Difference between revisions of "Team:DTU-Denmark/achievements"

 
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        <h1>Overview</h1>
 
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        <h1>Medal requirements</h1>
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                    <div class="col-md-5 col-sm-5 col-xs-12 title"> <!-- the approximate max number of characters ~ 400 --> <!-- EDIT -->
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                        <h1>Achievements<p class="lead">We have fulfilled all bronze medal requirements, all the requirements for the silver medal and three of the four criteria for achieving a gold medal. Furthermore, we have qualified for three special prizes: Education and Public Engagement award, Software award, and Hardware award.</p></h1>
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                    <div class="col-md-5 col-sm-5 hidden-xs intro"> <!-- will be hidden on phones, duplicate the text to blockquote down below first section header, to show it there, when it dissapear-->
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                        <blockquote class="blockquote-reverse"> <!-- EDIT -->
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                            <p>"Only those who attempt the absurd can achieve the impossible"</p>
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                            <small>Albert Einstein<cite title="Source Title"></cite></small>
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                        </blockquote>     
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    <div class="col-md-9 col-sm-10 colLeft"> <!-- LEFT -->
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        <div><a class="anchor" id="section-1"></a>
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        <h2 class="h2">Medal Requirements</h2>
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             <blockquote class="visible-xs"> <!-- quote from masterhead duplicate -->
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                <p>"Only those who attempt the absurd can achieve the impossible"</p>
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                <small>Albert Einstein<cite title="Source Title"></cite></small>
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            </blockquote>
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            <h3 class="h3">Bronze</h3>
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            <div class="grid-row">
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                <div class="col-md-3 col-sm-3 col-xs-12">
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                    <p style="text-align:left;"><span class="check">&#10003;</span> Register and attend</p>
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                <div class="col-md-9 col-sm-9 col-xs-12">
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                    <p>We registered for iGEM and had a great and educational (and sometimes frustrating) summer. We will also attended the Giant Jamboree. </p>
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                </div>
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            <div class="grid-row">
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                <div class="col-md-3 col-sm-3 col-xs-12">
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                    <p style="text-align:left;"><span class="check">&#10003;</span> Deliverables</p>
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                <div class="col-md-9 col-sm-9 col-xs-12">
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                    <p>Yes, we met all the deliverables. Take a look around on our awesome Wiki. We have registered and submitted all our 
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                    <a href="https://2016.igem.org/Team:DTU-Denmark/Description">parts</a>. We have filled out the safety, judging and registry forms as required. The team is ready with the presentation and poster for the Giant Jamboree.</p>
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                <div class="col-md-3 col-sm-3 col-xs-12">
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                    <p style="text-align:left;"><span class="check">&#10003;</span> Attribution</p>
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                <div class="col-md-9 col-sm-9 col-xs-12">
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                    <p>Even though this project was driven and conducted by the team only, we have gotten a lot of much appreciated help during this project. Everyone should of course be credited for their attributions. Please see our <a href="https://2016.igem.org/Team:DTU-Denmark/Attributions">attribution page</a>.</p>
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            <div class="grid-row">
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                <div class="col-md-3 col-sm-3 col-xs-12">
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                    <p style="text-align:left;"><span class="check">&#10003;</span> Part</p>
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                <div class="col-md-9 col-sm-9 col-xs-12">
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                    <p>We have registered and submitted our new part <a href="http://parts.igem.org/Part:BBa_K2117003">BBa_K2117003</a>. This part encodes the human proinsulin peptide. The gene has been codon-optimized for the yeast <i>Yarrowia lipolytica</i> using a DTU-Denmark iGEM 2016 team designed <a href="https://2016.igem.org/Team:DTU-Denmark/Software">codon-optimization tool</a> that also considers illegal restriction sites.</p>
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            </div> <!-- /grid-row -->
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            <h3 class="h3">Silver</h3>
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            <div class="grid-row">
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                <div class="col-md-3 col-sm-3 col-xs-12">
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                    <p style="text-align:left;"><span class="check">&#10003;</span> Validated Part</p>
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                </div>
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                <div class="col-md-9 col-sm-9 col-xs-12">
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                    <p>Our new BioBrick device <a href="http://parts.igem.org/Part:BBa_K2117005">BBa_K2117005</a> encodes the humanized <i>Renilla reniformis</i> green fluorescent protein (hrGFP) codon-optimized for <i>Y. lipolytica</i> and the translation elongation factor-1α (TEF1) promoter. We have used this device to demonstrate heterologous protein expression in <i>Y. lipolytica</i> and experimentally validated it through confocal laser scanning microscopy. </p>
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                <div class="col-md-3 col-sm-3 col-xs-12">
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                    <p style="text-align:left;"><span class="check">&#10003;</span> Collaboration</p>
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                </div>
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                <div class="col-md-9 col-sm-9 col-xs-12">
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                    <p>We have helped different iGEM teams during the summer: <a href="https://2016.igem.org/Team:Uppsala/Collaborations">Uppsala iGEM</a>, <a href="https://2016.igem.org/Team:UNIK_Copenhagen/Collaborations">UNIK_Copenhagen</a>, <a href="https://2016.igem.org/Team:SDU-Denmark/Collaborations">SDU-Denmark</a>. For more information please see our <a href="https://2016.igem.org/Team:DTU-Denmark/Collaborations">collaborations page.</a></p>
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                <div class="col-md-3 col-sm-3 col-xs-12">
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                    <p style="text-align:left;"><span class="check">&#10003;</span> Human Practices</p>
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                <div class="col-md-9 col-sm-9 col-xs-12">
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                    <p>We sure went beyond the lab bench during this project. Our biggest achievement was the launch of the <a href="https://2016.igem.org/Team:DTU-Denmark/Engagement">Biosensor project</a>, a platform for allowing over 200 high schools nationwide to work with synthetic biology. We also held a meet-up for other iGEM teams, presented our project at different events and got media coverage. Please see our <a href="https://2016.igem.org/Team:DTU-Denmark/HP/Silver">practices page</a> for elaboration.</p>
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            </div> <!-- /grid-row -->
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            <h3 class="h3">Gold</h3>
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            <div class="grid-row">
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                <div class="col-md-3 col-sm-3 col-xs-12">
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                    <p style="text-align:left;"><span class="check">&#10003;</span> Integrated Human Practices</p>
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                </div>
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                <div class="col-md-9 col-sm-9 col-xs-12">
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                    <p>Throughout our project we have been in close contact and collaboration with the industry. We started out searching for abundant waste streams in Denmark by contacting and visiting local factories, we then presented our idea to biotech manufacturing companies and all together the feedback made us more aware of the challenges our technology is facing. This ultimately led us to a more feasible product. Please see the <a href="https://2016.igem.org/Team:DTU-Denmark/HP/Gold">Integrated practice page</a> for elaboration.</p>
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                <div class="col-md-3 col-sm-3 col-xs-12">
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                    <p style="text-align:left;"><span class="check">&#10003;</span> Improve a previous part</p>
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                <div class="col-md-9 col-sm-9 col-xs-12">
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                    <p>We have improved the two BioBricks; <a href="http://parts.igem.org/Part:BBa_K530001">BBa_K530001</a> (<i>crtE</i>) and <a href="http://parts.igem.org/Part:BBa_K530002">BBa_K530002</a> (<i>crtI</i>) created by the John Hopkins iGEM team 2011. We used site directed mutagenesis to successfully remove two illegal restriction sites and we furthermore improved the characterization. Please see the <a href="https://2016.igem.org/Team:DTU-Denmark/Description">parts page</a> for elaboration.</p>
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            <div class="grid-row">
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                <div class="col-md-3 col-sm-3 col-xs-12">
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                    <p style="text-align:left;"><span class="check">&#10003;</span> Proof of concept</p>
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                </div>
 +
                <div class="col-md-9 col-sm-9 col-xs-12">
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                    <p>We successfully designed a functional plasmid (<a href="http://parts.igem.org/Part:BBa_K2117009">pSBB1A8YL</a>) for transformation and replication in both <em>Escherichia coli</em> and <em>Y. lipolytica</em>. pSBB1A8YL is also compatible with the BioBrick standard by assembly with our own BioBrick device <a href="http://parts.igem.org/Part:BBa_K2117005">BBa_K2117005</a>. This was proved by showing that we could utilize the construct in <em>Y. lipolytica</em> to express a heterologous protein, hrGFP. Please see the <a href="https://2016.igem.org/Team:DTU-Denmark/Proof">proof of concept page</a> for elaboration.</p>
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            <div class="grid-row">
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                <div class="col-md-3 col-sm-3  col-xs-12">
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                    <p style="text-align:left;"><span class="check">&#10007;</span> Demonstrate your work</p>
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                </div>
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                <div class="col-md-9 col-sm-9 col-xs-12">
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                    <p>We unfortunately did not have time to check our construct under simulated real-world conditions.</p>
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            </div> <!-- /grid-row -->
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        </div> <!-- /overview-->
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        <div><a class="anchor" id="section-2"></a>
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        <h2 class="h2">Special prizes</h2>
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            <p>
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                We have worked hard during the summer to obtain our goals. The results of our efforts are presented below.
 +
            </p>
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 +
            <h3 class="h3">Education and Public Engagement</h3>
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            <p>
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            The Biosensor project is an outstanding project, where kits for genetically modified organism (GMO) exercises are sent for free to all highschools in Denmark. The Biosensor kit contains everything needed for making 100 biosensors; deoxyribonucleic acid (DNA) with BioBricks from the iGEM registry, enzymes, antibiotics, buffers, ligases, cells and sterile equipment.
 +
            The students can create biosensors by assembling a detection and response gene using 3A assembly to genetically modify <em>E. coli.</em> Until now GMO exercises have been unavailable for Danish highschools due to costs and law, but with the biosensor project it is no longer a problem. We tested the kit at a local highschool and raised almost 135,000 USD from both Danish and international sponsors and we expect the kit to be distributed by the end of this year. We hope it will inspire and encourage the next generation to work in the field of synthetic biology. Please see the <a href="https://2016.igem.org/Team:DTU-Denmark/Engagement">Biosensor page</a>
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            </p>
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            <h3 class="h3">Software Tool</h3> 
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            <p>
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            One of the numerous capabilities and features that iGEM is providing to current and future science disciplines and societies around the globe, is the ability of “building interdisciplinary bridges”. Therefore, the DTU BioBuilders team confidently believes that the developed TaiCO tool will bring wetlabs and computational biology a step closer to bidirectional understanding. This tool is a stand-alone cross-platform software developed in Python (using only standard libraries) and provides comprehensive codon optimization of DNA sequences from protein sequences. Its uniqueness lies in the fact that the researcher can specify the organism and the desired protein sequences to optimize according to the tRNA adaptation index (TAI) for the specified organism. This is novel in terms of codon optimization methods approach is framed by a user friendly GUI along with the option of removal of desired restriction sites from the resulting DNA sequences. Please see the <a href="https://2016.igem.org/Team:DTU-Denmark/Software">codon optimization page</a> for elaboration.
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            </p>
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            <h3 class="h3">Hardware</h3>
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            <p>
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            When taking your synbio project to real applications, fast growth is crucial for the viability. The optical density is commonly used as a proximation for cell count and numerous instructions for DIY spectrophotometers exist. However, in order to estimate growth rates, cultures must be sampled over a long period of time. During our project, this was done by a robot handling microtiter plates. We are aware that this is a technology not everybody has access to. Therefore, we took the concept of a DIY spectrophotometer and expanded it to a platform that carries out small scale fermentations comparing growth of your modifed strain to a wild type or other organisms. To take it even further, we encapsuled it in a compact housing that fits on any lab bench. It can be rebuild or modified by anyone with access to a PC, a 3D-printer and a laser cutter. Please see the <a href="https://2016.igem.org/Team:DTU-Denmark/Hardware">microfermentation platform page</a> for elaboration.
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         <h1>Bronze</h1>
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         <h2 class="h2">Milestones</h2>
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<p>The DTU BioBuilders 2016 team formed! </p>
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<p>We decided on a project! To utilize a waste source as a substrate for a production organism to produce something valuable such as insulin! </p>
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<p>The DTU annual BioBrick Tutorial was hosted for Danish iGEM teams from SDU and KU.</p>
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<p>Our preliminary idea for glycerol as the ideal waste substrate was shot down by industry. Keep going! </p>
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<p>Getting approached by local journalists - our vision is reaching the greater public!</p>
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<p>Found a great waste source in form of cold-pressed canola oil sediment, that is just burned off. Out to find an organism that can utilize this waste! </p>
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<p>Preliminary versions of our Codon Optimization Software was used for the first time to codon optimize the proinsulin gene for <em>Y. lipolytica</em>, our organism of choice!</p>
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<p>Our BioBrick plasmid, pSB1A8YL, was finally constructed!</p>
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<p>We approached industry with our idea, and after going back and forth we decided a clear path for our project.</p>
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<p>Color proteins encoded in pSB1A8YL was successfully expressed in <em>E. coli</em>! </p>
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<p>After 10 weeks of trial and error, a transformation protocol compliant with <em>Y. lipolytica</em> was obtained. Making this yeast engineerable is getting closer!</p>
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<p>Our goal to fund the project with 60,000 USD was way over achieved, when the final funding totaled at 120,000 USD! Now we can start buying equipment for our own DTU iGEM lab for future teams.  </p>
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<p>Getting rid of the breadboards! The DIY microfermentation platform has been finally fit into the housing using the printed circuit board we designed. </p>
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<p>Genome scale modeling is coming along. We achieved getting the same PHPP values for growth rate changes in <em>E. coli</em> when varying oxygen and nutrient uptake rates, as in published papers.</p>
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<p>Our DIY lab is coming along, with the first growth curve measured with the final prototype of our microfermentation platform. </p>
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<p>Sequencing confirmed that we constructed the BioBrick Device pTEF:ProInsulin (BBa_K2117002) for optimized proinsulin expression in <em>Y. lipolytica</em>! </p>
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<p>We optimized preexisting &beta;-Carotene BioBricks by removing illegal restriction sites!</p>
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<p>Sequencing confirmed that we constructed the BioBrick Device pTEF:HrGFP (BBa_K2117005) for optimized GFP expression in <em>Y. lipolytica</em>! </p>
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<p>After months of laboratory work and planning, we unleashed the BioSensor project at a local high school with great success! </p>
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<p>Finally! We managed to insert a gene (<em>URA3</em>) in the <em>Y. lipolytica</em> genome by CRISPR induced homologous recombination. Where is the limit now?! </p>
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<p>We managed to use FSEOF to stimulate gene amplification targets to optimize &beta;-Carotene production in <em>Y. lipolytica</em>. Hopefully we can replicate these results in the lab. </p>
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<p>We can express proteins in <em>Y. lipolytica</em> by our BioBrick plasmid pSB1A8YL! pTEF:HrGFP was successfully integrated into pSB1A8YL and transformed into <em>Y. lipolytica</em> and convincing GFP expression was observed! </p>
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<p>Eureka! <em>Y. lipolytica</em> PO1f colonies with changed morphology was observed, indicating that we have successfully knocked out a gene by CRISPR induced error prone NHEJ. Sequencing awaits! </p>
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<p>Our DIY micro fermentation platform was successfully tested by prospective users: a high school student and a local hackerspace. </p>
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<p>Our Codon Optimization software finally has a great Graphic User Interface, so we can share this tool with everyone! </p>
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<p>Giant Jamboree! We can’t wait to show off our hard work! </p>
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Achievements

We have fulfilled all bronze medal requirements, all the requirements for the silver medal and three of the four criteria for achieving a gold medal. Furthermore, we have qualified for three special prizes: Education and Public Engagement award, Software award, and Hardware award.


Medal Requirements

"Only those who attempt the absurd can achieve the impossible"

Albert Einstein

Bronze

✓ Register and attend

We registered for iGEM and had a great and educational (and sometimes frustrating) summer. We will also attended the Giant Jamboree.

✓ Deliverables

Yes, we met all the deliverables. Take a look around on our awesome Wiki. We have registered and submitted all our parts. We have filled out the safety, judging and registry forms as required. The team is ready with the presentation and poster for the Giant Jamboree.

✓ Attribution

Even though this project was driven and conducted by the team only, we have gotten a lot of much appreciated help during this project. Everyone should of course be credited for their attributions. Please see our attribution page.

✓ Part

We have registered and submitted our new part BBa_K2117003. This part encodes the human proinsulin peptide. The gene has been codon-optimized for the yeast Yarrowia lipolytica using a DTU-Denmark iGEM 2016 team designed codon-optimization tool that also considers illegal restriction sites.

Silver

✓ Validated Part

Our new BioBrick device BBa_K2117005 encodes the humanized Renilla reniformis green fluorescent protein (hrGFP) codon-optimized for Y. lipolytica and the translation elongation factor-1α (TEF1) promoter. We have used this device to demonstrate heterologous protein expression in Y. lipolytica and experimentally validated it through confocal laser scanning microscopy.

✓ Collaboration

We have helped different iGEM teams during the summer: Uppsala iGEM, UNIK_Copenhagen, SDU-Denmark. For more information please see our collaborations page.

✓ Human Practices

We sure went beyond the lab bench during this project. Our biggest achievement was the launch of the Biosensor project, a platform for allowing over 200 high schools nationwide to work with synthetic biology. We also held a meet-up for other iGEM teams, presented our project at different events and got media coverage. Please see our practices page for elaboration.

Gold

✓ Integrated Human Practices

Throughout our project we have been in close contact and collaboration with the industry. We started out searching for abundant waste streams in Denmark by contacting and visiting local factories, we then presented our idea to biotech manufacturing companies and all together the feedback made us more aware of the challenges our technology is facing. This ultimately led us to a more feasible product. Please see the Integrated practice page for elaboration.

✓ Improve a previous part

We have improved the two BioBricks; BBa_K530001 (crtE) and BBa_K530002 (crtI) created by the John Hopkins iGEM team 2011. We used site directed mutagenesis to successfully remove two illegal restriction sites and we furthermore improved the characterization. Please see the parts page for elaboration.

✓ Proof of concept

We successfully designed a functional plasmid (pSBB1A8YL) for transformation and replication in both Escherichia coli and Y. lipolytica. pSBB1A8YL is also compatible with the BioBrick standard by assembly with our own BioBrick device BBa_K2117005. This was proved by showing that we could utilize the construct in Y. lipolytica to express a heterologous protein, hrGFP. Please see the proof of concept page for elaboration.

✗ Demonstrate your work

We unfortunately did not have time to check our construct under simulated real-world conditions.

Special prizes

We have worked hard during the summer to obtain our goals. The results of our efforts are presented below.

Education and Public Engagement

The Biosensor project is an outstanding project, where kits for genetically modified organism (GMO) exercises are sent for free to all highschools in Denmark. The Biosensor kit contains everything needed for making 100 biosensors; deoxyribonucleic acid (DNA) with BioBricks from the iGEM registry, enzymes, antibiotics, buffers, ligases, cells and sterile equipment. The students can create biosensors by assembling a detection and response gene using 3A assembly to genetically modify E. coli. Until now GMO exercises have been unavailable for Danish highschools due to costs and law, but with the biosensor project it is no longer a problem. We tested the kit at a local highschool and raised almost 135,000 USD from both Danish and international sponsors and we expect the kit to be distributed by the end of this year. We hope it will inspire and encourage the next generation to work in the field of synthetic biology. Please see the Biosensor page

Software Tool

One of the numerous capabilities and features that iGEM is providing to current and future science disciplines and societies around the globe, is the ability of “building interdisciplinary bridges”. Therefore, the DTU BioBuilders team confidently believes that the developed TaiCO tool will bring wetlabs and computational biology a step closer to bidirectional understanding. This tool is a stand-alone cross-platform software developed in Python (using only standard libraries) and provides comprehensive codon optimization of DNA sequences from protein sequences. Its uniqueness lies in the fact that the researcher can specify the organism and the desired protein sequences to optimize according to the tRNA adaptation index (TAI) for the specified organism. This is novel in terms of codon optimization methods approach is framed by a user friendly GUI along with the option of removal of desired restriction sites from the resulting DNA sequences. Please see the codon optimization page for elaboration.

Hardware

When taking your synbio project to real applications, fast growth is crucial for the viability. The optical density is commonly used as a proximation for cell count and numerous instructions for DIY spectrophotometers exist. However, in order to estimate growth rates, cultures must be sampled over a long period of time. During our project, this was done by a robot handling microtiter plates. We are aware that this is a technology not everybody has access to. Therefore, we took the concept of a DIY spectrophotometer and expanded it to a platform that carries out small scale fermentations comparing growth of your modifed strain to a wild type or other organisms. To take it even further, we encapsuled it in a compact housing that fits on any lab bench. It can be rebuild or modified by anyone with access to a PC, a 3D-printer and a laser cutter. Please see the microfermentation platform page for elaboration.

Milestones

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The DTU BioBuilders 2016 team formed!

February
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We decided on a project! To utilize a waste source as a substrate for a production organism to produce something valuable such as insulin!

April
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The DTU annual BioBrick Tutorial was hosted for Danish iGEM teams from SDU and KU.

May
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Our preliminary idea for glycerol as the ideal waste substrate was shot down by industry. Keep going!

June
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Getting approached by local journalists - our vision is reaching the greater public!

June
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Found a great waste source in form of cold-pressed canola oil sediment, that is just burned off. Out to find an organism that can utilize this waste!

June
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Preliminary versions of our Codon Optimization Software was used for the first time to codon optimize the proinsulin gene for Y. lipolytica, our organism of choice!

July
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Our BioBrick plasmid, pSB1A8YL, was finally constructed!

July
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We approached industry with our idea, and after going back and forth we decided a clear path for our project.

July
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Color proteins encoded in pSB1A8YL was successfully expressed in E. coli!

July
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After 10 weeks of trial and error, a transformation protocol compliant with Y. lipolytica was obtained. Making this yeast engineerable is getting closer!

August
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Our goal to fund the project with 60,000 USD was way over achieved, when the final funding totaled at 120,000 USD! Now we can start buying equipment for our own DTU iGEM lab for future teams.

August
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Getting rid of the breadboards! The DIY microfermentation platform has been finally fit into the housing using the printed circuit board we designed.

September
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Genome scale modeling is coming along. We achieved getting the same PHPP values for growth rate changes in E. coli when varying oxygen and nutrient uptake rates, as in published papers.

September
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Our DIY lab is coming along, with the first growth curve measured with the final prototype of our microfermentation platform.

September
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Sequencing confirmed that we constructed the BioBrick Device pTEF:ProInsulin (BBa_K2117002) for optimized proinsulin expression in Y. lipolytica!

September
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We optimized preexisting β-Carotene BioBricks by removing illegal restriction sites!

October
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Sequencing confirmed that we constructed the BioBrick Device pTEF:HrGFP (BBa_K2117005) for optimized GFP expression in Y. lipolytica!

October
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After months of laboratory work and planning, we unleashed the BioSensor project at a local high school with great success!

October
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Finally! We managed to insert a gene (URA3) in the Y. lipolytica genome by CRISPR induced homologous recombination. Where is the limit now?!

October
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We managed to use FSEOF to stimulate gene amplification targets to optimize β-Carotene production in Y. lipolytica. Hopefully we can replicate these results in the lab.

Month
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We can express proteins in Y. lipolytica by our BioBrick plasmid pSB1A8YL! pTEF:HrGFP was successfully integrated into pSB1A8YL and transformed into Y. lipolytica and convincing GFP expression was observed!

October
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Eureka! Y. lipolytica PO1f colonies with changed morphology was observed, indicating that we have successfully knocked out a gene by CRISPR induced error prone NHEJ. Sequencing awaits!

October
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Our DIY micro fermentation platform was successfully tested by prospective users: a high school student and a local hackerspace.

October
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Our Codon Optimization software finally has a great Graphic User Interface, so we can share this tool with everyone!

October
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Giant Jamboree! We can’t wait to show off our hard work!

October
★

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  • MAIN SPONSORS:
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