Difference between revisions of "Team:Cambridge-JIC/Description"

 
(114 intermediate revisions by 4 users not shown)
Line 4: Line 4:
 
<body>
 
<body>
  
 +
<style>
 +
.darkWhite:hover
 +
{
 +
color:#fff;
 +
}
  
−
<div class="column full_size judges-will-not-evaluate">
+
.darkBlue:link
−
<h3>★  ALERT! </h3>
+
{
−
<p>This page is used by the judges to evaluate your team for the<a href="https://2016.igem.org/Judging/Medals"> improve a previous part or project gold medal criterion</a>. </p>
+
        color:#000;
−
<p> Delete this box in order to be evaluated for this medal. See more information at <a href="https://2016.igem.org/Judging/Pages_for_Awards/Instructions"> Instructions for Pages for awards</a>.</p>
+
        text-decoration:none;
−
</div>
+
   
 +
}
  
 +
.darkBlue:hover
 +
{
 +
        color:#B7E2F0;
 +
        text-decoration:none;
 +
}
  
−
<div class="column full_size">
+
.darkWhite, .darkBlue{
 +
        color: #000
 +
        font-weight: bold;
 +
        font-size: 100%;
 +
}
  
−
<p>Tell us about your project, describe what moves you and why this is something important for your team.</p>
+
.darkBlue:active
 +
{
 +
        color:##B7E2F0;
 +
        text-decoration:none;
 +
}
  
 +
ol
 +
{
 +
        font-size:130%;
 +
        font-weight:bold;
 +
        font-family: 'Arvo';
 +
        list-style-position: inside;
 +
        text-align:center:
 +
}
  
−
<h5>What should this page contain?</h5>
+
hr
−
<ul>
+
{
−
<li> A clear and concise description of your project.</li>
+
        height: 3px;
−
<li>A detailed explanation of why your team chose to work on this particular project.</li>
+
        color: #B7E2F0;
−
<li>References and sources to document your research.</li>
+
        background-color: #B7E2F0;
−
<li>Use illustrations and other visual resources to explain your project.</li>
+
}
−
</ul>
+
  
 +
</style>
  
−
</div>
+
<section style="background-color:#fff; text-align: center; padding: 10% 0%">
 +
    <div class="container">
 +
    <h1 style="font-family:Open Sans">DESCRIPTION</h1>
 +
    <hr>
 +
    <p style="font-family:Open Sans; font-size:150%;">We have built a toolbox for chloroplast transformation. In our chosen organism Chlamydomonas reinhardtii (Chlamy) we have targeted all the transformation steps and improved each of them. We have built a library of tested parts optimised for Chlamydomonas or related chloroplasts. We built a gene gun which is less than 1/100 of commercial price and an incubator for our cells with many functions. Moreover we modelled the behaviour of transformed systems. Finally we designed a wetlab tool which could help achieve essential homoplasmy (transformation of all copies of chloroplast DNA) in one generation instead of 2-3 months of selection. Our design incorporated numerous discussions about biosafety and our library contains the relevant parts for practical implementation!</p>
 +
    <hr>
 +
    </div>
 +
</section>
  
−
<div class="column full_size" >
+
<section style="background-color:#3d3d3d; text-align: center; padding: 15% 0%">
 +
    <div class="container" style="color:#fff">
 +
    <p class="darkBlue" style="font-family:Open Sans; font-size:180%; text-align:center">Why Chlamydomonas?</p>
 +
    </div>
 +
</section>
 +
 +
<section style="background-color:#fff; text-align: center; padding: 10% 0%">
 +
    <div class="container" style="color:#000">
 +
    <div class="col-md-4">
 +
    <p style="font-family:Open Sans; font-size:150%; text-align:center;">Chlamydomonas, a single-celled alga with only one chloroplast, has its natural advantage over many other single-celled organisms in the lab such as E.coli and yeast. It is a perfect chassis for prototyping plant work in iGEM time scales.</p>
 +
    </div>
 +
    <div class="col-md-4">
 +
    </div>
 +
    <div class="col-md-4" style="margin-right: 0px">
 +
    <hr>
 +
    <p style="font-family:Arvo; font-size: 150%; text-align:right">Unlike E. coli or yeast it does not need extra carbon source such as glucose. This will make a huge difference in an industrial scale.<br><br>The plant cell systems allows post-translational modification such as complex folding and glycosylation.</p>
 +
    <hr>
 +
    </div>
 +
    </div>
 +
</section>
  
−
<h5>Advice on writing your Project Description</h5>
+
<section style="background-color:#3d3d3d; text-align: center; padding: 15% 0%">
 +
    <div class="container" style="color:#fff">
 +
    <p class="darkBlue" style="font-family:Open Sans; font-size:180%; text-align:center">Why Chloroplasts?</p>
 +
    </div>
 +
</section>
  
−
<p>
+
<section style="background-color:#fff; text-align: center; padding: 10% 0%">
−
We encourage you to put up a lot of information and content on your wiki, but we also encourage you to include summaries as much as possible. If you think of the sections in your project description as the sections in a publication, you should try to be consist, accurate and unambiguous in your achievements.
+
    <div class="container" style="color:#000">
−
</p>
+
    <div class="col-md-4">
 +
    <hr>
 +
    <p style="font-family:Open Sans; font-size:150%; text-align:center;">Higher transgene yields than nucleus<br><br>
 +
Allows precise editing because DNA integration occurs almost exclusively through homologous integration in Chlamydomonas chloroplast</p>
 +
    <hr>
 +
    </div>
 +
    <div class="col-md-4">
 +
    </div>
 +
    <div class="col-md-4" style="margin-right: 0px">
 +
    <p style="font-family:Arvo; font-size: 180%; text-align:right">Naturally specialized in synthesis</p>
 +
    </div>
 +
    </div>
 +
</section>
  
−
<p>
+
<section style="background-color:#3d3d3d; text-align: center; padding: 15% 0%">
−
Judges like to read your wiki and know exactly what you have achieved. This is how you should think about these sections; from the point of view of the judge evaluating you at the end of the year.
+
    <div class="container" style="color:#fff">
−
</p>
+
    <p class="darkBlue" style="font-family:Open Sans; font-size:180%; text-align:center">What are the problems?</p>
 +
    </div>
 +
</section>
  
−
</div>
+
<section style="background-color:#fff; text-align: center; padding: 10% 0%">
 +
    <div class="container" style="color:#000">
 +
    <div class="col-md-4">
 +
    <hr>
 +
    <p style="font-family:Open Sans; font-size:150%; text-align:center;">Complex cloning design<br><br>Equipment is expensive and sometimes inaccessible<br><br>More time-consuming than bacteria engineering<br><br>Multiple plastid genomes to transform </p>
 +
    <hr>
 +
    </div>
 +
    <div class="col-md-4">
 +
    </div>
 +
    <div class="col-md-4" style="margin-right: 0px">
 +
    <img src="https://static.igem.org/mediawiki/2016/2/22/T--Cambridge-JIC--description--icon1.png" style="max-width:100%; max-height:100%">
 +
    </div>
 +
    </div>
 +
</section>
  
 +
<section style="background-color:#3d3d3d; text-align: center; padding: 15% 0%">
 +
    <div class="container" style="color:#fff">
 +
    <p class="darkBlue" style="font-family:Open Sans; font-size:180%; text-align:center">Improving Chloroplast Transformation Step by Step</p>
 +
    </div>
 +
</section>
  
−
<div class="column half_size" >
+
<section style="background-color:#fff; text-align: center; padding: 10% 0%">
 +
    <div class="container" style="color:#000">
 +
    <div class="col-md-4">
 +
   
 +
    <a class="darkBlue" href="https://2016.igem.org/Team:Cambridge-JIC/Parts"><h3 style="font-weight:bold; text-align:left">Library of Parts</h3></a>
 +
<hr>
 +
<p style="font-family:Open Sans; font-size:150%; text-align:left;">Our library of parts contains many parts necessary for synthetic biology of chloroplasts. They have been tested by cloning in E. coli, some by shooting into Chlamy and extracting, some even by sequencing. They all were designed with the intention to facilitate bringing our homoplasmy tool into practice.</p>
 +
    <hr>
 +
    </div>
 +
    <div class="col-md-4">
 +
    <p style="font-family:Open Sans; font-size:150%; text-align:left;"><b>Our Improved parts:</b>
 +
    <br><a href="http://parts.igem.org/wiki/index.php?title=Part:BBa_K2148013">BBa_K2148013</a>
 +
    <br>Cas9 is a molecular tool which together with its guide RNA can cut DNA sequences at sequence-specific places. Our Cas9 is codon-optimized for Chlamydomonas reinhardtii chloroplast chassis (likely useable in other chloroplasts). Additionally it has a fusion tag to link reporter genes such as fluorescent proteins. It is fully compatible with the increasingly popular Phytobrick standard.
 +
    </p>
 +
    </div>
 +
    <div class="col-md-4" style="margin-right: 0px">
 +
    <p style="font-family:Open Sans; font-size:150%; text-align:right;">
 +
    <br>
 +
    <a href="http://parts.igem.org/wiki/index.php?title=Part:BBa_K2148009">BBa_K2148009</a>
 +
    <br>GFP is the most classic fluorescent reporter protein with very wide range of usage. Our GFP is again codon-optimised for Chlamydomonas reinhardtii chloroplast. Moreover it is compatible with Phytobrick standard.</p>
 +
    </div>
 +
    </div>
 +
</section>
  
−
<h5>References</h5>
+
<section style="background-color:#3d3d3d; text-align: center; padding: 15% 0%">
−
<p>iGEM teams are encouraged to record references you use during the course of your research. They should be posted somewhere on your wiki so that judges and other visitors can see how you thought about your project and what works inspired you.</p>
+
    <div class="container" style="color:#fff">
 +
    <p class="darkBlue" style="font-family:Open Sans; font-size:180%; text-align:center">Gene Gun</p>
 +
    </div>
 +
</section>
  
−
</div>
+
<section style="background-color:#fff; text-align: center; padding: 10% 0%">
 +
    <div class="container" style="color:#000">
 +
    <div class="col-md-4">
 +
    <hr>
 +
    <p style="font-family:Open Sans; font-size:150%; text-align:center;">Our complete Do-It-Yourself Gene Gun with all necessary documentation is less than one-hundredth of the commercial price! And it has been firing DNA onto samples! </p>
 +
    <hr>
 +
    </div>
 +
    <div class="col-md-4">
 +
    </div>
 +
    <div class="col-md-4" style="margin-right: 0px">
 +
    <a href="https://2016.igem.org/Team:Cambridge-JIC/Biolistics"><img src="https://static.igem.org/mediawiki/2016/4/46/T--Cambridge-JIC--description--icon2.jpg" style="max-width:100%; max-height:100%"></a>
 +
    </div>
 +
    </div>
 +
</section>
  
 +
<section style="background-color:#3d3d3d; text-align: center; padding: 15% 0%">
 +
    <div class="container" style="color:#fff">
 +
    <p class="darkBlue" style="font-family:Open Sans; font-size:180%; text-align:center">Growth Facility</p>
 +
    </div>
 +
</section>
  
−
<div class="column half_size" >
+
<section style="background-color:#fff; text-align: center; padding: 10% 0%">
−
<h5>Inspiration</h5>
+
    <div class="container" style="color:#000">
−
<p>See how other teams have described and presented their projects: </p>
+
    <div class="col-md-4">
 +
    <hr>
 +
    <p style="font-family:Open Sans; font-size:150%; text-align:center;">Always wanted to have a portable controlled environment for your Petri dishes full of organisms which can even Tweet pictures of itself? We have made one! It has various functions, is cheap, well documented and again DIY. This can really bring algae into small and community labs and make synthetic biology accessible and understandable to public!</p>
 +
    <hr>
 +
    </div>
 +
    <div class="col-md-4">
 +
    </div>
 +
    <div class="col-md-4" style="margin-right: 0px">
 +
    <a href="https://2016.igem.org/Team:Cambridge-JIC/GrowthFacility"><img src="https://static.igem.org/mediawiki/2016/d/d5/T--Cambridge-JIC--description--icon3.jpg" style="max-width:100%; max-height:100%"></a>
 +
    </div>
 +
    </div>
 +
</section>
  
−
<ul>
+
<section style="background-color:#3d3d3d; text-align: center; padding: 15% 0%">
−
<li><a href="https://2014.igem.org/Team:Imperial/Project"> Imperial</a></li>
+
    <div class="container" style="color:#fff">
−
<li><a href="https://2014.igem.org/Team:UC_Davis/Project_Overview"> UC Davis</a></li>
+
    <p class="darkBlue" style="font-family:Open Sans; font-size:180%; text-align:center">Homoplasmy</p>
−
<li><a href="https://2014.igem.org/Team:SYSU-Software/Overview">SYSU Software</a></li>
+
    </div>
−
</ul>
+
</section>
−
</div>
+
 
 +
<section style="background-color:#fff; text-align: center; padding: 10% 0%">
 +
    <div class="container" style="color:#000">
 +
    <div class="col-md-4">
 +
    <hr>
 +
    <p style="font-family:Open Sans; font-size:150%; text-align:center;">Our ultimate wetlab goal was to build a very modular device based on CRISPR/Cas9 which would accelerate the post-transformation process. To get your genes into all the copies of chloroplast DNA has never been so quick! As we are pioneers in using plant and algal chloroplasts in iGEM, our tool is theoretical but well thought through (see our Notebook for details), incorporating all environmental safety advice from scientists and the library of parts is designed specifically to facilitate this to happen in real!</p>
 +
    <hr>
 +
    </div>
 +
    <div class="col-md-4">
 +
    </div>
 +
    <div class="col-md-4" style="margin-right: 0px">
 +
    <a href="https://2016.igem.org/Team:Cambridge-JIC/Homoplasmy"><img src="https://static.igem.org/mediawiki/2016/6/63/T--Cambridge-JIC--description--icon4.jpg" style="max-width:100%; max-height:100%"></a>
 +
    </div>
 +
    </div>
 +
</section>
 +
 
 +
<section style="background-color:#3d3d3d; text-align: center; padding: 15% 0%">
 +
    <div class="container" style="color:#fff">
 +
    <p class="darkBlue" style="font-family:Open Sans; font-size:180%; text-align:center">Project References</p>
 +
    </div>
 +
</section>
 +
 +
<section style="background-color:#fff; text-align: center; padding: 10% 0%">
 +
    <div class="container" style="color:#000">
 +
    <p style="font-family:Open Sans; font-size:150%; text-align:center;"><ul style="font-size: 120%">
 +
      <li>Mayfield, S. P. (2005); Contribution of 5’ and 3’ untranslated regions of plastid mRNAs to the expression of Chlamydomonas reinhardtii chloroplast genes. Mol Gen Genomics 274: 625–636 DOI 10.1007/s00438-005-0055-y
 +
      <li>Verma, D., Daniell, H. (2007) Chloroplast Vector Systems for Biotechnology Applications. Plant Physiol. Vol. 145
 +
      <li>Engler, C., Youles, M., Gruetzner, R., Ehnert, T. M., Werner, S., Jones, J. D., Marillonnet, S. (2014). A golden gate modular cloning toolbox for plants. ACS Synthetic Biology,3(11), 839–843.
 +
<li>Krichevsky, A., Meyers, B., Vainstein, A., Maliga, P. and Citovsky, V. (2010) Autoluminescent plants. PLoS ONE 5,e15461.
 +
<li>Bock, R (2015). Engineering Plastid Genomes: Methods, Tools, and Applications in Basic Research and Biotechnology. Annual Review of Plant Biology, Vol. 66: 211 -241
 +
<li>Jiang W, Brueggeman AJ, Horken KM, Plucinak TM, Weeks DP. (2014) Successful Transient Expression of Cas9 and Single Guide RNA Genes in Chlamydomonas reinhardtii. Eukaryotic Cell. 2014;13(11):1465-1469. doi:10.1128/EC.00213-14.
 +
<li>Jin S, Daniell (2015) H. Engineered Chloroplast Genome just got Smarter Trends in plant science. 2015;20(10):622-640. doi:10.1016/j.tplants.2015.07.004.
 +
<li>Wannathong, T., Waterhouse, J.C., Young, R.E.B. et al. (2016) New tools for chloroplast genetic engineering allow the synthesis of human growth hormone in the green alga Chlamydomonas reinhardtii. Appl Microbiol Biotechnol 100: 5467. doi:10.1007/s00253-016-7354-6
 +
<li>Gangl, Doris; Zedler, Julie A. Z.; Rajakumar, Priscilla D.; Ramos Martinez, Erick Miguel; Riseley, Anthony; Wlodarczyk, Artur Jacek; Purton, Saul; Sakuragi, Yumiko; Howe, Christopher J.; Jensen, Poul Erik; Robinson, Colin. (2015) Biotechnological exploitation of microalgae. Journal of Experimental Botany, Vol. 66, No. 22, 2015, p. 6975-6990.
 +
    </ul></p>
 +
    </div>
 +
</section>
  
  
 
</body>
 
</body>
 
</html>
 
</html>
 +
{{Cambridge-JIC/Templates/Footer}}

Latest revision as of 00:46, 20 October 2016

Cambridge-JIC

DESCRIPTION

We have built a toolbox for chloroplast transformation. In our chosen organism Chlamydomonas reinhardtii (Chlamy) we have targeted all the transformation steps and improved each of them. We have built a library of tested parts optimised for Chlamydomonas or related chloroplasts. We built a gene gun which is less than 1/100 of commercial price and an incubator for our cells with many functions. Moreover we modelled the behaviour of transformed systems. Finally we designed a wetlab tool which could help achieve essential homoplasmy (transformation of all copies of chloroplast DNA) in one generation instead of 2-3 months of selection. Our design incorporated numerous discussions about biosafety and our library contains the relevant parts for practical implementation!

Why Chlamydomonas?

Chlamydomonas, a single-celled alga with only one chloroplast, has its natural advantage over many other single-celled organisms in the lab such as E.coli and yeast. It is a perfect chassis for prototyping plant work in iGEM time scales.

Unlike E. coli or yeast it does not need extra carbon source such as glucose. This will make a huge difference in an industrial scale.

The plant cell systems allows post-translational modification such as complex folding and glycosylation.

Why Chloroplasts?

Higher transgene yields than nucleus

Allows precise editing because DNA integration occurs almost exclusively through homologous integration in Chlamydomonas chloroplast

Naturally specialized in synthesis

What are the problems?

Complex cloning design

Equipment is expensive and sometimes inaccessible

More time-consuming than bacteria engineering

Multiple plastid genomes to transform

Improving Chloroplast Transformation Step by Step

Library of Parts

Our library of parts contains many parts necessary for synthetic biology of chloroplasts. They have been tested by cloning in E. coli, some by shooting into Chlamy and extracting, some even by sequencing. They all were designed with the intention to facilitate bringing our homoplasmy tool into practice.

Our Improved parts:
BBa_K2148013
Cas9 is a molecular tool which together with its guide RNA can cut DNA sequences at sequence-specific places. Our Cas9 is codon-optimized for Chlamydomonas reinhardtii chloroplast chassis (likely useable in other chloroplasts). Additionally it has a fusion tag to link reporter genes such as fluorescent proteins. It is fully compatible with the increasingly popular Phytobrick standard.


BBa_K2148009
GFP is the most classic fluorescent reporter protein with very wide range of usage. Our GFP is again codon-optimised for Chlamydomonas reinhardtii chloroplast. Moreover it is compatible with Phytobrick standard.

Gene Gun

Our complete Do-It-Yourself Gene Gun with all necessary documentation is less than one-hundredth of the commercial price! And it has been firing DNA onto samples!

Growth Facility

Always wanted to have a portable controlled environment for your Petri dishes full of organisms which can even Tweet pictures of itself? We have made one! It has various functions, is cheap, well documented and again DIY. This can really bring algae into small and community labs and make synthetic biology accessible and understandable to public!

Homoplasmy

Our ultimate wetlab goal was to build a very modular device based on CRISPR/Cas9 which would accelerate the post-transformation process. To get your genes into all the copies of chloroplast DNA has never been so quick! As we are pioneers in using plant and algal chloroplasts in iGEM, our tool is theoretical but well thought through (see our Notebook for details), incorporating all environmental safety advice from scientists and the library of parts is designed specifically to facilitate this to happen in real!

Project References

  • Mayfield, S. P. (2005); Contribution of 5’ and 3’ untranslated regions of plastid mRNAs to the expression of Chlamydomonas reinhardtii chloroplast genes. Mol Gen Genomics 274: 625–636 DOI 10.1007/s00438-005-0055-y
  • Verma, D., Daniell, H. (2007) Chloroplast Vector Systems for Biotechnology Applications. Plant Physiol. Vol. 145
  • Engler, C., Youles, M., Gruetzner, R., Ehnert, T. M., Werner, S., Jones, J. D., Marillonnet, S. (2014). A golden gate modular cloning toolbox for plants. ACS Synthetic Biology,3(11), 839–843.
  • Krichevsky, A., Meyers, B., Vainstein, A., Maliga, P. and Citovsky, V. (2010) Autoluminescent plants. PLoS ONE 5,e15461.
  • Bock, R (2015). Engineering Plastid Genomes: Methods, Tools, and Applications in Basic Research and Biotechnology. Annual Review of Plant Biology, Vol. 66: 211 -241
  • Jiang W, Brueggeman AJ, Horken KM, Plucinak TM, Weeks DP. (2014) Successful Transient Expression of Cas9 and Single Guide RNA Genes in Chlamydomonas reinhardtii. Eukaryotic Cell. 2014;13(11):1465-1469. doi:10.1128/EC.00213-14.
  • Jin S, Daniell (2015) H. Engineered Chloroplast Genome just got Smarter Trends in plant science. 2015;20(10):622-640. doi:10.1016/j.tplants.2015.07.004.
  • Wannathong, T., Waterhouse, J.C., Young, R.E.B. et al. (2016) New tools for chloroplast genetic engineering allow the synthesis of human growth hormone in the green alga Chlamydomonas reinhardtii. Appl Microbiol Biotechnol 100: 5467. doi:10.1007/s00253-016-7354-6
  • Gangl, Doris; Zedler, Julie A. Z.; Rajakumar, Priscilla D.; Ramos Martinez, Erick Miguel; Riseley, Anthony; Wlodarczyk, Artur Jacek; Purton, Saul; Sakuragi, Yumiko; Howe, Christopher J.; Jensen, Poul Erik; Robinson, Colin. (2015) Biotechnological exploitation of microalgae. Journal of Experimental Botany, Vol. 66, No. 22, 2015, p. 6975-6990.