Difference between revisions of "Team:Mingdao/Collaborations"

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<h2> Collaborations</h2>
 
  
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Sharing and collaboration are core values of iGEM. We encourage you to reach out and work with other teams on difficult problems that you can more easily solve together.
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<h4> Which other teams can we work with? </h4>
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You can work with any other team in the competition, including software, hardware, high school and other tracks. You can also work with non-iGEM research groups, but they do not count towards the <a hreef="https://2015.igem.org/Judging/Awards#Medals">iGEM team collaboration gold medal criterion</a>.
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In order to meet the gold medal criteria on helping another team, you must complete this page and detail the nature of your collaboration with another iGEM team.
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Here are some suggestions for projects you could work on with other teams:
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        <a class="anchor_item colelem" id="collaboration"></a>
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        <a class="anchor_item colelem" id="data-mining"></a>
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<li> Improve the function of another team's BioBrick Part or Device</li>
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<li> Characterize another team's part </li>
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          <img class="grpelem" id="u4044-4" alt="Data mining" width="266" height="48" src="images/u4044-4.png"/><!-- rasterized frame -->
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<li> Debug a construct </li>
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<li> Model or simulating another team's system </li>
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          <p>*</p>
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<li> Test another team's software</li>
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<li> Help build and test another team's hardware project</li>
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<li> Mentor a high-school team</li>
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          <p>*</p>
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        <p>After understanding of protein composition required for fire retardant effectiveness, we would like to find a novel protein candiate with fire retardant properties. We decided to use protein data mining approach in bioinformatics for our purpose.</p>
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        <p>&nbsp;</p>
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        <p>We contacted&nbsp; and asked iGEM team, NCTU&#45;Formosa for collaboration with data mining and programming. Chao&#45;Di Chang, who is an advisor of team <a class="nonblock" href="https://2014.igem.org/Team:NCTU_Formosa/team">NCTU&#45;Formosa</a>&nbsp;in 2014, taught us a lot in the field of bioinformatics and protein databases such as NCBI, UniProtKB and dbPTM. The super advisor, Prof. Wen&#45;Liang Chen gave us many great advices and shared experiences in the previous iGEM projects and Jamboree.</p>
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        <p>&nbsp;</p>
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        <p>This year, the members of NCTU&#45;Formosa helped us finding out the fire retardant target in the protein data bank. And Yi&#45;Ru Liu of team Mingdao wrote a programming code (see here) and NCTU&#45;Formosa gave us a lot of comments on the code. With the thanks of NCTU&#45;Formosa, we found the ideal target with high serine and arginine contents in protein composition from Uniprot database (see the result).</p>
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      <p>*</p>
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      <p>*</p>
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    <p>We’ve created BioBricks of SR/pSB1C3 (<a class="nonblock" href="http://parts.igem.org/Part:BBa_K1608000">BBa_K1608000</a>), SRPK/pSB1C3 (<a class="nonblock" href="http://parts.igem.org/Part:BBa_K1608001">BBa_K1608001</a>) and cloned the genes to the commercial expression vectors, i.e., SR/pGEX&#45;2T and SRPK/pET&#45;29b.</p>
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    <p>Credit: <a class="nonblock" href="https://2012.igem.org/Team:Uppsala_University/Chromoproteins">iGEM Team Uppsala 2012</a></p>
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    <div class="clearfix colelem" id="u4090-34"><!-- content -->
 +
    <p>In order to test the expression system, we request some BioBricks carrying the genes (amajLime, <a class="nonblock" href="http://parts.igem.org/Part:BBa_K1033915">BBa_K1033915</a>; asPink, <a class="nonblock" href="http://parts.igem.org/wiki/index.php/Part:BBa_K1033933">BBa_K1033933</a>; eforRed, <a class="nonblock" href="http://parts.igem.org/Part:BBa_K592012">BBa_K592012</a>&nbsp;tsPurple, <a class="nonblock" href="http://parts.igem.org/Part:BBa_K1033905">BBa_K1033905</a>) of chromoproteins from iGEM Team <a class="nonblock" href="https://2015.igem.org/Team:Uppsala">Uppsala</a>. The work was done in 2012.</p>
 +
    <p>We transferred the parts to pGEX&#45;2T followed by transforming E. coli BL21. Color proteins seen by naked eyes are the indicator of success of protein induction and expreesion system. In addition to validation of BioBricks created previously, it also can be used to optimize the condition of protein induction system.</p>
 +
    <p>&nbsp;</p>
 +
    <p>The experiment procedure was described briefly as follows:</p>
 +
    <p>↓ Culture E. coli BL21 O/N, which carry indicated BioBricks from the stocks at &#45;80°C.</p>
 +
    <p>&nbsp;↓ Dilute 100X in the fresh media (LB with 100 ug/ml Ampicillin) for 2 hr</p>
 +
    <p>↓ Till OD600 = 06~1.0, 1mM IPTG was added and incubate for 4~5 hr at 37°C</p>
 +
    <p>↓ Transfer 1 ml of bacteria and centrifuge for 1.5 min</p>
 +
    <p>↓ Observe color expression</p>
 +
    </div>
 +
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 +
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 +
    </div>
 +
    <div class="clearfix colelem" id="u4097-16"><!-- content -->
 +
    <p>The expression of color genes after IPTG induction in pGEX&#45;2T system. Left ot right: amajLime (<a class="nonblock" href="http://parts.igem.org/Part:BBa_K1033915">BBa_K1033915</a>), asPink (<a class="nonblock" href="http://parts.igem.org/wiki/index.php/Part:BBa_K1033933">BBa_K1033933</a>), eforRed ( <a class="nonblock" href="http://parts.igem.org/Part:BBa_K592012">BBa_K592012</a>), tsPurple (<a class="nonblock" href="http://parts.igem.org/Part:BBa_K1033905">BBa_K1033905</a>), BL21 (pGEX&#45;2T empty vector)</p>
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Revision as of 13:30, 16 September 2015

Collaboration

Collaboration
Data mining

*

*

After understanding of protein composition required for fire retardant effectiveness, we would like to find a novel protein candiate with fire retardant properties. We decided to use protein data mining approach in bioinformatics for our purpose.

 

We contacted  and asked iGEM team, NCTU-Formosa for collaboration with data mining and programming. Chao-Di Chang, who is an advisor of team NCTU-Formosa in 2014, taught us a lot in the field of bioinformatics and protein databases such as NCBI, UniProtKB and dbPTM. The super advisor, Prof. Wen-Liang Chen gave us many great advices and shared experiences in the previous iGEM projects and Jamboree.

 

This year, the members of NCTU-Formosa helped us finding out the fire retardant target in the protein data bank. And Yi-Ru Liu of team Mingdao wrote a programming code (see here) and NCTU-Formosa gave us a lot of comments on the code. With the thanks of NCTU-Formosa, we found the ideal target with high serine and arginine contents in protein composition from Uniprot database (see the result).

Code data for data mining of fire retardant protein
BioBrick parts validation

*

*

We’ve created BioBricks of SR/pSB1C3 (BBa_K1608000), SRPK/pSB1C3 (BBa_K1608001) and cloned the genes to the commercial expression vectors, i.e., SR/pGEX-2T and SRPK/pET-29b.

In order to test the expression system, we request some BioBricks carrying the genes (amajLime, BBa_K1033915; asPink, BBa_K1033933; eforRed, BBa_K592012 tsPurple, BBa_K1033905) of chromoproteins from iGEM Team Uppsala. The work was done in 2012.

We transferred the parts to pGEX-2T followed by transforming E. coli BL21. Color proteins seen by naked eyes are the indicator of success of protein induction and expreesion system. In addition to validation of BioBricks created previously, it also can be used to optimize the condition of protein induction system.

 

The experiment procedure was described briefly as follows:

↓ Culture E. coli BL21 O/N, which carry indicated BioBricks from the stocks at -80°C.

 ↓ Dilute 100X in the fresh media (LB with 100 ug/ml Ampicillin) for 2 hr

↓ Till OD600 = 06~1.0, 1mM IPTG was added and incubate for 4~5 hr at 37°C

↓ Transfer 1 ml of bacteria and centrifuge for 1.5 min

↓ Observe color expression

The expression of color genes after IPTG induction in pGEX-2T system. Left ot right: amajLime (BBa_K1033915), asPink (BBa_K1033933), eforRed ( BBa_K592012), tsPurple (BBa_K1033905), BL21 (pGEX-2T empty vector)