Difference between revisions of "Team:Washington/Parts"

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<h2> Part Documentation</h2>
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    <div id="menuContainer">
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        <!-- This list is your menu, every list item is a menu button and nested listed become submenu buttons -->
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        <ul>
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            <a href="https://2015.igem.org/Team:Washington">
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                <li>Home
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                  <ul>
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                    <li><a href="https://2014.igem.org/Team:Washington">UW 2014</a></li>
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                    <li><a href="https://2013.igem.org/Team:Washington">UW 2013</a></li>
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                    <li><a href="https://2012.igem.org/Team:Washington">UW 2012</a></li>
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                    <li><a href="https://2011.igem.org/Team:Washington">UW 2011</a></li>
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                    <li><a href="https://2010.igem.org/Team:Washington">UW 2010</a></li>
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                    <li><a href="https://2009.igem.org/Team:Washington">UW 2009</a></li>
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                    <li><a href="https://2008.igem.org/Team:University_of_Washington">UW 2008</a></li>
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                    <li><a href="https://2013.igem.org/Main_Page">iGEM Homepage</a></li>
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                  </ul>
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</li>
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            </a>
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            <a href="https://2015.igem.org/Team:Washington/Auxin">
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                <li>Auxin
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                    <div class="collapse navbar-collapse" id="bs-example-navbar-collapse-1">
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                        <ul class="nav navbar-nav">
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                            <li>
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                                <a href="https://2015.igem.org/Team:Washington/Auxin#Introduction">Introduction</a>
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                            </li>
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                            <li>
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                                <a href="https://2015.igem.org/Team:Washington/Auxin#Methods">Methods</a>
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                            </li>
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                            <li>
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                                <a href="https://2015.igem.org/Team:Washington/Auxin#Results">Results</a>
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                            </li>
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                            <li>
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                                <a href="https://2015.igem.org/Team:Washington/Auxin#Conclusion">Conclusion</a>
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                            </li>
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                            <li>
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                                <a href="https://2015.igem.org/Team:Washington/Auxin#Biobrick">Biobrick</a>
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                            </li>
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                        </ul>
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                    </div>
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                </li>
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            </a>
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            <a href="https://2015.igem.org/Team:Washington/Aptazyme">
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                <li>Aptazyme
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                    <ul>
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                            <li>
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                                <a href="https://2015.igem.org/Team:Washington/Aptazyme#Introduction">Introduction</a>
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                            </li>
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                            <li>
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                                <a href="https://2015.igem.org/Team:Washington/Aptazyme#Methods">Methods</a>
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                            </li>
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                            <li>
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                                <a href="https://2015.igem.org/Team:Washington/Aptazyme#Results">Results</a>
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                            </li>
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                            <li>
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                                <a href="https://2015.igem.org/Team:Washington/Aptazyme#Conclusion">Conclusion</a>
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                            </li>
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                            <li>
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                                <a href="https://2015.igem.org/Team:Washington/Aptazyme#Biobrick">Biobrick</a>
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                            </li>
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                    </ul>
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                </li>
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            </a>
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            <a href="https://2015.igem.org/Team:Washington/Paper_Device">
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                <li>Paper Device             
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                    <ul>
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                        <li>
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                            <a href="https://2015.igem.org/Team:Washington/Paper_Device#Introduction">Introduction</a>
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                        </li>
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                        <li>
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                            <a href="https://2015.igem.org/Team:Washington/Paper_Device#Methods">Methods</a>
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                        </li>
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                            <li>
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                                <a href="https://2015.igem.org/Team:Washington/Design">Design</a>
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                            </li>
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                            <li>
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                                <a href="https://2015.igem.org/Team:Washington/Paper_Device#Results">Results</a>
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                            </li>
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                            <li>
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                                <a href="https://2015.igem.org/Team:Washington/Paper_Device#Conclusion">Conclusion</a>
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                            </li>
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                    </ul>
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                </li>
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            </a>
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            <a href="https://2015.igem.org/Team:Washington/Modeling">
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                <li>Modeling             
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                    <ul>
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                        <li>
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                            <a href="https://2015.igem.org/Team:Washington/Modeling#Paper_Device">Paper Device</a>
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                        </li>
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                        <li>
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                            <a href="https://2015.igem.org/Team:Washington/Modeling#Aptamer">Aptamer</a>
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                        </li>
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                    </ul>
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                </li>
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            </a>
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            <a href="https://2015.igem.org/Team:Washington/Practices">
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                <li>Human Practices             
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                    <ul>
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                        <li>
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                            <a href="https://2015.igem.org/Team:Washington/Practices#Outreach">Outreach</a>
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                        </li>
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                        <li>
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                            <a href="https://2015.igem.org/Team:Washington/Practices#Integrated">Integrated</a>
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                        </li>
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                    </ul>
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                </li>
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            </a>
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            <a href="https://2015.igem.org/Team:Washington/Protocols">
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                <li>Protocols
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                    <ul>
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                        <li>
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                            <a href="https://2015.igem.org/Team:Washington/Protocols#Experiments">Experiments</a>
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                        </li>
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                        <li>
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                            <a href="https://2015.igem.org/Team:Washington/Protocols#Safety">Safety</a>
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                        </li>
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                    </ul>
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                </li>
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            </a>
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            <a href="https://2015.igem.org/Team:Washington/Team">
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                <li>Team                       
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                    <ul>
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                        <li>
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                            <a href="https://2015.igem.org/Team:Washington/Team#Members">Members</a>
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                        </li>
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                        <li>
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                            <a href="https://2015.igem.org/Team:Washington/Team#Attributions">Attributions</a>
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                        </li>
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                        <li>
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                            <a href="https://2015.igem.org/Team:Washington/Team#Sponsors">Sponsors</a>
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                        </li>
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                        <li>
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                            <a href="https://2015.igem.org/Team:Washington/Team#Judging_Form">Judging Form</a>
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                        </li>
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                    </ul>
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                </li>
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            </a>
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        </ul>
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    </div>
  
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<p>Each team will make new parts during iGEM and will submit them to the Registry of Standard Biological Parts. The iGEM software provides an easy way to present the parts your team has created. The <code>&lt;groupparts&gt;</code> tag (see below) will generate a table with all of the parts that your team adds to your team sandbox.</p>
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<p>Remember that the goal of proper part documentation is to describe and define a part, so that it can be used without needing to refer to the primary literature. Registry users in future years should be able to read your documentation and be able to use the part successfully. Also, you should provide proper references to acknowledge previous authors and to provide for users who wish to know more.</p>
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            <div id="Biobrick"> Biobricks </div>
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<h4>Parts in the registry</h4>
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<h4>Note</h4>
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<p>Note that parts must be documented on the <a href="http://parts.igem.org/Main_Page"> Registry</a>. This page serves to <i>showcase</i> the parts you have made. Future teams and other users and are much more likely to find parts by looking in the Registry than by looking at your team wiki.</p>
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<center>
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<groupparts>iGEM015 Washington</groupparts>
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We also have an automatically generated <a href="http://partsregistry.org/cgi/partsdb/pgroup.cgi?pgroup=iGEM2015&group=Washington">Team Parts</a> page.
  
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                    <h2>Auxin</h2>
  
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<p align = "justify"> This part, called AFB2, is an F-box protein that binds the common plant hormone auxin. F-box proteins contain an F-box domain that mediates degradation of other proteins by recognizing substrates for ubiquitination. </p>
  
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<h4>Adding parts to the registry</h4>
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<p align = "justify"> In our system, a dCas9-degron-repressor complex represses expression of lacZ. In the presence of auxin, the F-box protein and the presence of auxin, the AFB2 binds to auxin and auxin also binds to a degron; the F-box protein then recruits the ubiquitin ligase to degrade the dCas9-degron-repressor complex. When this occurs, lacZ is no longer repressed and production of beta galactosidase occurs. Beta galactosidase acts as a reporter for the presence of auxin. </p>
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<p>You can add parts to the Registry at our <a href="http://parts.igem.org/Add_a_Part_to_the_Registry">Add a Part to the Registry</a> link.</p>
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<p>We encourage teams to start completing documentation for their parts on the Registry as soon as you have it available. The sooner you put up your parts, the better you will remember all the details about your parts. Remember, you don't need to send us the DNA sample before you create an entry for a part on the Registry. (However, you <b>do</b> need to send us the DNA sample before the Jamboree. If you don't send us a DNA sample of a part, that part will not be eligible for awards and medal criteria.)</p>
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      <h2>Apatazyme</h2>
  
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<h4>What information do I need to start putting my parts on the Registry?</h4>
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<h2>yeVenus-TheoA; Coding sequence for enhanced YFP and theophylline-sensative aptazyme</h2>
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<p>The information needed to initially create a part on the Registry is:</p>
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<ul>
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<li>Part Name</li>
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<li>Part type</li>
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<li>Creator</li>
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<li>Sequence</li>
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<li>Short Description (60 characters on what the DNA does)</li>
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<li>Long Description (Longer description of what the DNA does)</li>
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<li>Design considerations</li>
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</ul>
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<p>
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<center><a href="http://parts.igem.org/Part:BBa_K1711001">BBa_K1711001</a></center>
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We encourage you to put up <em>much more</em> information as you gather it over the summer. If you have images, plots, characterization data and other information, please also put it up on the part page. </p>
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<p>The part contains the coding sequence for yeast enhanced yellow fluorescent protein (yeVenus), linked to it is a gene for a theophylline sensitive riboswitch aptazyme. The aptazyme portion of the transcript self-cleaves in the absence of theophylline and no YFP should be produced. The theophylline bound state stabilizes the transcript, which translates to the protein and fluorescence should be observed.</p>
  
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<h2>yeVenus-PEST-TheoA; Coding sequence for destabilized YFP Venus and theophylline-sensitive aptazyme</h2>
  
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<center><a href="http://parts.igem.org/Part:BBa_K1711002">BBa_K1711002</a></center>
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<p>This part, yeVenus-PEST-TheoA, contains the coding sequence for a hybrid protein made of yeast enhanced yellow fluorescent protein (yeVenus) fused in frame with the CDS of the PEST-rich 178 c-terminal residues of Cln2, which targets the protein for ubiquitin dependent degradation. These coding sequences are fused with a gene for a theophylline sensitive riboswitch aptazyme. The aptazyme portion of the transcript self-cleaves in the absence of theophylline and no YFP should be produced. The theophylline bound state stabilizes the transcript, which translates to the protein and fluorescence should be observed.</p>
  
  
  
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<h4>Inspiration</h4>
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<p>We have a created  a <a href="http://parts.igem.org/Well_Documented_Parts">collection of well documented parts</a> that can help you get started.</p>
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<p> You can also take a look at how other teams have documented their parts in their wiki:</p>
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<ul>
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<li><a href="https://2014.igem.org/Team:MIT/Parts"> 2014 MIT </a></li>
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<li><a href="https://2014.igem.org/Team:Heidelberg/Parts"> 2014 Heidelberg</a></li>
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<li><a href="https://2014.igem.org/Team:Tokyo_Tech/Parts">2014 Tokyo Tech</a></li>
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</ul>
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<h4>Part Table </h4>
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<groupparts>iGEM015 Example</groupparts>
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Latest revision as of 03:37, 19 September 2015



Biobricks

Parts in the registry

<groupparts>iGEM015 Washington</groupparts>

We also have an automatically generated Team Parts page.

Auxin

This part, called AFB2, is an F-box protein that binds the common plant hormone auxin. F-box proteins contain an F-box domain that mediates degradation of other proteins by recognizing substrates for ubiquitination.

In our system, a dCas9-degron-repressor complex represses expression of lacZ. In the presence of auxin, the F-box protein and the presence of auxin, the AFB2 binds to auxin and auxin also binds to a degron; the F-box protein then recruits the ubiquitin ligase to degrade the dCas9-degron-repressor complex. When this occurs, lacZ is no longer repressed and production of beta galactosidase occurs. Beta galactosidase acts as a reporter for the presence of auxin.

Apatazyme

yeVenus-TheoA; Coding sequence for enhanced YFP and theophylline-sensative aptazyme

BBa_K1711001

The part contains the coding sequence for yeast enhanced yellow fluorescent protein (yeVenus), linked to it is a gene for a theophylline sensitive riboswitch aptazyme. The aptazyme portion of the transcript self-cleaves in the absence of theophylline and no YFP should be produced. The theophylline bound state stabilizes the transcript, which translates to the protein and fluorescence should be observed.

yeVenus-PEST-TheoA; Coding sequence for destabilized YFP Venus and theophylline-sensitive aptazyme

BBa_K1711002

This part, yeVenus-PEST-TheoA, contains the coding sequence for a hybrid protein made of yeast enhanced yellow fluorescent protein (yeVenus) fused in frame with the CDS of the PEST-rich 178 c-terminal residues of Cln2, which targets the protein for ubiquitin dependent degradation. These coding sequences are fused with a gene for a theophylline sensitive riboswitch aptazyme. The aptazyme portion of the transcript self-cleaves in the absence of theophylline and no YFP should be produced. The theophylline bound state stabilizes the transcript, which translates to the protein and fluorescence should be observed.