CH391L/S12
CH391L: Synthetic Biology
Spring 2012
Mondays 2-5 PM MBB 2.204
Instructor: Dr. Jeffrey Barrick <jbarrick AT cm DOT utexas PERIOD edu>
Course web page: The course web site on OpenWetWare.org http://openwetware.org/wiki/CH391L/S12 will host course handouts, readings, and assignments.
Motivation
The purpose of this course is to become familiar with the techniques, biological parts, accomplishments, problems, and challenges of synthetic biology. For the most part, we will focus on E. coli and yeast systems as chassis. Participants will be expected to individually contribute to OWW pages describing the history, development, and implementation details of engineered parts and organisms from the scientific literature. Then, they will be expected to create a proposal as part of a group with specific experimental and modeling details for using synthetic biology to solve an outstanding problem with technological or societal impact.
Assignments
Coursework will consist of in-class oral presentations on scientific papers or research proposals and a "written" component consisting of Wiki page edits on OpenWetWare. All participants in the course will be expected to provide feedback concerning the content of presentations and the content of Wiki pages.
Topics
Introduction - Barrick
- Definitions of synthetic biology
- A short history of synthetic biology
- Ethical issues in synthetic biology
- Challenges and open problems
Methods
(Approximately 3 class periods)
Making or finding parts
- iGEM Registry
- BioBricks
- BglBricks
- Bioprospecting new parts using Metagenomics
- Rational design
- Directed evolution / in vitro selection
Assembling parts into systems
- Gene/genome synthesis
- Restriction enzyme cloning
- PCR techniques
- Gibson assembly, SLIC, CPEC
Computational methods
- TBD
Parts
(Approximately 6 class periods)
- Chassis (organism)
- Replication origins (plasmids and artificial chromosomes)
- Transcriptional promoters
- Ribosome binding sites
- Codon optimization (other factors controlling protein expression)
- Transcription terminators
- Selectable and counter-selectable genetic markers
- Toxin-Antitoxin genes
- Reporter genes
- Sensor genes (quorum sensing, light)
- Transcriptional regulatory proteins / riboswitches
- Locomotion/chemotaxis
Systems
(Approximately 6 class periods)
- Refactored T7 (Endy)
- Represillator (Elowitz and Leibler)
- Toggle switch (Collins)
- Counter (Church and Collins)
- Edge detection (Ellington, Voigt, etc.)
- Yeast producing artemisinic acid (Keasling)
- Atrazine seek and destroy (Gallivan)
- Synthetic chromosome arms in yeast (Boeke)
- Synthetic ecologies
- MAGE increased lycopene production (Church).
- And many more...
