | <ul> | |
− | + | <li><a class="index_link" href="#1">Overview</a></li> | |
− | + | <li><a class="index_link" href="#2">Previous Parts</a></li> | |
− | + | <li><a class="index_link" href="#3">Basic Parts</a></li> | |
− | + | <li><a class="index_link" href="#4">Composite Parts</a></li> | |
− | </ | + | <li><a class="index_link" href="#5">Improvement</a></li> |
− | < | + | </ul> |
− | + | </section> | |
− | + | </div> | |
− | < | + | </div> |
− | <p> | + | </div> |
− | + | ||
− | + | <div class="col-md-8 p-5"> | |
− | + | <div class="mt-5"> | |
− | + | <p class="py-3" id="1"> | |
− | + | </p> | |
− | + | <h2>Overview</h2> | |
− | + | <p>Due to the novel approaches taken while pursuing this project, we found ourselves using new parts that had not been given in the iGEM registry. In total, we developed 37 new basic parts (either entirely new or by modifying previously existing ones). We strongly believe that these two collections can be exploited to their full potential by the subsequent iGEM generations.</p> | |
− | < | + | |
− | < | + | <p id="2">Furthermore, we have designed and used multiple combinations of basic parts as given in the composite part section.These composite parts can be used in multiple settings depending on the requirements of the projects.</p> |
− | + | ||
− | + | <p>The parts used in our project are as follows:</p> | |
− | + | <h2 class="pt-3">Previous Parts used:</h2> | |
− | + | <div class="table-responsive"> | |
− | <p> | + | <table class="table table-striped table-bordered"> |
− | + | <thead> | |
− | + | <tr style="background-color: #bb2f5c;color: white;"> | |
− | + | <td > | |
− | + | <p><strong>BioBrick ID</strong></p> | |
− | < | + | </td> |
− | + | <td> | |
− | < | + | <p><strong>Name</strong></p> |
− | <p> | + | </td> |
− | + | <td> | |
− | + | <p><strong>Length</strong></p> | |
− | + | </td> | |
− | + | <td> | |
− | + | <p><strong>Description</strong></p> | |
− | + | </td> | |
− | + | </tr> | |
− | + | </thead> | |
− | + | <tbody> | |
− | + | <tr> | |
− | + | <td> | |
− | + | <p><a href="http://parts.igem.org/Part:BBa_K316001"><em>BBa_K316001</em></a></p> | |
− | + | </td> | |
− | + | <td> | |
− | < | + | <p>pVeg</p> |
− | <p> | + | </td> |
− | + | <td> | |
− | <p> | + | <p>97 bp</p> |
− | + | </td> | |
− | + | <td> | |
− | + | <p>Constitutive natural promoter under Sig A transcription factor</p> | |
− | + | </td> | |
− | + | </tr> | |
− | < | + | <tr> |
− | < | + | <td> |
− | <p> | + | <p><a href="http://parts.igem.org/Part:BBa_K143013">BBa_K143013</a></p> |
− | + | </td> | |
− | + | <td> | |
− | + | <p>P43</p> | |
− | + | </td> | |
− | + | <td> | |
− | + | <p>56 bp</p> | |
− | + | </td> | |
− | + | <td> | |
− | < | + | <p>Constitutive natural promoter under Sig A and SigB transcription factor</p> |
− | + | </td> | |
− | + | </tr> | |
− | + | <tr> | |
− | + | <td> | |
− | + | <p><a href="http://parts.igem.org/Part:BBa_K143014">BBa_K143014</a></p> | |
− | < | + | </td> |
− | <p> | + | <td> |
− | <p> | + | <p>pxylA</p> |
− | < | + | </td> |
− | < | + | <td> |
− | < | + | <p>82 bp</p> |
− | <p> | + | </td> |
− | + | <td> | |
− | + | <p>Xylose dependent natural promoter (repressed by xylR)</p> | |
− | + | </td> | |
− | < | + | </tr> |
− | + | <tr> | |
− | + | <td> | |
− | + | <p><a href="http://parts.igem.org/Part:BBa_C0053">BBa_C0053</a></p> | |
− | + | </td> | |
− | + | <td> | |
− | < | + | <p>P22 repressor</p> |
− | + | </td> | |
− | <p> | + | <td> |
− | < | + | <p>712 bp</p> |
− | < | + | </td> |
− | < | + | <td> |
− | + | <p>DNA binding repressor protein</p> | |
− | + | </td> | |
− | + | </tr> | |
− | + | <tr> | |
− | + | <td> | |
− | + | <p><a href="http://parts.igem.org/Part:BBa_K2333002">BBa_K2333002</a></p> | |
− | + | </td> | |
− | + | <td> | |
− | + | <p>Protein degradation tag B</p> | |
− | + | </td> | |
− | + | <td> | |
− | + | <p>87 bp</p> | |
− | + | </td> | |
− | + | <td> | |
− | + | <p>mf-Lon specific Protein Degradation Tag B (medium-strong)</p> | |
− | + | </td> | |
− | + | </tr> | |
− | + | <tr> | |
− | + | <td> | |
− | + | <p><a href="http://parts.igem.org/Part:BBa_K1351031">BBa_K13510</a>28</p> | |
− | + | </td> | |
− | + | <td> | |
− | + | <p>RBS</p> | |
− | + | </td> | |
− | + | <td> | |
− | + | <p>11 bp</p> | |
− | + | </td> | |
− | + | <td> | |
− | + | <p>RBS for <em>B. subtilis</em></p> | |
− | + | </td> | |
+ | </tr> | ||
+ | <tr> | ||
+ | <td> | ||
+ | <p><a href="http://parts.igem.org/Part:BBa_K1351030">BBa_K1351030</a></p> | ||
+ | </td> | ||
+ | <td> | ||
+ | <p>RBS</p> | ||
+ | </td> | ||
+ | <td> | ||
+ | <p>11 bp</p> | ||
+ | </td> | ||
+ | <td> | ||
+ | <p>RBS for <em>B. subtilis</em></p> | ||
+ | </td> | ||
+ | </tr> | ||
+ | <tr> | ||
+ | <td> | ||
+ | <p><a href="http://parts.igem.org/Part:BBa_K1351031">BBa_K1351031</a></p> | ||
+ | </td> | ||
+ | <td> | ||
+ | <p>RBS</p> | ||
+ | </td> | ||
+ | <td> | ||
+ | <p>11 bp</p> | ||
+ | </td> | ||
+ | <td> | ||
+ | <p>RBS for <em>B. subtilis</em></p> | ||
+ | </td> | ||
+ | </tr> | ||
+ | <tr> | ||
+ | <td> | ||
+ | <p><a href="http://parts.igem.org/Part:BBa_K1351033">BBa_K1351033</a></p> | ||
+ | </td> | ||
+ | <td> | ||
+ | <p>RBS</p> | ||
+ | </td> | ||
+ | <td> | ||
+ | <p>11 bp</p> | ||
+ | </td> | ||
+ | <td> | ||
+ | <p>RBS for <em>B. subtilis</em></p> | ||
+ | </td> | ||
+ | </tr> | ||
+ | <tr> | ||
+ | <td> | ||
+ | <p><a href="http://parts.igem.org/Part:BBa_J06504">BBa_J06504</a></p> | ||
+ | </td> | ||
+ | <td> | ||
+ | <p>mCherry</p> | ||
+ | </td> | ||
+ | <td> | ||
+ | <p>714 bp</p> | ||
+ | </td> | ||
+ | <td> | ||
+ | <p>Red fluorescent tag </p> | ||
+ | </td> | ||
+ | </tr> | ||
+ | <tr> | ||
+ | <td> | ||
+ | <p><a href="http://parts.igem.org/Part:BBa_B0015">BBa_B0015</a></p> | ||
+ | </td> | ||
+ | <td> | ||
+ | <p>Terminator</p> | ||
+ | </td> | ||
+ | <td> | ||
+ | <p>129 bp</p> | ||
+ | </td> | ||
+ | <td> | ||
+ | <p>Double terminator consisting of BBa_B0010 and BBa_B0012</p> | ||
+ | </td> | ||
+ | </tr> | ||
+ | <tr> | ||
+ | <td> | ||
+ | <p><a href="https://parts.igem.org/Part:BBa_B0010">BBa_B0010</a></p> | ||
+ | </td> | ||
+ | <td> | ||
+ | <p>Terminator</p> | ||
+ | </td> | ||
+ | <td> | ||
+ | <p>80 bp</p> | ||
+ | </td> | ||
+ | <td> | ||
+ | <p id="3">Relatively warker Terminator as compared to <a href="http://parts.igem.org/Part:BBa_B0015">BBa_B0015</a></p> | ||
+ | </td> | ||
+ | </tr> | ||
+ | </tbody> | ||
</table> | </table> | ||
− | </div> | + | </div> |
− | <p> | + | |
− | + | <h2 class="pt-3">Basic Parts: </h2> | |
− | <p> | + | <div class="table-responsive"> |
− | <p> | + | <table class="table table-striped table-bordered"> |
− | <p> | + | <thead> |
− | <p> | + | <tr style="background-color: #bb2f5c;color: white;"> |
− | <p> | + | <td> |
− | < | + | <p><strong>Part No:</strong></p> |
− | <p> | + | </td> |
− | < | + | <td> |
− | <p> | + | <p><strong>Name</strong></p> |
− | < | + | </td> |
− | <p> | + | <td> |
− | < | + | <p><strong>Length</strong></p> |
− | + | </td> | |
− | + | <td> | |
− | + | <p><strong>Description </strong></p> | |
− | + | </td> | |
− | + | </tr> | |
− | + | </thead> | |
− | + | <tbody> | |
− | + | <tr> | |
− | + | <td> | |
− | + | <p><a href="http://parts.igem.org/Part:BBa_K3889000">BBa_K3889000</a></p> | |
− | + | </td> | |
− | + | <td> | |
− | + | <p>Azurite BFP (BFP.B3)</p> | |
− | + | </td> | |
− | + | <td> | |
− | + | <p>717 bp</p> | |
− | + | </td> | |
− | + | <td> | |
− | + | <p>Blue fluorescent tag </p> | |
− | + | </td> | |
+ | </tr> | ||
+ | <tr> | ||
+ | <td> | ||
+ | <p><a href="http://parts.igem.org/Part:BBa_K3889002">BBa_K3889002</a></p> | ||
+ | </td> | ||
+ | <td> | ||
+ | <p>modified_sfGFP</p> | ||
+ | </td> | ||
+ | <td> | ||
+ | <p>720 bp</p> | ||
+ | </td> | ||
+ | <td> | ||
+ | <p>Green fluorescent tag </p> | ||
+ | </td> | ||
+ | </tr> | ||
+ | <tr> | ||
+ | <td> | ||
+ | <p><a href="http://parts.igem.org/Part:BBa_K3889010">BBa_K3889010</a></p> | ||
+ | </td> | ||
+ | <td> | ||
+ | <p>SP126</p> | ||
+ | </td> | ||
+ | <td> | ||
+ | <p>52 bp</p> | ||
+ | </td> | ||
+ | <td> | ||
+ | <p>Promoter from synthetic library of Bacillus subtilis</p> | ||
+ | </td> | ||
+ | </tr> | ||
+ | <tr> | ||
+ | <td> | ||
+ | <p><a href="http://parts.igem.org/Part:BBa_K3889011">BBa_K3889011</a></p> | ||
+ | </td> | ||
+ | <td> | ||
+ | <p>SP146</p> | ||
+ | </td> | ||
+ | <td> | ||
+ | <p>52 bp</p> | ||
+ | </td> | ||
+ | <td> | ||
+ | <p>Promoter from synthetic library of Bacillus subtilis</p> | ||
+ | </td> | ||
+ | </tr> | ||
+ | <tr> | ||
+ | <td> | ||
+ | <p><a href="http://parts.igem.org/Part:BBa_K3889012">BBa_K3889012</a></p> | ||
+ | </td> | ||
+ | <td> | ||
+ | <p>SP200</p> | ||
+ | </td> | ||
+ | <td> | ||
+ | <p>52 bp</p> | ||
+ | </td> | ||
+ | <td> | ||
+ | <p>Promoter from synthetic library of Bacillus subtilis</p> | ||
+ | </td> | ||
+ | </tr> | ||
+ | <tr> | ||
+ | <td> | ||
+ | <p><a href="http://parts.igem.org/Part:BBa_K3889013">BBa_K3889013</a></p> | ||
+ | </td> | ||
+ | <td> | ||
+ | <p>pgsiB</p> | ||
+ | </td> | ||
+ | <td> | ||
+ | <p>300 bp</p> | ||
+ | </td> | ||
+ | <td> | ||
+ | <p>Natural promoter of Bacillus subtilis under control of general stress SigB transcription factor</p> | ||
+ | </td> | ||
+ | </tr> | ||
+ | <tr> | ||
+ | <td> | ||
+ | <p><a href="http://parts.igem.org/Part:BBa_K3889014">BBa_K3889014</a></p> | ||
+ | </td> | ||
+ | <td> | ||
+ | <p>pGAL1 Yeast Promoter</p> | ||
+ | </td> | ||
+ | <td> | ||
+ | <p>531 bp</p> | ||
+ | </td> | ||
+ | <td> | ||
+ | <p>Galactose inducible yeast promoter</p> | ||
+ | </td> | ||
+ | </tr> | ||
+ | <tr> | ||
+ | <td> | ||
+ | <p><a href="http://parts.igem.org/Part:BBa_K3889020">BBa_K3889020</a></p> | ||
+ | </td> | ||
+ | <td> | ||
+ | <p>P22 c2 repressor</p> | ||
+ | </td> | ||
+ | <td> | ||
+ | <p>648 bp</p> | ||
+ | </td> | ||
+ | <td> | ||
+ | <p>DNA binding that represses gene expression</p> | ||
+ | </td> | ||
+ | </tr> | ||
+ | <tr> | ||
+ | <td> | ||
+ | <p><a href="http://parts.igem.org/Part:BBa_K3889021">BBa_K3889021</a></p> | ||
+ | </td> | ||
+ | <td> | ||
+ | <p>Steroid responsive Transcription Factor (SRTF1)</p> | ||
+ | </td> | ||
+ | <td> | ||
+ | <p>567 bp</p> | ||
+ | </td> | ||
+ | <td> | ||
+ | <p>Transcription factor that can bind to specific DNA sequence to repress gene expression and is inhibited by progesterone</p> | ||
+ | </td> | ||
+ | </tr> | ||
+ | <tr> | ||
+ | <td> | ||
+ | <p><a href="http://parts.igem.org/Part:BBa_K3889022">BBa_K3889022</a></p> | ||
+ | </td> | ||
+ | <td> | ||
+ | <p>Human Ovastacin protease phosphomimic_A</p> | ||
+ | </td> | ||
+ | <td> | ||
+ | <p>594 bp</p> | ||
+ | </td> | ||
+ | <td> | ||
+ | <p>Epitope region of the human protease ovastacin containing active site for ZP2 protein cleavage</p> | ||
+ | </td> | ||
+ | </tr> | ||
+ | <tr> | ||
+ | <td> | ||
+ | <p><a href="http://parts.igem.org/Part:BBa_K3889023">BBa_K3889023</a></p> | ||
+ | </td> | ||
+ | <td> | ||
+ | <p>Human Ovastacin protease phosphomimic_B</p> | ||
+ | </td> | ||
+ | <td> | ||
+ | <p>594 bp</p> | ||
+ | </td> | ||
+ | <td> | ||
+ | <p>Human protease ovastacin with phospho mimic tyrosine</p> | ||
+ | </td> | ||
+ | </tr> | ||
+ | <tr> | ||
+ | <td> | ||
+ | <p><a href="http://parts.igem.org/Part:BBa_K3889024">BBa_K3889024</a></p> | ||
+ | </td> | ||
+ | <td> | ||
+ | <p>Human Ovastacin protease </p> | ||
+ | </td> | ||
+ | <td> | ||
+ | <p>594 bp</p> | ||
+ | </td> | ||
+ | <td> | ||
+ | <p>Human protease ovastacin with phospho mimic tyrosine and serine</p> | ||
+ | </td> | ||
+ | </tr> | ||
+ | <tr> | ||
+ | <td> | ||
+ | <p><a href="http://parts.igem.org/Part:BBa_K3889025">BBa_K3889025</a></p> | ||
+ | </td> | ||
+ | <td> | ||
+ | <p>yqcG toxin (RFC1000 compatible)</p> | ||
+ | </td> | ||
+ | <td> | ||
+ | <p>1593 bp</p> | ||
+ | </td> | ||
+ | <td> | ||
+ | <p>Toxin part of type 2 toxin-antitoxin system of Bacillus subtilis (DNase)</p> | ||
+ | </td> | ||
+ | </tr> | ||
+ | <tr> | ||
+ | <td> | ||
+ | <p><a href="http://parts.igem.org/Part:BBa_K3889026">BBa_K3889026</a></p> | ||
+ | </td> | ||
+ | <td> | ||
+ | <p>ytvA light sensor (RFC1000 compatible)</p> | ||
+ | </td> | ||
+ | <td> | ||
+ | <p>783 bp</p> | ||
+ | </td> | ||
+ | <td> | ||
+ | <p>Blue light sensor that positively regulates SigB</p> | ||
+ | </td> | ||
+ | </tr> | ||
+ | <tr> | ||
+ | <td> | ||
+ | <p><a href="http://parts.igem.org/Part:BBa_K3889027">BBa_K3889027</a></p> | ||
+ | </td> | ||
+ | <td> | ||
+ | <p>bovine pancreatic DNase 1</p> | ||
+ | </td> | ||
+ | <td> | ||
+ | <p>846 bp</p> | ||
+ | </td> | ||
+ | <td> | ||
+ | <p>Highly potential and efficient endonuclease (Toxin)</p> | ||
+ | </td> | ||
+ | </tr> | ||
+ | <tr> | ||
+ | <td> | ||
+ | <p><a href="http://parts.igem.org/Part:BBa_K3889028">BBa_K3889028</a></p> | ||
+ | </td> | ||
+ | <td> | ||
+ | <p>mfLon protease</p> | ||
+ | </td> | ||
+ | <td> | ||
+ | <p>2361 bp</p> | ||
+ | </td> | ||
+ | <td> | ||
+ | <p>Lon Protease from Mesoplasma florum bacteria</p> | ||
+ | </td> | ||
+ | </tr> | ||
+ | <tr> | ||
+ | <td> | ||
+ | <p><a href="http://parts.igem.org/Part:BBa_K3889029">BBa_K3889029</a></p> | ||
+ | </td> | ||
+ | <td> | ||
+ | <p>Human Zona pellucida ZP2 protein partial</p> | ||
+ | </td> | ||
+ | <td> | ||
+ | <p>1800 bp</p> | ||
+ | </td> | ||
+ | <td> | ||
+ | <p>ZP2 protein that is cleaved by ovastacin</p> | ||
+ | </td> | ||
+ | </tr> | ||
+ | <tr> | ||
+ | <td> | ||
+ | <p><a href="http://parts.igem.org/Part:BBa_K3889030">BBa_K3889030</a></p> | ||
+ | </td> | ||
+ | <td> | ||
+ | <p>SRTF 1 Binding Site</p> | ||
+ | </td> | ||
+ | <td> | ||
+ | <p>20 bp</p> | ||
+ | </td> | ||
+ | <td> | ||
+ | <p>SRTF1 binds to this DNA sequence to negatively regulate gene expression</p> | ||
+ | </td> | ||
+ | </tr> | ||
+ | <tr> | ||
+ | <td> | ||
+ | <p><a href="http://parts.igem.org/Part:BBa_K3889040">BBa_K3889040</a></p> | ||
+ | </td> | ||
+ | <td> | ||
+ | <p>Bacillus subtilis Spacer Sequence</p> | ||
+ | </td> | ||
+ | <td> | ||
+ | <p>40 bp</p> | ||
+ | </td> | ||
+ | <td> | ||
+ | <p>Spacer sequence without any promoter, RBS or terminator activity</p> | ||
+ | </td> | ||
+ | </tr> | ||
+ | <tr> | ||
+ | <td> | ||
+ | <p><a href="http://parts.igem.org/Part:BBa_K3889050">BBa_K3889050</a></p> | ||
+ | </td> | ||
+ | <td> | ||
+ | <p>Bacillus subtilis TAT signal peptide phoD</p> | ||
+ | </td> | ||
+ | <td> | ||
+ | <p>168 bp</p> | ||
+ | </td> | ||
+ | <td> | ||
+ | <p>Signal Peptide for TAT secretion system in Bacillus subtilis</p> | ||
+ | </td> | ||
+ | </tr> | ||
+ | <tr> | ||
+ | <td> | ||
+ | <p><a href="http://parts.igem.org/Part:BBa_K3889051">BBa_K3889051</a></p> | ||
+ | </td> | ||
+ | <td> | ||
+ | <p>Bacillus subtilis TAT signal peptide YwnB</p> | ||
+ | </td> | ||
+ | <td> | ||
+ | <p>84 bp</p> | ||
+ | </td> | ||
+ | <td> | ||
+ | <p>Signal Peptide for TAT secretion system in Bacillus subtilis</p> | ||
+ | </td> | ||
+ | </tr> | ||
+ | <tr> | ||
+ | <td> | ||
+ | <p><a href="http://parts.igem.org/Part:BBa_K3889069">BBa_K3889069</a></p> | ||
+ | </td> | ||
+ | <td> | ||
+ | <p>P2A Peptide Linker PTV</p> | ||
+ | </td> | ||
+ | <td> | ||
+ | <p>66 bp</p> | ||
+ | </td> | ||
+ | <td> | ||
+ | <p>Self cleaving peptide sequence which separates two proteins during translation in same operon</p> | ||
+ | </td> | ||
+ | </tr> | ||
+ | <tr> | ||
+ | <td> | ||
+ | <p><a href="http://parts.igem.org/Part:BBa_K3889070">BBa_K3889070</a></p> | ||
+ | </td> | ||
+ | <td> | ||
+ | <p>Bacillus subtilis oriented double terminator nagP</p> | ||
+ | </td> | ||
+ | <td> | ||
+ | <p>122 bp</p> | ||
+ | </td> | ||
+ | <td> | ||
+ | <p>Fused product of nagP and <a href="http://parts.igem.org/Part:BBa_B0010">BBa_B0010</a> (Improvement in <a href="http://parts.igem.org/Part:BBa_B0010">BBa_B0010</a>)</p> | ||
+ | </td> | ||
+ | </tr> | ||
+ | <tr> | ||
+ | <td> | ||
+ | <p><a href="http://parts.igem.org/Part:BBa_K3889080">BBa_K3889080</a></p> | ||
+ | </td> | ||
+ | <td> | ||
+ | <p>P22 binding site A</p> | ||
+ | </td> | ||
+ | <td> | ||
+ | <p>18 bp</p> | ||
+ | </td> | ||
+ | <td> | ||
+ | <p>P22 binds to this DNA sequence to negatively regulate gene expression</p> | ||
+ | </td> | ||
+ | </tr> | ||
+ | <tr> | ||
+ | <td> | ||
+ | <p><a href="http://parts.igem.org/Part:BBa_K3889081">BBa_K3889081</a></p> | ||
+ | </td> | ||
+ | <td> | ||
+ | <p>P22 binding site B</p> | ||
+ | </td> | ||
+ | <td> | ||
+ | <p>18 bp</p> | ||
+ | </td> | ||
+ | <td> | ||
+ | <p>P22 binds to this DNA sequence to negatively regulate gene expression</p> | ||
+ | </td> | ||
+ | </tr> | ||
+ | <tr> | ||
+ | <td> | ||
+ | <p><a href="http://parts.igem.org/Part:BBa_K3889082">BBa_K3889082</a></p> | ||
+ | </td> | ||
+ | <td> | ||
+ | <p>P22 binding site C</p> | ||
+ | </td> | ||
+ | <td> | ||
+ | <p>18 bp</p> | ||
+ | </td> | ||
+ | <td> | ||
+ | <p>P22 binds to this DNA sequence to negatively regulate gene expression</p> | ||
+ | </td> | ||
+ | </tr> | ||
+ | <tr> | ||
+ | <td> | ||
+ | <p><a href="http://parts.igem.org/Part:BBa_K3889083">BBa_K3889083</a></p> | ||
+ | </td> | ||
+ | <td> | ||
+ | <p>P22 binding site D</p> | ||
+ | </td> | ||
+ | <td> | ||
+ | <p>18 bp</p> | ||
+ | </td> | ||
+ | <td> | ||
+ | <p>P22 binds to this DNA sequence to negatively regulate gene expression</p> | ||
+ | </td> | ||
+ | </tr> | ||
+ | <tr> | ||
+ | <td> | ||
+ | <p><a href="http://parts.igem.org/Part:BBa_K3889084">BBa_K3889084</a></p> | ||
+ | </td> | ||
+ | <td> | ||
+ | <p>P22 binding site E</p> | ||
+ | </td> | ||
+ | <td> | ||
+ | <p>18 bp</p> | ||
+ | </td> | ||
+ | <td> | ||
+ | <p>P22 binds to this DNA sequence to negatively regulate gene expression</p> | ||
+ | </td> | ||
+ | </tr> | ||
+ | <tr> | ||
+ | <td> | ||
+ | <p><a href="http://parts.igem.org/Part:BBa_K3889085">BBa_K3889085</a></p> | ||
+ | </td> | ||
+ | <td> | ||
+ | <p>P22 binding site F</p> | ||
+ | </td> | ||
+ | <td> | ||
+ | <p>18 bp</p> | ||
+ | </td> | ||
+ | <td> | ||
+ | <p>P22 binds to this DNA sequence to negatively regulate gene expression</p> | ||
+ | </td> | ||
+ | </tr> | ||
+ | <tr> | ||
+ | <td> | ||
+ | <p><a href="http://parts.igem.org/Part:BBa_K3889086">BBa_K3889086</a></p> | ||
+ | </td> | ||
+ | <td> | ||
+ | <p>P22 binding site G</p> | ||
+ | </td> | ||
+ | <td> | ||
+ | <p>18 bp</p> | ||
+ | </td> | ||
+ | <td> | ||
+ | <p>P22 binds to this DNA sequence to negatively regulate gene expression</p> | ||
+ | </td> | ||
+ | </tr> | ||
+ | <tr> | ||
+ | <td> | ||
+ | <p><a href="http://parts.igem.org/Part:BBa_K3889087">BBa_K3889087</a></p> | ||
+ | </td> | ||
+ | <td> | ||
+ | <p>P22 binding site H</p> | ||
+ | </td> | ||
+ | <td> | ||
+ | <p>18 bp</p> | ||
+ | </td> | ||
+ | <td> | ||
+ | <p>P22 binds to this DNA sequence to negatively regulate gene expression</p> | ||
+ | </td> | ||
+ | </tr> | ||
+ | <tr> | ||
+ | <td> | ||
+ | <p><a href="http://parts.igem.org/Part:BBa_K3889088">BBa_K3889088</a></p> | ||
+ | </td> | ||
+ | <td> | ||
+ | <p>P22 binding site I</p> | ||
+ | </td> | ||
+ | <td> | ||
+ | <p>18 bp</p> | ||
+ | </td> | ||
+ | <td> | ||
+ | <p>P22 binds to this DNA sequence to negatively regulate gene expression</p> | ||
+ | </td> | ||
+ | </tr> | ||
+ | <tr> | ||
+ | <td> | ||
+ | <p><a href="http://parts.igem.org/Part:BBa_K3889089">BBa_K3889089</a></p> | ||
+ | </td> | ||
+ | <td> | ||
+ | <p>P22 binding site J</p> | ||
+ | </td> | ||
+ | <td> | ||
+ | <p>18 bp</p> | ||
+ | </td> | ||
+ | <td> | ||
+ | <p>P22 binds to this DNA sequence to negatively regulate gene expression</p> | ||
+ | </td> | ||
+ | </tr> | ||
+ | <tr> | ||
+ | <td> | ||
+ | <p><a href="http://parts.igem.org/Part:BBa_K3889090">BBa_K3889090</a></p> | ||
+ | </td> | ||
+ | <td> | ||
+ | <p>P22 binding site K</p> | ||
+ | </td> | ||
+ | <td> | ||
+ | <p>18 bp</p> | ||
+ | </td> | ||
+ | <td> | ||
+ | <p>P22 binds to this DNA sequence to negatively regulate gene expression</p> | ||
+ | </td> | ||
+ | </tr> | ||
+ | <tr> | ||
+ | <td> | ||
+ | <p><a href="http://parts.igem.org/Part:BBa_K3889091">BBa_K3889091</a></p> | ||
+ | </td> | ||
+ | <td> | ||
+ | <p>P22 binding site L</p> | ||
+ | </td> | ||
+ | <td> | ||
+ | <p>18 bp</p> | ||
+ | </td> | ||
+ | <td> | ||
+ | <p>P22 binds to this DNA sequence to negatively regulate gene expression</p> | ||
+ | </td> | ||
+ | </tr> | ||
+ | <tr> | ||
+ | <td> | ||
+ | <p><a href="http://parts.igem.org/Part:BBa_K3889092">BBa_K3889092</a></p> | ||
+ | </td> | ||
+ | <td> | ||
+ | <p>XylR</p> | ||
+ | </td> | ||
+ | <td> | ||
+ | <p>1050 bp</p> | ||
+ | </td> | ||
+ | <td> | ||
+ | <p>pXylA repressor which provides xylose inducible gene expression</p> | ||
+ | </td> | ||
+ | </tr> | ||
+ | <tr> | ||
+ | <td> | ||
+ | <p><a href="http://parts.igem.org/Part:BBa_K3889093">BBa_K3889093</a></p> | ||
+ | </td> | ||
+ | <td> | ||
+ | <p>yqcF</p> | ||
+ | </td> | ||
+ | <td> | ||
+ | <p>576 bp</p> | ||
+ | </td> | ||
+ | <td> | ||
+ | <p id="4">Anti-toxin of yqcG (a kind of DNase)</p> | ||
+ | </td> | ||
+ | </tr> | ||
+ | </tbody> | ||
+ | </table> | ||
+ | </div> | ||
+ | |||
+ | |||
+ | |||
+ | |||
+ | <h2 class="pt-3">Composite Parts: </h2> | ||
+ | <div class="table-responisve"> | ||
+ | <table class="table table-striped table-bordered"> | ||
+ | <tbody> | ||
+ | <tr style="background-color: #bb2f5c;color: white;"`> | ||
+ | <td > | ||
+ | <p><strong>Part No:</strong></p> | ||
+ | </td> | ||
+ | <td> | ||
+ | <p><strong>Name</strong></p> | ||
+ | </td> | ||
+ | <td> | ||
+ | <p><strong>Length</strong></p> | ||
+ | </td> | ||
+ | <td> | ||
+ | <p><strong>Description </strong></p> | ||
+ | </td> | ||
+ | </tr> | ||
+ | <tr> | ||
+ | <td> | ||
+ | <p><a href="http://parts.igem.org/Part:BBa_K3889100">BBa_K3889100</a></p> | ||
+ | </td> | ||
+ | <td> | ||
+ | <p>SRTF1 Cassette</p> | ||
+ | </td> | ||
+ | <td> | ||
+ | <p>1539 bp</p> | ||
+ | </td> | ||
+ | <td> | ||
+ | <p>Constitutive production of SRTF1 being reported by mCherry</p> | ||
+ | </td> | ||
+ | </tr> | ||
+ | <tr> | ||
+ | <td> | ||
+ | <p><a href="http://parts.igem.org/Part:BBa_K3889101">BBa_K3889101</a></p> | ||
+ | </td> | ||
+ | <td> | ||
+ | <p>P22 Cassette</p> | ||
+ | </td> | ||
+ | <td> | ||
+ | <p>1643 bp</p> | ||
+ | </td> | ||
+ | <td> | ||
+ | <p>Progesterone inducible production due to fusion of SRTF1 binding site to the promoter reported by Azurite</p> | ||
+ | </td> | ||
+ | </tr> | ||
+ | <tr> | ||
+ | <td> | ||
+ | <p><a href="http://parts.igem.org/Part:BBa_K3889102">BBa_K3889102</a></p> | ||
+ | </td> | ||
+ | <td> | ||
+ | <p>Ovastacin Cassette</p> | ||
+ | </td> | ||
+ | <td> | ||
+ | <p>1042 bp</p> | ||
+ | </td> | ||
+ | <td> | ||
+ | <p>P22 controlled (indirect progesterone control) ovastacin production reported by sfGFP </p> | ||
+ | </td> | ||
+ | </tr> | ||
+ | <tr> | ||
+ | <td> | ||
+ | <p><a href="http://parts.igem.org/Part:BBa_K3889110">BBa_K3889110</a></p> | ||
+ | </td> | ||
+ | <td> | ||
+ | <p>xylR cassette</p> | ||
+ | </td> | ||
+ | <td> | ||
+ | <p>2032 bp</p> | ||
+ | </td> | ||
+ | <td> | ||
+ | <p>Constitutive production of XylR being reported by sfGFP</p> | ||
+ | </td> | ||
+ | </tr> | ||
+ | <tr> | ||
+ | <td> | ||
+ | <p><a href="http://parts.igem.org/Part:BBa_K3889111">BBa_K3889111</a></p> | ||
+ | </td> | ||
+ | <td> | ||
+ | <p>yqcG cassette</p> | ||
+ | </td> | ||
+ | <td> | ||
+ | <p>1815 bp</p> | ||
+ | </td> | ||
+ | <td> | ||
+ | <p>Xylose inducible production of YqcG</p> | ||
+ | </td> | ||
+ | </tr> | ||
+ | <tr> | ||
+ | <td> | ||
+ | <p><a href="http://parts.igem.org/Part:BBa_K3889112">BBa_K3889112</a></p> | ||
+ | </td> | ||
+ | <td> | ||
+ | <p>yqcF cassette</p> | ||
+ | </td> | ||
+ | <td> | ||
+ | <p>1548 bp</p> | ||
+ | </td> | ||
+ | <td> | ||
+ | <p>Constitutive production of YqcF being reported by mCherry</p> | ||
+ | </td> | ||
+ | </tr> | ||
+ | <tr> | ||
+ | <td> | ||
+ | <p><a href="http://parts.igem.org/Part:BBa_K3889120">BBa_K3889120</a></p> | ||
+ | </td> | ||
+ | <td> | ||
+ | <p>ytvA cassette</p> | ||
+ | </td> | ||
+ | <td> | ||
+ | <p>1759 bp</p> | ||
+ | </td> | ||
+ | <td> | ||
+ | <p>Constitutive production of YtvA being reported by mCherry</p> | ||
+ | </td> | ||
+ | </tr> | ||
+ | <tr> | ||
+ | <td> | ||
+ | <p><a href="http://parts.igem.org/Part:BBa_K3889121">BBa_K3889121</a></p> | ||
+ | </td> | ||
+ | <td> | ||
+ | <p>bpDnase 1 cassette</p> | ||
+ | </td> | ||
+ | <td> | ||
+ | <p>1275 bp</p> | ||
+ | </td> | ||
+ | <td> | ||
+ | <p>Light inducible production of bpDNase 1 </p> | ||
+ | </td> | ||
+ | </tr> | ||
+ | <tr> | ||
+ | <td> | ||
+ | <p><a href="http://parts.igem.org/Part:BBa_K3889122">BBa_K3889122</a></p> | ||
+ | </td> | ||
+ | <td> | ||
+ | <p>mfLon cassette</p> | ||
+ | </td> | ||
+ | |||
+ | <td> | ||
+ | <p>Constitutive production of mfLon being reported by sfGFP</p> | ||
+ | </td> | ||
+ | </tr> | ||
+ | <tr> | ||
+ | <td> | ||
+ | <p><a href="http://parts.igem.org/Part:BBa_K3889127">BBa_K3889127</a></p> | ||
+ | </td> | ||
+ | <td> | ||
+ | <p>bpDnase 1 + mfLon tag</p> | ||
+ | </td> | ||
+ | <td> | ||
+ | <p>933 bp</p> | ||
+ | </td> | ||
+ | <td> | ||
+ | <p>bpDnase 1 fused with protein degradation tag of mfLon</p> | ||
+ | </td> | ||
+ | </tr> | ||
+ | <tr> | ||
+ | <td> | ||
+ | <p><a href="http://parts.igem.org/Part:BBa_K3889130">BBa_K3889130</a></p> | ||
+ | </td> | ||
+ | <td> | ||
+ | <p>Spacer Cassette for Terminator check in Bacillus subtilis</p> | ||
+ | </td> | ||
+ | <td> | ||
+ | <p>1722 bp</p> | ||
+ | </td> | ||
+ | <td> | ||
+ | <p>Spacer in between of two reporters mCherry and sfGFP which provides with basal level expression of downstream genes in absence of a terminator</p> | ||
+ | </td> | ||
+ | </tr> | ||
+ | <tr> | ||
+ | <td> | ||
+ | <p><a href="http://parts.igem.org/Part:BBa_K3889131">BBa_K3889131</a></p> | ||
+ | </td> | ||
+ | <td> | ||
+ | <p>Improvement Cassette BBa_B0010</p> | ||
+ | </td> | ||
+ | <td> | ||
+ | <p>1762 bp</p> | ||
+ | </td> | ||
+ | <td> | ||
+ | <p>Replacing spacer with terminator in <a href="http://parts.igem.org/Part:BBa_K3889130">BBa_K3889130</a> for checking terminator efficiency of <a href="http://parts.igem.org/Part:BBa_B0010"><strong>BBa_B0010</strong></a></p> | ||
+ | </td> | ||
+ | </tr> | ||
+ | <tr> | ||
+ | <td> | ||
+ | <p><a href="http://parts.igem.org/Part:BBa_K3889132">BBa_K3889132</a></p> | ||
+ | </td> | ||
+ | <td> | ||
+ | <p>Improvement Cassette BBa_B0010+nagP</p> | ||
+ | </td> | ||
+ | <td> | ||
+ | <p>1804 bp</p> | ||
+ | </td> | ||
+ | <td> | ||
+ | <p>Replacing spacer with terminator in <a href="http://parts.igem.org/Part:BBa_K3889130">BBa_K3889130</a> for checking terminator efficiency of <a href="http://parts.igem.org/Part:BBa_K3889070">BBa_K3889070</a></p> | ||
+ | </td> | ||
+ | </tr> | ||
+ | <tr> | ||
+ | <td> | ||
+ | <p><a href="http://parts.igem.org/Part:BBa_K3889150">BBa_K3889150</a></p> | ||
+ | </td> | ||
+ | <td> | ||
+ | <p>SP200+SRTF1 Binding Site+ RBS</p> | ||
+ | </td> | ||
+ | <td> | ||
+ | <p>83 bp</p> | ||
+ | </td> | ||
+ | <td> | ||
+ | <p>SRTF1 binding site fused with SP200 promoter for progesterone inducible gene expression</p> | ||
+ | </td> | ||
+ | </tr> | ||
+ | <tr> | ||
+ | <td> | ||
+ | <p><a href="http://parts.igem.org/Part:BBa_K3889151">BBa_K3889151</a></p> | ||
+ | </td> | ||
+ | <td> | ||
+ | <p>P43+P22 Binding Site L +RBS</p> | ||
+ | </td> | ||
+ | <td> | ||
+ | <p>85 bp</p> | ||
+ | </td> | ||
+ | <td> | ||
+ | <p id="5">P22 binding site fused with P43 for P22 controlled gene expression</p> | ||
+ | </td> | ||
+ | </tr> | ||
+ | </tbody> | ||
+ | </table> | ||
+ | </div> | ||
+ | <h1>Improvement:</h1> | ||
+ | |||
+ | <p><strong>Introduction:</strong></p> | ||
+ | <figure class="col-12 col-md-8 p-5 m-auto"> | ||
+ | <img src="./assets/c3p2 (1).svg" alt="Trulli" style="width:100%"> | ||
+ | </figure> | ||
+ | <p>While engineering any new circuit, there is always a need for well-characterized and predictable parts. Not only should the circuit function as expected, but it should also be orthogonal to irrelevant cell processes, thereby increasing the need to have efficient production and, in some cases, more importantly, efficient termination. While there are several well-studied and efficient terminators for <em>E.coli</em>, we found no specific efficient single terminator on the iGEM registry that could stand out for <em>B.subtilis</em> chassis. Hence, we decided to improvise a terminator which might fulfil this gap.</p> | ||
+ | |||
+ | <p><strong>Measuring efficiency:</strong></p> | ||
+ | <p>The experiment is divided into two cassettes: one reference and the other is a test cassette containing a terminator whose efficiency needs to be determined as shown by Gale et al.[1].</p> | ||
+ | |||
+ | <figure class="col-12 col-md-8 p-5 m-auto"> | ||
+ | <img src="./assets/c3p2 (1).svg" alt="Trulli" style="width:100%"> | ||
+ | </figure> | ||
+ | <p>The reference and the test cassette provide us the expression levels of both the fluorescent proteins which could be compared to tell us how efficiently the terminator is working.</p> | ||
+ | <p><br /><br /></p> | ||
+ | <p>Formulae for terminator efficiency<a style="color: #8d1063;" href="#ref5">[5]</a></p> | ||
+ | |||
+ | $TE_{Device}=\frac{mCherry_{0}}{sfGFP_{0}}$ (1) | ||
+ | <br> | ||
+ | where, | ||
+ | <br> | ||
+ | <br> | ||
+ | $mCherry_{0}\rightarrow$ mCherry produced by device without terminator<br><br> | ||
+ | $sfGFP_{0}\rightarrow$ sfGFP produced by device without terminator<br><br> | ||
+ | Using the device without any changes, $TE_{Device}$ can be calculated which gives the expression of <br>$mCherry$ in absence of a terminator.<br><br> | ||
+ | $TE=100-\left[\left(\frac{mCherry}{sfGPF}\right)\times\left(\frac{1}{TE_{Device}}\right)\times100\right]$ (2)<br><br> | ||
+ | where, <br><br> | ||
+ | $mCherry$ $\rightarrow$ mCherry produced by device with the terminator that needs to checked<br><br> | ||
+ | $sfGFP$ $\rightarrow$ sfGFP produced by device with the terminator that needs to checked<br><br> | ||
+ | <p><br /><br /></p> | ||
+ | <p><strong>d-score:</strong></p> | ||
+ | <p>For <em>E. coli </em>terminators d'Aubenton Carafa [3] gave a scoring system as shown below:</p> | ||
+ | |||
+ | <p>$d=96.59 \times \frac{-\Delta G/(kcal/mol)}{n{SL}} + 18.16 \times T_{score} -116.87$</p> | ||
+ | |||
+ | <p>Where </p> | ||
+ | <p>d is the d-score</p> | ||
+ | <p>$-\Delta G$ is the Gibbs free energy of stem-loop formation in kcal/mole</p> | ||
+ | <p>nSL is the length of the stem loop</p> | ||
+ | <p>TScore is the score for T-stretch of the terminators</p> | ||
+ | <p>Coefficients are according to fitting the d'Aubenton Carafa’s model </p> | ||
+ | |||
+ | <p>The T<sub>Score</sub>b> is calculated as follows:</p> | ||
+ | <p>$T_{score}= \sum_{i=0}^{\ 14} x _i$</p> | ||
+ | <p>Where</p> | ||
+ | <p>$x_0 = 0.9$</p> | ||
+ | <p>$x_i = 0.9$ if $i^{th}$ nucleotide is thymine</p> | ||
+ | <p>$x_i = 0.6 \times x_{i-1}$ if $i^{th}$ nucleotide is not thymine</p> | ||
+ | |||
+ | <p>These scoring system was modified by de Hoon et al. [2] for <em>Bacillus subtilis</em> as per their model which is as follows:</p> | ||
+ | |||
+ | <p>$d=7.90 \times \frac{-\Delta G/(kcal/mol)}{n{SL}} + 2.67 \times T{score} -14.91$</p> | ||
+ | |||
+ | <p>Where </p> | ||
+ | <p>d is the d-score</p> | ||
+ | <p>$-\Delta$ G is the Gibbs free energy of stem-loop formation in kcal/mole</p> | ||
+ | <p>nSL is the length of the stem loop</p> | ||
+ | <p>TScore is the score for T-stretch of the terminators</p> | ||
+ | <p>Coefficients are according to fitting the model </p> | ||
+ | <p>Here the TScore is calculated as follows:</p> | ||
+ | |||
+ | <p>$T= \sum_{i=0}^{\ 14} e^{- \lambda _i} \delta_i$</p> | ||
+ | <p>Where</p> | ||
+ | <p>$\lambda _i = 0.144$ as per the fitting of the model</p> | ||
+ | <p>$\delta_i = 0$ if $i^{th}$ nucleotide is not thymine </p> | ||
+ | <p>$\delta_i = 1$ if $i^{th}$ nucleotide is thymine</p> | ||
+ | |||
+ | <p>.As the d-score takes into account the Gibbs free energy, length of the stem loop and the richness of thymine in T-stretch which are essential for a rho independent terminator. Hence, the d-score can provide a rough idea about how good a terminator is. In other words, higher the d-score higher will be the terminator efficiency.[3]</p> | ||
+ | <p><br /><br /></p> | ||
+ | <p><strong>Improvement:</strong></p> | ||
+ | <p>We decided to improve BBa_B0010 in order to make a strong terminator which can be used for primarily the B.subtilis chassis while still retaining its efficiency in E.coli. For doing this we modified the tail of Bba_B0010 and fused another rho-independent terminator from the Bacillus subtilis genome on the basis of its d-Score. </p> | ||
+ | |||
+ | <p>From a list of 425 native B.subtilis terminators taken from the study conducted by Michiel et al [2], we calculated the d-score of each terminator to get a rough idea of their efficiency. Based on the results the highest d-score= 5.666126119 was of the terminator belonging to the gene nagP. Both BBa_B0010 and nagP terminators were ligated to form a double terminator.</p> | ||
+ | |||
+ | <p>Based on our calculations, we decided to go with nagP terminator. We modified the end regions of BBa_B0010 and ligated to it the nagP terminator to create an improved version(PARTNO). Using the server <a href="http://rna.tbi.univie.ac.at/cgi-bin/RNAWebSuite/RNAfold.cgi">RNAFold</a> we calculated the minimum energy to show in silico that the improved terminator will have more negative Minimum Free energy as shown. </p> | ||
+ | |||
+ | <table class="table table-bordered table-striped"> | ||
+ | <thead> | ||
+ | <tr style="background-color: #8D1063; color: #FDF8D7;"> | ||
+ | <td></td> | ||
+ | <td> | ||
+ | <p>BBa_B0010</p> | ||
+ | </td> | ||
+ | <td> | ||
+ | <p>BBa_B0010+nagP</p> | ||
+ | </td> | ||
+ | </tr> | ||
+ | </thead> | ||
+ | <tbody> | ||
+ | <tr> | ||
+ | <td> | ||
+ | <p>Minimum Free Energy (kcal/mol)</p> | ||
+ | </td> | ||
+ | <td> | ||
+ | <p>-40</p> | ||
+ | </td> | ||
+ | <td> | ||
+ | <p>-64.6</p> | ||
+ | </td> | ||
+ | </tr> | ||
+ | </tbody> | ||
+ | </table> | ||
+ | |||
+ | <p>The predicted structure for these two terminators as given by RnaFold server is:</p> | ||
+ | <ol> | ||
+ | <li>BBa_B0010: | ||
+ | <figure class="col-12 col-md-8 p-5 m-auto"> | ||
+ | <img src="./assets/c3p2 (1).svg" alt="Trulli" style="width:100%"> | ||
+ | </figure> | ||
+ | </li> | ||
+ | <li>BBa_B0010+nagP: | ||
+ | <figure class="col-12 col-md-8 p-5 m-auto"> | ||
+ | <img src="./assets/c3p2 (1).svg" alt="Trulli" style="width:100%"> | ||
+ | </figure> | ||
+ | </li> | ||
+ | </ol> | ||
+ | <p>Data</p> | ||
+ | <p>Zip file containing excel sheet of all terminators,2*t score calculators, one raw data sheet excel file,readme file</p> | ||
+ | <h1>References:</h1> | ||
+ | <p>[1] Gale, G. A. R., Wang, B., & McCormick, A. J. (2021). Evaluation and Comparison of the Efficiency of Transcription Terminators in Different Cyanobacterial Species. Frontiers in Microbiology, 11. https://doi.org/10.3389/fmicb.2020.624011 : </p> | ||
+ | |||
+ | <p>[2] de Hoon, M. J. L., Makita, Y., Nakai, K., & Miyano, S. (2005). Prediction of Transcriptional Terminators in Bacillus subtilis and Related Species. PLoS Computational Biology, 1(3), e25. https://doi.org/10.1371/journal.pcbi.0010025 </p> | ||
+ | |||
+ | <p>[3] Carafa, Y. d’Aubenton, Brody, E., & Thermes, C. (1990). Prediction of rho-independent Escherichia coli transcription terminators. Journal of Molecular Biology, 216(4), 835–858. https://doi.org/10.1016/s0022-2836(99)80005-9 </p> | ||
+ | |||
+ | </div> | ||
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+ | <button type="button" class="btn button-dark btn-floating btn-lg" id="btn-back-to-top"><i class="fas fa-arrow-up"></i></button> | ||
</main> | </main> | ||
− | |||
Revision as of 15:21, 16 October 2021
Overview
Due to the novel approaches taken while pursuing this project, we found ourselves using new parts that had not been given in the iGEM registry. In total, we developed 37 new basic parts (either entirely new or by modifying previously existing ones). We strongly believe that these two collections can be exploited to their full potential by the subsequent iGEM generations.
Furthermore, we have designed and used multiple combinations of basic parts as given in the composite part section.These composite parts can be used in multiple settings depending on the requirements of the projects.
The parts used in our project are as follows:
Previous Parts used:
BioBrick ID |
Name |
Length |
Description |
pVeg |
97 bp |
Constitutive natural promoter under Sig A transcription factor |
|
P43 |
56 bp |
Constitutive natural promoter under Sig A and SigB transcription factor |
|
pxylA |
82 bp |
Xylose dependent natural promoter (repressed by xylR) |
|
P22 repressor |
712 bp |
DNA binding repressor protein |
|
Protein degradation tag B |
87 bp |
mf-Lon specific Protein Degradation Tag B (medium-strong) |
|
RBS |
11 bp |
RBS for B. subtilis |
|
RBS |
11 bp |
RBS for B. subtilis |
|
RBS |
11 bp |
RBS for B. subtilis |
|
RBS |
11 bp |
RBS for B. subtilis |
|
mCherry |
714 bp |
Red fluorescent tag |
|
Terminator |
129 bp |
Double terminator consisting of BBa_B0010 and BBa_B0012 |
|
Terminator |
80 bp |
Relatively warker Terminator as compared to BBa_B0015 |
Basic Parts:
Part No: |
Name |
Length |
Description |
Azurite BFP (BFP.B3) |
717 bp |
Blue fluorescent tag |
|
modified_sfGFP |
720 bp |
Green fluorescent tag |
|
SP126 |
52 bp |
Promoter from synthetic library of Bacillus subtilis |
|
SP146 |
52 bp |
Promoter from synthetic library of Bacillus subtilis |
|
SP200 |
52 bp |
Promoter from synthetic library of Bacillus subtilis |
|
pgsiB |
300 bp |
Natural promoter of Bacillus subtilis under control of general stress SigB transcription factor |
|
pGAL1 Yeast Promoter |
531 bp |
Galactose inducible yeast promoter |
|
P22 c2 repressor |
648 bp |
DNA binding that represses gene expression |
|
Steroid responsive Transcription Factor (SRTF1) |
567 bp |
Transcription factor that can bind to specific DNA sequence to repress gene expression and is inhibited by progesterone |
|
Human Ovastacin protease phosphomimic_A |
594 bp |
Epitope region of the human protease ovastacin containing active site for ZP2 protein cleavage |
|
Human Ovastacin protease phosphomimic_B |
594 bp |
Human protease ovastacin with phospho mimic tyrosine |
|
Human Ovastacin protease |
594 bp |
Human protease ovastacin with phospho mimic tyrosine and serine |
|
yqcG toxin (RFC1000 compatible) |
1593 bp |
Toxin part of type 2 toxin-antitoxin system of Bacillus subtilis (DNase) |
|
ytvA light sensor (RFC1000 compatible) |
783 bp |
Blue light sensor that positively regulates SigB |
|
bovine pancreatic DNase 1 |
846 bp |
Highly potential and efficient endonuclease (Toxin) |
|
mfLon protease |
2361 bp |
Lon Protease from Mesoplasma florum bacteria |
|
Human Zona pellucida ZP2 protein partial |
1800 bp |
ZP2 protein that is cleaved by ovastacin |
|
SRTF 1 Binding Site |
20 bp |
SRTF1 binds to this DNA sequence to negatively regulate gene expression |
|
Bacillus subtilis Spacer Sequence |
40 bp |
Spacer sequence without any promoter, RBS or terminator activity |
|
Bacillus subtilis TAT signal peptide phoD |
168 bp |
Signal Peptide for TAT secretion system in Bacillus subtilis |
|
Bacillus subtilis TAT signal peptide YwnB |
84 bp |
Signal Peptide for TAT secretion system in Bacillus subtilis |
|
P2A Peptide Linker PTV |
66 bp |
Self cleaving peptide sequence which separates two proteins during translation in same operon |
|
Bacillus subtilis oriented double terminator nagP |
122 bp |
Fused product of nagP and BBa_B0010 (Improvement in BBa_B0010) |
|
P22 binding site A |
18 bp |
P22 binds to this DNA sequence to negatively regulate gene expression |
|
P22 binding site B |
18 bp |
P22 binds to this DNA sequence to negatively regulate gene expression |
|
P22 binding site C |
18 bp |
P22 binds to this DNA sequence to negatively regulate gene expression |
|
P22 binding site D |
18 bp |
P22 binds to this DNA sequence to negatively regulate gene expression |
|
P22 binding site E |
18 bp |
P22 binds to this DNA sequence to negatively regulate gene expression |
|
P22 binding site F |
18 bp |
P22 binds to this DNA sequence to negatively regulate gene expression |
|
P22 binding site G |
18 bp |
P22 binds to this DNA sequence to negatively regulate gene expression |
|
P22 binding site H |
18 bp |
P22 binds to this DNA sequence to negatively regulate gene expression |
|
P22 binding site I |
18 bp |
P22 binds to this DNA sequence to negatively regulate gene expression |
|
P22 binding site J |
18 bp |
P22 binds to this DNA sequence to negatively regulate gene expression |
|
P22 binding site K |
18 bp |
P22 binds to this DNA sequence to negatively regulate gene expression |
|
P22 binding site L |
18 bp |
P22 binds to this DNA sequence to negatively regulate gene expression |
|
XylR |
1050 bp |
pXylA repressor which provides xylose inducible gene expression |
|
yqcF |
576 bp |
Anti-toxin of yqcG (a kind of DNase) |
Composite Parts:
Part No: |
Name |
Length |
Description |
SRTF1 Cassette |
1539 bp |
Constitutive production of SRTF1 being reported by mCherry |
|
P22 Cassette |
1643 bp |
Progesterone inducible production due to fusion of SRTF1 binding site to the promoter reported by Azurite |
|
Ovastacin Cassette |
1042 bp |
P22 controlled (indirect progesterone control) ovastacin production reported by sfGFP |
|
xylR cassette |
2032 bp |
Constitutive production of XylR being reported by sfGFP |
|
yqcG cassette |
1815 bp |
Xylose inducible production of YqcG |
|
yqcF cassette |
1548 bp |
Constitutive production of YqcF being reported by mCherry |
|
ytvA cassette |
1759 bp |
Constitutive production of YtvA being reported by mCherry |
|
bpDnase 1 cassette |
1275 bp |
Light inducible production of bpDNase 1 |
|
mfLon cassette |
Constitutive production of mfLon being reported by sfGFP |
||
bpDnase 1 + mfLon tag |
933 bp |
bpDnase 1 fused with protein degradation tag of mfLon |
|
Spacer Cassette for Terminator check in Bacillus subtilis |
1722 bp |
Spacer in between of two reporters mCherry and sfGFP which provides with basal level expression of downstream genes in absence of a terminator |
|
Improvement Cassette BBa_B0010 |
1762 bp |
Replacing spacer with terminator in BBa_K3889130 for checking terminator efficiency of BBa_B0010 |
|
Improvement Cassette BBa_B0010+nagP |
1804 bp |
Replacing spacer with terminator in BBa_K3889130 for checking terminator efficiency of BBa_K3889070 |
|
SP200+SRTF1 Binding Site+ RBS |
83 bp |
SRTF1 binding site fused with SP200 promoter for progesterone inducible gene expression |
|
P43+P22 Binding Site L +RBS |
85 bp |
P22 binding site fused with P43 for P22 controlled gene expression |
Improvement:
Introduction:
While engineering any new circuit, there is always a need for well-characterized and predictable parts. Not only should the circuit function as expected, but it should also be orthogonal to irrelevant cell processes, thereby increasing the need to have efficient production and, in some cases, more importantly, efficient termination. While there are several well-studied and efficient terminators for E.coli, we found no specific efficient single terminator on the iGEM registry that could stand out for B.subtilis chassis. Hence, we decided to improvise a terminator which might fulfil this gap.
Measuring efficiency:
The experiment is divided into two cassettes: one reference and the other is a test cassette containing a terminator whose efficiency needs to be determined as shown by Gale et al.[1].
The reference and the test cassette provide us the expression levels of both the fluorescent proteins which could be compared to tell us how efficiently the terminator is working.
Formulae for terminator efficiency[5]
$TE_{Device}=\frac{mCherry_{0}}{sfGFP_{0}}$ (1)where,
$mCherry_{0}\rightarrow$ mCherry produced by device without terminator
$sfGFP_{0}\rightarrow$ sfGFP produced by device without terminator
Using the device without any changes, $TE_{Device}$ can be calculated which gives the expression of
$mCherry$ in absence of a terminator.
$TE=100-\left[\left(\frac{mCherry}{sfGPF}\right)\times\left(\frac{1}{TE_{Device}}\right)\times100\right]$ (2)
where,
$mCherry$ $\rightarrow$ mCherry produced by device with the terminator that needs to checked
$sfGFP$ $\rightarrow$ sfGFP produced by device with the terminator that needs to checked
d-score:
For E. coli terminators d'Aubenton Carafa [3] gave a scoring system as shown below:
$d=96.59 \times \frac{-\Delta G/(kcal/mol)}{n{SL}} + 18.16 \times T_{score} -116.87$
Where
d is the d-score
$-\Delta G$ is the Gibbs free energy of stem-loop formation in kcal/mole
nSL is the length of the stem loop
TScore is the score for T-stretch of the terminators
Coefficients are according to fitting the d'Aubenton Carafa’s model
The TScoreb> is calculated as follows:
$T_{score}= \sum_{i=0}^{\ 14} x _i$
Where
$x_0 = 0.9$
$x_i = 0.9$ if $i^{th}$ nucleotide is thymine
$x_i = 0.6 \times x_{i-1}$ if $i^{th}$ nucleotide is not thymine
These scoring system was modified by de Hoon et al. [2] for Bacillus subtilis as per their model which is as follows:
$d=7.90 \times \frac{-\Delta G/(kcal/mol)}{n{SL}} + 2.67 \times T{score} -14.91$
Where
d is the d-score
$-\Delta$ G is the Gibbs free energy of stem-loop formation in kcal/mole
nSL is the length of the stem loop
TScore is the score for T-stretch of the terminators
Coefficients are according to fitting the model
Here the TScore is calculated as follows:
$T= \sum_{i=0}^{\ 14} e^{- \lambda _i} \delta_i$
Where
$\lambda _i = 0.144$ as per the fitting of the model
$\delta_i = 0$ if $i^{th}$ nucleotide is not thymine
$\delta_i = 1$ if $i^{th}$ nucleotide is thymine
.As the d-score takes into account the Gibbs free energy, length of the stem loop and the richness of thymine in T-stretch which are essential for a rho independent terminator. Hence, the d-score can provide a rough idea about how good a terminator is. In other words, higher the d-score higher will be the terminator efficiency.[3]
Improvement:
We decided to improve BBa_B0010 in order to make a strong terminator which can be used for primarily the B.subtilis chassis while still retaining its efficiency in E.coli. For doing this we modified the tail of Bba_B0010 and fused another rho-independent terminator from the Bacillus subtilis genome on the basis of its d-Score.
From a list of 425 native B.subtilis terminators taken from the study conducted by Michiel et al [2], we calculated the d-score of each terminator to get a rough idea of their efficiency. Based on the results the highest d-score= 5.666126119 was of the terminator belonging to the gene nagP. Both BBa_B0010 and nagP terminators were ligated to form a double terminator.
Based on our calculations, we decided to go with nagP terminator. We modified the end regions of BBa_B0010 and ligated to it the nagP terminator to create an improved version(PARTNO). Using the server RNAFold we calculated the minimum energy to show in silico that the improved terminator will have more negative Minimum Free energy as shown.
BBa_B0010 |
BBa_B0010+nagP |
|
Minimum Free Energy (kcal/mol) |
-40 |
-64.6 |
The predicted structure for these two terminators as given by RnaFold server is:
- BBa_B0010:
- BBa_B0010+nagP:
Data
Zip file containing excel sheet of all terminators,2*t score calculators, one raw data sheet excel file,readme file
References:
[1] Gale, G. A. R., Wang, B., & McCormick, A. J. (2021). Evaluation and Comparison of the Efficiency of Transcription Terminators in Different Cyanobacterial Species. Frontiers in Microbiology, 11. https://doi.org/10.3389/fmicb.2020.624011 :
[2] de Hoon, M. J. L., Makita, Y., Nakai, K., & Miyano, S. (2005). Prediction of Transcriptional Terminators in Bacillus subtilis and Related Species. PLoS Computational Biology, 1(3), e25. https://doi.org/10.1371/journal.pcbi.0010025
[3] Carafa, Y. d’Aubenton, Brody, E., & Thermes, C. (1990). Prediction of rho-independent Escherichia coli transcription terminators. Journal of Molecular Biology, 216(4), 835–858. https://doi.org/10.1016/s0022-2836(99)80005-9