Team:UCSF UCB/team.html

From 2014.igem.org

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                             <h2>Website Materials</h2>
                             <h2>Website Materials</h2>
                             <p>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 <a href = "https://github.com/vixis/angularplasmid/blob/master/README.md">here</a>.</p>
                             <p>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 <a href = "https://github.com/vixis/angularplasmid/blob/master/README.md">here</a>.</p>
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Revision as of 04:47, 15 October 2014

Eleanor Amidei is a recent graduate of ALHS and is heading to UC Berkeley in the spring studying whatever undecided students study -- possibly molecular cell biology or maybe political science, but leaning towards public health. Most nights, after hours spent in the lab, you can find Eleanor in the weight room at ALHS working out and contemplating the myriad of reasons she decided to forgo sleep the night before (thanks, Netflix), only to give into the temptation again. While sometimes wishing she were already in school, iGEM has been an invaluable educational experience.

Sabrina Chu aka 'greatest driver on earth' is a recent graduate from Abraham Lincoln High School who is attending UC Davis as a freshman in the fall. She plans to major in Biochemistry and Molecular Biology. She also plans on minoring in accounting and is very excited to finally attend college. She gained much of her wetlab experience during high school in her Biotechnology class at Abraham Lincoln High School in San Francisco. Because of her many hours using the FACS machine, she is also known as the "Flow Master."

Shuaixin He will be in her third year at Peking University. She majors in Life Sciences and is interested in observing and thinking about biological phenomena at microcosmic level. She was a lab manager of 2013 Peking iGEM team and this is her second time participating in iGEM. In this year's project, she managed the strain construction and characterization of positive & negative feedback. She has really enjoyed a pleasant time with S. cerevisiae as well as her fellow teammates.

Jessica Hsueh is a third year bioengineering major at UC Berkeley. She is from Fremont, California, which means she enjoys an hour and a half commute from home to the lab in San Francisco. Jessica likes learning about a variety of topics, from working with yeast to programming Kilobots. Outside of research and academics, Jessica also enjoys good food, books, movies, puzzles, Quidditch, and archery.

Derrick Lee is currently a sophomore at City College of San Francisco, majoring in Molecular Cell Biology. He intends to transfer to either UC Davis or UC Berkley and eventually pursue a PhD. This is his second year as a member of the UCSF-UCB iGEM Team and he is an Abraham Lincoln High School alumnus. In his off-time, Derrick enjoys binge-watching TV shows, rooting for the Golden State Warriors and the San Francisco 49ers, and finding the best places to eat in San Francisco. He also has a somewhat unhealthy attachment to the Internet.

Jeffrey Shu, a recent graduate from Abraham Lincoln High School, is currently studying as a freshman at UC Berkeley and intending to major in Molecular and Cell Biology. Jeffrey was drawn to iGEM for its innovative approach to collaborative science and its exciting opportunity to try new things. When not in the lab, you can find him cleaning and organizing things, curling up reading a good book, obsessively binge-watching shows and movies on his bucket list, or loudly singing show tunes in the shower. Jeffrey is excited to start his new life in college and be a part of such an exciting scientific venture alongside his amazing teammates.

Eric Wong is a second year student with the UCSF-UCB iGEM team. Like many of his teammates, he is also an Abraham Lincoln High School alumnus. Eric currently attends the College of San Mateo and is interested in transferring to either UC-Berkeley or UC-Davis to study Molecular Cell Biology. iGEM gave him the opportunity to dive straight into hands-on, innovative research that he would otherwise not have been able to do. He feels that it has been a pleasure to be a part of this enormous community where people all work together to discover and create things we never imagined or thought possible.

Robert Wong is a recent graduate from Abraham Lincoln High School and is currently at College of San Mateo. He plans to move onto UC Davis or UC Berkeley after finishing his GE’s at CSM. Right now he’s headed in the direction of Molecular Cell Biology as a major and hopes to eventually earn his PhD. In his free time he likes to find good food places. “I'M A BIG FOODIE!”

Ianto Lin Xi is a fourth year undergraduate student at UC Berkeley studying Molecular and Cell Biology with an emphasis in immunology. Outside of iGEM, Ianto works at the Children’s Hospital Oakland Research Institute, where he can be found programming pipelines to analyze sequencing data. He is also a coordinator at the Berkeley Free Clinic, where he manages the routine operations of the Men’s STI Clinic. In his free time, Ianto forgoes the stability of the earth and prefers to dangle dangerously from rocks.

Born and raised as a 2nd generation immigrant, George Yip has adopted both Chinese and American cultures. He is a recent graduate of Abraham Lincoln High School and has his road paved towards CSM. The idea of learning and gathering knowledge was an essential motivator for him to join iGEM. Real world experience and the trials of everyday scientists are seldom found in literature, and George is certain that being a participant in the world of science will further reinforce his understanding of this field as well as open up insights for him to investigate.

Advisors

This is Kara Helmke’s second year working with the iGEM team. She just completed her graduate work at UC Berkeley studying mitosis in frogs. As a cell biologist and microscopist by training, the field of synthetic biology has been both challenging and exciting for her to learn about alongside the students.

Wendell Lim has had a lab at UCSF for over 15 years and has been an adviser to the UCSF team since it started in 2007. He enjoys working with bright, open-minded young scientists and seeing their ideas develop into scientific projects.

Hyun Youk is a former postdoc in the Lim Lab and now an assistant professor of physics and nanobiology at the Delft University of Technology, currently setting up his new lab. His main passion is seeking core mathematical/physical principles that govern dynamics of biological systems, such as genetic circuits and multicellular entities. Among his many responsibilities, one that particularly excites him is learning from and mentoring young students as they embark on their research careers.

Mentors

Zairan Liu is a second year graduate student at University of California, San Francisco. She is part of the integrated program of quantitative biology (iPQB) and just joined the Weiner lab. With interest in systems and synthetic biology, she wants to study development of early zebrafish embryos using optogenetic tools.

Anusuya Ramasubramanian is a fourth year Bioengineering Ph.D. student in the UCSF/UC Berkeley joint program, where she works at the nexus of tissue engineering, biomaterials and synthetic biology. She has an undergraduate degree in Biomechanical Engineering from Stanford University. Having participated in iGEM twice as an undergrad at Stanford - once as team member and once as a mentor - she couldn't help but get involved with iGEM as a graduate student. This is Anusuya's second year mentoring the UCSF iGEM team. Mentoring this team, which has a unique mix of high school and undergraduate members, has been an incredibly enriching and rewarding experience. Anusuya has been really impressed with the progress of this year's team and can't wait to see the impact of their work at the Jamboree and beyond!

Kevin Hartman is a second year Bioinformatics PhD student at UCSF. He received his Bachelor’s degree from the California Institute of Technology in Chemical Engineering. Following that, he worked in the biofuels industry for two years. He helped the iGEM team develop data analysis computational tools.

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 progess, the team attended group meetings to present a weekly update to both the 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. 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 progess, the team attended group meetings to present a weekly update to both the students and mentors on individual progress.

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 on 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 XXXX number of 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 in S. 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.

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