Difference between revisions of "Team:Kyoto/Parts"
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| − | <td> | + | <td>BBa_K3815001</td> |
| − | <td> | + | <td>Protein Coding</td> |
| − | <td> | + | <td>ELK16-PT linker-Mxe Gyr intein-CecropinA</td> |
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<td><a href="https://2021.igem.org/Team:Kyoto/Attributions">https://2021.igem.org/Team:Kyoto/Attributions</a></td> | <td><a href="https://2021.igem.org/Team:Kyoto/Attributions">https://2021.igem.org/Team:Kyoto/Attributions</a></td> | ||
| − | <td> | + | <td>Koudai Shiotsu</td> |
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| − | <td> | + | <td>BBa_K3815002</td> |
| − | <td> | + | <td>Protein Coding</td> |
| − | <td> | + | <td>ELK16-PT linker-Mxe Gyr intein-Defensin1</td> |
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<td><a href="https://2021.igem.org/Team:Kyoto/Description">https://2021.igem.org/Team:Kyoto/Description</a></td> | <td><a href="https://2021.igem.org/Team:Kyoto/Description">https://2021.igem.org/Team:Kyoto/Description</a></td> | ||
| − | <td> | + | <td>Koudai Shiotsu</td> |
</tr> | </tr> | ||
<tr> | <tr> | ||
| − | <td> | + | <td>BBa_K3815002</td> |
| − | <td> | + | <td>Protein Coding</td> |
| − | <td> | + | <td>ELK16-PT linker-Mxe Gyr intein-Defensin1</td> |
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<td ><a href="https://2021.igem.org/Team:Kyoto/Contribution">https://2021.igem.org/Team:Kyoto/Contribution</a></td> | <td ><a href="https://2021.igem.org/Team:Kyoto/Contribution">https://2021.igem.org/Team:Kyoto/Contribution</a></td> | ||
| − | <td > | + | <td >Koudai Shiotsu</td> |
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| − | + | <td><a href="http://parts.igem.org/Part:BBa_K3815003">BBa_K3815003</a></td> | |
| − | + | <td>Protein Coding</td> | |
| − | + | <td>ELK16-PT linker-Mxe Gyr intein-LL37</td> | |
| − | + | <td></td> | |
| − | + | <td>Koudai Shiotsu</td> | |
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Revision as of 12:26, 21 October 2021
Parts
| Name | Type | Part Name | Diagram | Designer |
|---|---|---|---|---|
| BBa_K3815000 | Protein Coding | ELK16-PT linker-Mxe Gyr intein | a | Koudai Shiotsu |
| BBa_K3815001 | Protein Coding | ELK16-PT linker-Mxe Gyr intein-CecropinA | <a href="https://2021.igem.org/Team:Kyoto/Attributions">https://2021.igem.org/Team:Kyoto/Attributions</a> | Koudai Shiotsu |
| BBa_K3815002 | Protein Coding | ELK16-PT linker-Mxe Gyr intein-Defensin1 | <a href="https://2021.igem.org/Team:Kyoto/Description">https://2021.igem.org/Team:Kyoto/Description</a> | Koudai Shiotsu |
| BBa_K3815002 | Protein Coding | ELK16-PT linker-Mxe Gyr intein-Defensin1 | <a href="https://2021.igem.org/Team:Kyoto/Contribution">https://2021.igem.org/Team:Kyoto/Contribution</a> | Koudai Shiotsu | <a href="http://parts.igem.org/Part:BBa_K3815003">BBa_K3815003</a> | Protein Coding | ELK16-PT linker-Mxe Gyr intein-LL37 | Koudai Shiotsu |
| 2 | Collaboration | <svg xmlns="http://www.w3.org/2000/svg" width="16" height="16" fill="currentColor" class="bi bi-check2-square" viewBox="0 0 16 16">
<path d="M3 14.5A1.5 1.5 0 0 1 1.5 13V3A1.5 1.5 0 0 1 3 1.5h8a.5.5 0 0 1 0 1H3a.5.5 0 0 0-.5.5v10a.5.5 0 0 0 .5.5h10a.5.5 0 0 0 .5-.5V8a.5.5 0 0 1 1 0v5a1.5 1.5 0 0 1-1.5 1.5H3z"/> <path d="m8.354 10.354 7-7a.5.5 0 0 0-.708-.708L8 9.293 5.354 6.646a.5.5 0 1 0-.708.708l3 3a.5.5 0 0 0 .708 0z"/></svg> |
<a href="https://2021.igem.org/Team:Kyoto/Collaborations">https://2021.igem.org/Team:Kyoto/Collaborations</a> | This is a list of the many interactions we have had with iGEM teams during the process of our project and what we have learned from each interaction. |
| 3 | Human Practices | <svg xmlns="http://www.w3.org/2000/svg" width="16" height="16" fill="currentColor" class="bi bi-check2-square" viewBox="0 0 16 16">
<path d="M3 14.5A1.5 1.5 0 0 1 1.5 13V3A1.5 1.5 0 0 1 3 1.5h8a.5.5 0 0 1 0 1H3a.5.5 0 0 0-.5.5v10a.5.5 0 0 0 .5.5h10a.5.5 0 0 0 .5-.5V8a.5.5 0 0 1 1 0v5a1.5 1.5 0 0 1-1.5 1.5H3z"/> <path d="m8.354 10.354 7-7a.5.5 0 0 0-.708-.708L8 9.293 5.354 6.646a.5.5 0 1 0-.708.708l3 3a.5.5 0 0 0 .708 0z"/></svg> |
<a href="https://2021.igem.org/Team:Kyoto/Human_Practices">https://2021.igem.org/Team:Kyoto/Human_Practices</a> | We learned what is needed in the field from interviews with various people in the flower industry, and we showed that. In order to indicate the cultural importance of flowers, we also described what we learned from our teacher about Ikebana, a Japanese cultural art form. |
| 4 | Proposed Implementation | <svg xmlns="http://www.w3.org/2000/svg" width="16" height="16" fill="currentColor" class="bi bi-check2-square" viewBox="0 0 16 16">
<path d="M3 14.5A1.5 1.5 0 0 1 1.5 13V3A1.5 1.5 0 0 1 3 1.5h8a.5.5 0 0 1 0 1H3a.5.5 0 0 0-.5.5v10a.5.5 0 0 0 .5.5h10a.5.5 0 0 0 .5-.5V8a.5.5 0 0 1 1 0v5a1.5 1.5 0 0 1-1.5 1.5H3z"/> <path d="m8.354 10.354 7-7a.5.5 0 0 0-.708-.708L8 9.293 5.354 6.646a.5.5 0 1 0-.708.708l3 3a.5.5 0 0 0 .708 0z"/></svg> |
<a href="https://2021.igem.org/Team:Kyoto/Implementation">https://2021.igem.org/Team:Kyoto/Implementation</a> | We described the application of our project in the real world. |
| Gold Criteria | ||||
| Number | Check | Criteria | URL | Contents |
| 1 | Integrated Human Practices | <svg xmlns="http://www.w3.org/2000/svg" width="16" height="16" fill="currentColor" class="bi bi-check2-square" viewBox="0 0 16 16">
<path d="M3 14.5A1.5 1.5 0 0 1 1.5 13V3A1.5 1.5 0 0 1 3 1.5h8a.5.5 0 0 1 0 1H3a.5.5 0 0 0-.5.5v10a.5.5 0 0 0 .5.5h10a.5.5 0 0 0 .5-.5V8a.5.5 0 0 1 1 0v5a1.5 1.5 0 0 1-1.5 1.5H3z"/> <path d="m8.354 10.354 7-7a.5.5 0 0 0-.708-.708L8 9.293 5.354 6.646a.5.5 0 1 0-.708.708l3 3a.5.5 0 0 0 .708 0z"/></svg> |
<a href="https://2021.igem.org/Team:Kyoto/Human_Practices">https://2021.igem.org/Team:Kyoto/Human_Practices</a> | We repeatedly listen to various people in the flower industry to evaluate our solutions. By doing this, we understood what is needed in the field. and we improved our project.
As a result, we understood our project more deeply. In addition, the project itself got better in many ways than projects we thought at first. |
| 2 | Improvement of an Existing Part | <svg xmlns="http://www.w3.org/2000/svg" width="16" height="16" fill="currentColor" class="bi bi-check2-square" viewBox="0 0 16 16">
<path d="M3 14.5A1.5 1.5 0 0 1 1.5 13V3A1.5 1.5 0 0 1 3 1.5h8a.5.5 0 0 1 0 1H3a.5.5 0 0 0-.5.5v10a.5.5 0 0 0 .5.5h10a.5.5 0 0 0 .5-.5V8a.5.5 0 0 1 1 0v5a1.5 1.5 0 0 1-1.5 1.5H3z"/> <path d="m8.354 10.354 7-7a.5.5 0 0 0-.708-.708L8 9.293 5.354 6.646a.5.5 0 1 0-.708.708l3 3a.5.5 0 0 0 .708 0z"/></svg> |
To extend the general applicability of the production system we developed, we improved it by mutating the sequence of the proteolytic tag, SsrA tag. This improvement is based on the suggestions obtained from modeling. Although the SsrA tag usually induces very fast proteolysis in E. coli, we have created many variants and established a set of variants with different degradation rates. The collection of these parts is a resource that can be used extensively to control the rate of protein turnover within E. coli. Degradation activity was evaluated by sfGFP intensity and compared to the original parts (wild-type SsrA tag). | |
| 3 | Project Modeling | <svg xmlns="http://www.w3.org/2000/svg" width="16" height="16" fill="currentColor" class="bi bi-check2-square" viewBox="0 0 16 16">
<path d="M3 14.5A1.5 1.5 0 0 1 1.5 13V3A1.5 1.5 0 0 1 3 1.5h8a.5.5 0 0 1 0 1H3a.5.5 0 0 0-.5.5v10a.5.5 0 0 0 .5.5h10a.5.5 0 0 0 .5-.5V8a.5.5 0 0 1 1 0v5a1.5 1.5 0 0 1-1.5 1.5H3z"/> <path d="m8.354 10.354 7-7a.5.5 0 0 0-.708-.708L8 9.293 5.354 6.646a.5.5 0 1 0-.708.708l3 3a.5.5 0 0 0 .708 0z"/></svg> |
<a href="https://2021.igem.org/Team:Kyoto/Model">https://2021.igem.org/Team:Kyoto/Model</a> | We simulated the production system we developed, and confirmed that the production system based on asymmetric plasmid partitioning behaves as intended. We also used this model to evaluate the effect of varying parameters on the time of the expression of the two reporters proteins. From the above analysis, we predicted that the "repressor degradation rate" is the most sensitive parameter to control the timing of reporter expression in our production system. This prediction provided valuable suggestions for the improvement experiments of the parts described in Improvement of an Existing Part above.
In addition to the two-plasmid system that was actually used in this project, a similar model was constructed for a three-plasmid system, and we confirmed that the two-step continuous asymmetric partitioning can occur as intended. By doing this, we were able to clarify the scalability of our production system. We have also simulated the application to actual biomolecular production. This quantitatively demonstrated its superiority to ordinary continuous culture systems. |
| 4 | Proof of Concept | <svg xmlns="http://www.w3.org/2000/svg" width="16" height="16" fill="currentColor" class="bi bi-check2-square" viewBox="0 0 16 16">
<path d="M3 14.5A1.5 1.5 0 0 1 1.5 13V3A1.5 1.5 0 0 1 3 1.5h8a.5.5 0 0 1 0 1H3a.5.5 0 0 0-.5.5v10a.5.5 0 0 0 .5.5h10a.5.5 0 0 0 .5-.5V8a.5.5 0 0 1 1 0v5a1.5 1.5 0 0 1-1.5 1.5H3z"/> <path d="m8.354 10.354 7-7a.5.5 0 0 0-.708-.708L8 9.293 5.354 6.646a.5.5 0 1 0-.708.708l3 3a.5.5 0 0 0 .708 0z"/></svg> |
<a href="https://2021.igem.org/Team:Kyoto/Proof_Of_Concept">https://2021.igem.org/Team:Kyoto/Proof_Of_Concept</a> | Toward the implementation of our project in a relevant context, we completed proof of concept experiments. First, to solve the problem of viral infection in flowering plants, our experiments and prototypes include an enzymatic detection method, image-based software AI, and an integrated hardware system. Additionally, we performed experiments to address the control of plant pests, as well as conceptualized and modeled an improved biomolecule production system with broad applications in our own project and general bioprocesses. The following results establish proof of concept for each component and the project as a whole. |
| 5 | Partnership | <svg xmlns="http://www.w3.org/2000/svg" width="16" height="16" fill="currentColor" class="bi bi-check2-square" viewBox="0 0 16 16">
<path d="M3 14.5A1.5 1.5 0 0 1 1.5 13V3A1.5 1.5 0 0 1 3 1.5h8a.5.5 0 0 1 0 1H3a.5.5 0 0 0-.5.5v10a.5.5 0 0 0 .5.5h10a.5.5 0 0 0 .5-.5V8a.5.5 0 0 1 1 0v5a1.5 1.5 0 0 1-1.5 1.5H3z"/> <path d="m8.354 10.354 7-7a.5.5 0 0 0-.708-.708L8 9.293 5.354 6.646a.5.5 0 1 0-.708.708l3 3a.5.5 0 0 0 .708 0z"/></svg> |
<a href="https://2021.igem.org/Team:Kyoto/Partnership">https://2021.igem.org/Team:Kyoto/Partnership</a> | We described our efforts throughout the year in collaboration with other iGEM teams. Not only did we share information about the progress of their projects, but we actually conducted experiments to complement each other's projects by exchanging DNA, peptides, enzymes, and other molecules. These collaborations played a major role in making the projects of both teams more valuable. |
| 6 | Education & Communication | <svg xmlns="http://www.w3.org/2000/svg" width="16" height="16" fill="currentColor" class="bi bi-check2-square" viewBox="0 0 16 16">
<path d="M3 14.5A1.5 1.5 0 0 1 1.5 13V3A1.5 1.5 0 0 1 3 1.5h8a.5.5 0 0 1 0 1H3a.5.5 0 0 0-.5.5v10a.5.5 0 0 0 .5.5h10a.5.5 0 0 0 .5-.5V8a.5.5 0 0 1 1 0v5a1.5 1.5 0 0 1-1.5 1.5H3z"/> <path d="m8.354 10.354 7-7a.5.5 0 0 0-.708-.708L8 9.293 5.354 6.646a.5.5 0 1 0-.708.708l3 3a.5.5 0 0 0 .708 0z"/></svg> |
<a href="https://2021.igem.org/Team:Kyoto/Communication">https://2021.igem.org/Team:Kyoto/Communication</a> | We described the educational activities we have conducted to promote synthetic biology. This activity was not only an opportunity to provide new knowledge to high school students interested in synthetic biology but also an opportunity for our team to understand the significance of synthetic biology more deeply by giving lectures to students. The linked page provides the actual materials used for education for future teams to develop similar educational activities. |
| 7 | Excellence in Another Area | <svg xmlns="http://www.w3.org/2000/svg" width="16" height="16" fill="currentColor" class="bi bi-check2-square" viewBox="0 0 16 16">
<path d="M3 14.5A1.5 1.5 0 0 1 1.5 13V3A1.5 1.5 0 0 1 3 1.5h8a.5.5 0 0 1 0 1H3a.5.5 0 0 0-.5.5v10a.5.5 0 0 0 .5.5h10a.5.5 0 0 0 .5-.5V8a.5.5 0 0 1 1 0v5a1.5 1.5 0 0 1-1.5 1.5H3z"/> <path d="m8.354 10.354 7-7a.5.5 0 0 0-.708-.708L8 9.293 5.354 6.646a.5.5 0 1 0-.708.708l3 3a.5.5 0 0 0 .708 0z"/></svg> |
<a href="https://2021.igem.org/Team:Kyoto/Gift_from_Synthetic_Biology">https://2021.igem.org/Team:Kyoto/Gift_from_Synthetic_Biology</a> | What can synthetic biology and participating in iGEM bring to students? This time, we visited new startups founded by the members of iGEM Kyoto 10 years ago. We interviewed them to find out how their experience at iGEM has changed their lives and helped them to launch their startups. By listening to and thinking about the stories of our seniors, the true meaning of our activities at iGEM, which we hadn't noticed before, gradually began to emerge. |
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