Outreach & Teaching


iCLEM program

In 2008, James co-founded the Introduction to College Level Experience in Microbiology (iCLEM) program at UC Berkeley and the Joint BioEnergy Institute, a paid summer internship in bioenergy-related research for low income high school students in the San Francisco Bay Area. In the past five years the program has had 35 students, all of whom come from families with little or no history of college attendance, and 15 credentialed High School Science Teacher Fellows and Teachers-in-Training (Above, 2012 Student Researchers are shown in the lab with Teacher Fellows). The program has been covered in newspaper and television press and is now a major outreach/education activity of the Synthetic Biology Engineering Research Center (SynBERC) and the Joint BioEnergy Institute (JBEI).  

To aid efforts to efficiently convert renewable plant materials into transportation fuels, the iCLEM interns have worked to isolate and characterize cellulose-degrading organisms from environmental samples. The program also includes college prep activities and career exploration through field trips to local biotech companies and lunchtime discussions with practicing scientists. The Science Teacher Fellows develop and give lessons focused on fundamental concepts in microbiology, molecular biology, biochemistry, genomics, bioengineering and synthetic biology. To broaden the impact of the program, the Teacher Fellows create specific plans to transfer their Summer Fellowship experiences to their classrooms.

iCLEM students:
  • High school sophomores and juniors from the San Francisco Bay Area (San Francisco, Alameda and Contra Costa Counties) from low income families with little or no history of college attendance
  • Promising students for whom the experience would make a critical difference in their lives
  • Annual number of applications: >200 (acceptance rate < 10%)
  • 76% are low-income, 2/3 are the first in their families to attend college
  • 100% of iCLEM students enroll in college, 70% major in science or engineering
  • National data for students with similar backgrounds show that only 53% would be likely to attend college

Main outcomes:

  • Students experience biotechnology as participants in an 8 week, team-oriented bioenergy research project
  • Didactic reading, writing and discussion teach fundamental concepts in microbiology, molecular biology, biochemistry and synthetic biology
  • Students improve communication skills by preparing data for publication, maintaining lab records, writing reports, giving presentations and developing scientific posters
  • Students are exposed to careers in science and biotechnology through lunchtime discussions with scientists and field trips to local biotech companies
  • Students improve readiness for the college application process and college coursework
  • Formal written student evaluations are given throughout the program
  • With guidance, Science Teacher Fellows develop specific plans to transfer their Summer Fellowship experience back to their school sites-- 1500 Bay Area students benefit from these well-trained teachers each year

HIGHLIGHTED IN:  2012 LBL News |ABC Bay Area TV | San Jose Mercury News |UC Berkeley News | Berkeley Alumni News | Berkeley Daily Planet

Advanced Synthetic Biology for Applications

Spring Quarter 2013

ChemE 498/599; BioE 424/524; EE 424/524; CSE 487/587

Tues and Thus, 11:30am-12:50pm

MOL 1st Floor Conference Room (note room change)

Prof. James M. Carothers

Office hours:
MolES 322, Tues and Thur, 1pm-2pm (by appointment).

40% written paper critiques

40% final written project SBIR mini-proposal
20% final oral project presentation SBIR mini-proposal
Extra credit will be recorded and used subjectively when determining letter grades. All assignments must be turned in on time. Late assignments will not be accepted except for prearranged travel or unexpected illness.

Dropbox URL:

Discussion Board URL:


Through the careful application of genetic engineering, synthetic biological systems can be engineered to help meet unmet needs in the production of renewable chemicals and fuels, materials for global health, and the development of novel cell-based therapeutics. This course will use application testbeds to explore how computational approaches, including coarse-grained biochemical modeling, and sensitivity analysis can be integrated with experimental approaches for directed evolution and combinatorial screening to drive the design of functional systems. Although the primary focus will be on systems-level engineering in microbes and cultured mammalian cells, this course will also touch on practical aspects of process design for industrial and medical biotechnology. The course will consist of background lectures, in-depth student-led discussions of topical literature, and in-class 'tech charrettes'. Final projects will involve using modeling to analyze a system engineered to solve real-world problems.

Knowledge of basic molecular biology, biochemistry, and math through differential equations will be assumed. The Introduction to Synthetic Biology course, and experience with computational modeling of biological systems is recommended, but not required. At a minimum, course participants should review the basic molecular biology of gene expression in prokaryotes and eukaryotes before the first class session.

Course Schedule:


 WkTopicTuesThursThurs Mini lectureKey Dates 
 1IntroductionIntro to applied synthetic biology and tech charretteHands-on: Intro to dynamic modelingIsoprenoid pathway engineering  
 2Drug pathway constructionPaper: Ro et al. 2006. Nature.Hands-on: Reaction rate equationsFitness landscapes4/9 Ro et al. Critique Due 
 3Drug pathway optimizationPaper: Ajikumar et al. 2010. Science.Hands-on: Isoprenoid pathway modelIntro to industrial biotechnology4/16 Ajikumar et al. Critique Due 
 4Bioreactor strain engineeringPaper: Moser et al. 2012. ACS Synth. Biol.Hands-on: Intro to statistical analysis with REngineering genetic control parts4/23 Moser et al. Paper Critique Due 
 5Model-driven circuit constructionPaper: Ellis et al. 2009. Nat. Biotechnol.Hands-on: Genetic circuit modelingRNA synthetic biology4/30 Ellis et al. Paper Critique Due 
 6Design-driven genetic device engineeringPaper: Carothers et al. 2011. Science.Hands-on: One-at-a-time sensitivity analysisGlobal sensitivity analysis5/7 Carothers et al. Paper Critique Due 
 7Dynamic controls for metabolic engineeringPaper: Zhang et al. 2012. Nat. Biotechnol.Hands-on: Global sensitivity analysisMammalian synthetic biology5/14 Zhang et al. Paper Critique Due 
 8Mammalian cell-cell communicationPaper: Bacchus et al. 2012. Nat. Biotechnol.Tech charrette to identify final projectsIdentifying market opportunities5/21 Bacchus et al. Paper Critique Due 
 9Model-driven mammalian synthetic biologyPaper: Miller et al. 2012. PloS Comp Biol.Mid-way project presentations (SBIR mini-proposal)5/28 Miller et al. Paper Critique Due 
 10Final PresentationsFinal Presentations 1 (SBIR mini-proposal)Final Presentations 2 (SBIR mini-proposal)6/10 SBIR mini-proposal due 

Written paper critiques:
Professional scientists and engineers in academia, industry, government, finance, law, etc. are routinely called on to critically-review papers and generate new ideas based on those papers. Each person will write a 400-500 word written critique of the eight papers discussed in the Tuesday class sessions Write-ups should be submitted to the course dropbox before the start of the Tuesday class. Dues dates are listed in the 'Key Dates' chart; late submissions cannot be accepted and will receive a score of 0. Peer grading will be used to evaluate the written critiques, with spot-checking performed by the Instructor and Reader to ensure rigor and fairness. A general outline for the write-up is given below.
First paragraph should succinctly restate, in your own words, what was accomplished. 2) Second paragraph should describe and evaluate the soundness of the technical approach 3) Third and fourth paragraphs should identify future directions and interesting experiments that are enabled by the work described in the paper. The future directions should be original and distinct from the ones identified by the authors. Although it is important to have a solid understanding of the paper (i.e., demonstrate this in paragraphs 1 & 2), the bulk of the score will come from the specificity and creativity of the future directions.

Paper assignments:

Each Tuesday discussion will be lead by 1-3 students. Assignments will be made during first class session.
1. D.-K. Ro et al., Production of the antimalarial drug precursor artemisinic acid in engineered yeast,Nature 440, 940–943 (2006).
2. P. K. Ajikumar et al., Isoprenoid Pathway Optimization for Taxol Precursor Overproduction in Escherichia coli, Science 330, 70–74 (2010).
3. F. Moser et al., Genetic Circuit Performance under Conditions Relevant for Industrial Bioreactors,ACS Synthetic Biology 1, 555–564 (2012).
4. T. Ellis, X. Wang, J. J. Collins, Diversity-based, model-guided construction of synthetic gene networks with predicted functions, Nat. Biotechnol. 27, 465–471 (2009).
5. J. M. Carothers, J. A. Goler, D. Juminaga, J. D. Keasling, Model-Driven Engineering of RNA Devices to Quantitatively Program Gene Expression, Science 334, 1716–1719 (2011).
6. F. Zhang, J. M. Carothers, J. D. Keasling, Design of a dynamic sensor-regulator system for production of chemicals and fuels derived from fatty acids, Nat. Biotechnol. 30, 354–359 (2012).
7. W. Bacchus et al., Synthetic two-way communication between mammalian cells, Nat. Biotechnol.(2012).
8. M. Miller et al., Modular Design of Artificial Tissue Homeostasis: Robust Control through Synthetic Cellular Heterogeneity, PLoS Computational Biology 8, e1002579 (2012).

Hands-on, in-class workshops:

Details will be given during class.

Final projects:

From the National Science Foundation (NSF) Small Business Innovation Research grant website:

The Small Business Innovation Research (SBIR) Program stimulates technological innovation in the private sector by strengthening the role of small business concerns in meeting Federal research and development needs, increasing the commercial application of federally supported research results, and fostering and encouraging participation by socially and economically disadvantaged and women-owned small businesses.

NSF SBIR Evaluation criteria:

Intellectual merit. What is the problem to be solved? How will the problem be solved? What is the innovation in the proposed approach?

Broader impacts. Why is your solution better than competitive technologies? Who is going to buy your solution? Who are the other key players?

Final projects will involve writing a 2-3 page executive summary for an SBIR proposal that is supported by mechanistic modeling and sensitivity analysis learned in the class. Scores will be derived from the the originality of the proposal, the effectiveness of the modeling and sensitivity analysis in supporting the technical proposal, and the quality of the oral and written presentations. Further details will be provided in class.