Team:UCSF UCB/judging.html

From 2014.igem.org

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<p class = "requirement">Team Registration</p>
<p class = "requirement">Team Registration</p>
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<p>Team UCSF_UCB is signed up for the collegiate division of the iGEM competition. <a href = "https://igem.org/Team.cgi?id=1346">Our official team registration</a>.</p>
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<p>Team UCSF_UCB is signed up for the collegiate division of the iGEM competition as an "undergraduate" team. <a href = "https://igem.org/Team.cgi?id=1346">Our official team registration</a>.</p>
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<p class = "requirement">Improve the function OR characterization of an existing BioBrick Part or Device (created by another team or your own institution in a previous year), enter this information in the Registry. </p>
<p class = "requirement">Improve the function OR characterization of an existing BioBrick Part or Device (created by another team or your own institution in a previous year), enter this information in the Registry. </p>
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<p>UCSF_UCB has improved the characterization for the yeast TEF1 promoter. This part has been submitted multiple times by multiple teams, resulting in 3 twin parts in the registry (BBa_K431008, BBa_K563004, and BBA_K319003).  We have improved all of these parts by adding on a graph displaying the expression strength the TEF1 promoter. We measured the expression level of GFP and compared it alongside pTEF1 mutants and established a comparison of its strength as a constitutive promoter.</p>
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<p>UCSF_UCB has improved the characterization for the yeast TEF1 promoter. This part has been submitted multiple times by multiple teams, resulting in 3 twin parts in the registry (<a href = "http://parts.igem.org/Part:BBa_K431008">BBa_K431008</a>,<a href = "http://parts.igem.org/Part:BBa_K563004"> BBa_K563004</a>, and <a href = "http://parts.igem.org/Part:BBa_K319003">BBa_K319003</a>).  We have improved all of these parts by adding on a graph displaying the expression strength the TEF1 promoter. We measured the expression level of GFP and compared it alongside pTEF1 mutants and established a comparison of its strength as a constitutive promoter.</p>
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<p class = "requirement">Help any registered iGEM team from another school or institution by, for example, characterizing a part, debugging a construct, or modeling or simulating their system</p>
<p class = "requirement">Help any registered iGEM team from another school or institution by, for example, characterizing a part, debugging a construct, or modeling or simulating their system</p>
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<p>In addition, our human practices were designed primarily to educate the public about synthetic biology in hopes of dispelling detrimental myths and creating awareness about the helpful applications of science in their daily lives. To do so, we presented a public outreach event at the Exploratorium and educated the public on the topic of “fact and fiction” in synthetic biology. Through a creative spin of superheroes on the matter, our team excited the public with the potential of synthetic biology, while promoting public involvement in science. Following this event, we have adapted our presentation into a curriculum and lesson packet) capable of introducing middle school and high school students to synthetic biology, in hopes of furthering science education. Toward this, our team also met with San Francisco city supervisors to discuss our project this year, garnering public support and advocating higher science education at the public school level. Through our project and public interactions this summer, we are optimistic in our approach to move science towards a transparent, exciting, and involved field.</p>
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<p>We have collaborated with an assortment of other iGEM teams to assist in their projects. In particular, we highlight our collaboration with the Nevada iGEM team — we were able to provide them with yeast strains and shuttle vectors to help them get their project going. We additionally helped them troubleshoot expression problems and provided them with our characterized pTEF1 promoter. We are very excited about the growth of yeast projects in this year’s iGEM! A complete list and description of our collaborations can be found <a href = "https://2014.igem.org/Team:UCSF_UCB/hp.html#collaborations">on our wiki</a>.</p>
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                     <p> Safety, both of our team as researchers as well as the community at large, is of primary importance. We have taken significant measures to minimize risk inside the lab and out, and we are confident in our approach to safety for the 2014 project. We encourage you to read about our safety precautions on <a href = "https://igem.org/Safety/Safety_Form?team_id=1346">our team safety form:  </a>.</p>
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                     <p> Safety, both of our team as researchers as well as the community at large, is of primary importance. We have taken significant measures to minimize risk inside the lab and out, and we are confident in our approach to safety for the 2014 project. We encourage you to read about our safety precautions on <a href = "https://igem.org/Safety/Safety_Form?team_id=1346">our team safety form</a>.</p>
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Revision as of 17:32, 15 October 2014

Medal Requirements

Safety

Implications

Bronze Medal Requirements

  1. Team Registration

    Team UCSF_UCB is signed up for the collegiate division of the iGEM competition as an "undergraduate" team. Our official team registration.

  2. Complete Judging Form

    Done!

  3. Team Wiki

    You're looking at it! The homepage can be found at https://2014.igem.org/Team:UCSF_UCB

  4. Present a poster and a talk at the iGEM Jamboree.

    We are registered and en route to the 2014 Giant Jamboree.

  5. The description of each project must clearly attribute work done by the students and distinguish it from work done by others, including host labs, advisors, instructors, sponsors, professional website designers, artists, and commercial services.

    On our website we have made it clear as to individual attributions of work as well as including the contributions and aid our mentors provided. Please see our attributions here.

  6. Document at least one new standard BioBrick Part or Device used in your project/central to your project and submit this part to the iGEM Registry.

    One of our team goals this year was to expand the library of parts available for use in single-celled eukaryotes, particularly the yeast Saccharomyces cerevisiae. Combined with the awesome power of yeast genetics, working with eukaryotes provides additional functionality and complexity not available with many bacterial species. To this end, we have submitted an arsenal of parts to the iGEM headquarters for use in yeast. We have synthesized and delivered a variety of Alpha-responsive promoters and constitutive promoters in the PSB1C3 backbone. Specific part details as well as catalog number can be found on our iGEM parts registry page and on our wiki.

Silver Medal Requirements

  1. Experimentally validate that at least one new BioBrick Part or Device of your own design and construction works as expected.

    We verified and classified our parts/devices by means of flow cytometry analysis. We validated the expression strength of our promoters by creating circuits in which GFP was behind our promoters and running the circuits under flow cytometry. By measuring the GFP outputs of each promoter, we can determine the expression strength of each promoter. Results for each individual part can be found on our wiki.

  2. Document the characterization of this part in the “Main Page” section of that Part’s/Device’s Registry entry.

    We have documented the expression levels of our parts alongside graphical comparisons to some of our other characterized parts. The characterization can be found at our iGEM parts registry, or on our wiki.

  3. Submit this new part to the iGEM Parts Registry.

    Our parts our integrated within the PSB1C3 plasmid and have no restriction sites within its sequence, thus adhering to iGEM guidelines. All parts delivered are risk group one organisms and do not violate any safety standards.

  4. iGEM projects involve important questions beyond the bench, for example relating to (but not limited to) ethics, sustainability, social justice, safety, security, or intellectual property rights. Articulate at least one question encountered by your team, and describe how your team considered the(se) question(s) within your project. Include attributions to all experts and stakeholders consulted.

    Scientific research comes with many complex implications, and we have considered many, including not only the basic science of our project but how our project relates to the community. We have discussed these questions on our wiki. Additionally, our team participated in an ethics discussion organized by UC-Santa Cruz at the West Coast iGEM Meetup. We debated the importance of sustainability of large-scale research, land occupation and resource distribution. We also discussed intellectual property rights and how withholding information from competing companies can deter the progress of research.

Gold Medal Requirements

  1. Improve the function OR characterization of an existing BioBrick Part or Device (created by another team or your own institution in a previous year), enter this information in the Registry.

    UCSF_UCB has improved the characterization for the yeast TEF1 promoter. This part has been submitted multiple times by multiple teams, resulting in 3 twin parts in the registry (BBa_K431008, BBa_K563004, and BBa_K319003). We have improved all of these parts by adding on a graph displaying the expression strength the TEF1 promoter. We measured the expression level of GFP and compared it alongside pTEF1 mutants and established a comparison of its strength as a constitutive promoter.

  2. Help any registered iGEM team from another school or institution by, for example, characterizing a part, debugging a construct, or modeling or simulating their system

    We have collaborated with an assortment of other iGEM teams to assist in their projects. In particular, we highlight our collaboration with the Nevada iGEM team — we were able to provide them with yeast strains and shuttle vectors to help them get their project going. We additionally helped them troubleshoot expression problems and provided them with our characterized pTEF1 promoter. We are very excited about the growth of yeast projects in this year’s iGEM! A complete list and description of our collaborations can be found on our wiki.

Medal Requirements

Safety

Implications

Safety, both of our team as researchers as well as the community at large, is of primary importance. We have taken significant measures to minimize risk inside the lab and out, and we are confident in our approach to safety for the 2014 project. We encourage you to read about our safety precautions on our team safety form.

Medal Requirements

Safety

Implications

The Science of Collective Behaviors

Our inspiration for this project stems from the lack of comprehensive understanding of cellular collective behavior. In synthetic biology, it is particularly important to understand population mechanisms and collective behavior in order to properly replicate and study natural systems in a laboratory setting. From the study of T cell communication in immune responses to correcting for quorum sensing in bacterial cultures, collective behavior is a powerful, inevitable and largely unknown phenomenon in biological systems. Our project aims to create a synthetic cell circuit capable of not only modeling natural collective systems, but quantitatively analyzing such interactions.

As the biological sciences are making a shift from a qualitative science to a quantitative science, our team is making an effort to support this transformation by creating methods for replicable and standardized measurement of biological phenomena. By designing a solely synthetic circuit with modular parts, we are able to fine tune collective responses using various feedback loops and stimuli. Through this modular approach, we hope to expand this cell circuit to be able to replicate/simulate all different kinds of collective responses from autoimmune responses to cell adhesion. In addition, a key design feature of our cell circuit is an autonomous/community-coordinated readout able to be quantitatively measured with flow cytometry. Our cell circuit impacts science at the research level, helping scientists understand natural phenomena and providing a novel measurement tool. A standardized quantitative method of measurement, opposed to qualitative observations, will create a more transparent and un-biased data analysis tool for scientists to use and relay data to the public. We hope that our project will be able to provide novel insights into cellular communities and provide a tool to study various natural systems, with implications reaching into everything from pharmaceuticals to tissue-biology.

Scientist - Community Interactions

Outside of the wetlab, our research-driven approach in this year’s project hopes to combat the growing stigma of science in the public. Through media propaganda and general ignorance of the subject, biotechnology is generally looked upon as “elitist” and “secretive.” In the philosophy of iGEM, the UCSF/UCB team made it a primary goal this year to act as a bridge between the public and scientists to make science more accessible, transparent, and publicly involved.

In addition, our human practices were designed primarily to educate the public about synthetic biology in hopes of dispelling detrimental myths and creating awareness about the helpful applications of science in their daily lives. To do so, we presented a public outreach event at the Exploratorium and educated the public on the topic of “fact and fiction” in synthetic biology. Through a creative spin of superheroes on the matter, our team excited the public with the potential of synthetic biology, while promoting public involvement in science. Following this event, we have adapted our presentation into a curriculum and lesson packet) capable of introducing middle school and high school students to synthetic biology, in hopes of furthering science education. Toward this, our team also met with San Francisco city supervisors (pictured on the right) to discuss our project this year, garnering public support and advocating higher science education at the public school level. Through our project and public interactions this summer, we are optimistic in our approach to move science towards a transparent, exciting, and involved field.

Open Source Science

As part of this year’s West Coast iGEM Meetup, the teams present participated in an ethics forum organized by UCSC (pictured on the right). A panel of faculty members in science, policy, and ethics moderated the discussion and provided perspective to team questions and concerns.

Of particular interest was discussion about the issue of making data freely available to the public. There are many arguments for (e.g. providing tax-payer access to data resulting from their investment, increasing speed of progress and development, reducing barriers) and against (e.g. knowledge could be repurposed for malicious intents or marketed) open access data sharing. This is a complex issue, and there are no right or wrong answers. Ultimately, we came away with a more in- depth understanding of our responsibility as scientists to practice safe science and be cognizant of the downstream developments and implications of our work.

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