Click on a medal to jump to its section.
As part of the iGEM Competition, our team worked diligently to fulfill the requirements for the bronze, silver, and gold medals. Below details our progress and completion of the requirements.
- Register for iGEM, have a great summer, and attend the Giant Jamboree.
The UCSF team is signed up for the collegiate division of the iGEM competition as an "undergraduate" team.
- Complete the Judging Form.
This was completed.
- Create and share a Description of the team's project using the iGEM wiki, and document the team's parts using the Registry of Standard Biological Parts.
This is it! The homepage can be found at 2015.igem.org/Team:UCSF.
- Present a poster and a talk at the iGEM Jamboree.
We are registered for and are going to the 2015 Giant Jamboree.
- Create a page on your team wiki with clear attribution of each aspect of your project. This page 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.
The individual attributions of each team member are provided on our website as well as the contributions and aid from our mentors. Please see our Attributions Page for more information.
- 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 goals is to help add to the available basic parts for using yeast as a chassis. For our project this year, we needed to make plasmids that contained multiple genes that used, but did not share, the same promoter. We had to use the terminators tEno2 (BBa_K1829003) and tFba1 (BBa_K1829004) to separate the end of one gene from the beginning of the next promoter. By using these terminators, we were able to make a plasmid that contained three different genes with three copies of the same promoter. All of the parts were submitted on the pSB1C3 backbone. Specific part details can be found on our iGEM parts registry page and our Parts Page.
- Experimentally validate that at least one new BioBrick Part or Device of your own design and construction works as expected. Document the characterization of this part in the Main Page section of the Registry entry for that Part/Device. This working part must be different from the part you documented in Bronze medal criterion #6.
We verified and classified our parts/devices by means of flow cytometry analysis. We validated the expression strength of three different alpha-factor responsive promoters by creating circuits in which fluorescent reporters were being driven by the promoter. We induced these promoters with purified alpha factor and measured them with flow cytometry to determine the expression strength of each promoter. The promoters characterized were pFig2c (BBa_K1829002), pBar1 (BBa_K1829001), and pAga1 (BBa_K1829005); all are endogenous yeast promoters that participate in the mating response pathway. We additionally submitted the yeast protease Bar1 (BBa_K1829000) which cleaves alpha factor, and made silent mutations to make it BioBrick compatible. We characterized the effect of adding Bar1 to our communication circuit with alpha factor, showing it effectively degrades alpha factor and reduces circuit sensitivity. Our parts were integrated within the pSB1C3 plasmid. All parts delivered are risk group one organisms and do not violate any safety standards. Specific part details can be found on our iGEM parts registry page and our Parts Page.
- Submit this new part to the iGEM Parts Registry.
The parts have been submitted!
- iGEM projects involve important questions beyond the bench, for example relating to (but not limited to) ethics, sustainability, social justice, safety, security, and intellectual property rights. We refer to these activities as Human Practices in iGEM. Demonstrate how your team has identified, investigated and addressed one or more of these issues in the context of your project.
This year, in addition to addressing cellular communication, we wanted to explore other issues of communication, specifically between the scientific community and the general public. Despite the breadth of iGEM and the open-source nature of its data reporting, the wikis and science content still remain very complex and not easily accessed by members of the general public. We addressed this with three ambitious projects:
- We utilized social media, such as Twitter and Youtube, as a way of conveying scientific research to the general public through a video series on synthetic biology and research.
- We contributed to the planning of a Synthetic Biology conference -- the Sierra Systems and SynBio Symposium -- which highlights undergraduate research in synbio. As a part of that conference, we organized an iGEM Meetup and coordinated 4 other teams attending as well as science presentations and social activities.
- We started a new initiative called Wiki Flicks, where we encouraged the other iGEM teams, including ourselves, to create a short, interesting video about their project that is easy for ANYONE understand.
We have much more information, including successes and challenges, on all of these initiatives on our Practices Page.
- Choose one of these two options: (1) Expand on your silver medal Human Practices activity by demonstrating how you have integrated the investigated issues into the design and/or execution of your project. OR (2) Demonstrate an innovative Human Practices activity that relates to your project (this typically involves educational, public engagement, and/or public perception activities; see the Human Practices Hub for information and examples of innovative activities from previous teams).
Our new initiative -- iGEM Wiki Flicks -- is an innovative and much-needed contribution to iGEM projects. The goal here is simple - to create a platform to easily, quickly, and simply explain an iGEM project so that anyone can access it and understand the projects. We have been in contact with iGEM HQ and they are very excited about the idea and want to partner in moving this forward! However, there are many limitations, including the ability of the iGEM website to host the content instead of a third-party site (like YouTube) which may be inaccessible to many teams. Our attempt this year was to garner interest (and we have several interested teams!), while the goal next year will be to formalize participation and provide infrastructure through the iGEM server to be able to host the videos for all teams. See our descriptions, 2015 participants, successes and challenges on our Practices and Wiki Flicks pages!
- Help any registered iGEM team from a high-school, different track, another university, or institution in a significant way by, for example, mentoring a new team, characterizing a part, debugging a construct, modeling/simulating their system or helping validate a software/hardware solution to a synbio problem.
This year, we interacted with over 25 other iGEM teams in a variety of activities! We have documented these in detail in our Collaborations section of our wiki. Our key contributions to the research of other teams were (1) a collaboration with the University of Georgia iGEM team, where we helped them characterize a library of RBS mutants by taking fluorescence measurements for their Archaeal Collaboration study, and (2) providing iGEM Tuebingen with a construct containing e-cadherin developed by UCSF iGEM 2011.
- Improve the function OR characterization of a previously existing BioBrick Part or Device (created by another team, or by your own team in in a previous year of iGEM), and enter this information in the part's page on the Registry. Please see the Registry Contribution help page for help on documenting a contribution to an existing part. This part must not come from your team's 2015 range of part numbers.
Our team has improved two existing parts in our project. For all parts, please see our Parts Page. The first is the receptor for alpha factor, Ste2 (BBa_I766204), used in our positive feedback component of our circuit. It was submitted to the Parts Registry by UCSF iGEM 2007, yet no sample of it currently exists for other teams to use. We contributed in two ways: (1) by submitting a sequence-verified version of Ste2 (BBa_I766204) to the Registry and (2) by additionally improving the original gene by making it BioBrick compatible by creating a silent mutation to remove an internal PstI cutsite (BBa_K1829007). Both contributions have been noted in the original part experience page. We also improved upon the characterization of the clustering proteins expressed by yeast mating display as developed by UCSF 2011, including mussel foot protein Mgfp-5 (BBa_K197018), E-cadherin (BBa_K644000), and hyphal wall protein1 Hwp1 (BBa_K644001).