Difference between revisions of "Team:Peking/Notebook"

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    <meta name="description" content="Wiki of Peking iGEM 2016" />
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      <meta name="description" content="Wiki of Peking iGEM 2016" />
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    <meta name="author" content="Li Jiamian & Wang Yuqing">
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      <meta name="author" content="Li Jiamian & Wang Yuqing">
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      <a class="show-menu" data-toggle="collapse" data-target=".nav-collapse"><span class="show-menu-bar"></span>
 
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    </a>
 
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      <div id="logo" style="max-width:170px"><a class="" href="https://2016.igem.org/Team:Peking"></a></div>
 
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        <div class="nav-collapse collapse">
 
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      <ul class="nav">
 
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        <li class="menu-1"><a class="colapse-menu1" href="https://2016.igem.org/Team:Peking" >Home</a></li>
 
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        <li class="dropdown menu-2"><a class="dropdown-toggle" data-toggle="dropdown" href="#">Project</a>
 
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                  <ul class="dropdown-menu">
 
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                      <li><a href="https://2016.igem.org/Team:Peking/Description" >Decription</a></li>
 
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                      <li><a href="https://2016.igem.org/Team:Peking/Design" >Design</a></li>
 
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                      <li><a href="https://2016.igem.org/Team:Peking/Proof" >Proof of Concept</a></li>
 
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                      <li><a href="https://2016.igem.org/Team:Peking/Demonstrate" >Demonstrate</a></li>
 
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                  </ul>
 
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                </li>
 
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        <li class="dropdown menu-3"><a class="dropdown-toggle" data-toggle="dropdown" href="#" >Parts</a>
 
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                  <ul class="dropdown-menu">
 
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                      <li><a href="https://2016.igem.org/Team:Peking/Basic_Part" >Basic parts</a></li>
 
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                      <li><a href="https://2016.igem.org/Team:Peking/Composite_Part" >Composite parts</a></li>
 
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                      <li><a href="https://2016.igem.org/Team:Peking/Part_Collection" >Parts collection</a></li>
 
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                  </ul>
 
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                </li>
 
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        <li class="menu-4"><a class="colapse-menu1" href="https://2016.igem.org/Team:Peking/Human_Practices" >Practices</a></li>
 
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        <li class="menu-5"><a class="colapse-menu1" href="https://2016.igem.org/Team:Peking/Collaborations" >Collaboration</a></li>
 
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        <li class="menu-6"><a class="colapse-menu1" href="https://2016.igem.org/Team:Peking/Model" >Modeling</a></li>
 
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                <li class="dropdown menu-7"><a class="dropdown-toggle" data-toggle="dropdown" href="#" >Lab</a>
 
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                  <ul class="dropdown-menu">
 
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                        <li><a class="" href="https://2016.igem.org/Team:Peking/Team" >Team</a></li>
 
−
                        <li><a class="" href="https://2016.igem.org/Team:Peking/Attributions" >Attribution</a></li>
 
−
                        <li><a class="" href="https://2016.igem.org/Team:Peking/Notebook" >Notebook</a></li>
 
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          </ul>
 
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                </li>
 
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                <li class="dropdown menu-8"><a class="colapse-menu1" data-toggle="dropdown" href="https://2016.igem.org/Team:Peking/Interlab" >Interlab</a>
 
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                </li>
 
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  </div>
 
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  <!-- CSS======================================================================================= -->
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<link rel="stylesheet" href="https://2016.igem.org/Template:Peking/css/notebook_panel?action=raw&ctype=text/css">
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<style type="text/css">
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.panel-default > .panel-heading { /* Notebooks */
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            <h1>Attributions<span>.</span></h1>
 
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            <p class="title1" style="text-align:center">The idea of this project was conceived by the team; advisors and instructors gave advices and suggestions on the implementation of this idea.</p>
 
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      </a>
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        <div id="logo" style="max-width:170px"><a class="" href="https://2016.igem.org/Team:Peking"></a></div>
 +
         
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          <div class="nav-collapse collapse">
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        <ul class="nav">
 +
          <li class="menu-1"><a class="colapse-menu1" href="https://2016.igem.org/Team:Peking" >Home</a></li>
 +
          <li class="dropdown menu-2"><a class="dropdown-toggle" data-toggle="dropdown" href="#">Project</a>
 +
                    <ul class="dropdown-menu">
 +
                        <li><a href="https://2016.igem.org/Team:Peking/Description" >Decription</a></li>
 +
                        <li><a href="https://2016.igem.org/Team:Peking/Design" >Design</a></li>
 +
                        <li><a href="https://2016.igem.org/Team:Peking/Proof" >Proof of Concept</a></li>
 +
                        <li><a href="https://2016.igem.org/Team:Peking/Demonstrate" >Demonstrate</a></li>
 +
                    </ul>
 +
                  </li>
 +
          <li class="dropdown menu-3"><a class="dropdown-toggle" data-toggle="dropdown" href="#" >Parts</a>
 +
                    <ul class="dropdown-menu">
 +
                        <li><a href="https://2016.igem.org/Team:Peking/Basic_Part" >Basic parts</a></li>
 +
                        <li><a href="https://2016.igem.org/Team:Peking/Composite_Part" >Composite parts</a></li>
 +
                        <li><a href="https://2016.igem.org/Team:Peking/Part_Collection" >Parts collection</a></li>
 +
                    </ul>
 +
                  </li>
 +
          <li class="menu-4"><a class="colapse-menu1" href="https://2016.igem.org/Team:Peking/Human_Practices" >Practices</a></li>
 +
          <li class="menu-5"><a class="colapse-menu1" href="https://2016.igem.org/Team:Peking/Collaborations" >Collaboration</a></li>
 +
          <li class="menu-6"><a class="colapse-menu1" href="https://2016.igem.org/Team:Peking/Model" >Modeling</a></li>
 +
                  <li class="dropdown menu-7"><a class="dropdown-toggle" data-toggle="dropdown" href="#" >Lab</a>
 +
                    <ul class="dropdown-menu">
 +
                          <li><a class="" href="https://2016.igem.org/Team:Peking/Team" >Team</a></li>
 +
                          <li><a class="" href="https://2016.igem.org/Team:Peking/Attributions" >Attribution</a></li>
 +
                          <li><a class="" href="https://2016.igem.org/Team:Peking/Notebook" >Notebook</a></li>
 +
            </ul>
 +
                  </li>
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                  <li class="dropdown menu-8"><a class="colapse-menu1" data-toggle="dropdown" href="https://2016.igem.org/Team:Peking/Interlab" >Interlab</a>
 +
                  </li>
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    </div>
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    </div>
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              <h1>Notebook<span>.</span></h1>
 +
              <p class="title1" style="text-align:center">In this page, you can view how we worked on our project.</p>
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          </div>
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        </div>
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    </div>
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    <!-- Page Title End-->
  
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<h3 style="text-align:center"> Diary</h3>
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                <h4 class="panel-title" style="color:white;">
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                    <a data-toggle="collapse" href="#collapseOne">Week 1 (6/26/2016-7/02/2016)</a>
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                </h4>
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            </div>
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            <div id="collapseOne" class="panel-collapse collapse">
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                <div class="panel-body">
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                    <ul>
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                        <li>We transformed BioBricks from the distribution:</li>
 +
                            <ul>
 +
                                <li><a href="http://parts.igem.org/Part:BBa_J33201" target="_blank">BBa_J33201</a> (arsR)</li>
 +
                                <li><a href="http://parts.igem.org/Part:BBa_K516030" target="_blank">BBa_K516030</a> (mRFP1 with RBS and terminator)</li>
 +
                                <li>Colonies were used to inoculate overnight cultures.</li>
 +
                                <li>Plasmids were isolated using a miniprep kit.</li>
 +
                        </ul>
 +
                    </ul>
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                </div>
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            </div>
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        </div>
  
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        <div class="panel panel-default">
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            <div class="panel-heading">
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                <h4 class="panel-title">
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                    <a data-toggle="collapse" href="#collapse2">Week 2 (4/20/2015-4/26/2015)</a>
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                </h4>
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            </div>
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            <div id="collapse2" class="panel-collapse collapse">
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                <div class="panel-body">
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                    <p>...</p>
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                </div>
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            </div>
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        </div>
  
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                <h4 class="panel-title">
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                    <a data-toggle="collapse" href="#collapse3">Week 3 (4/20/2015-4/26/2015)</a>
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                </h4>
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            </div>
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            <div id="collapse3" class="panel-collapse collapse">
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                <div class="panel-body">
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                    <p>...</p>
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                </div>
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            </div>
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        </div>
  
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        <div class="panel panel-default">
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            <div class="panel-heading">
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                <h4 class="panel-title">
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                    <a data-toggle="collapse" href="#collapse4">Week 4 (4/20/2015-4/26/2015)</a>
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                </h4>
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            </div>
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            <div id="collapse4" class="panel-collapse collapse">
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                <div class="panel-body">
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                    <p>...</p>
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            </div>
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        </div>
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        <div class="panel panel-default">
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            <div class="panel-heading">
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                <h4 class="panel-title">
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                    <a data-toggle="collapse" href="#collapse5">Week 5 (4/20/2015-4/26/2015)</a>
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                </h4>
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            </div>
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            <div id="collapse5" class="panel-collapse collapse">
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                <div class="panel-body">
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                    <p>...</p>
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            </div>
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        </div>
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  <h4>Attributions</h4>
 
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    <ul>
 
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        <li><a href="#members">Members'</a></li>
 
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        <li><a href="#acknowledgement">Acknowledgement</a></li>
 
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                <h3 class="classic-title";"><span>Member’s Attributions</span></h3>                     
 
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                <p>All the data presented on this wiki was measured, collected, and analyzed by the team members. All the plasmids directly involved in the data presented on this wiki were constructed by the team members. The idea conceiving, content planning, execution, and result analysis of human practice were all done by the team members. The following is the detailed attribution:
 
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</p>
 
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                <p>
 
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                <strong>LI Cheng</strong> is the team leader of Peking iGEM 2016. He participated in conceiving the project, took charge of troubleshooting, and managed the experiments, guaranteeing the normal operation of the lab.<br/>
 
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                <strong>YANG Xiaoyu</strong>  was committed to ameliorate the paired dCas9 (PC) reporter system, namely, to enhance the sensitivity and robustness. Early in the project, he was also responsible for information gathering, experiment design, and lab management<br/>
 
  
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                <strong>BAI Ke</strong> was in charge of Human Practice and also worked in the wet lab to construct and prepare plasmids for gRNA in vitro transcription.<br/>
 
−
                <strong>DONG Yiming</strong>
 
−
                was responsible for designing and manufacturing the portable electronic device that convert optical signal into analogue electrical signal.<br/>
 
−
                <strong>LI Yuexuan</strong> worked as the financial manager of the team. She was also responsible for plasmid construction and submission.<br/>
 
−
                <strong>YANG Changru</strong> was in charge of building <i>M.tuberculosis</i>-sensing system using Molecule Beacon. He was also engaged in the protein purification of dCas9 fusion proteins.<br/>
 
−
                <strong>ZHAO Shijun</strong> was in charge of measuring the luminescence intensity of PC reporter system. She analyzed the entire experimental data.<br/>
 
−
                <strong>LV Nayun</strong> helped to complete the plasmid construction of sgRNA and was in part responsible for human practice.<br/>
 
−
                <strong>WANG Dingyu</strong> was in charge of the construction of CRISPR gRNA as well as RNA scaffold in the beginning. Later she was working on the purification of dCas9 fusion protein.<br/>
 
−
                <strong>LI Jiamian</strong> took the task of cloning dCas9-luciferase. She was also responsible for the testing of PC reporter system.<br/>
 
−
                <strong>WEI Jingyi</strong> participated in plasmid construction, protein purification, and wiki building. She was also the designer of our PowerPoint slides.<br/>
 
−
                <strong>WANG Yuqing</strong> was in charge of Modeling. His main task was to computationally search for the suitable guide sequences. Also, he was the lab manager for the normal operation of our lab.<br/>
 
−
                <strong>TENG Huaiyuan</strong>was in charge of Modeling. His main task was to computationally search for the suitable guide sequences. Also, he was the lab manager for the normal operation of our lab.<br/>
 
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                <a id="acknowledgement"></a>
 
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                  <h3 class="classic-title";"><span>Acknowledgement</span></h3>                             
 
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                  <p>We'd like to thank all those who have helped us over the summer, without whose sincere support The Uranium Reaper Project goals would have not been achieved.
 
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</p>
 
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                <h4>General support</h4>
 
−
                <p><strong>Prof. OUYANG Qi, Prof. LOU Chunbo, Dr. ZHANG Haoqian</strong> and other teachers helped us during our brainstorming and gave us useful suggestions.<br>
 
−
                <strong>Prof. OUYANG Qi</strong> and<strong> Prof. LIU Chunli</strong> kindly provided the laboratory to us for experiments.
 
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                </p>
 
  
−
                <h4>Materials support</h4>
 
−
                <p><strong>Dr. ZHANG Wenbing</strong> provided us with the plasmid of 3B(Tri-SpyCatcher within 15X linker).<br>
 
−
                    <strong> Prof. ZHOU Lu</strong> provided us with Uranyl-binding Protein, also called SUP.<br>
 
−
                    <strong>Prof. LIU Chunli</strong>allowed us to use his lab to do experiments on uranyl ion. The uranyl nitrate solution and Arsenazo III was provided by Prof. LIU.<br>
 
−
                  <strong>Prof. LOU Chunbo</strong> provided us with the strain B.Subtilis and mSA, heavy metal ions binding proteins: lead-binding protein, mercury-binding protein and cadmium-binding protein.<br>
 
−
                  <strong>Dr. DU Pei</strong> provided the beads to us and gave us experimental guidance.<br>
 
−
                  <strong>BIT-China</strong> gave us the important Interlab kit.
 
−
                </p>
 
  
−
                <h4>Experiment equipment support</h4>
 
−
                <p><strong>Prof. OUYANG Qi</strong> lent the Akta Pure to us for all proteins purification.<br>
 
−
                    <strong>Prof. CHANG Zengyi</strong> and <strong>Dr. WANG Qingsong</strong> provided us with Scanner and helped with the setup and scan of gels.<br>
 
−
                  <strong>Prof. LIU Chunli</strong> provided us with Geiger counter to test the radiation level in and around our lab.<br>
 
−
                  <strong>Core Facilities</strong>, School of Life Sciences, Peking University,assisted us with ITC.<br>
 
−
                  <strong>the State Key Laboratory of environmental simulation and pollution control</strong> provided the Aurora M90 mass spectrograph.
 
−
                </p>
 
  
−
                <h4>Theoretical guidance</h4>
 
−
                <p> <strong>ZHANG Yihao</strong> and <strong>WANG Yu</strong>,The wiki designers of Peking iGEM 2015,gave us many suggestions about wiki building.<br>
 
−
                    <strong>Dr. YU Daqi</strong> of Prof. OUYANG Qi’s lab helped us a lot in experimental operating and data analysis.<br>
 
−
                    <strong>Prof. ZHANG Wenbing, Prof. LOU Chunbo</strong> and <strong>Dr. YU Daqi</strong> kindly helped our team with modeling of the project.<br>
 
−
                  <strong>Prof. OUYANG Qi, Prof. LOU Chunbo, Dr. ZHANG Haoqian</strong> and <strong>ZHANG Yihao</strong>,the instructors, coached us for the presentation.<br>
 
−
                    <strong>Prof. LAI Luhua</strong> and <strong>Prof. RAO Yi</strong> participated in our presentation rehearsal and gave suggestions for revisions.
 
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                </p>
 
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                <h4>Synthetic biology course</h4>
 
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                <p>From March to June, an introductory course of synthetic biology was hold by College of Life Sciences, Peking University.During the course, the teachers, also the instructors gave us kind guidance and judged our project design. In late June, we started in the lab to start our project.
 
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Revision as of 08:54, 30 September 2016

  
  
  
  
      
    
      
      
      
      



  
    
  
      
  
     
     
  
      
      
      
      
  
     
     
     
     
 
 		
  








  


  
   
      
      






  
     

        

           

              
Notebook.

              
In this page, you can view how we worked on our project.

           

        

     
 
     




 

      

   
        

  

  		

  		

  	 


       						

 Diary


 	


        

            

                

                    Week 1 (6/26/2016-7/02/2016)
                

            

            

                

                    
    
                        
  • We transformed BioBricks from the distribution:
    • 
                            
      
                                
    • BBa_J33201 (arsR)
      • 
                                
    • BBa_K516030 (mRFP1 with RBS and terminator)
      • 
                                
    • Colonies were used to inoculate overnight cultures.
      • 
                                
    • Plasmids were isolated using a miniprep kit.
      • 
                        	
    
                    

                

            

        


        

            

                

                    Week 2 (4/20/2015-4/26/2015)
                

            

            

                

                    
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                    Week 3 (4/20/2015-4/26/2015)
                

            

            

                

                    
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                    Week 4 (4/20/2015-4/26/2015)
                

            

            

                

                    
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                    Week 5 (4/20/2015-4/26/2015)
                

            

            

                

                    
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                    Week 6 (4/20/2015-4/26/2015)
                

            

            

                

                    
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                    Week 7 (4/20/2015-4/26/2015)
                

            

            

                

                    
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                    Week 8 (4/20/2015-4/26/2015)
                

            

            

                

                    
...

                

            

        

        
        

            

                

                    Week 9 (4/20/2015-4/26/2015)
                

            

            

                

                    
...

                

            

        

        
     

     





 Protocols