Difference between revisions of "Team:Peking/Design"

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<h2>Design</h2>
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    </style>
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</head>
  
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<p>
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<body>
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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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    <!-- 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>
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                    </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;padding-top:10px">
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                            <li>
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                                <a href="https://2015.igem.org/Team:Peking/JudgingCriteria">Achievements</a>
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                                <ul class="dropdown">
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                                    <li><a href="https://2015.igem.org/Team:Peking/JudgingCriteria">Judging Criteria</a>
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                                    </li>
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                                    <li><a href="https://2015.igem.org/Team:Peking/Parts">Parts</a>
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                                    </li>
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                                    <li><a href="https://2015.igem.org/Team:Peking/Collaborations">Collaborations</a>
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                                    </li>
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                                </ul>
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                            </li>
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                            <li>
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                                <a class="active" href="https://2015.igem.org/Team:Peking/Design">Project</a>
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                                <ul class="dropdown">
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                                    <li><a class="active" href="https://2015.igem.org/Team:Peking/Design">Overview</a>
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                                    </li>
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<li><a href="https://2015.igem.org/Team:Peking/Design/PC_Reporter">Paired<span style="text-transform:lowercase"> d</span>Cas9 Reporter</a>
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                                    </li>
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                                    <li><a href="https://2015.igem.org/Team:Peking/Design/Isothermal">Iso-<span style="text-transform:lowercase">t</span>hermal Amplification</a>
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                                    <li><a href="https://2015.igem.org/Team:Peking/Device">Hardware</a>
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                                    </li>
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                                    <li><a href="https://2015.igem.org/Team:Peking/Design/Speculation">Speculation</a>
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                                    </li>
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                                </ul>
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                            </li>
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                            <li>
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                                <a href="https://2015.igem.org/Team:Peking/Modeling">Modeling</a>
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                                <ul class="dropdown">
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                                    <li><a href="https://2015.igem.org/Team:Peking/Modeling">Array Design</a>
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                                    </li>
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                                    <li><a href="https://2015.igem.org/Team:Peking/Modeling/Analysis">Analysis algorithm</a>
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                                    </li>
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                                </ul>
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                            </li>
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                            <li>
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                                <a href="https://2015.igem.org/Team:Peking/Practices">Practices</a>
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                                <ul class="dropdown">
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                                    <li><a href="https://2015.igem.org/Team:Peking/Practices">Overview</a>
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                                    </li>
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                                    <li><a href="https://2015.igem.org/Team:Peking/Practices/Background">Facts about TB</a>
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                                    </li>
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                                    <li><a href="https://2015.igem.org/Team:Peking/Practices/Consultation">Consultation and Interview</a>
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                                    </li>
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                                    <li><a href="https://2015.igem.org/Team:Peking/Practices/Engagement">Public Engagement</a>
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                                    </li>
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                                    <li><a href="https://2015.igem.org/Team:Peking/Practices/Outreach">Ethics and Economics Issues</a>
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                                    </li>
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                                </ul>
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                            </li>
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                            <li>
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                                <a href="https://2015.igem.org/Team:Peking/Team">Lab</a>
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                                <ul>
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                                    <li><a href="https://2015.igem.org/Team:Peking/Team">Team</a>
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                                    </li>
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                                    <li><a href="https://2015.igem.org/Team:Peking/Notebook">Notebook</a>
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                                    </li>
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                                    <li><a href="https://2015.igem.org/Team:Peking/Attributions">Attributions</a>
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                                    </li>
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                                    <li><a href="https://2015.igem.org/Team:Peking/Safety">Safety</a>
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                                    </li>
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                                </ul>
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                            </li>
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                        </ul>
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                        <!-- End Navigation List -->
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    <!-- Start Page Banner -->
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    <div class="page-banner" >
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      <div class="container">
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        <div class="row">
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          <div class="col-md-6">
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            <h2 style="font-size:20px; margin-bottom:5px; padding-bottom:0">P<span style="text-transform:lowercase">roject</span></h2>
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            <p style="margin-top:0px;font-size:14px">It takes half your life before you discover life is a do-it-yourself project.</p>
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          </div>
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          <div class="col-md-6">
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            <ul class="breadcrumbs">
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              <li><a href="https://2015.igem.org/Team:Peking">Home</a></li>
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              <li>Project</li>
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            </ul>
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          </div>
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        </div>
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<h4>Note</h4>
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    <div id="content">
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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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      <div class="container">
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        <div class="row blog-page">
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          <!--Sidebar-->
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          <div class="col-md-3 sidebar left-sidebar">
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            <!-- Categories Widget -->
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            <div id="sidebar1"class="widget widget-categories" >
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              <h4 style="font-size:18px">O<span style="text-transform:lowercase">verview</span><span class="head-line"></span></h4>
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            </div>
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            <div id="sidebar2"class="widget widget-categories">
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              <h4 style="font-size:18px">O<span style="text-transform:lowercase">verview<span class="head-line"></span></h4>
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            </div>
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          </div>
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          <!--End sidebar-->
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  <!-- Page Content -->
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          <div class="col-md-9 page-content" style="text-align:justify;">
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            <div id="project">
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            <!-- Classic Heading -->
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              <div id="overview">
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                <div>
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                  <h3 class="classic-title" style="margin-top:50px"><span><a style="color:#00afd1;" href="#">Overview</a></span></h3>
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                  <div style="margin-top:30px; margin-bottom:0">
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<p>Tuberculosis (TB), caused by <I>Mycobacterium tuberculosis</I>, 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 the lack of effective identification of those in need of therapy. Case detection is currently the rate-limiting step in TB control.</p>
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<p>The currently widely-used TB detection methods all have their own problems. Nucleic Acid Detection (NAD) is a safer, faster, and more sensitive detection method. However, its shortcoming is critical: the high false-positive rate from non-specific amplification, and the requirement of extremely expensive clumsy instruments; these make NAD not common for TB diagnosis. </p>
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<p>To obviate such shortcoming, Peking iGEM developed a novel detection system, paired dCas9 (PC) reporter, that converts the sequence-specific information of pathogenic bacteria's genome (in our case, <i>M. tuberculosis</i>, MTB) into easily readable signal including bioluminescence, pigment, or electric current. Our PC Reporter was successfully applied to the detection of <span style="color:#00afd1;"><B>real pathogenic <I>M.Tuberculosis</I> H37Rv</B></span> (<b>isolated genomic DNA that is absolutely safe, prepared by our collaborator, not by us</b>). Combined with our work in multiple-marker array (using MTB-specific markers extracted from the entire genome of MTB) and hardware development, our PC reporter system is expected to be a powerful tool in TB diagnosis, with a huge potential for various applications and extensions.</p>
  
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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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                  </div>
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              <h3 class="classic-title"  style="margin-top:50px"><span><a style="color:#00afd1;" href="https://2015.igem.org/Team:Peking/Design/PC_Reporter">Paired dCas9 reporter</a></span></h3>
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              <div style="margin-top:30px; margin-bottom:0">
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                <div class="row">
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                  <div class="col-md-6">
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                    <img style="max-with:400px;" src="https://static.igem.org/mediawiki/2015/4/4e/Peking-Project-Overview1.png">
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                  </div>
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                  <div class="col-md-6">
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                <p> It is well known that CRISPR/dCas9 has a unique ability to be programmed to bind any sequence with the assistance of sgRNA; it was conventionally used for DNA editing or genome study. In our project, however, we integrate split reporters into CRISPR/Cas9 by translationally fusing two fragments of a split reporter to dCas9, respectively, to convert the sequence-specific information of pathogenic bacteria's genome (in our case, <i>M. tuberculosis</i>) into easily readable signal including bioluminescence or pigment. We demonstrated that the PC reporter is highly compatible with NAD-based diagnosis using isolated genomic DNA of MTB.</p>
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                </div>
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              </div>
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            </div>
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            <h3 class="classic-title"  style="margin-top:50px"><span><a style="color:#00afd1;" href="https://2015.igem.org/Team:Peking/Design/PC_Reporter#array">Multi-marker array</a></span></h3>
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              <div style="margin-top:30px; margin-bottom:0">
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                <div class="row">
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                  <div class="col-md-6">
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                    <img style="max-with:400px;" src="https://static.igem.org/mediawiki/2015/9/98/Peking-Project-Overview2.png">
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                  </div>
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                  <div class="col-md-6">
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                <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 sequence information from the entire genome of <i>M. tuberculosis</i>, for our PC Reporter to measure multiple sites on the target genome at one time, thus to improve the reliability of diagnosis. By statistics analysis, we are able to present the readouts in a quantitative way.</p>
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                </div>
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              </div>
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            </div>
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            <h3 class="classic-title"  style="margin-top:50px"><span><a style="color:#00afd1;" href="https://2015.igem.org/Team:Peking/Device">Hardware</a></span></h3>
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            <div style="margin-top:30px; margin-bottom:0">
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                <div class="row">
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                  <div class="col-md-6">
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                    <img style="max-with:400px;" src="https://static.igem.org/mediawiki/2015/0/0f/Peking-Project-Overview3.png">
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                    </div>
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                  <div class="col-md-6">
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                <p>Noticing that most TB cases occur in developing areas, we built an electronic device (despite prototype), which was portable, affordable, and easy to use for local medical workers.</p>
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                </div>
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              </div>
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            </div>
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            <h3 class="classic-title"  style="margin-top:50px"><span><a style="color:#00afd1;" href=""https://2015.igem.org/Team:Peking/Design/Isothermal>Simplified isothermal amplification</a></span></h3>
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            <div style="margin-top:30px; margin-bottom:0">
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                <div class="row">
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                  <div class="col-md-6">
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                    <img style="max-with:400px;" src="https://static.igem.org/mediawiki/2015/2/2c/Peking-Project-Overview4.png">
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                    </div>
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                  <div class="col-md-6">
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                <p>In order to popularize our diagnosis method in developing areas, we invented two novel isothermal amplification methods whose mechanism and operation requirements have been significantly simplified.</p>
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                </div>
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              </div>
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            </div>
  
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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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      <!--FOOTER************FOOTER*******************FOOTER***************FOOTER************-->
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<!--******************************* the only thing to CHANGE is the SHARE LINK******************************-->
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    <footer style="margin-top:30px; padding:0">
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      <div class="container" >
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          <!-- Start Subscribe & Social Links Widget -->
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                            <h4>Share This<span class="head-line"></span></h4>
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Latest revision as of 06:57, 16 November 2015

Peking iGEM 2015

Project

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

Overview

Overview

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 the lack of effective identification of those in need of therapy. Case detection is currently the rate-limiting step in TB control.

The currently widely-used TB detection methods all have their own problems. Nucleic Acid Detection (NAD) is a safer, faster, and more sensitive detection method. However, its shortcoming is critical: the high false-positive rate from non-specific amplification, and the requirement of extremely expensive clumsy instruments; these make NAD not common for TB diagnosis.

To obviate such shortcoming, Peking iGEM developed a novel detection system, paired dCas9 (PC) reporter, that converts the sequence-specific information of pathogenic bacteria's genome (in our case, M. tuberculosis, MTB) into easily readable signal including bioluminescence, pigment, or electric current. Our PC Reporter was successfully applied to the detection of real pathogenic M.Tuberculosis H37Rv (isolated genomic DNA that is absolutely safe, prepared by our collaborator, not by us). Combined with our work in multiple-marker array (using MTB-specific markers extracted from the entire genome of MTB) and hardware development, our PC reporter system is expected to be a powerful tool in TB diagnosis, with a huge potential for various applications and extensions.

Paired dCas9 reporter

It is well known that CRISPR/dCas9 has a unique ability to be programmed to bind any sequence with the assistance of sgRNA; it was conventionally used for DNA editing or genome study. In our project, however, we integrate split reporters into CRISPR/Cas9 by translationally fusing two fragments of a split reporter to dCas9, respectively, to convert the sequence-specific information of pathogenic bacteria's genome (in our case, M. tuberculosis) into easily readable signal including bioluminescence or pigment. We demonstrated that the PC reporter is highly compatible with NAD-based diagnosis using isolated genomic DNA of 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 sequence information from the entire genome of M. tuberculosis, for our PC Reporter to measure multiple sites on the target genome at one time, thus to improve the reliability of diagnosis. By statistics analysis, we are able to present the readouts in a quantitative way.

Hardware

Noticing that most TB cases occur in developing areas, we built an electronic device (despite prototype), which was portable, affordable, and easy to use for local medical workers.

Simplified isothermal amplification

In order to popularize our diagnosis method in developing areas, we invented two novel isothermal amplification methods whose mechanism and operation requirements have been significantly simplified.