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Synthetic Biology Engineering Research Center

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What can Synberc do in one year?

Synberc brings together about 500 students, professors, educators and industry partners to make biology easier and safer to engineer. What can this extraordinary group do in a twelve-month period? Here's a snapshot of some of the research, education and broader achievements of the Synberc community for 2014-2015:

Research and technological outcomes at the system level and the integrated systems test beds:

  • D-glucaric acid production in E. coli and S. cerevisiae: A project to produce glucaric acid in the yeast S. cerevisiae was initiated in 2014 with the goal of achieving a titer equal or greater than that currently achieved in E. coli (5 g/L) by 2016.  A more stable derivative of the glucaric acid pathway enzyme MIOX was achieved through a fusion with SUMO. This will be used for subsequent work to improve the activity of this enzyme 
  • Nitrogen Fixation (Nif): Starting from the original refactored Nif cluster from K. oxytoca, we improved our Nif synthetic cluster using multiple rounds of design-build-test-learn to 57% of the wild-type level. Subsequent designed rounds of improvement are now possible using the current version of the refactored nif cluster
  • Programmable Organoids: We developed and deployed a highly multiplexed screen for differentiation-inducing factors in iPS cells using the CRISPR-Cas System, which allows us to screen sgRNA libraries for genes that can drive differentiation when overexpressed

Research and technological outcomes at the enabling technologies and cross-cutting activities level, and the enabling technology testbeds:

  • Yeast genome engineering: We adapted the CRISPR-Cas9 system for use in yeast and have observed high-frequency directed genome editing. This system now allows multiplex genome editing in yeast 
  • We developed a new version of Clotho, a biocad platform for engineering synthetic biological systems and managing the data used to create them. It now modularizes workflow into Functions and Schemas to maximize their dynamic reusability
  • Part Assembly: The Dueber group developed methodologies for the rapid construction of devices consisting of multiple biological parts, a key bottleneck in the development of functional parts that work predictably in different contexts. 

Research at the fundamental science and engineering level:

  • We created a new device, termed DNAi, which is derived from the CRISPi system to destroy specifically targeted DNA (designated by the experimenter) at times in the growth/production cycle when no longer required 
  • Synthetic Memory Device: The Weiss lab modified the synthetic memory device, originally designed in the Silver lab to respond to hypoxia in human bone osteosarcoma epithelia cells, to respond to inflammation in beta-T6 cells. This demonstrates the reuse of this device in different hosts.

University education:

  • Synberc offered 23 courses this year that were based on ERC curriculum, including two new courses. Three of the most popular synthetic biology courses were made freely available. These include PowerPoint presentations, exams, assisignments, texts, and other resources. (http://synberc.org/featured-courses)
  • iGEM: Synberc is the single biggest sponsor of the International Genetically Engineered Machines (iGEM) Competition, the premiere undergraduate synthetic biology competition. This year we reached about 245 teams and about 3000 particpants from dozens of countries. We also started a new track in Policy & Practices, and partnered with Synthetic Genomics Inc to screen the entire iGEM registry for biosafety. 
  • Research Experiences for Undergraduates: Since 2007, the Synberc REU program has provided 93 undergraduate research experiences, 42% of which have gone to URMs. Of the REUs that completed their undergraduate degrees, we have long-term data for 82%, and of those students, 92% have pursued STEM careers and/or advanced degrees.

Pre-college education:

  • Synberc iCLEM: Since 2007, the iCLEM program has provided intensive eight-week research experiences to 50 high school students, nearly all of whom are women and/or underrepresented minorities. Of the 50 iCLEM graduates, 97% have gone on to college, and 81% have majored in STEM fields. (Section 7.6.3)
  • Since 2008, 71 pre-service and in-service teachers have participated in Synberc’s Berkeley RET program resulting in a broader reach to thousands of students through education transfer plans. Most in-service teachers serve at schools or community colleges in which the majority of students are socioeconomically disadvantaged. 
  • BioBuilder: After successfully establishing itself as an independent not-for-profit organization last year, this year BioBuilder held its first Master Teacher Workshop to further develop best practices for teaching synthetic biology in classrooms around the world. To date, BioBuilder has reached 457 teachers in 42 states, introducing students in over 200 classrooms to the Biobuilder curriculum. The BioBuilder textbook will soon be published by O’Reilly Media. 
  • iCLEM: The Introductory College-Level Experience in Microbiology (iCLEM) graduated its eighth cohort of high school researchers from underserved populations. Since 2007, iCLEM has provided intensive eight-week research experiences to 50 high school students, nearly all of whom are women and/or underrepresented minorities. Of the 50 iCLEM graduates, 97% have gone on to college, and 81% have majored in STEM fields. 

Public and policy engagement and communications:

  • Communications & Engagement Working Group: We initiated this working group to provide communications training and engagement opportunities to practitioners. It also aims to consider challenging topics in synthetic biology and explore strategies for addressing them. Seehttp://Synberc.org/engagement
  • Synberc on Capitol Hill: We coordinated a congressional briefing in partnership with Discover Magazine and NSF to emphasize the importance of sustaining U.S. leadership in biotech and synthetic biology. This was accompanied by visits to congressional offices, where we shared expertise relevant to draft congressional legislation for the Engineering Biology Research and Development Act of 2015. This bill was introduced on January 29, 2015. (see http://democrats.science.house.gov/press-release/ranking-member-johnson-and-rep-sensenbrenner-introduce-bipartisan-engineering-biology)
  • Taking synthetic biology into science museums: Synberc partnered with the Boston Museum of Science and AAAS on Multi-Site Public Engagement with Science (MSPES) in Synthetic Biology. This project will create conversations in science museums among scientists, engineers, and public audiences about synthetic biology. It will culminate in 200 synthetic biology learning kits being distributed throughout the U.S. in the summer of 2016. See http://dimensionsofpes.wikispaces.com/MSPES-SynBio
  • How to engage audiences about synthetic biology: The Synberc Student & Postdoc Association (SPA) led a Synthetic Biology Communication Workshop at MIT on Friday September 26, 2014, in partnership with the Alan Alda Center for Communicating Science at Stony Brook. The purpose of the workshop was to provide science practitioners with the skills and confidence needed to communicate and engage with general audiences about the importance and potential of engineering biology. 
  • We have boosted our social media outreach effort on platforms including Twitter, LinkedIn, Facebook, and others. A social media meet-up will take place on March 31, 2015, to describe best practices for social media and to identify challenging topics and potential strategies for approaching them. See https://twitter.com/Synberc

Diversity advances:

  • Expanding Potential: To overcome challenges to women in STEM, Synberc held its inaugural “Expanding Potential" workshop on November 15, 2014 to navigate the hurdles faced by women in STEM. The workshop opened a conversation about issues women often face in the workplace, and promoted career development and networking to encourage retention and diversity. Due to the tremendous response, we are planning a second workshop in Fall 2015 that will emphasize putting some of the ideas from the first workshop into action. 
  • Diversity at the podium: We initiated a program aimed initially at helping conference organizers to achieve gender balance in their speaker line-ups. The program webpage offers a suggested list of female speakers in synthetic biology related fields, as well as a sample letter for conference organizers on how to make their events more inclusive (e.g. ensuring women's restrooms are accessible, offering child care, offering travel funds to women/URM speakers, etc.). 
  • Synberc held an Implicit Bias Training Session at our Spring Retreat on March 25, 2014, attended by all Synberc community members. The session was led by Victoria Plout, an implicit bias expert at UC Berkeley. The purpose of the session was to reveal the subconscious biases that people may have, and describe ways of overcoming them. 

Technology transfer and commercialization:

  • Two more Synberc start-ups: Two new companies joined Synberc’s growing list of spin-offs in recent months. Both companies – 20n and De Novo DNA – are commercializing software tools originally co-developed with Synberc funding.  Founded by Synberc Affiliated PI Howard Salis, De Novo DNA is licensing advanced versions of the RBS calculator and other bioinformatics tools to established biotechnology companies.  Synberc PI Chris Anderson and colleagues’ brainchild 20n is developing the Act Synthesizer for license.
  • Two Synberc CRISPR/Cas9 patent applications: CRISPR/Cas9 technology, which enables rapid and precise genome editing in many organisms, is taking biotechnology by storm. Two patent applications pertaining to this technology, listing Synberc investigators Adam Arkin and George Church as co-inventors, were published in the last 12 months. With Multiplex Automated Genome Engineering (MAGE), George Church and colleagues took this technology one step further to enable the rapid re-engineering of entire genomes. In one instance, by generating genomic diversity, the team was able to make E. coli capable of producing five times the normal quantity of lycopene, an antioxidant, in a matter of days.

International partnerships/collaborations:

  • Synberc is developing a NSF SAVI proposal to create an international network of researchers that will form a global Web of Registries. The Web of Registries will adhere to and advance international standards for synthetic biology. It will include participants from the United Kingdom (Flowers Consortium), Denmark, and Singapore. 
  • Last year, the Synberc Student and Postdoc Association (SPA) appointed Christian Boehm (Cambridge University) as the SPA’s International Liaison. This year, Christian and the SPA are exploring ways to coordinate the SPA activities with those of the European Association of Students and Postdocs in Synthetic Biology (EUSynBioS, http://www.eusynbios.org.

Center infrastructure, including personnel:

  • Synberc looks ahead to sustainability: This year, we developed a Sustainability Working Group composed of a combination of Synberc PIs, Affiliate PIs, IAB members and SAB members. The findings from that group form the basis for our current Sustainability Plan. Our plan is becoming real as we anticipate establishing a not-for-profit like organization in the coming months. (seehttp://synberc.org/sustainability for our full plan)
  • In June 2014, Dr. Shaila Kotadia was hired to replace Kate Spohr as our Education & Outreach Manager. Dr. Kotada has a Ph.D. in genetics and development from University of Texas Southwestern Medical Center. She recently served as the American Society for Biochemistry and Molecular Biology (ASBMB)’s Science Policy Fellow in DC.  The leadership transition within our education program has been very smooth, and Shaila has brought a new energy and insight to our education and outreach programs.