New: Check out some of the gro simulations made by students in our Introduction to Synthetic Biology course on youtube.
Introduction to Synthetic Biology : Fall 2011
- BioE 423/523, CSE 486/586, EE 423/523
- Instructor: Prof. Eric Klavins
- Office Hours: Tu, Th 9:00AM - 10:20AM, CSE 236
- Teaching Assistant: Shelly Jang
- Office Hours: Mo, Fr, 10:00AM - 11:20AM, EEB M406
- MWF 11:30-12:20
- MOR 234
- Library proxy information: http://www.lib.washington.edu/help/connect.html
|1||9/28||Introduction||Special Issue of Science on Synthetic Biology: Read the introduction, news, reviews and perspectives sections. Optionally, check out various other reviews.||A1, due 10/5||A1 Solution|
|9/30||Growth||Various Optional Readings on Growth.|
|2||10/3||Simulation with gro||Read the gro documentation. There are some optional readings too.|
|10/5||Noise in Cells||Stochastic Gene Expression. Various other papers on noise are optional.||A2, due 10/12||A2 Solution|
|10/7||Probability||Nothing required, but you might want to check out this list of books on probability.|
|3||10/10||The Biology of Gene Expression||Check out various web resources on transcription and translation. Optional readings list textbooks and mathematical models.|
|10/12||Project Ideas||Read the iGEM project pages for ten 2011 regional gold medal teams.|
|10/14||The Math of Gene Expression||You can read my 2009 course notes on stochasticity. Other papers on noise in gene expression are optional.||A3, due 10/19||A3 Solution|
|4||10/17||Engineering Gene Expression||Read the overview by Collins on next generation gene networks.|
|10/19||Gene Regulation||Read Elowitz's Combinatorial Promoter paper.||A4, due 10/26||A4 Solution||-|
|10/21||Feedback||Read this paper and check out various others.||-||-|
|5||10/24||Bistability||Read the toggle switch paper by Collins et al. and look at various other papers on the reading list.||-||-|
|10/26||Noise and Feedback||Read Lestas, Vinnecombe, and Paulsson .|
|10/28||Bioweapons, Biosecurity, and Ethics||Look at the PBS Documentary on the Living Weapon. Various other links are here.||-||-|
|11/2||MIDTERM (Through 10/28)|
|12/4||Oscillators||Read the Represslator Paper. Other oscillator papers are listed Reading List.||A5, due 11/11|
|7||11/7||Signaling||Bonnie Bassler's TED Talk on quorum sensing and peruse other readings on signaling.|
|11/9||Auxin||Do Trees Grow on Money? plus other readings.|
|11/11||Veteran's Day||A6, due 11/23|
|11/16||Cellular Automata||Suggested readings|
|9||11/21||iGEM||Check out the UW Team's iGEM web site.|
|11/23||Evolution I||Suggested readings||A7, due 12/2|
|10||11/28||Evolution II||Dekel and Alon + other suggested readings|
|11/30||Protein Engineering (Guest Lecture by Niel King)||Nanohedra and suggested readings|
|12/2||Nucleic Acid Circuits (Guest Lecture by Georg Seelig)||A8, due 12/9
|12||12/14||FINAL (Comprehensive)||2:30-4:20 PM||-||-|
The following topics will be covered in this course, approximately in the order listed.
- Growth and cell division, mainly in bacteria. Dilution due to cell growth. Sources of noise. Sizes and numbers in cells.
- Gene expression and regulation. Bacterial promoters and ribosome binding sites. Inducers.
- Stohasticity. Intrinsic and extrinsic noise. Basics of probabilistic modeling. Negative feedback reduces noise. Noise in nature: bet-hedging, coin-flipping, symmetry breaking.
- State. The genetic toggle switch. Positive feedback. Distributed algorithms in bacterial micro-colonies. Leader election and symmetry breaking. Synthetic development and morphogenesis.
- Signalling. Two component systems, MAPK, quorum sensing, auxin signalling. Boolean logic, transfer functions, etc. implemented in cells.
- Dynamics. Synthetic oscillators: The repressilator. Synchronized oscillators. Other dynamic behaviors. Modeling and analysis of dynamic systems.
- Tuning. Sensitivity analysis. Fine tuning behaviors via promotors, ribosome binding sites, protein and RNA degradation rates. Recombineering and MAGE.
- Evolution. Basics of creating variation and selection. Mutation rates and DNA repair. Continuous culture devices. Examples of directed evolution.
In addition, the following topics will be interspersed as needed.
- Applications. Therapeutics, diagnostics, biofuels, bio-remediation, global health.
- Modeling. Deterministic, stochastic, black-box.
- Software. Various tools for modeling and designing synthetic biological systems.
- Data and parameter estimation.
- Construction. Gene synthesis, assembly, and verification. Plasmids, integrations, etc.
- Assays. Microscopy, cytometry, micro-fluidics, sequencing, plate-readers, etc.