Master Course Description No: EE 425 Title: LABORATORY METHODS IN SYNTHETIC BIOLOGY Credits: 4 UW Course Catalog Description: Design and build transgenic bacteria using promoters and genes taken from a variety of organisms. Construction techniques including recombination, gene synthesis, and gene extraction. Evaluation of designs using sequencing, fluorescence assays, enzyme activity assays, and single cell studies using time‐lapse microscopy. Offered jointly with BIOEN/CSE 424. Prerequisites: E E/CSE/BIOEN 423; CHEM 142 or CHEM 145 Instructor: Eric Klavins, Assistant Professor, Electrical Engineering Goals: For students to acquire the necessary tools for the analysis and design of linear feedback control systems. Learning Objectives: At the end of this course students will be able to: 1. Culture bacteria. 2. Manipulate DNA with restriction, ligation, PCR and gel electrophoresis. 3. Transform bacteria with recombinant DNA and screen for successful transformants. 4. Design genetic regulatory networks at the level of the DNA sequence. 5. Extract DNA from cells and prepare it for sequencing. 6. Perform fluorescence and growth assays with a fluorescence plate reader. 7. Use a fluorescence microscope to capture single cell behavior in time. 8. Analyze experimental data and fit it to mathematical models. 9. Understand the risks and ethical considerations of synthetic biology. Textbook: Klavins, Bishop, Egbert, House, and Oishi. Laboratory Methods in Synthetic Biology. Available online. Publication in progress. Reference text: (Optional) 1. Nelson and Cox, Principles of Biochemistry, 4th Edition, Freeman, 2004. 2. Micklos, Freyer and Crothy, DNA Science Cold Spring Harbor Laboratory Press, 2003. Prerequisites by Topic: 1. Introduction to synthetic biology (or similar) 2. Differential Equations 3. Linear Algebra 4. General Chemistry 5. Familiarity with the use of Matlab. NOTE: No biochemistry background is required. T i op cs: 1. The applications, risks and ethics of synthetic biology ng and sterile technique 2. Lab safety ti s 3. Basic lab techniques including pipet 4. Bacterial cultures and growth curve 5. Design of experiments and controls 6. Extraction of plasmid DNA from E. coli 7. Recombinant DNA techniques include restriction digests, gel purification, ligation, and PCR based methods 8. Sequencing for the purposes of debugging constructs 9. Fluorescence reporters and methods for measuring cell activity using fluorescence 10. Time lapse fluorescence microscopy 11. The application of differential equations and stochastic processes to predicting the behavior of synthetic biochemical networks 12. Parameter estimation and system identification Course Structure: The class meets for one lecture a week (Mondays) followed by two three‐hour lab sessions each week. Laboratory are done in groups of two. There will be weekly prelab quizzes and then lab reports. A final design project is due at the end of the quarter. Computer Resources: The course uses MATLAB for homework problems. The students complete an average of 3 hours of computer work per week. Outcome Coverage: (a) An ability to apply knowledge of mathematics, science, and engineering to the design of biochemical networks for specific applications. (b) An ability to design and conduct experiments, as well as to analyze and interpret data. Students will generate and analyze data from their own experiments. (c) An ability to design a system, component or process to meet desired needs within realistic constraints such as economic, environmental, social, political, ethical, health and safety, manufacturability and sustainability. Students are required to apply the skills acquired in this course to design control systems to meet specific performance requirements. (d) An ability to function on multi‐disciplinary teams. Lab work is done in teams and students typically come from EE, CSE and BioE. (f) An understanding of professional and ethical responsibilities related to introducing new genetic material into the ecosystem. (h) The broad education necessary to understand the impact of engineering biological solutions in a global, economic, environmental and societal context. (j) Knowledge of contemporary issues in genetic engineering, gene therapy, biofuels and energy, medicine and disease. (k) An ability to use the techniques, skills, and modern engineering tools necessary for engineering practice. Students use Matlab to analyze and design systems. Prepared By: Eric Klavins Last revised: 4/17/2009