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| | <div class="text">Design & integration</div> | | <div class="text">Design & integration</div> |
| | <div class="desc">OUTCASST toolkit and product design with factors such as bio-safety and user-friendliness taken into account.</div> | | <div class="desc">OUTCASST toolkit and product design with factors such as bio-safety and user-friendliness taken into account.</div> |
| | + | </div> |
| | + | <div class="section" data-url="outreach"> |
| | + | <div class="thumb"><img height="100" src=""></div> |
| | + | <div class="text">Outreach</div> |
| | + | <div class="desc">.</div> |
| | + | </div> |
| | + | <div class="section" data-url="collaborations"> |
| | + | <div class="thumb"><img height="100" src=""></div> |
| | + | <div class="text">Collaborations</div> |
| | + | <div class="desc">.</div> |
| | </div> | | </div> |
| | </div> | | </div> |
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| | We have also heard that the tool should have a low incidence of false positive and negative results and that our device should distinguish DNA strands with one different base pair. We want to take this information into account to decide the target DNA. There are two possibilities from which we can choose. The first option would be to permit certain mutations in the target DNA, to prevent getting a false negative result in some cases. The second option would be to use a very conserved domain as target DNA and don’t allow any mismatches. From our perspective, we think the second option would be more suitable, since the specificity in our system is a very valuable aspect of the design. We have chosen to use the satellite DNA, which is present in the T. cruzi parasite as a 195 base pair repeat with about 100,000 copies (Aldert Bart, Academical Medical Center Amsterdam: Clinical molecular parasitologist). | | We have also heard that the tool should have a low incidence of false positive and negative results and that our device should distinguish DNA strands with one different base pair. We want to take this information into account to decide the target DNA. There are two possibilities from which we can choose. The first option would be to permit certain mutations in the target DNA, to prevent getting a false negative result in some cases. The second option would be to use a very conserved domain as target DNA and don’t allow any mismatches. From our perspective, we think the second option would be more suitable, since the specificity in our system is a very valuable aspect of the design. We have chosen to use the satellite DNA, which is present in the T. cruzi parasite as a 195 base pair repeat with about 100,000 copies (Aldert Bart, Academical Medical Center Amsterdam: Clinical molecular parasitologist). |
| | | | |
| | + | </script> |
| | + | |
| | + | <script id="page-outreach" type="text/template"> |
| | + | <div class="page-heading">Outreach</div> |
| | + | Science can have an impact on the world in many ways. With our project, we are not only trying to make a difference by creating a diagnostic tool, but by reaching out to the public we hope to make science accessible for everyone. We try to achieve this by collaborating with ‘de Kennis van Nu’, a Dutch platform that brings different scientific themes to the general public in an understandable way. They aim to make science accessible to everyone, old and young, and encourage everyone to be curious and bring out the scientist in themselves! On this platform we explain the formation of Utrecht’s very first team, our design and how we are trying to solve healthcare problems. Through our whole iGEM experience, they will follow us from lab bench to Boston. |
| | + | <br><br> |
| | + | Below, you can find the short movies, articles and infographics that were so far made in cooperation with Kennis van Nu to reach out to the public. |
| | + | |
| | + | <br><br> |
| | + | <h2 class="subhead" id="subhead-2">Movie: iGEM Utrecht: an introduction</h2> |
| | + | |
| | + | <br><br> |
| | + | <h2 class="subhead" id="subhead-2">Movie: Meet the team</h2> |
| | + | |
| | + | <br><br> |
| | + | <h2 class="subhead" id="subhead-2">Movie: The problem; the detection of infectious disease has to be improved</h2> |
| | + | |
| | + | <br><br> |
| | + | <h2 class="subhead" id="subhead-2">Movie: Why Chagas Disease?</h2> |
| | </script> | | </script> |
| | | | |
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| | <div><b>Snapgene is a software company, providing useful software for molecular biology.</b> Snapgene offers fast and reliable software to visualize and design molecular biology experiments such as cloning and PCR experiments. They sponsored us with full team licenses for the Snapgene software, which we have used extensively during our project.</div> | | <div><b>Snapgene is a software company, providing useful software for molecular biology.</b> Snapgene offers fast and reliable software to visualize and design molecular biology experiments such as cloning and PCR experiments. They sponsored us with full team licenses for the Snapgene software, which we have used extensively during our project.</div> |
| | <div><b>eLabjournal is a product by BIO-ITECH BV, a company providing software as a service for research laboratories.</b> Their eLabjournal product offers a simple and effective software environment to keep our lab notes organized and allows easy access wherever and whenever we need it. eLabjournal sponsored us with full team licenses for their software.</div> | | <div><b>eLabjournal is a product by BIO-ITECH BV, a company providing software as a service for research laboratories.</b> Their eLabjournal product offers a simple and effective software environment to keep our lab notes organized and allows easy access wherever and whenever we need it. eLabjournal sponsored us with full team licenses for their software.</div> |
| − | <div><b>NTrans Technologies specializes in the delivery of content into cells using the iTOP technology which was developed in the Geijsen lab of the Hubrecht Institute.</b> NTrans offered us guidance and assistance with our project by facilitating a lab technician experienced in the work we had to do for our project. We thank them for Clara Martinez’ amazing assistance and patience with our silly questions.</div>
| |
| | <div><b>Integrated DNA Technologies (IDT) is a company focusing on the development and production of products for life sciences, both for research and diagnostic purposes.</b> They are an important supplier of synthetic DNA & RNA, next generation sequencing services and other tools and products for molecular biology. IDT supports us by offering us 20 kb of free custom DNA.</div> | | <div><b>Integrated DNA Technologies (IDT) is a company focusing on the development and production of products for life sciences, both for research and diagnostic purposes.</b> They are an important supplier of synthetic DNA & RNA, next generation sequencing services and other tools and products for molecular biology. IDT supports us by offering us 20 kb of free custom DNA.</div> |
| | <div><b>MathWorks is the leading company on mathematical computing software.</b> Their two primary products are MATLAB, for the development of algorithms and data-analysis, and Simulink, for designing and running simulations of dynamic, multidomain models. These products are a staple in innovation and development in life sciences as well as other fields. Furthermore, MathWorks’ tools are used in research and educational settings. MathWorks provided us with licenses for their fantastic software and technical support.</div> | | <div><b>MathWorks is the leading company on mathematical computing software.</b> Their two primary products are MATLAB, for the development of algorithms and data-analysis, and Simulink, for designing and running simulations of dynamic, multidomain models. These products are a staple in innovation and development in life sciences as well as other fields. Furthermore, MathWorks’ tools are used in research and educational settings. MathWorks provided us with licenses for their fantastic software and technical support.</div> |
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| | <div style="width: 300px;"><img src="https://static.igem.org/mediawiki/2017/3/38/Uusnapgene.png"></div> | | <div style="width: 300px;"><img src="https://static.igem.org/mediawiki/2017/3/38/Uusnapgene.png"></div> |
| | <div style="width: 275px;"><img src="https://static.igem.org/mediawiki/2017/e/e3/Uuelabjournal.png"></div> | | <div style="width: 275px;"><img src="https://static.igem.org/mediawiki/2017/e/e3/Uuelabjournal.png"></div> |
| − | <div style="width: 300px;"><img src="https://static.igem.org/mediawiki/2017/b/bb/Uuntrans.png"></div>
| |
| | <div style="width: 250px;"><img src="https://static.igem.org/mediawiki/2017/5/5c/Uuidt.jpg"></div> | | <div style="width: 250px;"><img src="https://static.igem.org/mediawiki/2017/5/5c/Uuidt.jpg"></div> |
| | <div style="width: 300px;"><img src="https://static.igem.org/mediawiki/2017/4/43/Uumathworks.png"></div> | | <div style="width: 300px;"><img src="https://static.igem.org/mediawiki/2017/4/43/Uumathworks.png"></div> |
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| | <div class="page-heading">Achievements</div> | | <div class="page-heading">Achievements</div> |
| | | | |
| − | Blabla
| + | This page will give an overview of the achievements of our team. These will be presented as the medal criteria we fulfilled to acquire the various medals. For several criteria we will provide a link to the page with more information on that item. |
| | | | |
| | <br><br> | | <br><br> |
| | | | |
| − | <h2 class="subhead" id="subhead-2">Bronze medals</h2> | + | <h2 class="subhead" id="subhead-2">Bronze</h2> |
| | <div class="achievements" style="width: 100%;"> | | <div class="achievements" style="width: 100%;"> |
| − | <div style="float: left; width: 300px;"> | + | <div style="float: left; width: 100%; margin: 0;"> |
| | <b>Register and attend</b><br> | | <b>Register and attend</b><br> |
| | We have registered for and will be attending the 2017 iGEM Jamboree in Boston! Our entire team, consisting of 15 students, 4 PIs and 1 supervisor, will be present. | | We have registered for and will be attending the 2017 iGEM Jamboree in Boston! Our entire team, consisting of 15 students, 4 PIs and 1 supervisor, will be present. |
| | </div> | | </div> |
| − | <div style="float: left; width: 300px;"> | + | <div style="float: left; width: 100%; margin: 0; margin-top: 20px;"> |
| | <b>Deliverables</b><br> | | <b>Deliverables</b><br> |
| | We have delivered all the required items on the iGEM deliverables page.<br> | | We have delivered all the required items on the iGEM deliverables page.<br> |
| | + | <table border="0" cellspacing="0" cellpadding="0" width="600"> |
| | + | <tr> |
| | + | <td width="250"> |
| | <ul> | | <ul> |
| − | <li /> Team wiki <a href=""> URL</a> | + | <li /><a href="">Team wiki</a> |
| − | <li /> Project attribution <a href=""> URL</a> | + | <li /><a href="">Project attribution</a> |
| − | <li /> Team poster <a href=""> URL</a> | + | <li /><a href="">Team poster</a> |
| − | <li /> Safety forms <a href=""> URL</a> | + | <li /><a href="">Team presentation</a> |
| − | <li />… | + | <li /><a href="">Safety forms</a> |
| | </ul> | | </ul> |
| | + | </td> |
| | + | <td width="350"> |
| | + | <ul> |
| | + | <li /><a href="">Judging form</a> |
| | + | <li /><a href="">Registry part pages</a> |
| | + | <li /><a href="">Sample submission</a> |
| | + | <li /><a href="">Project attribution</a> |
| | + | <li /><a href="">Contribution to InterLab Study</a> |
| | + | </ul> |
| | + | </td> |
| | + | </tr> |
| | + | </table> |
| | </div> | | </div> |
| − | <div style="float: left; width: 300px;">a</div>
| |
| − | <div style="float: left; width: 300px;">a</div>
| |
| − | <div style="float: left; width: 300px;">a</div>
| |
| | </div> | | </div> |
| | | | |
| | <div style="clear: both;"></div> | | <div style="clear: both;"></div> |
| | | | |
| − | <br><br>
| + | <br> |
| | <h2 class="subhead" id="subhead-2">Silver</h2> | | <h2 class="subhead" id="subhead-2">Silver</h2> |
| − | <div style="width: 100%;"> | + | <div class="achievements" style="width: 100%;"> |
| − | <div style="float: left; width: 200px;">a</div> | + | <div style="float: left; width: 100%; margin: 0;"> |
| − | <div style="float: left; width: 200px;">a</div>
| + | <b>Validate functionality of BioBrick</b><br> |
| − | <div style="float: left; width: 200px;">a</div> | + | <li />Part Ba_K2351009 (sCas9)<br> |
| − | <div style="float: left; width: 200px;">a</div>
| + | BioBrick Part Ba_K2351009 (sCas9) has been validated. This BioBrick is very special since our team successfully secreted CRISPR-associated proteins from HEK293 cells. To our knowledge, this is the first time that Cas9 has ever been expressed outside of the cell. |
| − | <div style="float: left; width: 200px;">a</div> | + | <br> |
| | + | LINKS to [Parts Page] |
| | + | </div> |
| | + | <div style="float: left; width: 100%; margin: 0; margin-top: 20px;"> |
| | + | <b>Collaboration</b><br> |
| | + | Our team collaborated with the Wageningen team to obtain independent validations of both our and their biobricks. In addition, we worked with the Rathenau Institute and the RIVM on our Human Practices and safety considerations. |
| | + | <br><br> |
| | + | Furthermore, we contributed a postcard design to the Düsseldorf Cologne postcards campaign. Although these are not, strictly speaking, collaborations, we have attended several meet-ups with Dutch and other European iGEM teams to exchange ideas. An overview of our collaboration efforts can be found on the Collaborations page (> Links to [Collaborations page]). |
| | + | </div> |
| | + | <div style="float: left; width: 100%; margin: 0; margin-top: 20px;"> |
| | + | <b>Human Practices</b><br> |
| | + | Our team has contacted professionals from many different backgrounds to find the setting wherein the OUTCASST system would be of most use and to identify where the requirements of the intended application affect the design of our tool. Through a series of interviews with several experts, we came to the conclusion that our tool would be most useful in diagnostics and pathogen detection in particular. By talking to a representative from ‘Doctors without borders’ and a parasitology expert, we discovered that Chagas disease is a neglected tropical disease with a large impact, yet a good diagnostic tool for this disease is still missing. Therefore, we chose to focus on Chagas disease in the further design of our tool. (> Links to [Human Practices] [End User]) |
| | + | <br><br> |
| | + | Besides the interviews to find the focus of our project, we also worked on outreach. In collaboration with ‘De Kennis van Nu’, a Dutch platform that brings different scientific themes to the general public, we made videos and wrote blogs about synthetic biology, the iGEM competition, lab safety, tropical diseases and our project. To raise more awareness for the competition and our project within our university, we wrote articles in several student magazines. (> Links to [Human Practices] [Outreach]) |
| | + | </div> |
| | </div> | | </div> |
| | | | |
| | <div style="clear: both;"></div> | | <div style="clear: both;"></div> |
| | | | |
| − | <br><br>
| + | <br> |
| | <h2 class="subhead" id="subhead-2">Gold</h2> | | <h2 class="subhead" id="subhead-2">Gold</h2> |
| − | <div style="width: 100%;"> | + | <div class="achievements" style="width: 100%;"> |
| − | <div style="float: left; width: 200px;">a</div> | + | <div style="float: left; width: 100%; margin: 0;"> |
| − | <div style="float: left; width: 200px;">a</div>
| + | <b>Integrated Human Practices</b><br> |
| − | <div style="float: left; width: 200px;">a</div> | + | We incorporated the feedback we got from various professionals into the design of our final product. Not only did the information we gained make us choose for Chagas disease as the focus of our project, it also made us think about the way our system could be used on location. Through our conversations with specialists, we realized the importance of simplicity in use and resistance to varying temperatures and humidity. Only tools which take these factors into account can be used without a need for further lab equipment or trained personnel. Furthermore, with safety considerations in mind, we designed our device to keep our system separated from the outside world, making it impossible for the GMO’s to escape into the environment. (> Link to [Human Practices][Design]) |
| − | <div style="float: left; width: 200px;">a</div>
| + | </div> |
| − | <div style="float: left; width: 200px;">a</div>
| + | <div style="float: left; width: 100%; margin: 0; margin-top: 20px;"> |
| | + | <b>Model your project</b><br> |
| | + | At the same time, our team worked on modeling our system. They first summarized the kinetics of our fusion proteins in a network of reactions. With this reaction network, we demonstrated that the system contains negative feedback on its own sensitivity and give some suggestions on how to alleviate that problem with additional bio-circuitry components. In addition, we show that the precision of the system may be increased by usage of a weaker protease. We subsequently used ODE reaction equations to test if differences in substrate affinity or protein production rates can alleviate sensitivity problems and if so, how. |
| | + | </div> |
| | </div> | | </div> |
| | | | |
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| | 2: "Toolkit design solutions", | | 2: "Toolkit design solutions", |
| | 3: "Additional considerations", | | 3: "Additional considerations", |
| | + | }, |
| | + | "outreach" : { |
| | + | 1: "Outreach", |
| | + | 2: "iGEM Utrecht: an introduction", |
| | + | 3: "Meet the team", |
| | + | 3: "The problem: the detection of …", |
| | + | 4: "The solution: a biosensor that …", |
| | + | 5: "Why Chagas Disease?" |
| | + | }, |
| | + | "collaborations" : { |
| | + | 1: "", |
| | + | 2: "", |
| | + | 3: "", |
| | }, | | }, |
| | "team" : { | | "team" : { |
