Team:TCU Taiwan/Parts

From 2014.igem.org

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<li><a href="#" style="cursor:default"><font size="5">Team</font></a>
<li><a href="#" style="cursor:default"><font size="5">Team</font></a>
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       <li><a href="https://2014.igem.org/Team:TCU_Taiwan/Team"><font size="3">Team Members</font></a></li>
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       <li><a href="https://2014.igem.org/Team:TCU_Taiwan/Team"><font size="3">Members</font></a></li>
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      <li><a href="https://2014.igem.org/Team:TCU_Taiwan/Achievements"><font size="3">Achievements</font></a></li>
       <li><a href="https://igem.org/Team.cgi?id=1473" target="_blank"><font size="3">Official Team Profile</font></a></li>
       <li><a href="https://igem.org/Team.cgi?id=1473" target="_blank"><font size="3">Official Team Profile</font></a></li>
       <li><a href="https://2014.igem.org/Team:TCU_Taiwan/Contact"><font size="3">Contact</font></a></li>
       <li><a href="https://2014.igem.org/Team:TCU_Taiwan/Contact"><font size="3">Contact</font></a></li>
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   <li><a href="#" style="cursor:default"><font size="5" style="color:#DBAC52">Project</font></a>
   <li><a href="#" style="cursor:default"><font size="5" style="color:#DBAC52">Project</font></a>
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       <li><a href="https://2014.igem.org/Team:TCU_Taiwan/Project"><font size="3">Project</font></a></li>
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       <li><a href="https://2014.igem.org/Team:TCU_Taiwan/Project"><font size="3">Introduction</font></a></li>
       <li><a href="https://2014.igem.org/Team:TCU_Taiwan/Parts" style="color:#DBAC52"><font size="3">Parts</font></a></li>
       <li><a href="https://2014.igem.org/Team:TCU_Taiwan/Parts" style="color:#DBAC52"><font size="3">Parts</font></a></li>
       <li><a href="https://2014.igem.org/Team:TCU_Taiwan/SystemDesign"><font size="3">System Design</font></a></li>
       <li><a href="https://2014.igem.org/Team:TCU_Taiwan/SystemDesign"><font size="3">System Design</font></a></li>
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<img src="https://static.igem.org/mediawiki/2014/c/c1/TCU-Line.png" width="100%"></td></tr>
<img src="https://static.igem.org/mediawiki/2014/c/c1/TCU-Line.png" width="100%"></td></tr>
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<!--Parts Submitted to the Registry  -->
<!--Parts Submitted to the Registry  -->
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   <td  style="background-color:#FFF2B5" height="20px" colspan="2"><font face="Trebuchet MS" size="6" color="#A66B38">Favorite parts</font></td>
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   <td  style="background-color:#FFF2B5" height="20px"><font face="Trebuchet MS" size="6" color="#A66B38">Favorite parts</font></td>
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   <td colspan="3" height="10px">&nbsp;</td>
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   <td colspan="3" height="10px"><img src="https://static.igem.org/mediawiki/2014/b/b8/TCU-Phage.png" width="35px"/><font face="Trebuchet MS" size="5" color="#90B849">BBa_K1473005</font></td>
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   <td height="10px">&nbsp;</td>
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  <td valign="top" rowspan="4" align="center"><div style="width: 520px; padding: 0em">
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<img alt=" change width 586 to 520 & 745 " style="float: left; position: relative; z-index: 2" src="https://static.igem.org/mediawiki/2014/0/0f/TCU_PART_10718959_854093597942524_327155245_o.jpg" onmouseover="this.style.width='745px'" onmouseout="this.style.width='520px'" width="100%"><font size="3" face="Verdana"><strong>Fig.1</strong></font>
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   <td><img src="https://static.igem.org/mediawiki/2014/b/b8/TCU-Phage.png" alt="" width="35px"/><font face="Trebuchet MS" size="5" color="#90B849">BBa_K1473005</font></td>
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  <td valign="top">&nbsp;</td>
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   <td colspan="2" valign="top"><font size="3" face="Verdana" color="#333">Phagemid pBluescript is a  special plasmid, it functions as a normal plasmid when transformed into  bacteria. But when helper phage M13KO7 infect the bacteria, it will produce  progeny M13 phage as vector for pBluescript.&nbsp;<br><br>
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   <td height="10px">&nbsp;</td>
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     pBluescript contains a f1 ori while M13KO7  helper phage&rsquo;s f1 ori has been knock-down. So after the infection of M13KO7,  its genome can produce protein and replicate but these proteins will package  pBluescript as their true &ldquo;genome&rdquo;. As a result, the progeny phage&rsquo;s genome  will only contains pBluescript&rsquo;s MCS, they cannot make next generation.</font></td>
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    <table width="100%" border="0" cellspacing="0" cellpadding="0">
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  <td valign="top" width="40%"><font size="3" face="Verdana" color="#333">Phagemid pBluescript is a  special plasmid, it functions as a normal plasmid when transformed into  bacteria. But when helper phage M13KO7 infect the bacteria, it will produce  phagemid-carrying phages.&nbsp;<br><br>
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        <td align="center"><img src="https://static.igem.org/mediawiki/2014/1/18/TCU_phagemid_POT.jpg" width="40%"></td>
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     pBluescript contains a f1 ori while M13KO7  helper phage&rsquo;s f1 ori has been mutated. So after the infection of M13KO7,  its genome can produce protein and replicate but these proteins will package  pBluescript as &quot;genome&quot;. As a result, the pahemid-carrying phaes will only contain pBluescript, they cannot make next generation.</font></td>
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        <td align="right"><em>Source </em>: XVIVO/Barcroft USA </td>
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   <td colspan="2" align="right"><a href="http://parts.igem.org/wiki/index.php?title=Part:BBa_K1473005" target="_blank"><img src="https://static.igem.org/mediawiki/2014/9/91/TCU-More-box.png" alt="BBa_K1473005" width="100px"></a></td>
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   <td align="right"><a href="http://parts.igem.org/wiki/index.php?title=Part:BBa_K1473005" target="_blank"><img src="https://static.igem.org/mediawiki/2014/9/91/TCU-More-box.png" alt="BBa_K1473005" width="100px"></a></td>
    
    
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   <td colspan="2" height="10px">&nbsp;</td>
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   <td colspan="3" height="1px" style="background-color:#90B849"></td>
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   <td colspan="2" height="1px" style="background-color:#90B849"></td>
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   <td colspan="2" height="10px">&nbsp;</td>
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   <td colspan="3" height="10px"><font face="Trebuchet MS" size="5" color="#0092C7"><img src="https://static.igem.org/mediawiki/2014/c/cc/TCU-Anti.png " alt="" width="30px"/>BBa_K1473009</font></td>
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   <td colspan="2" height="10px"><font face="Trebuchet MS" size="5" color="#0092C7"><img src="https://static.igem.org/mediawiki/2014/c/cc/TCU-Anti.png " alt="" width="30px"/>BBa_K1473009</font></td>
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   <td colspan="2" height="10px">&nbsp;</td>
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   <td colspan="2" valign="top"><font size="3" face="Verdana" color="#333">Here we combined a CRISPR system(BBa_K1218011) with an inducible promoter(BBa_K914003). The CRISPR system contains a tracrRNA , a Cas9 protein and a minimal  
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   <td valign="top"><font size="3" face="Verdana" color="#333">Here we combined a CRISPR system(<a href="http://parts.igem.org/Part:BBa_K1218011" target="_blank">BBa_K1218011</a>) with an inducible promoter(<a href="http://parts.igem.org/Part:BBa_K914003" target="_blank">BBa_K914003</a>). The CRISPR system contains a tracrRNA , a Cas9 protein and a minimal  
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     CRISPR array, it functions to knockout target gene. We give this system an inducible promoter so we can decided when to switch if on or off. </font></td>
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     CRISPR array, it functions to knockout target gene. We give this system an inducible promoter so we can decided when to switch it on or off. </font></td>
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     <td align="center"><table width="100%" border="0" cellspacing="0" cellpadding="0">
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     <td width="45%" align="center"><table width="100%" border="0" cellspacing="0" cellpadding="0">
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         <td align="center"><img src="https://static.igem.org/mediawiki/2014/c/c7/TCU_CRISPR_POT.jpg" alt="" width="30%"></td>
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         <td align="center"><img src="https://static.igem.org/mediawiki/2014/c/c7/TCU_CRISPR_POT.jpg" alt="" width="60%"></td>
       </tr>
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   <td colspan="2" align="right"><a href="http://parts.igem.org/wiki/index.php?title=Part:BBa_K1473009" target="_blank"><img src="https://static.igem.org/mediawiki/2014/9/91/TCU-More-box.png" alt="BBa_K1473009" width="100px"></a></td>
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   <td align="right"><a href="http://parts.igem.org/wiki/index.php?title=Part:BBa_K1473009" target="_blank"><img src="https://static.igem.org/mediawiki/2014/9/91/TCU-More-box.png" alt="BBa_K1473009" width="100px"></a></td>
   <td></td>
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   <td colspan="3" style="background-color:#FFF2B5"><font face="Trebuchet MS" size="6" color="#A66B38">Parts Sandbox</font></td>
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   <td colspan="2" style="background-color:#FFF2B5"><font face="Trebuchet MS" size="6" color="#A66B38">Parts Sandbox</font></td>
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   <td colspan="2" height="10px"><font size="3" face="Verdana" color="#333">Click on the name of the parts for detailed information.</font></td>
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  <td colspan="2" height="10px">&nbsp;</td>
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<table id="Table_2" class="pgrouptable addborder tablesorter" style="width: 925px;" cellpadding="0" cellspacing="0" align="center"><thead><tr><th colspan="1" style="width: .5em" nowrap="" class="header"></th><th colspan="1" style="width: .5em" nowrap="" class="header"></th><th style="width: 7em;" class="header">Name</th><th colspan="" style="padding-right:7px;" class="header">Type</th><th colspan="" style="padding-right:7px;" class="header">Description</th><th colspan="" style="padding-right:7px;" class="header">Designer</th><th colspan="" style="padding-right:7px;" class="header">Length</th><th class="blank_col"></th></tr></thead><tbody>
<table id="Table_2" class="pgrouptable addborder tablesorter" style="width: 925px;" cellpadding="0" cellspacing="0" align="center"><thead><tr><th colspan="1" style="width: .5em" nowrap="" class="header"></th><th colspan="1" style="width: .5em" nowrap="" class="header"></th><th style="width: 7em;" class="header">Name</th><th colspan="" style="padding-right:7px;" class="header">Type</th><th colspan="" style="padding-right:7px;" class="header">Description</th><th colspan="" style="padding-right:7px;" class="header">Designer</th><th colspan="" style="padding-right:7px;" class="header">Length</th><th class="blank_col"></th></tr></thead><tbody>
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<form method="post" action="/cgi/partsdb/pgroup.cgi?pgroup=iGEM2014&amp;group=TCU_Taiwan" enctype="multipart/form-data"></form>
<form method="post" action="/cgi/partsdb/pgroup.cgi?pgroup=iGEM2014&amp;group=TCU_Taiwan" enctype="multipart/form-data"></form>
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<input type="hidden" name="Editing" value="Editing"><input type="hidden" name="part" value="32275"><input type="hidden" name="pgroup" value="iGEM2014"><input type="hidden" name="group" value="TCU_Taiwan"></tr><tr><td class="status_cell cell_white" align="center"><img src="https://static.igem.org/mediawiki/2014/b/b8/TCU-Phage.png" width="250%"/></td><td class="status_cell cell_white">&nbsp;&nbsp;</td><td><a class="noul_link part_link" href="http://parts.igem.org/wiki/index.php?title=Part:BBa_K1473005" target="_blank" style="color:#90B849;">BBa_K1473005</a></td><td>Plasmid_Backbone</td><td>phagemid pBluescript </td><td width="100">Shan, Zhe</td><td align="right">2929</td><td class="blank_col"></td>
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<input type="hidden" name="Editing" value="Editing"><input type="hidden" name="part" value="32275"><input type="hidden" name="pgroup" value="iGEM2014"><input type="hidden" name="group" value="TCU_Taiwan"></tr><tr><td class="status_cell cell_white" align="left"><img src="https://static.igem.org/mediawiki/2014/b/b8/TCU-Phage.png" width="250%"/></td><td class="status_cell cell_white">&nbsp;&nbsp;</td><td><a class="noul_link part_link" href="http://parts.igem.org/wiki/index.php?title=Part:BBa_K1473005" target="_blank" style="color:#90B849;">BBa_K1473005</a></td><td>Plasmid_Backbone</td><td>phagemid pBluescript </td><td width="100">Shan, Zhe</td><td align="right">2929</td><td class="blank_col"></td>
<form method="post" action="/cgi/partsdb/pgroup.cgi?pgroup=iGEM2014&amp;group=TCU_Taiwan" enctype="multipart/form-data"></form>
<form method="post" action="/cgi/partsdb/pgroup.cgi?pgroup=iGEM2014&amp;group=TCU_Taiwan" enctype="multipart/form-data"></form>
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   <td colspan="3" height="10px" align="right"><font size="2" face="Verdana"><a href="http://parts.igem.org/cgi/partsdb/pgroup.cgi?pgroup=iGEM2014&group=TCU_Taiwan" target="_blank" title="Team Parts" style="text-decoration:none;color:#90B849;">TCU_Taiwan 2014 iGEM Team Parts</a></font></td>
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   <td colspan="2" height="10px" align="right"><font size="2" face="Verdana"><a href="http://parts.igem.org/cgi/partsdb/pgroup.cgi?pgroup=iGEM2014&group=TCU_Taiwan" target="_blank" title="Team Parts" style="text-decoration:none;color:#90B849;">TCU_Taiwan 2014 iGEM Team Parts</a></font></td>
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   <td colspan="3" style="background-color:#FFF2B5"><font face="Trebuchet MS" size="6" color="#A66B38">gRNA</font></td>
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   <td colspan="2" style="background-color:#FFF2B5"><font face="Trebuchet MS" size="6" color="#A66B38">gRNA</font></td>
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           <td align="center"><img src="https://static.igem.org/mediawiki/2014/8/8e/TCU_PHAGE_m13_%281%29.jpg" width="90%"></td>
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           <td align="center"><img src="https://static.igem.org/mediawiki/2014/7/7c/TCU_PART_10736069_854704547881429_1390079281_n.jpg" width="100%"></td>
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           <td align="center"><font size="3" face="Verdana"><strong>fig.1</strong></font></td>
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           <td align="center"><font size="3" face="Verdana"><strong>Fig.2</strong></font></td>
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      <td width="1">&nbsp;</td>
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          <td align="center"><img src="https://static.igem.org/mediawiki/2014/b/bf/TCU_SD_10733196_853652871319930_1466704235_o.jpg" width="100%"></td>
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          <td align="center"><font size="3" face="Verdana"><strong>Fig.3</strong></font></td>
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      <td width="15">&nbsp;</td>
 
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      <td>&nbsp;</td>
 
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       <td colspan="3"><font size="3" face="Verdana" color="#333"><p>We put a <em>sac</em>I restriction  cutting site downstream to gRNA (not shown in sequence information) and ligated  it back to pSB1C3 with correct prefix and surfix. Then we cut this recombinant  plasmid with <em>sac</em>I and run gel  electrophoresis for testing. As we can see in this image, because pSB1C3 only  contains 1 <em>sac</em>I cutting site itself,  so it would not be cut into 2 parts when no gRNA is ligated inside. But if  there is, then <em>sac</em>I will cut this  recombinant plasmid into 2 parts, whose lengths are 939 bp and 1159 bp.  Obviously, we have successfully synthesized this gRNA.</p></font></td>
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       <td colspan="3">
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      <p><font color="#333" size="3" face="Verdana">We put a <em>sac</em>I restriction  cutting site downstream to gRNA (not shown in sequence information) and ligated  it back to pSB1C3 with correct prefix and surffix. Then we cut this recombinant  plasmid with <em>sac</em>I and run gel  electrophoresis for checking. As we can see in this image, because pSB1C3 only  contains 1 <em>sac</em>I cutting site itself,  so it would not be cut into 2 parts when no gRNA is ligated inside. But if  there is, then <em>sac</em>I will cut this  recombinant plasmid into 2 parts, whose lengths are 939 bp and 1159 bp.  Obviously, we have successfully synthesized this gRNA.</font></p></td>
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  <td ><h3> Parts Submitted to the Registry </h3></td>
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  <td ><h3>What information do I need to start putting my parts on the Registry? </h3></td>
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  <td width="45%"  valign="top"><p> An important aspect of the iGEM competition is the use and creation of standard  biological parts. Each team will make new parts during iGEM and will submit them to the <a href="http://partsregistry.org"> Registry of Standard Biological Parts</a>. The iGEM software provides an easy way to present the parts your team has created. The "groupparts" tag will generate a table with all of the parts that your team adds to your team sandbox. 
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    <p> <strong>Note that if you want to document a part you need to document it on the <a href="http://partsregistry.org Registry"> Registry</a>, not on your team wiki.</strong> Future teams and other users and are much more likely to find parts on the Registry than on your team wiki. </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 a need 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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    <h3>When should you put parts into the Registry?</h3>
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    <p> As soon as possible! 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 recall you will have of all details surrounding your parts. Remember you don't need to send us the DNA to create an entry for a part on the Registry. However, you must send us the sample/DNA before the Jamboree. Only parts for which you have sent us samples/DNA are eligible for awards and medal requirements. </p></td>
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  <td ></td>
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  <td width="45%" valign="top"><p> The information needed to initially create a part on the Registry is: </p>
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      <li>Part Name</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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    </ol>
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    <p> 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. Check out part <a href="http://parts.igem.org/Part:BBa_K404003">BBa_K404003</a> for an excellent example of a highly characterized part. </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></td>
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   <td colspan="3"  height="15px"></td>
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   <td colspan="3" ><h3> Parts Table</h3></td>
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   <td colspan="2"  style="background-color:#FFF2B5"><font face="Trebuchet MS" size="6" color="#A66B38">Parts Table</font>
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  <p align="right">This table is from the Database of iGEM.</p></td>
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   <td width="45%" colspan="3"  valign="top"> Any parts your team has created will appear in this table below:</td>
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   <td width="45%" colspan="2"  valign="top"><font size="3" face="Verdana" color="#333">Any parts our team has created will appear in this table below:</font></td>
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<groupparts>iGEM013 TCU_Taiwan</groupparts>
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<groupparts>iGEM014 TCU_Taiwan</groupparts>
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Latest revision as of 21:09, 17 October 2014

 
Parts
  
Favorite parts
 
change width 586 to 520 & 745 Fig.1
BBa_K1473005  
   
Phagemid pBluescript is a special plasmid, it functions as a normal plasmid when transformed into bacteria. But when helper phage M13KO7 infect the bacteria, it will produce phagemid-carrying phages. 

pBluescript contains a f1 ori while M13KO7 helper phage’s f1 ori has been mutated. So after the infection of M13KO7, its genome can produce protein and replicate but these proteins will package pBluescript as "genome". As a result, the pahemid-carrying phaes will only contain pBluescript, they cannot make next generation.
BBa_K1473005
 
 
BBa_K1473009
 
Here we combined a CRISPR system(BBa_K1218011) with an inducible promoter(BBa_K914003). The CRISPR system contains a tracrRNA , a Cas9 protein and a minimal CRISPR array, it functions to knockout target gene. We give this system an inducible promoter so we can decided when to switch it on or off.
Source :Science

BBa_K1473009
 
 
 
Parts Sandbox
 
Click on the name of the parts for detailed information.
 
NameTypeDescriptionDesignerLength
  BBa_K1473001DNAgRNA 1 Shan, Zhe22
  BBa_K1473002DNAgRNA 2Shan, Zhe22
  BBa_K1473003DNAgRNA 3Shan, Zhe22
  BBa_K1473004DNAgRNA 4Shan, Zhe22
  BBa_K1473005Plasmid_Backbonephagemid pBluescript Shan, Zhe2929
  BBa_K1473006DNAgRNA for ampR 1Shan, Zhe22
  BBa_K1473007DNAgRNA for ampR 2Shan, Zhe22
  BBa_K1473008DNAgRNA for ampR 3Shan, Zhe22
 BBa_K1473009CodingpRha induced CRISPRShan, Zhe5011
  BBa_K1473010DNAgRNA for ampR 4Shan, Zhe22
  BBa_K1473011DNAgRNA for ampR 5Shan, Zhe22
  BBa_K1473012DNAgRNA for NeoR/kanR 1Shan, Zhe22
  BBa_K1473013DNAgRNA for NeoR/kanR 2Shan, Zhe22
  BBa_K1473014DNAgRNA for NeoR/kanR 3Shan, Zhe22
  BBa_K1473015DNAgRNA for NeoR/kanR 4Shan, Zhe22
  BBa_K1473016DNAgRNA for NeoR/kanR 5Shan, Zhe22
  BBa_K1473017DNAgRNA for tetR 1Shan, Zhe22
  BBa_K1473018DNAgRNA for tetR 2Shan, Zhe22
  BBa_K1473019DNAgRNA for tetR 3Shan, Zhe22
  BBa_K1473020DNAgRNA for tetR 4Shan, Zhe22
  BBa_K1473021DNAgRNA for tetR 5Shan, Zhe22
TCU_Taiwan 2014 iGEM Team Parts
gRNA
 
Fig.2
 
Fig.3

We put a sacI restriction cutting site downstream to gRNA (not shown in sequence information) and ligated it back to pSB1C3 with correct prefix and surffix. Then we cut this recombinant plasmid with sacI and run gel electrophoresis for checking. As we can see in this image, because pSB1C3 only contains 1 sacI cutting site itself, so it would not be cut into 2 parts when no gRNA is ligated inside. But if there is, then sacI will cut this recombinant plasmid into 2 parts, whose lengths are 939 bp and 1159 bp. Obviously, we have successfully synthesized this gRNA.
 
Parts Table

This table is from the Database of iGEM.
Any parts our team has created will appear in this table below:
<groupparts>iGEM014 TCU_Taiwan</groupparts>
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Team Members Project Parts Human Pratics Modeling Safety Notebook Attributions

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