Difference between revisions of "Team:Fudan/Basic Parts"
m |
|||
| (8 intermediate revisions by 3 users not shown) | |||
| Line 5: | Line 5: | ||
We make it compatible on laptop and mobile devices by using Materialize 1.0.0-rc.2. | We make it compatible on laptop and mobile devices by using Materialize 1.0.0-rc.2. | ||
--> | --> | ||
| + | <!-- LC check on 2018-10-18 --> | ||
<head> | <head> | ||
<meta charset="UTF-8"> | <meta charset="UTF-8"> | ||
| Line 12: | Line 13: | ||
<!-- Font-awesome icons 4.7.0 --> | <!-- Font-awesome icons 4.7.0 --> | ||
| − | <link href="https://2018.igem.org/wiki/index.php?title=Template:Fudan/font-awesome.css&action=raw&ctype=text/css" rel="stylesheet"> | + | <link href="https://2018.igem.org/wiki/index.php?title=Template:Fudan/font-awesome.css&action=raw&ctype=text/css" rel="stylesheet" /> |
<!-- Materialize 1.0.0-rc.2 (Material Design like) --> | <!-- Materialize 1.0.0-rc.2 (Material Design like) --> | ||
| Line 18: | Line 19: | ||
<!-- Clear default CSS settings; CSS reset --> | <!-- Clear default CSS settings; CSS reset --> | ||
| − | <style | + | <style> |
*{margin: 0;padding: 0;list-style: none;} | *{margin: 0;padding: 0;list-style: none;} | ||
/* via: https://blog.csdn.net/weixin_41014370/article/details/79523637 */ | /* via: https://blog.csdn.net/weixin_41014370/article/details/79523637 */ | ||
| Line 62: | Line 63: | ||
} | } | ||
</style> | </style> | ||
| + | <title>2018 iGEM Team:Fudan - Basic parts</title> | ||
</head> | </head> | ||
| Line 76: | Line 78: | ||
<div class="nav-wrapper"> | <div class="nav-wrapper"> | ||
<div id="teamLogo" class="brand-logo"> | <div id="teamLogo" class="brand-logo"> | ||
| − | <a href="https://2018.igem.org/Team:Fudan" target="_self"><img src="https://static.igem.org/mediawiki/2018/c/c4/T--Fudan--teamLogo.svg"></a> | + | <a href="https://2018.igem.org/Team:Fudan" target="_self"><img alt="2018 team Fudan logo" src="https://static.igem.org/mediawiki/2018/c/c4/T--Fudan--teamLogo.svg"></a> |
</div> | </div> | ||
<ul id="nav-mobile" class="right orangeBorder"> | <ul id="nav-mobile" class="right orangeBorder"> | ||
| Line 96: | Line 98: | ||
<!-- Dropdown and List elements in navigation bar --> | <!-- Dropdown and List elements in navigation bar --> | ||
<ul id="dropdown1" class="dropdown-content"> | <ul id="dropdown1" class="dropdown-content"> | ||
| − | <li><a href=" | + | <li><a href="/Team:Fudan/Demonstrate">Demonstration</a></li> |
| − | <li><a href=" | + | <li><a href="/Team:Fudan/Antigen_Receptors">Antigen, Receptors</a></li> |
| − | <li><a href=" | + | <li><a href="/Team:Fudan/Results">Transmembrane logic</a></li> |
</ul> | </ul> | ||
<ul id="dropdown2" class="dropdown-content"> | <ul id="dropdown2" class="dropdown-content"> | ||
| − | <li><a href=" | + | <li><a href="/Team:Fudan/Addon#ribo">Addon: ribo</a></li> |
| − | <li><a href=" | + | <li><a href="/Team:Fudan/Addon#TALE">Addon: TALE</a></li> |
| − | <li><a href=" | + | <li><a href="/Team:Fudan/Addon#T2">Addon: T2</a></li> |
| − | <li><a href=" | + | <li><a href="/Team:Fudan/Model#Transcriptional_Amplifer">Model: transcriptional amplifer</a></li> |
| − | <li><a href=" | + | <li><a href="/Team:Fudan/Model#NotchLigandKinetics">Model: Notch-ligand kinetics</a></li> |
| − | <li><a href=" | + | <li><a href="/Team:Fudan/Software">Software</a></li> |
</ul> | </ul> | ||
<ul id="dropdown3" class="dropdown-content"> | <ul id="dropdown3" class="dropdown-content"> | ||
| − | <li><a href=" | + | <li><a href="/Team:Fudan/InterLab">iGEM interLab</a></li> |
| − | <li><a href=" | + | <li><a href="/Team:Fudan/Notebook">Our notebook</a></li> |
| − | <li><a href=" | + | <li><a href="/Team:Fudan/Primers">Primers used</a></li> |
| − | <li><a href=" | + | <li><a href="/Team:Fudan/Protocols">Protocols</a></li> |
| − | <li><a href=" | + | <li><a href="/Team:Fudan/Safety">Safety</a></li> |
</ul> | </ul> | ||
<ul id="dropdown4" class="dropdown-content"> | <ul id="dropdown4" class="dropdown-content"> | ||
| − | <li><a href=" | + | <li><a href="/Team:Fudan/Basic_Parts">Basic parts</a></li> |
| − | <li><a href=" | + | <li><a href="/Team:Fudan/Composite_Parts">Composite parts</a></li> |
| − | <li><a href=" | + | <li><a href="/Team:Fudan/Optimization">Optimization</a></li> |
| − | <li><a href=" | + | <li><a href="/Team:Fudan/Parts_Collection">Parts collection</a></li> |
| − | <li><a href=" | + | <li><a href="/Team:Fudan/Improve">Parts improvement</a></li> |
| − | <li><a href=" | + | <li><a href="/Team:Fudan/Measurement">Quantification</a></li> |
</ul> | </ul> | ||
<ul id="dropdown5" class="dropdown-content"> | <ul id="dropdown5" class="dropdown-content"> | ||
| − | <li><a href=" | + | <li><a href="/Team:Fudan/Bio-Art">Bio-Art display</a></li> |
| − | <li><a href=" | + | <li><a href="/Team:Fudan/Collaborations">Collaborations</a></li> |
| − | <li><a href=" | + | <li><a href="/Team:Fudan/Design_Intention">Design intention</a></li> |
| − | <li><a href=" | + | <li><a href="/Team:Fudan/Human_Practices">Human practices</a></li> |
| − | <li><a href=" | + | <li><a href="/Team:Fudan/Public_Engagement">Public engagement</a></li> |
</ul> | </ul> | ||
<ul id="dropdown6" class="dropdown-content"> | <ul id="dropdown6" class="dropdown-content"> | ||
| − | <li><a href=" | + | <li><a href="/Team:Fudan/Acknowledgement">Acknowledgement</a></li> |
| − | <li><a href=" | + | <li><a href="/Team:Fudan/Attributions">Attributions</a></li> |
| − | <li><a href=" | + | <li><a href="/Team:Fudan/Heritage">Heritage</a></li> |
| − | <li><a href=" | + | <li><a href="/Team:Fudan/Team">Members</a></li> |
| − | <li><a href=" | + | <li><a href="/Team:Fudan/Sponsors">Sponsors</a></li> |
</ul> | </ul> | ||
| Line 147: | Line 149: | ||
<li> | <li> | ||
<ul class="collapsible expandable"> | <ul class="collapsible expandable"> | ||
| − | |||
| − | |||
<li>Navigator on wiki</li> | <li>Navigator on wiki</li> | ||
<li> | <li> | ||
| Line 154: | Line 154: | ||
<div class="collapsible-body"> | <div class="collapsible-body"> | ||
<ul> | <ul> | ||
| − | <li><a href=" | + | <li><a href="/Team:Fudan/Demonstrate">Demonstration</a></li> |
| − | <li><a href=" | + | <li><a href="/Team:Fudan/Antigen_Receptors">Antigen, Receptors</a></li> |
| − | <li><a href=" | + | <li><a href="/Team:Fudan/Results">Transmembrane logic</a></li> |
</ul> | </ul> | ||
</div> | </div> | ||
| Line 164: | Line 164: | ||
<div class="collapsible-body"> | <div class="collapsible-body"> | ||
<ul> | <ul> | ||
| − | <li><a href=" | + | <li><a href="/Team:Fudan/Addon#ribo">Addon: ribo</a></li> |
| − | <li><a href=" | + | <li><a href="/Team:Fudan/Addon#TALE">Addon: TALE</a></li> |
| − | <li><a href=" | + | <li><a href="/Team:Fudan/Addon#T2">Addon: T2</a></li> |
| − | <li><a href=" | + | <li><a href="/Team:Fudan/Model#Transcriptional_Amplifer">Model: transcriptional amplifer</a></li> |
| − | <li><a href=" | + | <li><a href="/Team:Fudan/Model#NotchLigandKinetics">Model: Notch-ligand kinetics</a></li> |
| − | <li><a href=" | + | <li><a href="/Team:Fudan/Software">Software</a></li> |
</ul> | </ul> | ||
</div> | </div> | ||
| Line 177: | Line 177: | ||
<div class="collapsible-body"> | <div class="collapsible-body"> | ||
<ul> | <ul> | ||
| − | <li><a href=" | + | <li><a href="/Team:Fudan/InterLab">iGEM interLab</a></li> |
| − | <li><a href=" | + | <li><a href="/Team:Fudan/Notebook">Our notebook</a></li> |
| − | <li><a href=" | + | <li><a href="/Team:Fudan/Primers">Primers used</a></li> |
| − | <li><a href=" | + | <li><a href="/Team:Fudan/Protocols">Protocols</a></li> |
| − | <li><a href=" | + | <li><a href="/Team:Fudan/Safety">Safety</a></li> |
</ul> | </ul> | ||
</div> | </div> | ||
| Line 189: | Line 189: | ||
<div class="collapsible-body"> | <div class="collapsible-body"> | ||
<ul> | <ul> | ||
| − | <li><a href=" | + | <li><a href="/Team:Fudan/Basic_Parts">Basic parts</a></li> |
| − | <li><a href=" | + | <li><a href="/Team:Fudan/Composite_Parts">Composite parts</a></li> |
| − | <li><a href=" | + | <li><a href="/Team:Fudan/Optimization">Optimization</a></li> |
| − | <li><a href=" | + | <li><a href="/Team:Fudan/Parts_Collection">Parts collection</a></li> |
| − | <li><a href=" | + | <li><a href="/Team:Fudan/Improve">Parts improvement</a></li> |
| − | <li><a href=" | + | <li><a href="/Team:Fudan/Measurement">Quantification</a></li> |
</ul> | </ul> | ||
</div> | </div> | ||
| Line 202: | Line 202: | ||
<div class="collapsible-body"> | <div class="collapsible-body"> | ||
<ul> | <ul> | ||
| − | <li><a href=" | + | <li><a href="/Team:Fudan/Bio-Art">Bio-Art display</a></li> |
| − | <li><a href=" | + | <li><a href="/Team:Fudan/Collaborations">Collaborations</a></li> |
| − | <li><a href=" | + | <li><a href="/Team:Fudan/Design_Intention">Design intention</a></li> |
| − | <li><a href=" | + | <li><a href="/Team:Fudan/Human_Practices">Human practices</a></li> |
| − | <li><a href=" | + | <li><a href="/Team:Fudan/Public_Engagement">Public engagement</a></li> |
</ul> | </ul> | ||
</div> | </div> | ||
| Line 214: | Line 214: | ||
<div class="collapsible-body"> | <div class="collapsible-body"> | ||
<ul> | <ul> | ||
| − | <li><a href=" | + | <li><a href="/Team:Fudan/Acknowledgement">Acknowledgement</a></li> |
| − | <li><a href=" | + | <li><a href="/Team:Fudan/Attributions">Attributions</a></li> |
| − | <li><a href=" | + | <li><a href="/Team:Fudan/Heritage">Heritage</a></li> |
| − | <li><a href=" | + | <li><a href="/Team:Fudan/Team">Members</a></li> |
| − | <li><a href=" | + | <li><a href="/Team:Fudan/Sponsors">Sponsors</a></li> |
</ul> | </ul> | ||
</div> | </div> | ||
| Line 238: | Line 238: | ||
</div> | </div> | ||
<div class="col s12 hide-on-med-and-up"> | <div class="col s12 hide-on-med-and-up"> | ||
| − | <span> | + | <span> </span> |
</div> | </div> | ||
</div> | </div> | ||
<div id="figureBannerTitle" class="hide-on-small-only"> | <div id="figureBannerTitle" class="hide-on-small-only"> | ||
<h1>Basic parts</h1> | <h1>Basic parts</h1> | ||
| − | <p><span> | + | <p><span> </span></p> |
</div> | </div> | ||
<div class="hide-on-small-only"> | <div class="hide-on-small-only"> | ||
| Line 274: | Line 274: | ||
<!-- @@@@ main content of the page --> | <!-- @@@@ main content of the page --> | ||
<div class="container"> | <div class="container"> | ||
| − | < | + | <main style="margin: 0"> |
| − | + | <div id="section1" class="section container"> | |
| − | + | <h2>BBa_K2549006 <a href="http://parts.igem.org/Part:BBa_K2549006" target=_blank>mouse Notch 1 core</a></h2> | |
| − | + | <p>Our favorite basic part for this year’s iGEM competition is mouse Notch 1 receptor’s core domain.<br/><img alt="006 screencapture" src="https://static.igem.org/mediawiki/2018/thumb/7/7e/T--Fudan--BBa_K2549006.png/1444px-T--Fudan--BBa_K2549006.png" /> | |
| − | + | </p><p> | |
| − | + | Notch core consists of the negatively regulated region and transmembrane region of the mouse Notch 1 receptor. It is the joint that empowers SynNotch the high modularity and proper activation. From the N terminal to C terminal, it is composed of three lin12-repeats (LNR) domains LNR-A, LNR-B, LNR-C, the heterodimerization domain (HD), and the transmembrane domain. The LNR-AB linker between LNR-A and B is like a plug that occludes ADAM from cleaving wild type extracellular domain can be substituted by antiGFP scFvs like LaG16 and anti-CD19, while its intracellular domain can be replaced by specialized transcription factors. Notch core is also the key to the activation of both wild type Notch receptors and SynNotch. | |
| − | + | </p> | |
| − | + | <div class="expFigureHolder" style="width:100%"> | |
| − | + | <div class="row" style="background: white"> | |
| − | + | <div class="col s12 m4"><img style="width:100%" src="https://static.igem.org/mediawiki/2018/9/9e/T--Fudan--bestpart1.png"></div> | |
| − | + | <div class="col s12 m4"><img style="width:100%" src="https://static.igem.org/mediawiki/2018/f/f1/T--Fudan--bestpart2.png"></div> | |
| − | + | <div class="col s12 m4"><img style="width:100%" src="https://static.igem.org/mediawiki/2018/8/80/T--Fudan--opt-gif.gif"></div> | |
| + | <div class="col s12 m4 offset-m1"><img style="width:100%" src="https://static.igem.org/mediawiki/2018/2/21/T--Fudan--bestpart3.png"></div> | ||
| + | <div class="col s12 m4 offset-m2"><img style="width:100%" src="https://static.igem.org/mediawiki/2018/8/81/T--Fudan--bestpart4.png"></div> | ||
| + | </div> | ||
| + | |||
| + | <p><b>Structure of the negative regulatory region of Notch 1 receptor, surface delivery, and optimization.</b><br/> | ||
| + | a-c. Shows structure of the Notch 1 core, with more detail on the NRR. (With structural information adapted from Gordon et al., 2009)<br/> | ||
| + | d. Shows that mouse SynNotch with LaG16-2 scFv (single chain fragment variants) as ectodomain is expressed on the 293T cell membrane as an example via anti-myc AF488 immunofluorescence staining. Shown here the light parts.<br/> | ||
| + | e. A conclusive diagram of our Notch optimization. We have 5 mutations that exhibit better activation performance to SynNotch with LaG17 as scFv. | ||
| + | </p> | ||
| + | |||
| + | </div> | ||
| + | <b class="tableHolder"> | ||
| + | <table> | ||
| + | <tr> | ||
| + | <th>SynNotch</th> | ||
| + | <th>Class</th> | ||
| + | <th>ARF<sub>aS</sub><sup>*)</sup></th> | ||
| + | <th>Preferred</th> | ||
| + | </tr> | ||
| + | <tr> | ||
| + | <td>LaG17-mN1c-tTAA</td> | ||
| + | <td>II</td> | ||
| + | <td>1.67 ± 0.20</td> | ||
| + | <td></td> | ||
| + | </tr> | ||
| + | <tr> | ||
| + | <td>LaG17-6G-LNRA[-]mN1c-tTAA</td> | ||
| + | <td>I</td> | ||
| + | <td>1.73 ± 0.29</td> | ||
| + | <td>☆</td> | ||
| + | </tr> | ||
| + | <tr> | ||
| + | <td>LaG17-LNRA cbs(D1433K)mN1c-tTAA</td> | ||
| + | <td>II</td> | ||
| + | <td>2.69 ± 0.11</td> | ||
| + | <td>☆</td> | ||
| + | </tr> | ||
| + | <tr> | ||
| + | <td>LaG17-LNRA cbs(D1433Q)mN1c-tTAA</td> | ||
| + | <td>II</td> | ||
| + | <td>Needs more repeat</td> | ||
| + | <td></td> | ||
| + | </tr> | ||
| + | <tr> | ||
| + | <td>LaG17-LNRAlnkr(L1457V)mN1c-tTAA</td> | ||
| + | <td>I</td> | ||
| + | <td>2.12 ± 0.39</td> | ||
| + | <td>☆</td> | ||
| + | </tr> | ||
| + | <tr> | ||
| + | <td>LaG17-LNRAlnkr(L1457G)mN1c-tTAA</td> | ||
| + | <td>II</td> | ||
| + | <td>2.55± 0.55</td> | ||
| + | <td></td> | ||
| + | </tr> | ||
| + | </table> | ||
| + | <p>*) <b>ARF<sub>aS</sub>:</b> activation ratio fold of activating-form SynNotch</p> | ||
| + | <p>See more in <a href="/Team:Fudan/Optimization">Optimization</a></p> | ||
| + | </div> | ||
| + | <p>It is suggested by recent research that Notch activation begin as the receptor is first "opened up" at its negatively regulatory region (NRR) by the mechanical force exerted by Notch-bound ligand endocytosis on signal-sender cell, exposing its cleavage sites to proteases. Intracellular proteolytic action releases the Notch intracellular domain (NICD). In the majority of cellular interactions, the free Notch intracellular domain then translocate into the cell nucleus via nuclear localization sequence to regulate downstream signaling. For wild type Notch, the Notch intracellular domain would interacted with its major downstream effector CBF-1/Suppressor of Hairless/Lag-1 (CSL) on their target DNA. Together they recruit co-factors to activate endogenous downstream transcription. For SynNotch, specialized transcription factors will exclusively participate in regulation of genetic circuits that allow user-defined cellular responses. | ||
| + | </p> | ||
</div> | </div> | ||
</main> | </main> | ||
| Line 293: | Line 354: | ||
<!--Abstract on content page--> | <!--Abstract on content page--> | ||
<div id="abstractContent" class="z-depth-2"> | <div id="abstractContent" class="z-depth-2"> | ||
| − | <a href="#!"><img src="https://static.igem.org/mediawiki/2018/9/96/T--Fudan--X.svg"></a> | + | <a href="#!"><img alt="2018 team Fudan abstract" src="https://static.igem.org/mediawiki/2018/9/96/T--Fudan--X.svg"></a> |
<div class="container"> | <div class="container"> | ||
<h2 style="margin: 0;padding: 10px 0;">Abstract</h2> | <h2 style="margin: 0;padding: 10px 0;">Abstract</h2> | ||
| Line 330: | Line 391: | ||
<div class="row"> | <div class="row"> | ||
<div id="sponsor" class="col m3 s12 row"> | <div id="sponsor" class="col m3 s12 row"> | ||
| − | <a href="https://2018.igem.org/Team:Fudan" target="_blank"><img class="col s3 m6 l3" style="position:relative; padding: 0 0.3rem; margin:-0.15rem 0; left: -0.45rem;" src="https://static.igem.org/mediawiki/2018/7/73/T--Fudan--teamLogoWhite.png"> | + | <a href="https://2018.igem.org/Team:Fudan" target="_blank"><img alt="2018 Team:Fudan logo white" class="col s3 m6 l3" style="position:relative; padding: 0 0.3rem; margin:-0.15rem 0; left: -0.45rem;" src="https://static.igem.org/mediawiki/2018/7/73/T--Fudan--teamLogoWhite.png"> |
</a><a href="http://www.fudan.edu.cn/en/" target="_blank"><img class="col s3 m6 l3" alt="Fudan University" src="https://static.igem.org/mediawiki/2018/f/f7/T--Fudan--schoolLogo.png"> | </a><a href="http://www.fudan.edu.cn/en/" target="_blank"><img class="col s3 m6 l3" alt="Fudan University" src="https://static.igem.org/mediawiki/2018/f/f7/T--Fudan--schoolLogo.png"> | ||
</a><a href="http://life.fudan.edu.cn/" target="_blank"><img class="col s3 m6 l3" style="margin-bottom: 4%;/* 该图比其他小一点，排版需要 */" alt="School of Life Sciences, Fudan University" src="https://static.igem.org/mediawiki/2018/1/1d/T--Fudan--schoolOfLifeSciencesIcon.png"> | </a><a href="http://life.fudan.edu.cn/" target="_blank"><img class="col s3 m6 l3" style="margin-bottom: 4%;/* 该图比其他小一点，排版需要 */" alt="School of Life Sciences, Fudan University" src="https://static.igem.org/mediawiki/2018/1/1d/T--Fudan--schoolOfLifeSciencesIcon.png"> | ||
| Line 342: | Line 403: | ||
<span>Project</span> | <span>Project</span> | ||
<ul> | <ul> | ||
| − | <li><a href=" | + | <li><a href="/Team:Fudan/Demonstrate">Demonstration</a></li> |
| − | <li><a href=" | + | <li><a href="/Team:Fudan/Antigen_Receptors">Antigen, Receptors</a></li> |
| − | <li><a href=" | + | <li><a href="/Team:Fudan/Results">Transmembrane logic</a></li> |
<li><a href="https://2017.igem.org/Team:Fudan">2017.iGEM</a></li> | <li><a href="https://2017.igem.org/Team:Fudan">2017.iGEM</a></li> | ||
</ul> | </ul> | ||
| Line 352: | Line 413: | ||
<span>Dry lab</span> | <span>Dry lab</span> | ||
<ul> | <ul> | ||
| − | <li><a href=" | + | <li><a href="/Team:Fudan/Addon#ribo">Addon: ribo</a></li> |
| − | <li><a href=" | + | <li><a href="/Team:Fudan/Addon#TALE">Addon: TALE</a></li> |
| − | <li><a href=" | + | <li><a href="/Team:Fudan/Addon#T2">Addon: T2</a></li> |
| − | <li><a href=" | + | <li><a href="/Team:Fudan/Model#Transcriptional_Amplifer">Model: transcriptional amplifer</a></li> |
| − | <li><a href=" | + | <li><a href="/Team:Fudan/Model#NotchLigandKinetics">Model: Notch-ligand kinetics</a></li> |
| − | <li><a href=" | + | <li><a href="/Team:Fudan/Software">Software</a></li> |
</ul> | </ul> | ||
</div> | </div> | ||
| Line 363: | Line 424: | ||
<span>Wet lab</span> | <span>Wet lab</span> | ||
<ul> | <ul> | ||
| − | <li><a href=" | + | <li><a href="/Team:Fudan/InterLab">iGEM interLab</a></li> |
| − | <li><a href=" | + | <li><a href="/Team:Fudan/Notebook">Our notebook</a></li> |
| − | <li><a href=" | + | <li><a href="/Team:Fudan/Primers">Primers used</a></li> |
| − | <li><a href=" | + | <li><a href="/Team:Fudan/Protocols">Protocols</a></li> |
| − | <li><a href=" | + | <li><a href="/Team:Fudan/Safety">Safety</a></li> |
</ul> | </ul> | ||
</div> | </div> | ||
| Line 375: | Line 436: | ||
<span>Toolbox</span> | <span>Toolbox</span> | ||
<ul> | <ul> | ||
| − | <li><a href=" | + | <li><a href="/Team:Fudan/Basic_Parts">Basic parts</a></li> |
| − | <li><a href=" | + | <li><a href="/Team:Fudan/Composite_Parts">Composite parts</a></li> |
| − | <li><a href=" | + | <li><a href="/Team:Fudan/Optimization">Optimization</a></li> |
| − | <li><a href=" | + | <li><a href="/Team:Fudan/Parts_Collection">Parts collection</a></li> |
| − | <li><a href=" | + | <li><a href="/Team:Fudan/Improve">Parts improvement</a></li> |
| − | <li><a href=" | + | <li><a href="/Team:Fudan/Measurement">Quantification</a></li> |
</ul> | </ul> | ||
</div> | </div> | ||
| Line 386: | Line 447: | ||
<span>Outreach</span> | <span>Outreach</span> | ||
<ul> | <ul> | ||
| − | <li><a href=" | + | <li><a href="/Team:Fudan/Bio-Art">Bio-Art display</a></li> |
| − | <li><a href=" | + | <li><a href="/Team:Fudan/Collaborations">Collaborations</a></li> |
| − | <li><a href=" | + | <li><a href="/Team:Fudan/Design_Intention">Design intention</a></li> |
| − | <li><a href=" | + | <li><a href="/Team:Fudan/Human_Practices">Human practices</a></li> |
| − | <li><a href=" | + | <li><a href="/Team:Fudan/Public_Engagement">Public engagement</a></li> |
</ul> | </ul> | ||
</div> | </div> | ||
| Line 396: | Line 457: | ||
<span>Team</span> | <span>Team</span> | ||
<ul> | <ul> | ||
| − | <li><a href=" | + | <li><a href="/Team:Fudan/Acknowledgement">Acknowledgement</a></li> |
| − | <li><a href=" | + | <li><a href="/Team:Fudan/Attributions">Attributions</a></li> |
| − | <li><a href=" | + | <li><a href="/Team:Fudan/Heritage">Heritage</a></li> |
| − | <li><a href=" | + | <li><a href="/Team:Fudan/Team">Members</a></li> |
| − | <li><a href=" | + | <li><a href="/Team:Fudan/Sponsors">Sponsors</a></li> |
</ul> | </ul> | ||
</div> | </div> | ||
| Line 409: | Line 470: | ||
<div class="footer-copyright"> | <div class="footer-copyright"> | ||
<div class="container"> | <div class="container"> | ||
| − | + | <div class="contactUS row"> | |
| − | + | <div class="col s12 m6 l4"><i class="fa fa-location-arrow"></i> Life Sci Bldg E301, 2005 Songhu Rd, Shanghai | |
| − | + | </div><div class="col s12 m6 l2"><i class="fa fa-fax"></i> +86-21-31246727 | |
| − | + | </div><div class="col s12 m6 l2"><i class="fa fa-envelope-o"></i> igem@fudan.edu.cn | |
| − | + | </div><div class="col s12 m6 l4"><i class="fa fa-twitter"></i> <i class="fa fa-wechat"></i> Fudan_iGEM | |
| − | + | </div> | |
| − | + | </div> | |
| − | + | </div> | |
</div> | </div> | ||
</footer> | </footer> | ||
Latest revision as of 15:09, 7 November 2018
- Addon: ribo
- Addon: TALE
- Addon: T2
- Model: transcriptional amplifer
- Model: Notch-ligand kinetics
- Software
Basic parts
BBa_K2549006 mouse Notch 1 core
Our favorite basic part for this year’s iGEM competition is mouse Notch 1 receptor’s core domain.
Notch core consists of the negatively regulated region and transmembrane region of the mouse Notch 1 receptor. It is the joint that empowers SynNotch the high modularity and proper activation. From the N terminal to C terminal, it is composed of three lin12-repeats (LNR) domains LNR-A, LNR-B, LNR-C, the heterodimerization domain (HD), and the transmembrane domain. The LNR-AB linker between LNR-A and B is like a plug that occludes ADAM from cleaving wild type extracellular domain can be substituted by antiGFP scFvs like LaG16 and anti-CD19, while its intracellular domain can be replaced by specialized transcription factors. Notch core is also the key to the activation of both wild type Notch receptors and SynNotch.
Structure of the negative regulatory region of Notch 1 receptor, surface delivery, and optimization.
a-c. Shows structure of the Notch 1 core, with more detail on the NRR. (With structural information adapted from Gordon et al., 2009)
d. Shows that mouse SynNotch with LaG16-2 scFv (single chain fragment variants) as ectodomain is expressed on the 293T cell membrane as an example via anti-myc AF488 immunofluorescence staining. Shown here the light parts.
e. A conclusive diagram of our Notch optimization. We have 5 mutations that exhibit better activation performance to SynNotch with LaG17 as scFv.
| SynNotch | Class | ARFaS*) | Preferred |
|---|---|---|---|
| LaG17-mN1c-tTAA | II | 1.67 ± 0.20 | |
| LaG17-6G-LNRA[-]mN1c-tTAA | I | 1.73 ± 0.29 | ☆ |
| LaG17-LNRA cbs(D1433K)mN1c-tTAA | II | 2.69 ± 0.11 | ☆ |
| LaG17-LNRA cbs(D1433Q)mN1c-tTAA | II | Needs more repeat | |
| LaG17-LNRAlnkr(L1457V)mN1c-tTAA | I | 2.12 ± 0.39 | ☆ |
| LaG17-LNRAlnkr(L1457G)mN1c-tTAA | II | 2.55± 0.55 |
*) ARFaS: activation ratio fold of activating-form SynNotch
See more in Optimization
It is suggested by recent research that Notch activation begin as the receptor is first "opened up" at its negatively regulatory region (NRR) by the mechanical force exerted by Notch-bound ligand endocytosis on signal-sender cell, exposing its cleavage sites to proteases. Intracellular proteolytic action releases the Notch intracellular domain (NICD). In the majority of cellular interactions, the free Notch intracellular domain then translocate into the cell nucleus via nuclear localization sequence to regulate downstream signaling. For wild type Notch, the Notch intracellular domain would interacted with its major downstream effector CBF-1/Suppressor of Hairless/Lag-1 (CSL) on their target DNA. Together they recruit co-factors to activate endogenous downstream transcription. For SynNotch, specialized transcription factors will exclusively participate in regulation of genetic circuits that allow user-defined cellular responses.
Abstract
Contact-dependent signaling is critical for multicellular biological events, yet customizing contact-dependent signal transduction between cells remains challenging. Here we have developed the ENABLE toolbox, a complete set of transmembrane binary logic gates. Each gate consists of 3 layers: Receptor, Amplifier, and Combiner. We first optimized synthetic Notch receptors to enable cells to respond to different signals across the membrane reliably. These signals, individually amplified intracellularly by transcription, are further combined for computing. Our engineered zinc finger-based transcription factors perform binary computation and output designed products. In summary, we have combined spatially different signals in mammalian cells, and revealed new potentials for biological oscillators, tissue engineering, cancer treatments, bio-computing, etc. ENABLE is a toolbox for constructing contact-dependent signaling networks in mammals. The 3-layer design principle underlying ENABLE empowers any future development of transmembrane logic circuits, thus contributes a foundational advance to Synthetic Biology.