Team:UNITN-Trento/Achievements

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<ul>
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<li><a href="https://2012.igem.org/Team:UNITN-Trento">Home</a></li>
<li><a href="https://2012.igem.org/Team:UNITN-Trento">Home</a></li>
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<li class="folder"><a href="javascript:void(0);">Project</a>
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<h2 style="text-align: center;">Achievements</h2>
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<h2 style="text-align: center;">Attributions</h2>
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<div class="content attributions" style="padding-left: 20px ;padding-right: 20px ;">
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<div id="medals" style="width: 251px; margin: 0 auto;"><img src="http://www.science.unitn.it/~igem/img/medals.png" alt="" /></div>
 
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<p style="text-align: center;">We believe our team deserves a <b>Gold</b> medal, because we met the following criteria:</p>
 
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<h3>Bronze Requirements:</h3>
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<h3>IDEA</h3>
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<ul class="judging">
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<p>The idea of Crustaway has been always in the back of our minds since Daniele proposed it in our first meeting in March. <br />
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<li><img class="medal" src="http://www.science.unitn.it/~igem/img/bronze.png"></img><img class="check" src="http://www.science.unitn.it/~igem/img/check.png"></img><a href="https://igem.org/Team.cgi?id=731">Register the team</a>, have a great summer, and plan to have fun at the Regional Jamboree.</li>
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However, the idea started to take off when Jason found an interesting paper by J. Keasling where they used two genes to reduce sulfate with the ultimate goal of precipitating metals. Since then everybody worked on the planning of the project. <br />
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<li><img class="medal" src="http://www.science.unitn.it/~igem/img/bronze.png"></img><img class="check" src="http://www.science.unitn.it/~igem/img/check.png"></img>Successfully complete and submit this iGEM 2012 Judging form.</li>
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Anna and Giacomo with some help from Sheref designed the Terminator 5 project.</p>
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<li><img class="medal" src="http://www.science.unitn.it/~igem/img/bronze.png"></img><img class="check" src="http://www.science.unitn.it/~igem/img/check.png"></img>Create and share a <a href="https://2012.igem.org/Team:UNITN-Trento/Project/CrustAway">Description of the team's project using the iGEM wiki</a> and the <a href="http://partsregistry.org/cgi/partsdb/pgroup.cgi?pgroup=iGEM2012&group=UNITN-Trento">team's parts using the Registry of Standard Biological Parts</a>.</li>
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<li><img class="medal" src="http://www.science.unitn.it/~igem/img/bronze.png"></img><img class="check" src="http://www.science.unitn.it/~igem/img/check.png"></img>Plan to present a Poster and Talk at the iGEM Jamboree.</li>
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<li><img class="medal" src="http://www.science.unitn.it/~igem/img/bronze.png"></img><img class="check" src="http://www.science.unitn.it/~igem/img/check.png"></img>
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<p>Enter information detailing at least one new standard BioBrick Part or Device in the Registry of Standard Biological Parts.</p>
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<p>We have planned, constructed <a href="http://partsregistry.org/cgi/partsdb/pgroup.cgi?pgroup=iGEM2012&group=UNITN-Trento">18 new Parts</a>. For each Part we have provided to the Registry:
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<ul>
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<li>Primary nucleic acid sequence</li>
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<li>Description of function</li>
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<li>Authorship</li>
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<li>Safety notes, if relevant.</li>
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<li>Acknowledgment of sources and references</li>
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</ul>
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    </p>
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</li>
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<li><img class="medal" src="http://www.science.unitn.it/~igem/img/bronze.png"></img><img class="check" src="http://www.science.unitn.it/~igem/img/check.png"></img><p>Submit DNA for at least one new BioBrick Part or Device to the Registry.</p><p>We have submitted to the Registry <a href="http://partsregistry.org/cgi/partsdb/pgroup.cgi?pgroup=iGEM2012&group=UNITN-Trento">18 new Parts</a> and 3 improved existing Parts</p></li>
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</ul>
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<h3>Additional Requirements for a Silver Medal</h3>
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<h3>CONSTRUCT DESIGN</h3>
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<ul class="judging">
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<h4>Crust Away</h4>
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<li><img class="medal" src="http://www.science.unitn.it/~igem/img/silver.png"></img><img class="check" src="http://www.science.unitn.it/~igem/img/check.png"></img>
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<p>Most of the constructs were planned by Giacomo and Daniele, with some help from Cristina.<br />
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<p>Demonstrate that at least one new BioBrick Part or Device of your own design and construction works as expected; characterize the operation of your new Part/Device.</p>
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The constructs for the GFP fusion were designed by Jason, Andrea and Francesco.</p>
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<p>We have characterized 15 new Parts/Devices.
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We have demonstrated that all 15 Parts worked as expected.  For a description of our Parts go to our <a href="https://2012.igem.org/Team:UNITN-Trento/Parts">Parts page</a>.
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Here is a brief description to our favorite parts:
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<ul>
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<li>K731030:  A serine acetyltransferase (CysE) controlled by an arabinose inducible system. This is a key part in our black crust project: a device used to reduce sulfate that ultimately produces cysteine</li>
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<li>K731400: Our favorite BioBrick encoding for a cysteine desulfhydrase, controlled by an IPTG inducible cassette. This is the second key part for the Crustaway project. This BioBrick produces an enzyme that uses cysteine as the substrate to form sulfidric acid.
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</li>
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<li>K731020: our new entry in the terminator collections of the Registry: a T7 terminator! This terminator was characterized with both T7 and <i>E. coli</i> polymerases.
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</li>
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</ul>
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</p>
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</li>
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<li><img class="medal" src="http://www.science.unitn.it/~igem/img/silver.png"></img><img class="check" src="http://www.science.unitn.it/~igem/img/check.png"></img>
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<p>Enter this information and other documentation on the Part's 'Main Page' section of the Registry.</p>
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<p>We have entered in the Registry informations and characterizations of the following Parts:</p>
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<ul>
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<li>Part Numbers: <a href="http://partsregistry.org/Part:BBa_K731000">BBa_K731000</a>, <a href="http://partsregistry.org/Part:BBa_K731010">BBa_K731010</a>, <a href="http://partsregistry.org/Part:BBa_K731020">BBa_K731020</a>, <a href="http://partsregistry.org/Part:BBa_K731030">BBa_K731030</a>, <a href="http://partsregistry.org/Part:BBa_K731040">BBa_K731040</a>, <a href="http://partsregistry.org/Part:BBa_K731201">BBa_K731201</a>, <a href="http://partsregistry.org/Part:BBa_K731250">BBa_K731250</a>, <a href="http://partsregistry.org/Part:BBa_K731255">BBa_K731255</a>, <a href="http://partsregistry.org/Part:BBa_K731400">BBa_K731400</a>, <a href="http://partsregistry.org/Part:BBa_K731480">BBa_K731480</a>, <a href="http://partsregistry.org/Part:BBa_K731520">BBa_K731520</a>, <a href="http://partsregistry.org/Part:BBa_K731700">BBa_K731700</a>, <a href="http://partsregistry.org/Part:BBa_K731701">BBa_K731701</a>, <a href="http://partsregistry.org/Part:BBa_K731702">BBa_K731702</a>, <a href="http://partsregistry.org/Part:BBa_K731710">BBa_K731710</a>, <a href="http://partsregistry.org/Part:BBa_K731711">BBa_K731711</a>, <a href="http://partsregistry.org/Part:BBa_K731712">BBa_K731712</a>, <a href="http://partsregistry.org/Part:BBa_K731721">BBa_K731721</a>
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</li>
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</ul>
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</li>
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</ul>
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<h3>Additional Requirements for a Gold Medal</h3>
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<h4>Terminator 5</h4>
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<ul class="judging">
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<p>We started to build our platform from a plasmid of the Mansy lab (RL024), made by one of our advisors Roberta Lentini. Starting from this construct we mutated three illegal sites and we added a prefix and a suffix between the two fluorescent proteins.<br />  
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<li><img class="medal" src="http://www.science.unitn.it/~igem/img/gold.png"></img><img class="check" src="http://www.science.unitn.it/~igem/img/check.png"></img>
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All the constructs for this project were designed by Giacomo and Anna, with initial help of Cristina.</p>
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<p>Improve an existing BioBrick Part or Device and enter this information back on the Experience Page of the Registry.</p>
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<p>We have improved 2 existing BioBricks from the registry: B0010 and K314111. Our new entries are:
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<h3>CLONING & CHARACTERIZATION</h3>
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<ul>
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<h4>CysDes Parts:</h4>
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<li><a href="http://partsregistry.org/Part:BBa_K731722">BBa_K731722</a> (new entry for B0010)</li>
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<p>Andrea built and characterized Parts: K731300, K731400, K731450 (i.e. K731400 in pSB4K5), K731480.<br />
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<li><a href="http://partsregistry.org/Part:BBa_K731300">BBa_K731300</a> (new entry for K314111)</li>
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The initial gene encoding CysDes was synthetized by Genescript and then subcloned into our Parts.<br />
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<li><a href="http://partsregistry.org/Part:BBa_K731722">BBa_K731500</a> (new entry for K314111)</li>
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Gas chromatography measurements were done by Damiano Avi.</p>
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</ul>
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<h4>CysE Parts:</h4>
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</p>
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<p>Jason has cloned and characterized Parts: K731000, K731010, K731020, K731030, K731025 (i.e. part K731020 in pSB3C5), K731035 (i.e. K731030 in pSB3C5), K731040, K731045 (i.e. K731040 in pSB3C5).</p>
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<p>With <a href="http://partsregistry.org/Part:BBa_K731722">BBa_K731722</a> we provided a valid functioning alternative to <a href="http://partsregistry.org/Part:BBa_B001">BBa_B0010</a>, which is a transcriptional terminator deposited in the Registry. Part <a href="http://partsregistry.org/Part:BBa_B001">BBa_B0010</a> from the registry was inconsistent (i.e. the gel did not show any insert of the right size) and no functional characterization was available. Others in the past have tried to use this part and failed.(http://partsregistry.org/Part:BBa_B0010:Experience , http://openwetware.org/wiki/Cconboy:Terminator_Characterization/Results). Therefore we have amplified <a href="http://partsregistry.org/Part:BBa_B001">BBa_B0010</a> from BBa_E0840 and subcloned into pSB1C3. We have now resubmitted a well functioning B0010 terminator and named it <a href="http://partsregistry.org/Part:BBa_K731722">BBa_K731722</a>.  We have documented our entry in the Experience section of <a href="http://partsregistry.org/Part:BBa_B001">BBa_B0010</a>. <br/> <br/></p>
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<h4>Promoters Parts:</h4>
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<p>With <a href="http://partsregistry.org/Part:BBa_K731300">BBa_K731300</a> and <a href="http://partsregistry.org/Part:BBa_K731500">BBa_K731500</a> we are providing two new ready to use IPTG inducible cassette that are an improvement of Part <a href="http://partsregistry.org/Part:K314111">BBa_K314111</a>. <br />
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<p>Daniele worked on the following Parts: K731200, K731201, K731250, K731255 , K731260 (i.e.  in pSB3C5).<br />
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Daniele also helped Jason with the characterization of K731040.<br />
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<a href="http://partsregistry.org/Part:BBa_K731300">BBa_K731300</a> is a part that encodes for the LacI protein controlled by the constitutive lacIq promoter in the reverse direction. We have chosen the reverse direction to avoid complications arising from RNA polymerases.<br />
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Francesco built and characterized Parts: K731500, K731510, K731520, K731530 and gave some help in characterizing K731480.</p>
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<a href="http://partsregistry.org/Part:BBa_K731500">BBa_K731500</a> is a composite part that consists of <a href="http://partsregistry.org/Part:BBa_K731300">BBa_K731300</a> followed by a tac promoter and a lac operator, both in the forward direction. Several entries are listed in the Registry for lacI or lacIq. However, there is no “ready to go” device available. Our two new entries make it easier for Registry users to build IPTG inducible devices.
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<h4>Terminators Parts:</h4>
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</p>
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<p>Anna and Giacomo built and characterized together all the Parts for the terminators project: K731700, K731701, K731710, K731711, K731721, K731722.<br />
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</li><br />
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Anna and Giacomo developed a new method to use the platform. Sheref contributed with both humor and important suggestions.</p>
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<li><img class="medal" src="http://www.science.unitn.it/~igem/img/gold.png"></img>Help another iGEM team</li>
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<li><img class="medal" src="http://www.science.unitn.it/~igem/img/gold.png"></img><img class="check" src="http://www.science.unitn.it/~igem/img/check.png"></img>
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<h3>APPLICATIONS</h3>
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<p>Outline and detail a new approach to an issue of Human Practice in synthetic biology as it relates to your project, such as safety, security, ethics, or ownership, sharing, and innovation.</p>
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<p>The black crust bioremediation pathway was put together by Daniele, Francesco e Jason.<br />
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<ul>
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The Crustanator was an idea of Cristina and was built by Daniele and Francesco with some technical suggestions of Damiano. <br />
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<li>We have compiled “The SRB handbook – safety guidelines for H<sub>2</sub>S producing bacteria” to share our experience and help other iGEM teams working safely with H<sub>2</sub>S and H<sub>2</sub>S producing bacteria in the laboratory. The handbook is available in our wiki page under the <a href="https://2012.igem.org/Team:UNITN-Trento/H2S">H<sub>2</sub>S</a> section of our lab notes.</li>
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Everybody had fun together cleaning the statues!</p>
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<li> We also have taken steps to introduce experts in the field to our new approach. We have interviewed a sculpturist, a geologist, a restorer, a chemical engineer who works in stone restoration, and one of the authority in conservation of arts and monuments of Trento. A merge between Art and Science to validate the usefulness of our method and how that would have an impact on the art of stones restoration and conservation. The results of our survey are posted in the <a href="https://2012.igem.org/Team:UNITN-Trento/ART">Art and Science</a> section of our wiki.</li>
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</ul>
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<p>Scanning Electron Microscopy Images were taken at the facility of SEM in the department of Engineering.</p>
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</li>
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</ul>
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<h3>WEBSITE</h3>
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<p>Our Wiki was designed by Jason, who also put all the content together. Everybody worked on the content of the Wiki.</p>
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<h3>ART & SCIENCE</h3>
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<p>Although, we all took part to the interviews, this aspect of the project was mostly cured by Andrea and Anna.</p>
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<h3>EVENTS</h3>
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<p>Anna organized with Roberta the “3 open days” at the Museum of Science for high school teachers.<br />
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Francesco and Roberta organized The Researchers Night.<br />
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Everybody participated to the events.</p>
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<h3>SAFETY</h3>
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<p>Francesco and Cristina wrote the SRB safety handbook. Marzia Filippi from the Safety office of the University of Trento revised the text. UniTN communication office helped with the graphic of the pamphlet.</p>
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<h3>POSTER, PRESENTATION & LOGO</h3>
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<p>Our poster was designed by Andrea with some help from Laura.<br />
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The logo was designed by Daniele.<br />
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Everybody worked on the presentation.</p>
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<h3>TRAINING and ICECREAMS…</h3>
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<p>…were brought in by Cristina.</p>
</div> <!--end content-->
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Revision as of 21:17, 19 September 2012

Attributions

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Attributions

IDEA

The idea of Crustaway has been always in the back of our minds since Daniele proposed it in our first meeting in March.
However, the idea started to take off when Jason found an interesting paper by J. Keasling where they used two genes to reduce sulfate with the ultimate goal of precipitating metals. Since then everybody worked on the planning of the project.
Anna and Giacomo with some help from Sheref designed the Terminator 5 project.

CONSTRUCT DESIGN

Crust Away

Most of the constructs were planned by Giacomo and Daniele, with some help from Cristina.
The constructs for the GFP fusion were designed by Jason, Andrea and Francesco.

Terminator 5

We started to build our platform from a plasmid of the Mansy lab (RL024), made by one of our advisors Roberta Lentini. Starting from this construct we mutated three illegal sites and we added a prefix and a suffix between the two fluorescent proteins.
All the constructs for this project were designed by Giacomo and Anna, with initial help of Cristina.

CLONING & CHARACTERIZATION

CysDes Parts:

Andrea built and characterized Parts: K731300, K731400, K731450 (i.e. K731400 in pSB4K5), K731480.
The initial gene encoding CysDes was synthetized by Genescript and then subcloned into our Parts.
Gas chromatography measurements were done by Damiano Avi.

CysE Parts:

Jason has cloned and characterized Parts: K731000, K731010, K731020, K731030, K731025 (i.e. part K731020 in pSB3C5), K731035 (i.e. K731030 in pSB3C5), K731040, K731045 (i.e. K731040 in pSB3C5).

Promoters Parts:

Daniele worked on the following Parts: K731200, K731201, K731250, K731255 , K731260 (i.e. in pSB3C5).
Daniele also helped Jason with the characterization of K731040.
Francesco built and characterized Parts: K731500, K731510, K731520, K731530 and gave some help in characterizing K731480.

Terminators Parts:

Anna and Giacomo built and characterized together all the Parts for the terminators project: K731700, K731701, K731710, K731711, K731721, K731722.
Anna and Giacomo developed a new method to use the platform. Sheref contributed with both humor and important suggestions.

APPLICATIONS

The black crust bioremediation pathway was put together by Daniele, Francesco e Jason.
The Crustanator was an idea of Cristina and was built by Daniele and Francesco with some technical suggestions of Damiano.
Everybody had fun together cleaning the statues!

Scanning Electron Microscopy Images were taken at the facility of SEM in the department of Engineering.

WEBSITE

Our Wiki was designed by Jason, who also put all the content together. Everybody worked on the content of the Wiki.

ART & SCIENCE

Although, we all took part to the interviews, this aspect of the project was mostly cured by Andrea and Anna.

EVENTS

Anna organized with Roberta the “3 open days” at the Museum of Science for high school teachers.
Francesco and Roberta organized The Researchers Night.
Everybody participated to the events.

SAFETY

Francesco and Cristina wrote the SRB safety handbook. Marzia Filippi from the Safety office of the University of Trento revised the text. UniTN communication office helped with the graphic of the pamphlet.

POSTER, PRESENTATION & LOGO

Our poster was designed by Andrea with some help from Laura.
The logo was designed by Daniele.
Everybody worked on the presentation.

TRAINING and ICECREAMS…

…were brought in by Cristina.

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