Difference between revisions of "Team:Peking/Design"

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{{Peking}}
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<!--[if IE 8 ]><html class="ie ie8" lang="en"> <![endif]-->
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<html>
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<html lang="en">
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<head>
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  <meta charset="utf-8">
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  <meta name="viewport" content="width=device-width, initial-scale=1, maximum-scale=1">
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  <meta name="Peking-iGEM-2015" content="iGEM - Peking iGEM 2015">
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  <!--add  ?action=raw&amp;ctype=text/css    when using Css-->
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  <link rel="stylesheet" href="https://2015.igem.org/Template:Peking/new?action=raw&amp;ctype=text/css" type="text/css" media="screen">
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  <link rel="stylesheet" type="text/css" href="https://2015.igem.org/Template:Peking/Style/new?action=raw&amp;ctype=text/css" media="screen">
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  <link rel="stylesheet" type="text/css" href="https://2015.igem.org/Template:Peking/Responsive/new?action=raw&amp;ctype=text/css" media="screen">
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  <link rel="stylesheet" type="text/css" href="https://2015.igem.org/Template:Peking/Animate/new?action=raw&amp;ctype=text/css" media="screen">
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  <link rel="stylesheet" type="text/css" href="https://2015.igem.org/Template:Peking/Blue/new?action=raw&amp;ctype=text/css " title="blue" media="screen" />
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  <style type="text/css">/*get rid of the annoying iGEM style*/
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      #content{padding:0;border:0;width:100%;}
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      .firstHeading{visibility:hidden;}
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      h2{border-bottom:none;padding-bottom:.5em;}  
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      .carousel-control.left, .carousel-control.right{background-image: none}
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    /* to style the sidebar*/
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        @media (min-width:1024px){
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      #sidebar1{position:relative;top:120px;max-width:200px;}
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      #sidebar2{display:none;}
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      #nav-top{height:88px;}
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    }
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      @media (max-width: 1023px){
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      #sidebar1{display:none;}
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      #sidebar2{display:block;}
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    }
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    .back-to-top{z-index:9999;}
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ul.dropdown{margin-left: 0px; margin-top: 0px;}
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.classic-title span {
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position: absolute;
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    margin-top: -30px;
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    border-bottom-color: #00afd1;
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}
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.page-banner{
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  background-color:#e0e0e0;margin-top:1%;margin-bottom:20px;padding:20px;padding-top:40px;
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}
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    </style>
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</head>
  
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<h2>Design</h2>
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<body>
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  <!-- Container -->
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  <div id="container">
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    <!-- Start Header -->
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    <header class="clearfix">
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        <!-- Start  Logo & Naviagtion  -->
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            <div class="navbar navbar-default navbar-top">
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                <div class="container">
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                    <div class="navbar-header" >
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                        <!-- Stat Toggle Nav Link For Mobiles -->
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                        <button type="button" class="navbar-toggle" data-toggle="collapse" data-target=".navbar-collapse" style="margin-top:40px">
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                            <i class="fa"><img  style="margin-left:0;height:30px;"src="https://static.igem.org/mediawiki/2015/4/45/Peking-Hambergur-1.png" ></i>
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                        </button>
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                        <!-- End Toggle Nav Link For Mobiles -->
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                        <a class="navbar-brand" href="https://2015.igem.org/Team:Peking">
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                            <img alt="Peking iGEM 2015" src="https://static.igem.org/mediawiki/2015/8/8b/Peking-header-logo-1.png" style="height:55px;margin-top:7px">
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                        </a>
 +
                    </div>
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                    <div class="navbar-collapse collapse"  style="padding-top:5px;padding-bottom:0">
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                        <!-- Start Navigation List -->
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                        <ul class="nav navbar-nav navbar-right " style="padding-bottom:15px;height:88px;padding-top:10px">
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                            <li>
 +
                                <a href="https://2015.igem.org/Team:Peking/JudgingCriteria">Achievements</a>
 +
                                <ul class="dropdown">
 +
                                    <li><a href="https://2015.igem.org/Team:Peking/JudgingCriteria">Judging Criteria</a>
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                                    </li>
 +
                                    <li><a href="https://2015.igem.org/Team:Peking/Parts">Parts</a>
 +
                                    </li>
 +
                                    <li><a href="https://2015.igem.org/Team:Peking/Collaborations">Collaborations</a>
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                                    </li>
 +
                                </ul>
 +
                            </li>
 +
                            <li>
 +
                                <a class="active" href="https://2015.igem.org/Team:Peking/Design">Project</a>
 +
                                <ul class="dropdown">
 +
                                    <li><a class="active" href="https://2015.igem.org/Team:Peking/Design">Overview</a>
 +
                                    </li>
 +
<li><a href="https://2015.igem.org/Team:Peking/Design/PC_Reporter">Paired<span style="text-transform:lowercase"> d</span>Cas9 Reporter</a>
 +
                                    </li>
 +
                                    <li><a href="https://2015.igem.org/Team:Peking/Design/Isothermal">Iso-<span style="text-transform:lowercase">t</span>hermal Amplification</a>
 +
                                    <li><a href="https://2015.igem.org/Team:Peking/Device">Hardware</a>
 +
                                    </li>
 +
                                    <li><a href="https://2015.igem.org/Team:Peking/Design/Speculation">Speculation</a>
 +
                                    </li>
 +
                                </ul>
 +
                            </li>
 +
                            <li>
 +
                                <a href="https://2015.igem.org/Team:Peking/Modeling">Modeling</a>
 +
                                <ul class="dropdown">
 +
                                    <li><a href="https://2015.igem.org/Team:Peking/Modeling">Array Design</a>
 +
                                    </li>
 +
                                    <li><a href="https://2015.igem.org/Team:Peking/Modeling/Analysis">Analysis algorithm</a>
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                                    </li>
 +
                                </ul>
 +
                            </li>
 +
                            <li>
 +
                                <a href="https://2015.igem.org/Team:Peking/Practices">Practices</a>
 +
                                <ul class="dropdown">
 +
                                    <li><a href="https://2015.igem.org/Team:Peking/Practices">Overview</a>
 +
                                    </li>
 +
                                    <li><a href="https://2015.igem.org/Team:Peking/Practices/Background">Facts about TB</a>
 +
                                    </li>
 +
                                    <li><a href="https://2015.igem.org/Team:Peking/Practices/Consultation">Consultation and Interview</a>
 +
                                    </li>
 +
                                    <li><a href="https://2015.igem.org/Team:Peking/Practices/Engagement">Public Engagement</a>
 +
                                    </li>
 +
                                    <li><a href="https://2015.igem.org/Team:Peking/Practices/Outreach">Ethics and Economics Issues</a>
 +
                                    </li>
 +
                                </ul>
 +
                            </li>
 +
                            <li>
 +
                                <a href="https://2015.igem.org/Team:Peking/Team">Lab</a>
 +
                                <ul>
 +
                                    <li><a href="https://2015.igem.org/Team:Peking/Team">Team</a>
 +
                                    </li>
 +
                                    <li><a href="https://2015.igem.org/Team:Peking/Notebook">Notebook</a>
 +
                                    </li>
 +
                                    <li><a href="https://2015.igem.org/Team:Peking/Attributions">Attributions</a>
 +
                                    </li>
 +
                                    <li><a href="https://2015.igem.org/Team:Peking/Safety">Safety</a>
 +
                                    </li>
 +
                                </ul>
 +
                            </li>
 +
                        </ul>
 +
                        <!-- End Navigation List -->
 +
                    </div>
 +
                </div>
 +
            </div>
 +
            <!-- End Header Logo & Naviagtion -->
 +
           
 +
        </header>
 +
        <!-- End Header Section -->
 +
   
 +
   
 +
    <!-- Start Page Banner -->
 +
    <div class="page-banner" >
 +
      <div class="container">
 +
        <div class="row">
 +
          <div class="col-md-6">
 +
            <h2 style="font-size:20px; margin-bottom:5px; padding-bottom:0">Project</h2>
 +
            <p style="margin-top:0px;font-size:14px">It takes half your life before you discover life is a do-it-yourself project.</p>
 +
          </div>
 +
          <div class="col-md-6">
 +
            <ul class="breadcrumbs">
 +
              <li><a href="https://2015.igem.org/Team:Peking">Home</a></li>
 +
              <li>Project</li>
 +
            </ul>
 +
          </div>
 +
        </div>
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      </div>
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    </div>
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    <!-- End Page Banner -->
  
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<p>
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    <!-- Start Content -->
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By talking about your design work on this page, there is one medal criterion that you can attempt to meet, and one award that you can apply for. If your team is going for a gold medal by building a functional prototype, you should tell us what you did on this page. If you are going for the <a href="https://2015.igem.org/Judging/Awards#SpecialPrizes">Applied Design award</a>, you should also complete this page and tell us what you did.  
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    <div id="content">
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</p>
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      <div class="container">
 +
        <div class="row blog-page">
 +
                 
 +
          <!--Sidebar-->
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          <div class="col-md-3 sidebar left-sidebar">
 +
            <!-- Categories Widget -->
 +
            <div id="sidebar1"class="widget widget-categories" >
 +
              <h4 style="font-size:18px">P<span style="text-transform:lowercase">roject</span><span class="head-line"></span></h4>
 +
             
 +
            </div>
 +
            <div id="sidebar2"class="widget widget-categories">
 +
              <h4 style="font-size:18px">P<span style="text-transform:lowercase">roject<span class="head-line"></span></h4>
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 +
            </div>
 +
          </div>
 +
          <!--End sidebar-->
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  <!-- Page Content -->
 +
          <div class="col-md-9 page-content">
 +
            <div id="project">
 +
            <!-- Classic Heading -->
 +
              <div id="overview">
 +
                <div>
 +
                  <h3 class="classic-title" style="margin-top:50px"><span><a href="#">Overview</a></span></h3>
 +
                  <div style="margin-top:30px; margin-bottom:0">
 +
<p>Tuberculosis (TB), caused by Mycobacterium tuberculosis, remains one of the world's most serious public health problems. Although tuberculosis is curable and the treatment success rate is high, it is still the second most common cause of death from infectious disease. Most of the deaths occur for lack of effective identification of those in need of therapy. Case detection is currently the rate-limiting step in TB control.</p>
 +
<p>The currently major TB detection methods all have their own problems. Nucleic Acid Detection (NAD) is a safer, faster, and more sensitive detection method available. However, it has short comes: the high false positive rate from non-specific amplification, and the requirement of extremely expensive clumsy instruments, which make NAD not common for TB diagnosis. </p>
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<p>To obviate such problems, Peking iGEM developed a novel detection system that can directly read out specific sequence information inside the PCR amplified product, and convert the information into visible signal. Combined with our work in multi-marker array design and hardware development, this new advanced system can be turned out as a powerful tool in TB diagnosis, with a huge potential for applications and extensions.</p>
  
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<div class="highlightBox">
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                  </div>
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<h4>Note</h4>
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<p>In order to be considered for the <a href="https://2015.igem.org/Judging/Awards#SpecialPrizes">Best Applied Design award</a> and/or the <a href="https://2015.igem.org/Judging/Awards#Medals">functional prototype gold medal criterion</a>, you must fill out this page.</p>
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              <h3 class="classic-title"  style="margin-top:50px"><span><a href="https://2015.igem.org/Team:Peking/Design/PC_Reporter">PC Reporter</a></span></h3>
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</div>
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              <div style="margin-top:30px; margin-bottom:0">
 +
                <div class="row">
 +
                  <div claa="col-md-6">
 +
                    <img src="https://static.igem.org/mediawiki/2015/4/4e/Peking-Project-Overview1.png">
 +
                  </div>
 +
                  <div class="col-md-6">
 +
                <p> With two fragments of split firefly luciferase separately fused to dCas9 protein, we successfully designed and built a paired dCas9 reporter (PC reporter) that can convert specific sequence information into light signal. We finished the characterization and optimization. Most importantly, we successfully demonstrated the PC reporter with isolated genomic DNA from a pathogenic MTB.</p>
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                </div>
 +
              </div>
 +
            </div>
 +
            <h3 class="classic-title"  style="margin-top:50px"><span>Multi-marker array</span></h3>
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              <div style="margin-top:30px; margin-bottom:0">
 +
                <div class="row">
 +
                  <div claa="col-md-4">
 +
                    <img src="https://static.igem.org/mediawiki/2015/9/98/Peking-Project-Overview2.png">
 +
                  </div>
 +
                  <div class="col-md-8">
 +
                <p>To deal with challenges from clinical practices, such as strain mutations, sample variations, and other uncontrollable environmental factors, we designed an array to extract more sequence information for our PC Reporter to test multiple sites on the target genome at one time to improve the reliability. With statistics analysis, we can analyze read-outs in a quantitative way.</p>
 +
                </div>
 +
              </div>
 +
            </div>
 +
            <h3 class="classic-title"  style="margin-top:50px"><span><a href="https://2015.igem.org/Team:Peking/Device">Hardware</a></span></h3>
 +
            <div style="margin-top:30px; margin-bottom:0">
 +
                <div class="row">
 +
                  <div claa="col-md-6">
 +
                    <img src="https://static.igem.org/mediawiki/2015/0/0f/Peking-Project-Overview3.png">
 +
                    </div>
 +
                  <div class="col-md-6">
 +
                <p>Noticing that most TB cases occur in developing areas, we designed and built a device (prototype), which was portable, affordable, and can be easily used by medical workers.</p>
 +
                </div>
 +
              </div>
 +
            </div>
 +
            <h3 class="classic-title"  style="margin-top:50px"><span><a href=""https://2015.igem.org/Team:Peking/Design/Isothermal>Specific isothermal amplification</a></span></h3>
 +
            <div style="margin-top:30px; margin-bottom:0">
 +
                <div class="row">
 +
                  <div claa="col-md-5">
 +
                    <img src="https://static.igem.org/mediawiki/2015/0/0f/Peking-Project-Overview3.png">
 +
                    </div>
 +
                  <div class="col-md-7">
 +
                <p>In order to popularize our detection system to developing areas, we invented two novel isothermal amplification methods that can use one pair of easily designed primers to achieve specific amplification.</p>
 +
                </div>
 +
              </div>
 +
            </div>
  
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<p>This is a prize for the team that has developed a synthetic biology product to solve a real world problem in the most elegant way. The students will have considered how well the product addresses the problem versus other potential solutions, how the product integrates or disrupts other products and processes, and how its lifecycle can more broadly impact our lives and environments in positive and negative ways.</p>
 
  
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<p>
 
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If you are working on art and design as your main project, please join the art and design track. If you are integrating art and design into the core of your main project, please apply for the award by completing this page.
 
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</p>
 
  
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</div>
 
  
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                </div>
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            </div>
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          </div>
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        </div>
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      </div>
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    </div>
 +
   
 +
      <!--FOOTER************FOOTER*******************FOOTER***************FOOTER************-->
 +
<!--******************************* the only thing to CHANGE is the SHARE LINK******************************-->
 +
    <!-- Start Footer -->
 +
    <footer style="margin-top:30px; padding:0">
 +
      <div class="container" >
 +
        <div class="row footer-widgets" style="padding:0:margin:0">
 +
         
 +
          <!-- Start Subscribe & Social Links Widget -->
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                    <div class="col-md-3">
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                          <div class="col-md-12 footer-widget social-widget row" style="padding-top:0:padding-bottom:0;margin-top:0;margin-bottom:0">
 +
                            <h4>Share This<span class="head-line"></span></h4>
 +
                            <ul class="social-icons" style="padding-top:0:padding-bottom:0;margin-top:0;margin-bottom:0">
 +
                                <li style="padding-top:0:padding-bottom:0;margin-top:0;margin-bottom:0"><!--HERE need to be changed-->
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                                    <a class="twitter" target="_blank" href="https://twitter.com/home/?status=https://2015.igem.org/Team:Peking/Practices/Background">
 +
                                      <i class="fa">
 +
                                        <img src="https://static.igem.org/mediawiki/2015/d/d0/Peking-twitter.png" style="height:20px;width:auto; margin-top:7px;">
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                                      </i>
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                                    </a>
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                                </li>
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                                <li style="padding-top:0:padding-bottom:0;margin-top:0;margin-bottom:0"><!--HERE need to be changed-->
 +
                                    <a class="facebook"target="_blank" href="https://www.facebook.com/sharer/sharer.php?u=https://2015.igem.org/Team:Peking/Practices/Background">
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                                      <i class="fa">
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                                        <img src="https://static.igem.org/mediawiki/2015/0/0e/Peking-facebook.png" style="height:20px; margin-top:7px;">
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                                      </i>
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                                    </a>
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Revision as of 22:05, 18 September 2015

Peking iGEM 2015

Project

It takes half your life before you discover life is a do-it-yourself project.

Project

Project

Overview

Tuberculosis (TB), caused by Mycobacterium tuberculosis, remains one of the world's most serious public health problems. Although tuberculosis is curable and the treatment success rate is high, it is still the second most common cause of death from infectious disease. Most of the deaths occur for lack of effective identification of those in need of therapy. Case detection is currently the rate-limiting step in TB control.

The currently major TB detection methods all have their own problems. Nucleic Acid Detection (NAD) is a safer, faster, and more sensitive detection method available. However, it has short comes: the high false positive rate from non-specific amplification, and the requirement of extremely expensive clumsy instruments, which make NAD not common for TB diagnosis.

To obviate such problems, Peking iGEM developed a novel detection system that can directly read out specific sequence information inside the PCR amplified product, and convert the information into visible signal. Combined with our work in multi-marker array design and hardware development, this new advanced system can be turned out as a powerful tool in TB diagnosis, with a huge potential for applications and extensions.

PC Reporter

With two fragments of split firefly luciferase separately fused to dCas9 protein, we successfully designed and built a paired dCas9 reporter (PC reporter) that can convert specific sequence information into light signal. We finished the characterization and optimization. Most importantly, we successfully demonstrated the PC reporter with isolated genomic DNA from a pathogenic MTB.

Multi-marker array

To deal with challenges from clinical practices, such as strain mutations, sample variations, and other uncontrollable environmental factors, we designed an array to extract more sequence information for our PC Reporter to test multiple sites on the target genome at one time to improve the reliability. With statistics analysis, we can analyze read-outs in a quantitative way.

Hardware

Noticing that most TB cases occur in developing areas, we designed and built a device (prototype), which was portable, affordable, and can be easily used by medical workers.

Specific isothermal amplification

In order to popularize our detection system to developing areas, we invented two novel isothermal amplification methods that can use one pair of easily designed primers to achieve specific amplification.