Difference between revisions of "Team:Vilnius-Lithuania/Medals"

 
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<h1 class="text-wall-heading">Medals</h1>
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    <h2 class="text-wall-area-box-heading">Getting the Metals</h2>
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      <h2 class="text-wall-area-box-heading">Getting the Metals</h2>
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        <p class="text-content">Cell-free systems are becoming an increasingly popular in vitro tool to study biological processes as it is accompanied by less intrinsic and extrinsic noise. Relying on fundamental concepts of synthetic biology, we apply a bottom-up forward engineering approach to create a novel cell-free system for unorthodox protein-evolution. The core of this system is cell-sized liposomes that serve as excellent artificial membrane models. By encapsulating genetic material and full in vitro protein transcription and translation systems within the liposomes, we create reliable and incredibly efficient nanofactories for the production of target proteins. Even though there are many alternative proteins that can be synthesized, our main focus is directed towards membrane proteins, which occupy approximately one third of living-cells’ genomes. Considering their significance, membrane proteins are spectacularly understudied since synthesis and thus characterization of them remain prevailing obstacles to this day. We aim to utilize liposomes as nanofactories for directed evolution of membrane proteins. Furthermore, by means of directed membrane protein-evolution, a universal exposition system will be designed in order to display any protein of interest on the surface of the liposome. This way, a system is built where a phenotype of a particular protein is expressed on the outside while containing its genotype within the liposome. To prove the concept, small antibody fragments will be displayed to create a single-chain variable fragment (scFv) library for rapid screening of any designated target.</p>
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        <p class="text-content">Our team did a miraculous job during the eight months of the SynDrop project. To ease the process of finding relevant documentation we have provided an overview which shows that we have achieved the requirements to be awarded the medals and special prizes at the iGEM 2018 competition.</p>
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        <h1>Description</h1>
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        <h1>Medals</h1>
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        <h2>What is SynORI?</h2>
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        <p>SynORI stands for synthetic origin of replication. It is a framework designed to make working with single
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             and multi-plasmid systems precise, easy and on top of that - more functional.</p>
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        <p>The SynORI framework enables scientists to build a multi-plasmid system in a standardized manner by:</p>
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                  <td class="s0"><span style="font-size:11pt;font-family:Calibri,Arial;">MEDAL</span></td>
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                  <td class="s0"><span style="font-size:11pt;font-family:Calibri,Arial;color:#000000;">CRITERIA</span></td>
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            <li>Selecting the number of plasmid groups</li>
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                  <td class="s0"><span style="font-size:11pt;font-family:Calibri,Arial;color:#000000;">FULFILLMENT</span></td>
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            <li>Choosing the copy number of each group</li>
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            <li>Picking the type of copy number control (specific to one group or regulating all of them at once).</li>
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                  <td style="background-color:#cd7f32" class="s1" rowspan="7"><span style="font-size:11pt;font-family:Calibri,Arial;">Bronze</span></td>
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                  <td class="s2"><span style="font-size:11pt;font-family:Calibri,Arial;color:#000000;">Registration and Giant Jamboree Attendance</span></td>
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        <p></p>
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                  <td class="s3"><span style="font-size:11pt;font-family:Calibri,Arial;color:#000000;">Team Vilnius-Lithuania (also known as Komanda X) is ready to attend the Giant Jamboree after having a great iGEM season.  </span></td>
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        <p>The framework also includes a possibility of adding a selection system that reduces the usage of antibiotics
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            (only 1 antibiotic for up to 5 different plasmids!) and an active partitioning system to make sure that low
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            copy number plasmid groups are not lost during the division.
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                  <td class="s2" rowspan="4"><span style="font-size:11pt;font-family:Calibri,Arial;color:#000000;">Competition Deliverables </span></td>
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        </p>
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                  <td class="s3"><span style="font-size:11pt;font-family:Calibri,Arial;color:#000000;">All of the stages of developing the SynDrop idea and presenting it to the general public are provided here, on our wiki page (<a href="https://2018.igem.org/Team:Vilnius-Lithuania/Main">https://2018.igem.org/Team:Vilnius-Lithuania/Main</a>). </span></td>
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                  <td class="s3"><span style="font-size:11pt;font-family:Calibri,Arial;color:#000000;">We have designed an informative poster in order to convey the idea of our project to the judges and other iGEM&#39;ers. </span></td>
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                  <td class="s3"><span style="font-size:11pt;font-family:Calibri,Arial;color:#000000;">The story of SynDrop was put into a 20 minute resumptive presentation, which will be held on Friday. </span></td>
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        <h2>Applications</h2>
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        <p>
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            <h5>Everyday lab work</h5>
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                  <td class="s3">The Judging Form<span style="font-size:11pt;font-family:Calibri,Arial;color:#000000;"> (<a href="https://igem.org/2018_Judging_Form?id=2622">https://igem.org/2018_Judging_Form?id=2622</a>) was completed responsibly to convince judges we have done our best.</span></td>
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                A multi-plasmid system that is easy to assemble and control. With our framework the need to limit your
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                research to a particular plasmid copy number just because there are not enough right replicons to
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                  <td class="s2"><span style="font-size:11pt;font-family:Calibri,Arial;color:#000000;">Attributions</span></td>
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                choose from, is eliminated. With SynORI you can easily create a vector with a desired copy number that
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                  <td class="s3"><span style="font-size:11pt;font-family:Calibri,Arial;color:#000000;">People who helped us throughout our project in areas where we needed their competences and advice are presented in the Attributions page (<a href="https://2018.igem.org/Team:Vilnius-Lithuania/Attributions">https://2018.igem.org/Team:Vilnius-Lithuania/Attributions</a>). </span></td>
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                suits your needs.</li>
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            <h5>Biological computing</h5>
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                  <td class="s5"><span style="font-size:11pt;font-family:Calibri,Arial;color:#000000;"> Characterization</span></td>
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            <p>
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                  <td class="s3"><span style="font-size:11pt;font-family:Calibri,Arial;color:#000000;">The InterLab Study (<a href="https://2018.igem.org/Team:Vilnius-Lithuania/InterLab">https://2018.igem.org/Team:Vilnius-Lithuania/InterLab</a>) succeeded in identifying and minimizing the sources of systematic variability in fluorescence measurements and the data was accepted by the Measurement Committee. </span></td>
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                The ability to choose a wide range of copy number options and their control types will make the
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                synthetic biology engineering much more flexible and predictable. Introduction of plasmid copy number
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                regulation is equivalent to adding a global parameter to a computer system. It enables the coordination
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                  <td style="background-color:#D3D3D3" class="s6" rowspan="3"><span style="font-size:11pt;font-family:Calibri,Arial;color:#000000;">Silver</span></td>
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                of multiple gene group expression.
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                  <td class="s7"><span style="font-size:11pt;font-family:Calibri,Arial;color:#000000;">Validated Part </span></td>
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            </p>
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                  <td class="s8"><span style="font-size:11pt;font-family:Calibri,Arial;color:#000000;">We have sent 48 BioBrick Parts : 25 basic parts and 23 composite parts. They can be found here (<a style="color:#002bb8" href="http://parts.igem.org/cgi/dna_transfer/one_batch.cgi?batch_id=5321">http://parts.igem.org/cgi/dna_transfer/one_batch.cgi?batch_id=5321</a>) and used by all in the iGEM community.</span></td>
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            <h5>Smart assembly of large protein complexes</h5>
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            <p>
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                The co-expression of multi-subunit complexes using different replicons brings incoherency to an already
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                  <td class="s9"><span style="font-size:11pt;font-family:Calibri,Arial;color:#000000;">Collaboration</span></td>
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                chaotic cell system. This can be avoided by using SynORI, as in this framework every plasmid group uses
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                  <td class="s8"><span style="font-size:11pt;font-family:Calibri,Arial;color:#000000;">We had 6 bi-directional and uni-directional collaborations with iGEM teams from different countries! All collaborations with descriptions can be found on Contributions (<a href="https://2018.igem.org/Team:Vilnius-Lithuania/Collaborations">https://2018.igem.org/Team:Vilnius-Lithuania/Collaborations</a>) page. </span></td>
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                the same type of control, and in addition can act in a group-specific manner.</p>
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            <h5>Metabolic engineering</h5>
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                  <td class="s9"><span style="font-size:11pt;font-family:Calibri,Arial;color:#000000;">Human Practices</span></td>
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            <p>
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                  <td class="s8"><span style="font-size:11pt;font-family:Calibri,Arial;color:#000000;">While passing on our experience to pupils and celebrating DNA Day with the community, we presented our project as widely applicable cell-free system. The &quot;DIY-science&quot; workshop successfully encouraged people to try scientists&#39; daily routine, as well as inspired us to educate them outside the laboratory.</span></td>
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                A big challenge for heterologous expression of multiple gene pathways is to accurately adjust the
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                levels of each enzyme to achieve optimal production efficiency. Precise promoter tuning in
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                transcriptional control and synthetic ribosome binding sites in translational control are already
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                  <td style="background-color:#FFD700" class="s10" rowspan="4"><span style="font-size:11pt;font-family:Calibri,Arial;color:#000000;">Gold</span></td>
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                widely used to maintain expression levels. In addition to current approaches, our framework allows a
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                  <td class="s11"><span style="font-size:11pt;font-family:Calibri,Arial;color:#000000;">Integrated Human Practices</span></td>
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                simultaneous multiple gene control. Furthermore, an inducible regulation that we offer, can make the
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                  <td class="s8"><span style="font-size:11pt;font-family:Calibri,Arial;color:#000000;">Inspired by discussions with the stakeholders during the DNA Day celebration, we had organised the international life sciences BioHackathon which helped spawn the base for our software tool LipoVision (<a href="https://2018.igem.org/Team:Vilnius-Lithuania/Software">https://2018.igem.org/Team:Vilnius-Lithuania/Software</a>).</span></td>
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                search for perfect conditions a lot easier.
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                  <td class="s11"><span style="font-size:11pt;font-family:Calibri,Arial;color:#000000;">Improve a previous part</span></td>
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                  <td class="s8"><span style="font-size:11pt;font-family:Calibri,Arial;color:#000000;">While using an existing BioBrick Part OmpA_full-His, we have created a new one (<a style="color:#002bb8" href="http://parts.igem.org/Part:BBa_K2622047">http://parts.igem.org/Part:BBa_K2622047</a>) by adding Mstx to it.</span></td>
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                  <td class="s11"><span style="font-size:11pt;font-family:Calibri,Arial;color:#000000;">Model your project</span></td>
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                  <td class="s8"><span style="font-size:11pt;font-family:Calibri,Arial;color:#000000;">We created several models that characterize and improve different parts of our project: membrane protein insertion, liposome synthesis through microfluidics, BamA transcription/translation in IVTT systems and efficiency of thermoswitches. All models can be found on our wiki page (<a href="https://2018.igem.org/Team:Vilnius-Lithuania/Model">Model</a>).</span></td>
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                  <td class="s11"><span style="font-size:11pt;font-family:Calibri,Arial;color:#000000;">Demonstrate your work</span></td>
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                  <td class="s8"><span style="font-size:11pt;font-family:Calibri,Arial;color:#000000;">Numerous experiments were conducted to ascertain that our system is functionally active. We obtained indisputable results and demonstrated that MPs can successefully be inserted into the liposome membrane and therefore can perform their intended function. SynDrop both works and complies with all rules and regulations approved by the iGEM Safety Committee. All results can be found in our wiki page (<a style="color:#002bb8" href="https://2018.igem.org/Team:Vilnius-Lithuania/Demonstrate">https://2018.igem.org/Team:Vilnius-Lithuania/Demonstrate</a>).</span></td>
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<td align='center'>Species sign in ODE system</td>
 
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<td align='center'>Species</td>
 
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<td align='center'>Initial concentration (M)</td>
 
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<td align='center'>A</td>
 
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<td align='center'>pDNA+RNA I+RNAII early</td>
 
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<td align='center'>0</td>
 
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<td align='center'>B</td>
 
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<td align='center'>pDNA+RNA II short</td>
 
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<td align='center'>RNAI</td>
 
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<td align='center'>RNA I</td>
 
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<td align='center'>1E-6</td>
 
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<td align='center'>D</td>
 
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<td align='center'>pDNA+RNA II long</td>
 
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<td align='center'>0</td>
 
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<td align='center'>E</td>
 
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<td align='center'>RNA II long</td>
 
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<td align='center'>0</td>
 
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<td align='center'>G</td>
 
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<td align='center'>4E-8*</td>
 
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<td align='center'>H</td>
 
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<td align='center'>0</td>
 
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<td align='center'>RNA II</td>
 
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<td align='center'>0</td>
 
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<td align='center'>J</td>
 
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Latest revision as of 20:31, 4 November 2018

Medals

Getting the Metals

Our team did a miraculous job during the eight months of the SynDrop project. To ease the process of finding relevant documentation we have provided an overview which shows that we have achieved the requirements to be awarded the medals and special prizes at the iGEM 2018 competition.

Medals

MEDAL CRITERIA FULFILLMENT
Bronze Registration and Giant Jamboree Attendance Team Vilnius-Lithuania (also known as Komanda X) is ready to attend the Giant Jamboree after having a great iGEM season.
Competition Deliverables All of the stages of developing the SynDrop idea and presenting it to the general public are provided here, on our wiki page (https://2018.igem.org/Team:Vilnius-Lithuania/Main).
We have designed an informative poster in order to convey the idea of our project to the judges and other iGEM'ers.
The story of SynDrop was put into a 20 minute resumptive presentation, which will be held on Friday.
The Judging Form (https://igem.org/2018_Judging_Form?id=2622) was completed responsibly to convince judges we have done our best.
Attributions People who helped us throughout our project in areas where we needed their competences and advice are presented in the Attributions page (https://2018.igem.org/Team:Vilnius-Lithuania/Attributions).
Characterization The InterLab Study (https://2018.igem.org/Team:Vilnius-Lithuania/InterLab) succeeded in identifying and minimizing the sources of systematic variability in fluorescence measurements and the data was accepted by the Measurement Committee.
Silver Validated Part We have sent 48 BioBrick Parts : 25 basic parts and 23 composite parts. They can be found here (http://parts.igem.org/cgi/dna_transfer/one_batch.cgi?batch_id=5321) and used by all in the iGEM community.
Collaboration We had 6 bi-directional and uni-directional collaborations with iGEM teams from different countries! All collaborations with descriptions can be found on Contributions (https://2018.igem.org/Team:Vilnius-Lithuania/Collaborations) page.
Human Practices While passing on our experience to pupils and celebrating DNA Day with the community, we presented our project as widely applicable cell-free system. The "DIY-science" workshop successfully encouraged people to try scientists' daily routine, as well as inspired us to educate them outside the laboratory.
Gold Integrated Human Practices Inspired by discussions with the stakeholders during the DNA Day celebration, we had organised the international life sciences BioHackathon which helped spawn the base for our software tool LipoVision (https://2018.igem.org/Team:Vilnius-Lithuania/Software).
Improve a previous part While using an existing BioBrick Part OmpA_full-His, we have created a new one (http://parts.igem.org/Part:BBa_K2622047) by adding Mstx to it.
Model your project We created several models that characterize and improve different parts of our project: membrane protein insertion, liposome synthesis through microfluidics, BamA transcription/translation in IVTT systems and efficiency of thermoswitches. All models can be found on our wiki page (Model).
Demonstrate your work Numerous experiments were conducted to ascertain that our system is functionally active. We obtained indisputable results and demonstrated that MPs can successefully be inserted into the liposome membrane and therefore can perform their intended function. SynDrop both works and complies with all rules and regulations approved by the iGEM Safety Committee. All results can be found in our wiki page (https://2018.igem.org/Team:Vilnius-Lithuania/Demonstrate).
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