Throughout the entire summer, each student had specific jobs that contributed to our project. In order to accomplish our goals, the individual students all came together to work as a team. We took inspiration for this year’s project from prior work done by our mentors (Youk and Lim, 2014) and we set out to engineer multiple autocrine/paracrine extracellular signaling circuits to reshape collective cell responses. To manage progress, the team attended group meetings to present a weekly update to both students and mentors on individual progress. Throughout the entire summer, each student had specific jobs that contributed to our project. In order to accomplish our goals, the individual students all came together to work as a team.
In addition to scientific research, the team participated in many collaborations with other teams and worked together to develop a human practices project geared towards educating the general public about synthetic biology, with potential expansion to school curricula.
Eleanor Amidei was one of the team leaders for Human Practices. She helped develop the proposal for and execution of our presentation at the Exploratorium. Additionally, Eleanor was in charge of construction of our parts to be sent to the Parts Registry. She has had her hand in almost everything done in the wetlab and has been instrumental in the continuation of final testing before the Jamboree. Eleanor will also represent the team by presenting at the Jamboree.
Sabrina Chu constructed the positive-feedback circuits containing alpha factor-responsive promoters driving rtTA expression (with Jessica Hsueh), which involved many rounds of troubleshooting and optimization. In the second half of the summer, she has lead circuit characterization through flow cytometry. Sabrina (along with Jeffrey Shu) has also been in charge of documentation and has completed the safety forms for the competition.
Shuaixin He worked on incorporating various methods of positive and negative feedback into our communication circuits. She created constructs with alpha-factor responsive promoters driving additional alpha factor production (positive-feedback) and worked on cloning the protease Bar1 as a means of negative feedback.
Jessica Hsueh constructed the positive-feedback circuits containing alpha factor-responsive promoters driving rtTA expression (with Sabrina Chu). She was also our iGEM Collaboration Captain, managing interactions with 10 teams this summer. Jessica also participated in a workshop learning to program the collective behavior robots, Kilobots, making a simulation of our communication circuits.
Derrick Lee is a returning member from the 2013 iGEM team and helped train and mentor the new students for this year’s team. He constructed many parts over the summer, including alpha factor-responsive promoters in front of GFP and Ste2 (alpha factor receptor). He led promoter characterization on the flow cytometer and assisted in data analysis/presentation. Derrick used the promoter data to characterize our parts in the iGEM Parts Registry.
Jeffrey Shu was primarily in charge of strain construction in S. cerevisiae. With George Yip, he was responsible for building multiple yeast strains containing iterations of our primary circuit (pTEF1 and its mutants driving rtTA, pTET-alpha factor, and alpha factor-responsive promoters with mCherry/BFP). Jeffrey was also one of our Human Practices captains and worked on establishing contact with the Exploratorium and has developed a curriculum for teaching students about Biotechnology. Jeffrey (along with Sabrina Chu) has also been in charge of documentation and has completed the safety and judging forms for the competition.
Eric Wong is also a returning member from the 2013 iGEM team and helped train and mentor the new students for this year’s team. He played a primary role in gathering data for the characterization of promoters as well as data of completed circuits through flow cytometry. He also helped construct and assemble 11 alpha factor-responsive promoters and rtTA. Eric also integrated several motifs of the constitutive promoter circuit into our yeast cell lines. In addition, he also helped create the slideshow presentation displayed at the Exploratorium event for our Human Practices.
Robert Wong mainly worked in the wetlab, building several constructs: alpha factor-responsive promoters driving Ste2 or mCherry, constitutive pTEF1 promoters driving GFP, and construction of parts to submit to the Parts Registry in the pSB1C3 backbone. Robert was also Social Media Captain (Twitter/Facebook).
Ianto Lin Xi led the initial alpha factor-responsive promoter identification and selection through literature searches. He spearheaded the characterization of these promoters through the construction of yeast strains with alpha factor-responsive promoters driving GFP. He helped set up initial flow cytometry experiments and programmed our flow cytometer data analysis and interpretation pipeline in both FlowJo and MatLab. Ianto is also in charge of our graphic design, developing our wiki and creating our poster. Ianto will also represent the team by presenting at the Jamboree.
George Yip has been primarily in charge of strain construction inS. cerevisiae. With Jeffrey Shu, he was responsible for building multiple yeast strains containing iterations of our primary circuit (pTEF1 and its mutants driving rtTA, pTET-alpha factor, and alpha factor-responsive promoters with mCherry/BFP). As the summer has drawn to an end, George has been essential for construction of all strains required to test the remaining parts of our circuit, doing hundreds (perhaps thousands) of colony PCRs. George has also been heavily involved in testing our final circuits in flow cytometry.
Hyun Youk is a team advisor and helped with conception and execution of this project. The inspiration for the 2014 UCSF-UCB iGEM project is based on his prior work characterizing sense-and-secrete circuits in yeast (Youk and Lim, 2014), and his insight and previous constructs gave us many of the building blocks for our circuits. He was involved in every step of the project, helping to train the team in data acquisition and analysis as well as project planning and troubleshooting.
Kara Helmke is the team advisor and coordinator and has helped with planning and execution of this project. She helped the team on a day-to-day basis in training, designing experiments, interpreting results, troubleshooting, and coordinating all of the individual efforts into a team result.
Wendell Lim is the faculty advisor for the 2014 UCSF-UCB iGEM team and was involved in the conception of this year’s project, based on prior work (Youk and Lim 2014). His lab is the host for the team and he has graciously supported them with time, materials, and guidance.
The amazing group of iGEM mentors (Kevin Hartman, Jonathan Asfaha, Anusuya Ramasubramanian, Zairan Lu, Michael Broeker, Alain Bonny, Ben Heineike, PJ Buske) provided training and support to the team all summer. Many were instructors in the iGEM Bootcamp at the beginning of the summer, providing much of the valuable background and training for the execution of the project. They attended countless group meetings, helping the team not only troubleshoot the project but also hone and practice scientific communication skills. Their support also made the Human Practices event at the Exploratorium possible.
Website Materials
Special thanks to Rehan Chawdry for his AngularPlasmid, which is used to generate plasmids found on this website. AngularPlasmid is licensed under the MIT license. The script and more information about the copyright can be found here. Many of the headings on our website used the free font-face Ostrich designed by Tyler Finck. Copyright information and download information for this font can be found here.
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