UCSF

center for systems

& synthetic biology

an NIGMS national systems biology center

banner_publication.jpg
 
 
 

education + outreach


K-12 Programs/Events

UCSF iGEM Program

The UCSF iGEM program combines high school and college outreach with the International Genetically Engineered Machines (iGEM) competition. Promising young students from San Francisco Unified School District’s Abraham Lincoln High School spend the summer working together as a team, along with researchers at the University of California San Francisco. In addition, two returning iGEM alumni (who are now undergraduate students) as well as a local community college student are part of the annual team. They design and implement a project in synthetic biology with which they compete at the iGEM Jamboree in the fall. The program is a partnership between our Center and Lincoln High School, which has a two-year biotechnology program led by George Cachianes. The UCSF iGEM program was developed to offer talented young biologists a unique summer research experience while also providing graduate students and postdoctoral fellows at UCSF with valuable mentoring and teaching opportunities. The UCSF iGEM program is also supported by the Synthetic Biology Engineering Research Center (SynBERC), which highlighted the use of synthetic biology as an education platform and our partnership with Lincoln High School in a recent video.

Abraham Lincoln High School serves a very diverse community with less than 10% of the student population identifying as Caucasian and ~25% as underrepresented minorities. In addition, greater than 50% of the students qualify for a free or reduced lunch and at least half of the students who worked directly with the UCSF iGEM team will be the first in their families to attend college. In the fall semester of each year, the recent alumni of our iGEM team return to ALHS and explain their research project and describe their experiences of working at a university research lab. In the spring of 2013, our Center Education Coordinator spent two weeks at ALHS teaching a molecular biology module to the second year biotechnology class (30 students) in order to provide further resources to the class and enhance the curriculum. Along with the ALHS biotechnology teacher, our Education coordinator also oversaw a collaboration between students in the ALHS biotechnology program and the ALHS Green Academy. Our goal is to continue to provide laboratory resources and curriculum supplements to a broader range of students at Lincoln High School.

Read about the 2014 iGEM team and their project here -- winners of a Gold Medal and Best Presentation Award.

 

CTE Advisory Board

The Center Education Coordinator is a member of the Career Technical Education Advisory Board which provides opportunities and curriculum advisement to three San Francisco high schools which have been certified as Health Science Academies. These schools – Philip and Sala Burton High School, Raoul Wallenberg High School, and Galileo Academy of Science and Technology – represent a student body which is 68% socioeconomically disadvantaged and less than 5% caucasian, and on average 50% underrepresented minorities. The goal of the Academies is to promote career and technical training for students entering health and biotech professions. The Advisory Board helps the CTE achieve its goals by providing quality work-based learning experiences (i.e. job shadows, internships, tours, etc), ongoing professional development for teachers, industry expertise to support Academy programs, and advocacy for Academies to educational, business, and political communities.

 

ASBMB HOPES Workshop

At its Annual Meeting in April 2014, the American Society for Biochemistry and Molecular Biology hosts a half-day workshop for the Hands-on Opportunities to Promote Engagement in Science (HOPES) program. The goal of the workshop is to aid K-12 and college educators’ partnerships by providing introductions and networking opportunities, examples for models of successful collaboration, and funding through seed grants to encourage development of these partnerships. The Center Education Coordinator was invited to speak on the UCSF/Lincoln High School iGEM partnership as one such example of successful collaboration. Since the first time the Center participated in this workshop in 2012, this program has resulted in 26 partnership projects in 22 cities across the United States, in part due to the efforts of the Center in educating about its novel iGEM partnership.

 

BERET Teacher Training

The Berkeley Engineering and Research Experiences for Teachers (BERET) Program places current and prospective teachers in summer research positions to encourage them to develop and teach lessons that connect life sciences and engineering research to K-12 math and science curricula in the classroom. In the summer of 2013, our Center sponsored a BERET teaching pair consisting of a veteran in-service teacher from Oakland High School, Suzi LeBaron, and a pre-service teaching student at UC Berkeley, Priyanka Dadlani. These teachers were incorporated as a mentor and participant, respectively, in the 2013 UCSF iGEM team. With our Education Coordinator, the teachers helped lead the team in developing their project in synthetic biology and helped mentor the students in their communication skills. As an outcome of their participation in the Center, during and after the summer the teaching pair worked together to develop a curriculum unit of several weeks to be jointly taught at the in-service teacher’s institution.

Science Fair Judging and Awards

Santa Clara Valley Science and Engineering Fair The Synopsis Championship brings over 1000 student science fair projects to the San Jose convention Center every March to promote research in science and engineering. At the 2014 Synopsis Championship (March 12th, 2014), volunteers from the Center participated as judges for biochemistry and biology projects at the middle and high school level. Judges reviewed student projects, interviewed top contenders and then worked in teams to nominate winners in various categories. The volunteers also had the opportunity to network with local scientists and speak to students about their experiences as a scientist at UCSF. For the second year, our Center sponsored a special award for projects that “demonstrated interdisciplinary and/or quantitative approaches to answering biological questions.” First and second place awards were given to the best projects in both the middle and high school grade levels and were chosen by a group of 6 Center scientists who participated as judges.


Undergraduate Programs/Events

UCSF Summer Research Training Program

Every year the Center for Systems and Synthetic Biology sponsors undergraduate students as part of the UCSF Summer Research Training Program (SRTP). The SRTP provides research opportunities in the biomedical and biological sciences for college students interested in pursuing a PhD in the field. Students spend up to 10 weeks working in the labs of Center and UCSF faculty on research projects, and participate in seminars, lectures, and social events throughout the summer. At the end of the program, students submit abstracts and give presentations of their research. Underrepresented minority, socio-economically disadvantage, first-generation college students, and students with limited access to research laboratories are particularly encouraged to apply to this program.

 

UCSF iGEM Program (2014 Team Website)

The UCSF iGEM program combines high school and college outreach with the International Genetically Engineered Machines (iGEM) competition. Promising young students from San Francisco Unified School District’s Abraham Lincoln High School spend the summer working together as a team, along with researchers at the University of California San Francisco. In addition, two returning iGEM alumni (who are now undergraduate students) as well as a local community college student are part of the annual team. They design and implement a project in synthetic biology with which they compete at the iGEM Jamboree in the fall. The program is a partnership between our Center and Lincoln High School, which has a two-year biotechnology program led by George Cachianes. The UCSF iGEM program was developed to offer talented young biologists a unique summer research experience while also providing graduate students and postdoctoral fellows at UCSF with valuable mentoring and teaching opportunities.

City College of San Francisco

City College of San Francisco (CCSF) is the largest community college in California and serves many first generation, low-income, and underrepresented students in the pursuit of higher education. CCSF provides several biotechnology majors and an extremely successful Bridge to Biosciences program (https://sites.google.com/site/ccsflabassistant/). Our Center Education Coordinator has started working with the faculty at CCSF to identify students for summer internships at UCSF and to organize volunteers from the Center to serve as classroom speakers, poster judges, and on networking panels. Our first summer intern, Yesenia Lopez, was a member of the UCSF iGEM team in 2012 and our second intern, Michael Broeker, joined us in summer 2013 to work in the lab of Center Systems Biology Fellow, Matt Thomson. His successes in his summer research project prompted his transition into a permanent Center position, and he is currently spearheading the development of several Center core facilities and services such as microfabrication, advanced cloning methods, and tissue culture.


UCSF iGEM Alumni Networking and Resource Group

The UCSF iGEM team has produced over 40 alumni in the last 6 years. These students are at various stages of their undergraduate, graduate, and postgraduate careers. We have started a LinkedIn Alumni Group, a Facebook page and email list to disseminate information on summer internship and research opportunities. We have started a Facebook page and email list to disseminate information on summer internship and research opportunities. Additionally, we are providing alumni with guidance and advice in developing their resume and cover letters when applying to these positions. The students can also serve as a resource to one another and we host an iGEM alumni gathering every January at UCSF to help facilitate the alumni networking opportunities.

Howard Hughes Medical Institute Exceptional Research Opportunities Program

The Exceptional Research Opportunities Program (EXROP) provides motivated students from disadvantaged backgrounds or traditionally underrepresented groups with summer research experience by matching them with labs across the country. This year, the Center incorporated its first EXROP student, Ian Ergui from the University of Miami, into the 2013 iGEM team. In addition to his contributions to the team, he also participated in aspects of the UCSF Summer Research Training Program (SRTP) which encourages developing presentation skills through symposia and poster presentations, as well as networking with over 50 other students in summer research positions.


Graduate Programs/Events

Integrative Program in Quantitative Biology

UCSF has an umbrella graduate program that brings together three programs focused on applying physical, mathematical, and systems approaches to biological problems. The Integrative Program in Quantitative Biology (IPQB) establishes an innovative common core curriculum drawn from the PhD curricula in Biophysics, Bioinformatics, and Complex Biological Systems. This program fits very well with the systems and quantitative biology themes of our Center. Thus, we have been contributing Center resources to course development in this UCSF graduate program. In the fall semesters, we participate in the development and execution of a Systems Biology Course organized by IPQB for first year graduate students. This course is co-taught by center deputy director and co-investigator Hana El-Samad, and teaching assistance has been provided by several Center-associated postdoctoral fellows and graduate students, as well as the Center’s Education & Outreach Coordinator. An emphasis on Complex Biological Systems was recently created in the IPQB program and its development is greatly benefiting from associations with our Center.

 

Minicourses within IPQB: Two of our Systems Biology Fellows, Matt Thomson and David Soloveichik, developed a Center-generated Minicourse for the 2012 spring semester of the IPQB program, entitled How do organisms, cells, and molecules organize themselves: distributed computation in biology.’ Biological systems often solve problems through distributed computations, where individual agents (proteins, cells, organisms) collect information and dynamically interact to accomplish a task. Examples of distributed computation exist across scales of biological organization: the computation of cell morphology by the actin cytoskeleton; the selection of high affinity B-cell clones by the immune system; sensory integration in the brain; choice of flight direction in bird flocks. Even regulatory networks can be thought of as multi-agent systems, in which a set of molecules has to make a concerted decision. Computer science and statistical physics have developed rich theoretical tools for studying multi-agent systems and collective behaviors. This course drew on this rich history, combining it with an analysis of specific biological examples, to discuss the development of a theory for distributed computation in biology. Topics included chemical reaction networks, cell polarity, immune system dynamics, Hopfield neural networks, and flocking. Theoretical investigation into distributed algorithms in biology could uncover common principles used across systems and common implementation challenges like the aggregation of noisy signals and decision making in groups. For the spring 2013 Minicourse series, Matt Thomson and seed grant recipient Zev Gartner are developing the Minicourse ‘Multicellular systems biology’.

 

Tetrad Program

The UCSF joint Tetrad Program includes the biochemistry and molecular biology, cell biology, genetics and developmental biology programs. Several graduate students who are members of Center labs are also part of this graduate program.


Graduate School Career Workshop

In February 2014, the Center Education Coordinator co-organized a workshop at Agnes Scott College, an ethnically diverse women’s college in Atlanta, Georgia. The workshop was titled “Is a Ph.D. for Me? What You Can Be with a Ph.D. in Engineering & Life Sciences” and focused on the varied reasons for pursuing a graduate degree and determining which university/graduate program would be the best fit for a student. Over 100 undergraduate students from Atlanta-area schools registered and attended the workshop which included speakers from Georgia Institute of Technology, MIT, UC Berkeley, Agnes Scott College, Arizona State University, and UCSF. The workshop was co-organized by our Center, SynBERC at UC Berkeley, and Agnes Scott College. This is the second such workshop we have helped host, the first held in November 2012 at Prairie View A&M University.

 

SACNAS Leadership Development and CIENCIA

The Center provided instrumental funding in 2013/2014 to the UCSF chapter of the Society for Advancement of Chicanos and Native Americans in Science (SACNAS, http://ucsf.orgsync.com/org/sacnas/) to help support leadership development and new organizational initiatives. SACNAS is a national organization, and the local UCSF chapter is focused on expanding opportunities available to underrepresented minorities and empowering them to become leaders, by organizing academic, professional, community service and social activities. The Center was able to send two active chapter members to the SACNAS National Conference in San Antonio, Texas October 2-6, 2013 by funding their registration, travel and lodging. Additionally, the Center sponsored leadership development by subsidizing the inaugural SACNAS UCSF Chapter Leadership Retreat held in January 2014. Finally, Center funding was used to sponsor the development of CIENCIA (http://ucsf.orgsync.com/org/ciencia/), a scientific Spanish seminar series and journal club held on the UCSF campus. The goal of CIENCIA is to foster Spanish-speaking skills and allow for the opportunity for the UCSF community to participate in specialized, scientific discourse in Spanish. Contributions to these events have proven invaluable and led to the rapid development and solidification of these organizations, especially the nascent CIENCIA program which is in its first year.


Center Meetings and Workshops

Monthly Scientific Meetings

The monthly Center scientific meetings have been significantly growing in attendance, and now include participants from the broader UCSF community.

 

Theorizza

A Center-generated activity has been to hold a biweekly theory discussion group on Friday afternoons (theory + pizza = theorizza). This discussion group was initiated by our Systems Biology Fellows to allow theoretical researchers to discuss their ideas within our Center, as well as within the broader UCSF community and beyond. The response to this initiative remains very positive, and something that the UCSF community has been lacking. Theoreticians both within and outside the Center now attend this regularly.

 

Practical Systems and Synthetic Biology Discussion Series

The 'pSysSynBio dGroup' is a forum to discuss roadblocks and solutions in transitioning systems knowledge to actionable tools in everyday synthetic, cellular and population biology.  The series was initiated by one of our direct trainees, Ignacio Zuleta, a postdoctoral fellow working with Hana El-Samad and Hao Li. Discussion topics include flux re-engineering, secretion, directed evolution, cellular stress management strategies, biosensors, high-throughput and scaleup innovation, fermentor dynamics, cell population control and analysis tools. The group consists of graduate students and postdoctoral fellows at UCSF, and also aims to engage the local Bay Area industry and start-up community to discuss everyday applications and new emerging technology, and how to overcome roadblocks along the way.

 

Multicellular Systems Biology Discussion Group

Our Center has launched a new discussion group in 2013 on the topic of "multicellular systems biology."  By bringing together a diverse group of individuals – ranging from developmental and cancer biologists, to theorists and tool builders – the hope is to catalyze conversation and the exchange of ideas between these traditionally separate groups. Our aim is to identify their commonalities under the umbrella of multicellular systems biology through the presentation of exciting science by students, postdocs, and faculty in the UCSF and Bay Area scientific community. The group is also interested in exploring related topics like self-organization. This group was launched by seed grant recipient Zev Gartner and postdoctoral fellow Leo Morsut. This initiative has also been a great way to reach out and engage several labs and departments from outside our Center (ie., developmental biology).

 

UCSF-PKU Systems & Synthetic Biology Summer Workshop and Exchange

In collaboration with our co-investigator Chao Tang who has recently transitioned to Peking University (PKU), we developed an innovative UCSF-PKU team challenge workshop, which took place at PKU from July 25-29th, 2012. In our workshop, we were interested in breaking down some of the cultural and language barriers between the US and China, and in experimenting with how scientists in the US and China interface. In addition, we were interested in joint brainstorming exercises to lay a roadmap for new cutting edge ideas in the life sciences, and which would act as a springboard for joint projects and student exchange between UCSF and PKU. At UCSF, we have experience in collaborative, team-based approaches to science. Many of our graduate school courses are now taught via ‘team-challenge’ mechanisms and incorporate principles of collaborative ‘design-thinking’ approaches developed by the highly successful Palo Alto-based design firm IDEO.

Our Center sent 14 UCSF Center faculty, postdoctoral fellows, and graduate students to participate in the workshop at PKU, while 32 select graduate and undergraduate students participated from PKU. We were divided into four teams, each focused on one of the team challenge topics:
1) What controls cell size?
2) What is the future of optogenetics?
3) How can microfluidics be used as cheap diagnostics?
4) How to manage cell stress in engineered metabolic pathways?

 

The teams went through successive rounds of brainstorming, idea synthesis and organization, voting on favorite ideas, project development, followed by daily presentations to the other teams and panel of faculty for feedback. At the end of the four days, the teams developed a roadmap and written proposal for their topic idea. PKU agreed to fund follow-up exchange students to do preliminary or proof of principle studies. Our first exchange student, Zairan Liu, was at UCSF for 3 months (mid Feb to mid April, 2013), performing experiments related to the optogenetics team challenge project. The rationale, organizational process, and outcomes of this workshop were described in an educational article entitled ‘Bridging cross-cultural gaps in scientific exchange through innovative team challenge workshops’ published in the inaugural issue of the newly launched journal Quantitative Biology.

 


Other Outreach and Community Activities and Past Events

 

San Francisco ExplOratorium

The 2013 UCSF iGEM team introduced the basic ideas of synthetic biology in a special presentation at the San Francisco ExplOratorium, the city’s premiere science and education museum. The ExplOratorium hosts monthly themed “After Dark” evening events attended by over a thousand guests. On September 5, 2013, focusing on the theme of “Transformations,” the group talked about the central dogma of biology and how scientists use this information to build and “transform” biological systems and operate them in living cells. Their presentation was titled ‘Micro-Transformations Can Bring Big Results’. With this new relationship established with the museum, we hope to become further involved in developing presentations and exhibits in the coming year.

 

AAAS Teacher-Scientist Partnership Conference

The UCSF Science & Health Education Partnership (SEP) works with scientists and teachers in the Bay Area to support science education and has been a valuable collaborator for educational opportunities. As a result of our successful iGEM program, we were invited to organize a workshop session at the First International Teacher-Scientist Partnership Conference. The conference was co-organized by SEP and AAAS and was held February 13-14, 2013, in Boston, MA, directly preceding the AAAS annual meeting. Our Center Education Coordinator and two former iGEM mentors presented an hour long session titled “UCSF iGEM Program: Team-based Science Education from the Classroom to the Laboratory.” During the session the speakers shared information on the UCSF iGEM team and how our approach to teaching synthetic biology to young scientists has positively affected both student and mentor participants over the years.

 

Public Lecture on ‘Science & Cooking’

The Center partnered with the departments of Cellular & Molecular Pharmacology and Anesthesia at UCSF to organize and host a special Chauncey D. Leake Lecture on ‘Science & Cooking’ on April 2, 2012, presented by Professor David Weitz of Harvard University and Chef Corey Lee of San Francisco. The idea for this lecture series was inspired by the popular Harvard University science undergraduate course on ‘Science & Cooking: from haute cuisine to the science of soft matter’, pioneered by two Harvard physicists, David Weitz and Michael Brenner. This Center-organized public lecture at UCSF was attended by over 300 people and was highlighted in the San Francisco Chronicle blog post. The full lecture is also available on YouTube.

 

Panel Discussion on Synthetic Biology

On December 14, 2011, we collaborated with Jay Keasling of UC Berkeley and scientific editors at CellPress to co-organize and host the Synthetic Biology Lablinks meeting. Over 300 participants registered for this free symposium, which included a panel discussion on ‘Synthetic Biology: Goals, Aspirations, and Implications,’ also intended to be of interest for the general public.

 

Bay Area Science Festival

Our Center collaborated with UC Berkeley SynBERC to create an interactive booth titled “Synthetic Biology: Making Biology Easier to Engineer.” This booth was displayed at the first annual Bay Area Science Festival’s Discovery Days event held at AT&T Park on November 6, 2011. The exhibit, which included a video display, informational poster, and a hands-on activity, was designed to teach children of all ages about the field of synthetic biology. The design and display of the booth involved graduate student and undergraduate volunteers who worked throughout the day to engage attendees and promote synthetic biology. Ours was one of 170 exhibits at the event, which was attended by over 21,000 people. The Bay Area Science Festival consisted of more than 100 events held over a week in November and was primarily organized by UCSF. The Center sponsored UCSF iGEM program was highlighted during press events held leading up to the festival, including being recognized by San Francisco Mayor Ed Lee. Mayor Lee visited with the team in the lab, learned about their project, and remarked on the accomplishments of the UCSF iGEM program when he spoke to the press. Our Center plans to be involved in several more events with the Festival in the coming years.

 

Capitol Hill Day

On September 21, 2011, Center members advocated for science funding during the Coalition for the Life Sciences ‘Capitol Hill Day’. They teamed up with scientists from UCLA as part of a California delegation, visiting the Washington DC offices of Senators Barbara Boxer and Dianne Feinstein, Representatives Adam Schiff, Anna Eshoo, and Xavier Becerra, as well as Democratic Leader Nancy Pelosi. The team thanked the Senators and Representatives for their support of scientific research and asked them to continue funding NIH and NSF at the highest possible levels.

 

San Francisco Bay Area Science Fair

As our Center seeks to expand volunteer opportunities for our members, we have identified the San Francisco Bay Area Science Fair as a local organization promoting science education among middle and high school students. The science fair is held every March at the San Francisco County Fair Building and selects over 300 students from eight Bay Area counties to enter the competition. On March 20th, 2013, four volunteers from the Center reviewed and scored projects from grades 7-12 and selected students to be interviewed for top awards. To promote systems biology among young scientists, we also plan to sponsor a special award for this fair in 2014.

 

IISME Teacher Training

The Industry Initiatives for Science and Math Education (IISME) program places K-12 teachers in summer fellowships to provide them with exposure to industry and academic research environments. The teaching fellows spend 90% of their time working on a research project with their host/mentor and 10% of their time on professional development (producing an Educational Transfer Plan to update their curriculum). In the summer of 2012 our Center sponsored an IISME fellowship for Stephen Wakulchik, a high school science teacher from Dewey Academy in Oakland, CA. Stephen worked directly with our education coordinator to lead the iGEM team in developing their synthetic biology project and working in the lab. Stephen learned many new laboratory techniques and knowledge about the field of synthetic biology that he is now incorporating into his classroom. Additionally, Stephen developed a plan of action for helping his school administrators and faculty troubleshoot and brainstorm to solve problems within the school. This plan of action was based on the method of group idea generation used with our IGEM team, which Stephen was able to be a part of several times during the summer.

 

Dewey High School Student Field Trip

Dewey Academy (Oakland, CA) serves students who are not on track to obtain a high school diploma at a “traditional” school such that they may earn their degree and continue their education at vocational, technical, or other colleges. The school serves approximately 250 students in grades 9-12, with 90% identifying as underrepresented minorities and 74% as economically disadvantaged. We worked with Dewey Academy’s science teacher, Stephen Wakulchik, to organize a field trip to UCSF for students currently enrolled in physics or biology courses. On March 8, 2013, nine students traveled to UCSF and participated in interactive tours of the campus, the UCSF 3D structural visualization Center (https://www.rbvi.ucsf.edu/) and the UCSF Lung Biology Center (http://lungbiology.ucsf.edu/). The visit concluded with a lunch hosted by UCSF graduate students and postdocs, where the Dewey Academy students had an opportunity to learn about life as an academic scientist and hear about other research areas at UCSF.