Course: BIOEN 425/525 Laboratory Methods in Synthetic Biology

Credits: 4

Instructor: Georg Seelig or Eric Klavins

Texts and Supplemental Materials: Klavins, Bishop, Egbert, House, and Oishi. Laboratory Methods in Synthetic Biology.

UW Catalog Description: Designs and builds transgenic bacterial using promoters and genes taken from a variety of organisms. Uses construction techniques including recombination, gene synthesis, and gene extraction. Evaluates designs using sequencing, fluorescence assays, enzyme activity assays, and single cell studies using time-lapse microscopy.

Prerequisites by Course: Either BIOEN 423, E E 423, or CSE 486; either CHEM 142, CHEM 144, or CHEM 145.

Required or Elective: Elective

Specific Outcomes: 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.

Outcomes Addressed by this Course:

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.

 Topics Covered:

  1. The applications, risks and ethics of synthetic biology
  2. Lab safety
  3. Basic lab techniques including pipetting and sterile technique
  4. Bacterial cultures and growth curves
  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

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