Difference between revisions of "Team:Fudan/Parts"

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<h2> Part Documentation</h2>
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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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PARTS
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<p>In order to fulfill our experiments and testing our device, we built dozens of biobricks. We devoted a lot to these vectors, and these vector works well in our project. However, our project is such a pioneer work that we have to explore different approaches to solve our problem. As a result, our vectors may combine diversified origin, which makes them really hard to be modified to the standard RFC. Though we works really hard these week, we cannot finish all the site-mutation work, especially those big long parts. Till now, we have modified half of our parts to the RFC10, which is still a large collection. </p>
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<p>Here is the list of parts that works well in our projects!</p>
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<p>All of our parts to build the “Ouroboros"are all proved to be working as expected, as the testing experiment. (For more information about our experiments, please check our <a href="https://2015.igem.org/Team:Fudan/Results">results</a> and <a href="https://2015.igem.org/Team:Fudan/Notebook">notebook</a> pages!) The testing of ouroboros is based on the complete part of cyclizing device（<a href="https://2015.igem.org/Team:Fudan/Notebook">BBa_K1777016</a>）, which is constructed based on many basic parts(<a href="http://parts.igem.org/Part:BBa_ K1777006">BBa_K1777006</a>, <a href="http://parts.igem.org/Part:BBa_ K1777001">BBa_K1777001</a>,  <a href="http://parts.igem.org/Part:BBa_ K1777002">BBa_K1777002</a>, <a href="http://parts.igem.org/Part:BBa_ K1777003">BBa_K1777003</a>, <a href="http://parts.igem.org/Part:BBa_ K1777015">BBa_K1777015</a>.</p>
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<p>Our mir-21 reporter also work as expected, which validate our design of mir-21 binding sites(<a href="http://parts.igem.org/Part:BBa_ K1777000">BBa_K1777000)</a>. (see our <a href="https://2015.igem.org/Team:Fudan/Design">design</a> page)</p>
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<p>We also use our cyclizing device to simulate the prototype in research program, in which we measured the half-life time of circRNA generated by our device(<a href="http://parts.igem.org/Part:BBa_ K1777015">BBa_K1777015</a>). (see our <a href="https://2015.igem.org/Team:Fudan/Results">results</a> page)</p>
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<p>We also improved several parts, and design several parts based on the idea of other parts. For more information, please see our <a href="https://2015.igem.org/Team:Fudan/Description">Description</a> page.<br />
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<p>We develop several linker based on former linker(BBa_K1486003). For part <a href="http://parts.igem.org/Part:BBa_ K1777017">BBa_K1777017</a>，We have optimized the codon for mammalian, and we insert a NLS to promote locating in cell nucleus. Besides ,we lengthen this linker to provide better separation of two domains. At last we avoid tandem repeat sequence(like GGGSPKKKRKVGGGS), which will facilitate fusing this linker to your domains via overlap PCR. (Part <a href="http://parts.igem.org/Part:BBa_ K1777005">BBa_K1777005</a>, <a href="http://parts.igem.org/Part:BBa_ K1777018">BBa_K1777018</a> are also designed based on similar consideration)</p>
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<p>Apart from that, we use beta-globin intron to provide SA and SD sequence in our circular RNA device(<a href="http://parts.igem.org/Part:BBa_ K1777001">BBa_K1777001</a>, <a href="http://parts.igem.org/Part:BBa_ K1777002">BBa_K1777002</a>, <a href="http://parts.igem.org/Part:BBa_ K1777003">BBa_K1777003</a>), which is inspired by the beta-globin intron parts（<a href="http://parts.igem.org/Part:BBa_ K404119">BBa_K404119</a>）. Beta-globin intron provides long flanking intron for circularizing exon and can increase the expression level. We use this character of Beta-globin intron to improve our circRNA expression level.</p>
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<p>Apart from all the parts listed above, we have acRNA biobricks and a dozen of cyclizing protein biobrick.( BBa_K1777008, BBa_K1777009, BBa_K1777010, BBa_K1777011, BBa_K1777012, BBa_K1777013, BBa_K1777014,  BBa_K1777004, BBa_K1777005, BBa_K1777017 )</p>
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</div>
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<div id="right_row">
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<div id="footer">
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<ul>
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<li><a href="https://2015.igem.org/Team:Fudan">Fudan HOME</a></li>
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<li><a href="https://2015.igem.org/Team:Fudan/Achievement">ACHIEVEMENT</a> | <a href="https://2015.igem.org/Team:Fudan/Design">DESIGN</a> | <a href="https://2015.igem.org/Team:Fudan/Parts">PARTS</a> | <a href="https://2015.igem.org/Team:Fudan/Result">RESULT</a></li>
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<li><a href="https://2015.igem.org/Team:Fudan/Attributions">ATTRIBUTION</a> | <a href="https://2015.igem.org/Team:Fudan/Practices">PRACTICE</a> | <a href="https://2015.igem.org/Team:Fudan/Collaborations">COLLABORATION</a> | <a href="https://2015.igem.org/Team:Fudan/Notebook">NOTEBOOK</a></li>
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<li><CONTACT US: bertalanffy@163.com</li>
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</ul>
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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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<h4>Adding parts to the registry</h4>
 
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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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<h4>What information do I need to start putting my parts on the Registry?</h4>
 
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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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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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<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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<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 03:24, 19 September 2015



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Parts
PARTS

In order to fulfill our experiments and testing our device, we built dozens of biobricks. We devoted a lot to these vectors, and these vector works well in our project. However, our project is such a pioneer work that we have to explore different approaches to solve our problem. As a result, our vectors may combine diversified origin, which makes them really hard to be modified to the standard RFC. Though we works really hard these week, we cannot finish all the site-mutation work, especially those big long parts. Till now, we have modified half of our parts to the RFC10, which is still a large collection.

Here is the list of parts that works well in our projects!

All of our parts to build the “Ouroboros"are all proved to be working as expected, as the testing experiment. (For more information about our experiments, please check our results and notebook pages!) The testing of ouroboros is based on the complete part of cyclizing device（BBa_K1777016）, which is constructed based on many basic parts(BBa_K1777006, BBa_K1777001, BBa_K1777002, BBa_K1777003, BBa_K1777015.

Our mir-21 reporter also work as expected, which validate our design of mir-21 binding sites(BBa_K1777000). (see our design page)

We also use our cyclizing device to simulate the prototype in research program, in which we measured the half-life time of circRNA generated by our device(BBa_K1777015). (see our results page)

We also improved several parts, and design several parts based on the idea of other parts. For more information, please see our Description page.

We develop several linker based on former linker(BBa_K1486003). For part BBa_K1777017，We have optimized the codon for mammalian, and we insert a NLS to promote locating in cell nucleus. Besides ,we lengthen this linker to provide better separation of two domains. At last we avoid tandem repeat sequence(like GGGSPKKKRKVGGGS), which will facilitate fusing this linker to your domains via overlap PCR. (Part BBa_K1777005, BBa_K1777018 are also designed based on similar consideration)

Apart from that, we use beta-globin intron to provide SA and SD sequence in our circular RNA device(BBa_K1777001, BBa_K1777002, BBa_K1777003), which is inspired by the beta-globin intron parts（BBa_K404119）. Beta-globin intron provides long flanking intron for circularizing exon and can increase the expression level. We use this character of Beta-globin intron to improve our circRNA expression level.

Apart from all the parts listed above, we have acRNA biobricks and a dozen of cyclizing protein biobrick.( BBa_K1777008, BBa_K1777009, BBa_K1777010, BBa_K1777011, BBa_K1777012, BBa_K1777013, BBa_K1777014, BBa_K1777004, BBa_K1777005, BBa_K1777017 )