Difference between revisions of "Team:Fudan-TSI/Demonstrate"

(LC hand over)
(0915)
Line 74: Line 74:
 
             <div id="emptyBar" style="position:relative;width: 100%;"></div>
 
             <div id="emptyBar" style="position:relative;width: 100%;"></div>
  
             <!-- Navigation bar -->
+
             <!-- Navigation bar 2019-9-15 -->
 +
            <nav id="topNav" class="white z-depth-0_5">
 +
                <div class="nav-wrapper">
 +
                    <div id="teamLogo" class="brand-logo">
 +
                        <a href="/Team:Fudan-TSI" target="_self"><img alt="2019 team logo" src="https://static.igem.org/mediawiki/2019/3/3c/T--Fudan-TSI--Logo0.gif"></a>
 +
                    </div>
 +
                    <ul id="nav-mobile" class="right">
 +
                        <li>
 +
                            <a id="navList" data-target="slide-out" class="waves-effect waves-light sidenav-trigger right">
 +
                                <i class="fa fa-navicon" style="font-size: 24px"></i>
 +
                            </a>
 +
                        </li>
 +
                    </ul>
 +
                </div>
 +
            </nav>
 
             <!-- Dropdown and List elements in navigation bar -->
 
             <!-- Dropdown and List elements in navigation bar -->
             <!-- Slide-out navigator contents -->
+
             <!-- Slide-out navigator contents 2019-9-15 -->
 +
            <ul id="slide-out" class="sidenav">
 +
                <li style="padding: 0"><div class="sidenavBanner">
 +
                    <div class="background">
 +
                    </div>
 +
                    <p style="width: 100%;text-align: center;font-size: 24px"><span class="white-text">Demonstration</span></p>
 +
                </div></li>
 +
                <li>
 +
                    <ul class="collapsible expandable">
 +
                        <li>On this page</li>
 +
                        <li class="onThisPageNav"><a href="#section1">div with id section1</a></li>
 +
                        <li class="onThisPageNav"><a href="#section2">div with id section2</a></li>
 +
                        <li class="onThisPageNav"><a href="#section3">div with id section3</a></li>
 +
                        <li class="onThisPageNav"><a href="#section4">div with id section4</a></li>
 +
                        <li class="onThisPageNav"><a href="#section5">div with id section5</a></li>
 +
                        <li>Team: Fudan-TSI</li>
 +
<li><div class="collapsible-header">Project</div>
 +
    <div class="collapsible-body"><ul>
 +
        <li><a href="/Team:Fudan-TSI/Description">Background</a></li>
 +
        <li><a href="/Team:Fudan-TSI/Design">Design</a></li>
 +
        <li><a href="/Team:Fudan-TSI/Applied_Design">Applied Design</a></li>
 +
        <li><a href="/Team:Fudan-TSI/Experiments">Experiments</a></li>
 +
        <li><a href="/Team:Fudan-TSI/Judging">Judging</a></li>
 +
    </ul></div>
 +
</li>
 +
<li><div class="collapsible-header">Results</div>
 +
    <div class="collapsible-body"><ul>
 +
        <li><a href="/Team:Fudan-TSI/Results#ReverseTranscription">Reverse Transcription</a></li>
 +
        <li><a href="/Team:Fudan-TSI/Results#Recombination">Recombination</a></li>
 +
        <li><a href="/Team:Fudan-TSI/Demonstrate">Demonstration</a></li>
 +
        <li><a href="/Team:Fudan-TSI/Measurement">Measurement</a></li>
 +
        <li><a href="/Team:Fudan-TSI/Notebook">Notebook</a></li>
 +
    </ul></div>
 +
</li>
 +
<li><div class="collapsible-header">Model</div>
 +
    <div class="collapsible-body"><ul>
 +
        <li><a href="/Team:Fudan-TSI/Model">Modeling</a></li>
 +
        <li><a href="/Team:Fudan-TSI/Software">Software</a></li>
 +
        <li><a href="/Team:Fudan-TSI/Hardware">Hardware</a></li>
 +
    </ul></div>
 +
</li>
 +
<li><div class="collapsible-header">Parts</div>
 +
    <div class="collapsible-body"><ul>
 +
        <li><a href="/Team:Fudan-TSI/Basic_Part">Basic parts</a></li>
 +
        <li><a href="/Team:Fudan-TSI/Composite_Part">Composite parts</a></li>
 +
        <li><a href="/Team:Fudan-TSI/Improve">Improved parts</a></li>
 +
        <li><a href="/Team:Fudan-TSI/Part_Collection">Part collection</a></li>
 +
    </ul></div>
 +
</li>
 +
<li><div class="collapsible-header">Outreach</div>
 +
    <div class="collapsible-body"><ul>
 +
        <li><a href="/Team:Fudan-TSI/Public_Engagement">Education &amp; Public engagement</a></li>
 +
        <li><a href="/Team:Fudan-TSI/Integrated_Human_Practice">Integrated human practice</a></li>
 +
        <li><a href="/Team:Fudan-TSI/Collaborations">Collaborations</a></li>
 +
        <li><a href="/Team:Fudan-TSI/Safety">Safety</a></li>
 +
    </ul></div>
 +
</li>
 +
<li><div class="collapsible-header">Team</div>
 +
    <div class="collapsible-body"><ul>
 +
        <li><a href="/Team:Fudan-TSI/Team">Members</a></li>
 +
        <li><a href="/Team:Fudan-TSI/Attributions">Attributions</a></li>
 +
        <li><a href="https://2018.igem.org/Team:Fudan/Heritage" target=_blank>Heritage</a></li>
 +
        <li><a href="/Team:Fudan-TSI">&copy; 2019</a></li>
 +
    </ul></div>
 +
</li>
 +
                    </ul><!-- .expandable -->
 +
                </li>
 +
                <li><div class="placeHolder"></div></li>
 +
            </ul>
 
         </header>
 
         </header>
  
Line 82: Line 164:
  
  
             <div id="contentBanner" class="figureBanner orangeBg">
+
             <div id="contentBanner" class="figureBanner">
 
                 <div class="row">
 
                 <div class="row">
 
                     <div class="col s12 hide-on-med-and-up">
 
                     <div class="col s12 hide-on-med-and-up">
Line 125: Line 207:
 
             <div class="container">
 
             <div class="container">
 
                 <main style="margin: 0">
 
                 <main style="margin: 0">
                     <div id="section1" class="section container">
+
                     <div class="section container" id="section1">
 
<h2>Video abstract</h2>
 
<h2>Video abstract</h2>
 
<video class="responsive-video" style="margin-top:23px;" controls>
 
<video class="responsive-video" style="margin-top:23px;" controls>
Line 140: Line 222:
  
 
                         </div>
 
                         </div>
                         <h3>Repeated Evolution in vivo
+
                         <h3>a sequence-specific toolbox for continuous mutagenesis
 
                         </h3>
 
                         </h3>
 
                         <p><b>
 
                         <p><b>
Line 205: Line 287:
 
                     </div>
 
                     </div>
  
<div class="expFigureHolder" style="width:100%">
 
    <img class="responsive-img" src="https://static.igem.org/mediawiki/2018/8/84/T--Fudan--LC-gj-use.png" />
 
    <p>In our GJ presentation (10/25 Room 311 9:00-9:25), we used the image above to show other how to use our ENABLE toolbox.</p>
 
</div>
 
<div class="expFigureHolder" style="width:100%">
 
    <img class="responsive-img" src="https://static.igem.org/mediawiki/2018/b/bc/T--Fudan--LC-gj-unlimited.png" />
 
    <p>In our GJ presentation (10/25 Room 311 9:00-9:25), we used the image above to demonstrate the unlimited potential of mammalian cell computation: complex logic in one cells, distributed computing using CellBricks, and cell messengers travel far distance.</p>
 
</div><br/><br/><br/>
 
 
                 </main>
 
                 </main>
 
             </div>
 
             </div>
Line 222: Line 296:
 
                 <div class="container">
 
                 <div class="container">
 
                     <h2 style="margin: 0;padding: 10px 0;">Project Summary</h2>
 
                     <h2 style="margin: 0;padding: 10px 0;">Project Summary</h2>
                     <p style="margin: 0">abstract abstract abstract abstract abstract abstract abstract abstract abstract abstract abstract abstract abstract abstract abstract abstract due sep 5 due sep 5 due sep 5 due sep 5 due sep 5 due sep 5 due sep 5 due sep 5 due sep 5 due sep 5 due sep 5 due sep 5
+
                     <p style="margin: 0">Mutation library generation is critical for biological and medical research, but current methods cannot mutate a specific sequence continuously without manual intervention. Here we present a toolbox for <i>in vivo</i> continuous mutation library construction. First, the target DNA is transcribed into RNA. Next, our reverse transcriptase reverts RNA into cDNA, during which the target is randomly mutated by enhanced error-prone reverse transcription. Finally, the mutated version replaces the original sequence through recombination. These steps will be carried out iteratively, generating a random mutation library of the target with high efficiency as mutations accumulate along with bacterial growth. Our toolbox is orthogonal and provides a wide range of applications among various species. R-Evolution could mutate coding sequences and regulatory sequences, which enables the <i>in vivo</i> evolution of individual proteins or multiple targets at a time, promotes high-throughput research, and serves as a foundational advance to synthetic biology.
 
                     </p>
 
                     </p>
 
                 </div>
 
                 </div>
Line 242: Line 316:
 
                     <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://2019.igem.org/Team:Fudan"><img alt="2018 Team:Fudan logo white" class="col s3 m6 l3" style="position:relative; padding: 0.5em 0.3rem; margin:-0.15rem 0; left: -0.45rem;" src="https://static.igem.org/mediawiki/2019/7/7f/T--Fudan-TSI--Logo0-crop-grey.png">
+
                             <a href="https://2019.igem.org/Team:Fudan-TSI"><img alt="2018 Team:Fudan logo white" class="col s3 m6 l3" style="position:relative; padding: 0.5em 0.3rem; margin:-0.15rem 0; left: -0.45rem;" src="https://static.igem.org/mediawiki/2019/7/7f/T--Fudan-TSI--Logo0-crop-grey.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">
 
                         </a><a href="http://www.yfc.cn/en/" target="_blank"><img class="col s3 m6 l3" style="padding: 0.15rem 0.9rem;" alt="Yunfeng Capital" src="https://static.igem.org/mediawiki/2018/e/e2/T--Fudan--yunfengLogo.png">
 
                         </a><a href="http://www.yfc.cn/en/" target="_blank"><img class="col s3 m6 l3" style="padding: 0.15rem 0.9rem;" alt="Yunfeng Capital" src="https://static.igem.org/mediawiki/2018/e/e2/T--Fudan--yunfengLogo.png">
 
                         </a>
 
                         </a>
                             <h3 class="col s12" style="text-align: left; color: rgba(255, 255, 255, 0.8); font-size: 18px">Repeated Evolution in vivo</h3>
+
                             <h3 class="col s12" style="text-align: left; color: rgba(255, 255, 255, 0.8); font-size:12px">R-Evolution: an <i>in vivo</i> sequence-specific toolbox for continuous mutagenesis</h3>
 
                         </div>
 
                         </div>
 
                         <div id="usefulLinks" class="col m9 s12 row">
 
                         <div id="usefulLinks" class="col m9 s12 row">
 
                             <div class="col s12 l6 row">
 
                             <div class="col s12 l6 row">
                                 <div class="col s12 m4">
+
                                 <div class="col s12 m4 active">
 
                                   <span><a href="/Team:Fudan-TSI/Description">Project</a></span>
 
                                   <span><a href="/Team:Fudan-TSI/Description">Project</a></span>
 
                                     <ul>
 
                                     <ul>

Revision as of 04:53, 15 September 2019

2019 Team:Fudan-TSI Demonstrate

Demonstration

Demonstration

Video abstract

Transmembrane Logic

Sensing and integrating various transmembrane signals is a key aspect of cellular decision making.

For example, activation of CD8+ cells requires co-activation of TCR and CD28 molecules, meanwhile, this activation can be inhibited by the PD-1 pathway (Hui et al., 2017). By abstracting this biological process, we can get: the activation of CD8+ cell = activated TCR AND (activated CD28 NIMPLY activated PD-1). Programming cells with predictable complex transmembrane signal inputs – customized intracellular signal outputs logic relationships are significant for expanding the widespread applications of mammalian cells, such as cellular immunotherapy (Fedorov et al., 2013; Kloss et al., 2013; Roybal et al., 2016a; Roybal et al., 2016b), tissue patterning (Morsut et al., 2016;Roybal et al., 2016; Toda et al., 2018).

a sequence-specific toolbox for continuous mutagenesis

The ingenious design of nature makes us amazing, and inspires us to explore new possibilities. By designing the ENABLE (Engineered, Across-membrane, Binary Logic in Eukaryotes) system and achieving the first complete transmembrane binary Boolean logic in mammals, we could make the pupil outdo the master, make cells even smarter.

Optimizing the Receptor, aims for reduced background activation

In order to be able to implement a custom multiplexed transmembrane signal input/output relationship, the first condition is that engineering modular receptor to enable it to recognize extracellular signals and transduce them into customized intracellular signals. SynNotch is a transmembrane receptor with high programmability. Therefore, we can use this tool to receive extracellular signals and output customized intracellular signals.

Good tools are prerequisite to the successful execution of a job. In order to make SynNotch more suitable as a tool for receiving complex extracellular signals, we have optimized it. Please visit Optimization page for more details.

Three-layer design for dual transmembrane signals

The expression of membrane proteins on the cell membrane is limited. Our modeling tells us how to make cells sensitive to the limited signal molecules, and perform function efficiently is the key to make the transmembrane logic gate system work.

Based on this, we developed the ENABLE system with a 3-layers design: Receptor, Amplifier, and Combiner. By adding an intermediate layer, the “Amplifier” layer, we are able to effectively amplify the transmembrane signal, thus enabling our intracellular components to effectively travel logic functions.

The 3-layer design principle underlying ENABLE empowers any future development of transmembrane logic circuits, thus contributes a foundational advance to synthetic biology.

Unified intracellular logic gates layout

In order to be able to receive dual transmembrane signals and produce complete binary Boolean logic, we designed a set of interactive grammar for the interaction between the "Amplifier" layer and the "Combiner" layer within the cell membrane. This grammar consists mainly of the following elements, a transcription system based on the activating-form, silencing-from or NIMPLY-form promoters (the three are collectively referred to as a synthetic transcription factor-promoter pairs based transcription system); intein-based protein in vivo fusion systems, proteolytic enzyme-based protein in vivo destruction systems (the two are collectively referred to as a protein fusion/destruction-based transcription factor logic). We have test them and report in Results page, as well as on parts.igem pages.

ENABLE logic gates

Below we show experimental verifications of six (OR, NOR, AND, NAND, IMPLY, NIMPLY) of the eight truly binary logics.

Here, we use the OR gate as a proof of concept for a three-layer transmembrane binary Boolean logic during tissue patterning.

Through dynamic and static observations, we can see that the Receiver cell with transmembrane OR gate can be activated by two Sender cells expressing different membrane antigens.

Public engagement and education

Our human practice activities include dialogues (debate and interviews), presentations, Bio-Art display and hands-on practices, all of which centered around farseeing. We want to unlock the creativity and intelligence in as many people as possible. Fully engaged with the public, we motivated by their openness and willingness, which reminds us why we initiated the research and why we work hard in the lab - for the good of the people, including ourselves.

project summary

Project Summary

Mutation library generation is critical for biological and medical research, but current methods cannot mutate a specific sequence continuously without manual intervention. Here we present a toolbox for in vivo continuous mutation library construction. First, the target DNA is transcribed into RNA. Next, our reverse transcriptase reverts RNA into cDNA, during which the target is randomly mutated by enhanced error-prone reverse transcription. Finally, the mutated version replaces the original sequence through recombination. These steps will be carried out iteratively, generating a random mutation library of the target with high efficiency as mutations accumulate along with bacterial growth. Our toolbox is orthogonal and provides a wide range of applications among various species. R-Evolution could mutate coding sequences and regulatory sequences, which enables the in vivo evolution of individual proteins or multiple targets at a time, promotes high-throughput research, and serves as a foundational advance to synthetic biology.