Difference between revisions of "Team:CSMU NCHU Taiwan/Parts"

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{{CSMU_NCHU_Taiwan}}
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{{:Team:CSMU_NCHU_Taiwan/Templates/Header}}
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<html lang="en">
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    <link href='https://fonts.googleapis.com/css?family=Arizonia' rel='stylesheet'>
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    <link href='https://fonts.googleapis.com/css?family=Open+Sans' rel='stylesheet'>
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    <title>Safety</title>
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<h1>Parts</h1>
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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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.pdf-container {
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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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<h5>Note</h5>
 
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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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            <h1>Parts</h1>
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            <p>This year, we CSMU_NCHU_Taiwan, brings you 15 new parts consisting of 12 basic parts and 3 composite parts.</p>
  
 +
              <br>
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              <img class="center" src="https://static.igem.org/mediawiki/2017/4/4a/Csmuxnchu_parts1.png" style="width:90%;" alt="">
  
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              <br>
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              <img class="center" src="https://static.igem.org/mediawiki/2017/0/0e/Csmuxnchu_part_form2.png" style="width:90%;" alt="">
  
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<h5>Adding parts to the registry</h5>
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<h2>Basic Parts</h2>
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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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<h3>FOR ANTIDOTE</h3>
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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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<p><br>
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</div>
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<b>MSMEG_5998 (<a href="http://parts.igem.org/Part:BBa_K2382001"style="color:#385e66;" target="_blank">BBa_K2382001</a>)</b><br>
 +
This is an enzyme that could degrade aflatoxin with the aid of coenzyme F420, also called Australian MSMEG_5998 in our project. It belongs to the
 +
F420H2-dependent reductases family from Mycobacterium Smegmatis.<br><br>
 +
<b>F420-Dependent Glucose-6- phosphate Dehydrogenase (<a href="http://parts.igem.org/Part:BBa_K2382002"style="color:#385e66;" target="_blank">BBa_K2382002</a>)</b><br>
 +
The working condition of MSMEG_5998 includes the help from coenzyme F420. F420-dependent
 +
glucose-6- phosphate dehydrogenase (FGD) is the enzyme that reduces the F420 being used by
 +
MSMEG_5998 and make it available again.<br><br>
 +
<b>T7 promoter &amp; Lac operator and RBS from PET-29a (<a href="http://parts.igem.org/Part:BBa_K2382003"style="color:#385e66;" target="_blank">BBa_K2382003</a>)</b><br>
 +
This part originated from pET-29 a (+) Vectors, and it is composed of T7 promoter, Lac operator,
 +
and RBS.<br><br>
 +
<b>Thioredoxin with polylinker(<a href="http://parts.igem.org/Part:BBa_K2382004"style="color:#385e66;" target="_blank">BBa_K2382004</a>)</b><br>
 +
This part previously functioned as a DNA recombination and repair protein in E. coli. It is also
 +
found that Thioredoxin is capable of increasing enzyme activity of our protein, MSMEG5998.
 +
We designed a polylinker that has multiple restriction cutting sites at the end of this part for
 +
future iGEM teams who want to make their protein more effective.<br><br>
 +
<b>Thioredoxin-MSMEG_5998 fusion protein (<a href="http://parts.igem.org/Part:BBa_K2382009" style="color:#385e66;"target="_blank">BBa_K2382009</a>)</b><br>
 +
This is a fusion protein of Thioredoxin (BBa_K2382004) and MSMEG_5998 (BBa_K2382001), also called synthetic MSMEG_5998 in our project. The
 +
ability of degrading aflatoxin is better than MSMEG_5998 alone.<br><br>
 +
<b>Thioredoxin-FGD fusion protein (<a href="http://parts.igem.org/Part:BBa_K2382015" style="color:#385e66;"target="_blank">BBa_K2382015</a>)</b><br>
 +
This is a fusion protein of Thioredoxin (BBa_K2382004) and FGD (BBa_K2382002).
 +
</p>
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<h3>FOR TEST STRIP</h3>
 +
<p><br>
 +
<b>Anti-aflatoxin scFv (with start codon) (<a href="http://parts.igem.org/Part:BBa_K2382007"style="color:#385e66;" target="_blank">BBa_K2382007</a>)</b><br>
 +
This is the single chain variable fragment (scFv) of an antibody that have ability of binding
 +
aflatoxin. This part basically shares the same sequence with BBa_K2382011, except for a start
 +
codon ATG at the beginning.<br><br>
 +
<b>6X His tag (Codon optimized) (<a href="http://parts.igem.org/Part:BBa_K2382008" style="color:#385e66;"target="_blank">BBa_K2382008</a>)</b><br>
 +
This part is a codon optimized 6X His tag for E.coli.<br><br>
 +
<b>Anti-aflatoxin scFv (<a href="http://parts.igem.org/Part:BBa_K2382011" style="color:#385e66;"target="_blank">BBa_K2382011</a>)</b><br>
 +
This is the single chain variable fragment (scFv) of an antibody that have ability of binding
 +
aflatoxin. Since bacteria cannot produce the whole antibody, we decide use scFv to replace it.
 +
It contains two polypeptide chains linked by a GS linker.<br><br>
 +
<b>EAAAK rigid linker (<a href="http://parts.igem.org/Part:BBa_K2382012" style="color:#385e66;"target="_blank">BBa_K2382012</a>)</b><br>
 +
A rigid linker that links two proteins to form one fusion protein. It repeats amino acids EAAAK
 +
three times to maintain distance of two proteins and preventing from interrupting each other
 +
while folding.<br><br>
 +
<b>RFP with EAAAK linker and His Tag (<a href="http://parts.igem.org/Part:BBa_K2382013" style="color:#385e66;"target="_blank">BBa_K2382013</a>)</b><br>
 +
This is a fragment of BBa_K2382010. We designed a restriction site, BamHI, before EAAAK rigid
 +
linker, so future iGEM teams could take advantage of this part to fuse their proteins with RFP as
 +
indicator.<br><br>
  
 +
This is also an improvement of previous BioBrick Part (BBa_E1010). It encodes an RFP that have
 +
the same amino acids as BBa_E1010 and having a His Tag at the end. Therefore, a fusion protein
 +
with this part may have red color and the ability to be purified easily.<br><br>
  
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<b>RFP without barcode (<a href="http://parts.igem.org/Part:BBa_K2382014" style="color:#385e66;"target="_blank">BBa_K2382014</a>)</b><br>
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This part encodes a RFP that has the same amino acids as BBa_E1010. The barcode of
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BBa_E1010 is removed, so this part does not contain stop codon. Therefore, future iGEM teams
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could fuse other protein at the C terminal of this RFP.
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</p>
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<h5>What information do I need to start putting my parts on the Registry?</h5>
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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>
 
<p>
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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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<br>
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<h2>Composite Parts</h2>
 +
<h3>FOR ANTIDOTE</h3>
 +
<p><br>
 +
<b>T7 promoter + Thioredoxin-FGD fusion protein (<a href="http://parts.igem.org/Part:BBa_K2382005" style="color:#385e66;"target="_blank">BBa_K2382005</a>)</b><br>
 +
This part contains a T7 promoter and Thioredoxin-FGD fusion protein, and terminators are
 +
included. By ligating these two different parts as a fusion protein, it is supposed to raise the
 +
solubility of our protein, F420-dependent glucose-6- phosphate dehydrogenase (FGD).<br><br>
 +
<b>T7 promoter + Thioredoxin-MSMEG_5998 fusion protein (<a href="http://parts.igem.org/Part:BBa_K2382006"style="color:#385e66;" target="_blank">BBa_K2382006</a>)</b><br>
 +
This part contains a T7 promoter and Thioredoxin-MSMEG_5998 fusion protein, and terminators
 +
are included. By ligating these two different parts as a fusion protein, it works better than
 +
MSMEG_5998 alone.
 +
</p>
 +
<h3>FOR TEST STRIP</h3>
 +
<p><br>
 +
<b>Anti-aflatoxin scFv fusion protein construction DNA sequence (<a href="http://parts.igem.org/Part:BBa_K2382010"style="color:#385e66;" target="_blank">BBa_K2382010</a>)</b><br>
 +
By ligating the constitutive promoter (BBa_J23101), strong ribosome binding site (BBa_B0034)
 +
and scFv-EAAAK- RFP-Histag, we were able to detect aflatoxin by the purified protein expressing
 +
in E. coli. Moreover, we designed a restriction site, BamHI, between scFv and EAAAK, so future
 +
iGEM teams could take advantage of this composite part to fuse their scFv with RFP as indicator,
 +
and make their own test strip!
 +
</p>
 +
</p>
 
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<h5>Inspiration</h5>
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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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      <img src="https://static.igem.org/mediawiki/2017/5/52/T--CSMU_NCHU_Taiwan--top.png" alt="">
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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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  </body>
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<ul>
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  <script type="text/javascript">
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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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      $('#parts-1').slideToggle("slow");
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<li><a href="https://2014.igem.org/Team:Tokyo_Tech/Parts">2014 Tokyo Tech</a></li>
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    });
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<h5>Part Table </h5>
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<p>Please include a table of all the parts your team has made during your project on this page. Remember part characterization and measurement data must go on your team part pages on the Registry. </p>
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<groupparts>iGEM17 CSMU_NCHU_Taiwan</groupparts>
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Latest revision as of 23:15, 1 November 2017

HOME
Safety

Parts

This year, we CSMU_NCHU_Taiwan, brings you 15 new parts consisting of 12 basic parts and 3 composite parts.



Basic Parts

FOR ANTIDOTE


MSMEG_5998 (BBa_K2382001)
This is an enzyme that could degrade aflatoxin with the aid of coenzyme F420, also called Australian MSMEG_5998 in our project. It belongs to the F420H2-dependent reductases family from Mycobacterium Smegmatis.

F420-Dependent Glucose-6- phosphate Dehydrogenase (BBa_K2382002)
The working condition of MSMEG_5998 includes the help from coenzyme F420. F420-dependent glucose-6- phosphate dehydrogenase (FGD) is the enzyme that reduces the F420 being used by MSMEG_5998 and make it available again.

T7 promoter & Lac operator and RBS from PET-29a (BBa_K2382003)
This part originated from pET-29 a (+) Vectors, and it is composed of T7 promoter, Lac operator, and RBS.

Thioredoxin with polylinker(BBa_K2382004)
This part previously functioned as a DNA recombination and repair protein in E. coli. It is also found that Thioredoxin is capable of increasing enzyme activity of our protein, MSMEG5998. We designed a polylinker that has multiple restriction cutting sites at the end of this part for future iGEM teams who want to make their protein more effective.

Thioredoxin-MSMEG_5998 fusion protein (BBa_K2382009)
This is a fusion protein of Thioredoxin (BBa_K2382004) and MSMEG_5998 (BBa_K2382001), also called synthetic MSMEG_5998 in our project. The ability of degrading aflatoxin is better than MSMEG_5998 alone.

Thioredoxin-FGD fusion protein (BBa_K2382015)
This is a fusion protein of Thioredoxin (BBa_K2382004) and FGD (BBa_K2382002).

FOR TEST STRIP


Anti-aflatoxin scFv (with start codon) (BBa_K2382007)
This is the single chain variable fragment (scFv) of an antibody that have ability of binding aflatoxin. This part basically shares the same sequence with BBa_K2382011, except for a start codon ATG at the beginning.

6X His tag (Codon optimized) (BBa_K2382008)
This part is a codon optimized 6X His tag for E.coli.

Anti-aflatoxin scFv (BBa_K2382011)
This is the single chain variable fragment (scFv) of an antibody that have ability of binding aflatoxin. Since bacteria cannot produce the whole antibody, we decide use scFv to replace it. It contains two polypeptide chains linked by a GS linker.

EAAAK rigid linker (BBa_K2382012)
A rigid linker that links two proteins to form one fusion protein. It repeats amino acids EAAAK three times to maintain distance of two proteins and preventing from interrupting each other while folding.

RFP with EAAAK linker and His Tag (BBa_K2382013)
This is a fragment of BBa_K2382010. We designed a restriction site, BamHI, before EAAAK rigid linker, so future iGEM teams could take advantage of this part to fuse their proteins with RFP as indicator.

This is also an improvement of previous BioBrick Part (BBa_E1010). It encodes an RFP that have the same amino acids as BBa_E1010 and having a His Tag at the end. Therefore, a fusion protein with this part may have red color and the ability to be purified easily.

RFP without barcode (BBa_K2382014)
This part encodes a RFP that has the same amino acids as BBa_E1010. The barcode of BBa_E1010 is removed, so this part does not contain stop codon. Therefore, future iGEM teams could fuse other protein at the C terminal of this RFP.


Composite Parts

FOR ANTIDOTE


T7 promoter + Thioredoxin-FGD fusion protein (BBa_K2382005)
This part contains a T7 promoter and Thioredoxin-FGD fusion protein, and terminators are included. By ligating these two different parts as a fusion protein, it is supposed to raise the solubility of our protein, F420-dependent glucose-6- phosphate dehydrogenase (FGD).

T7 promoter + Thioredoxin-MSMEG_5998 fusion protein (BBa_K2382006)
This part contains a T7 promoter and Thioredoxin-MSMEG_5998 fusion protein, and terminators are included. By ligating these two different parts as a fusion protein, it works better than MSMEG_5998 alone.

FOR TEST STRIP


Anti-aflatoxin scFv fusion protein construction DNA sequence (BBa_K2382010)
By ligating the constitutive promoter (BBa_J23101), strong ribosome binding site (BBa_B0034) and scFv-EAAAK- RFP-Histag, we were able to detect aflatoxin by the purified protein expressing in E. coli. Moreover, we designed a restriction site, BamHI, between scFv and EAAAK, so future iGEM teams could take advantage of this composite part to fuse their scFv with RFP as indicator, and make their own test strip!