Introduction to Synthetic Biology : Fall 2012
- BioE 423/523, CSE 486/586, EE 423/523
- Instructor: Prof. Eric Klavins
- Office Hours: Tu, Th 8:30AM - 10:30AM, CSE 236
- Teaching Assistant: Kevin Oishi
- Office Hours: Mo, Fr, 10:00AM - 11:20AM, Sieg 128
- MWF 11:30-12:20
- Grading (Undergrads): Homework : 30%, Midterm : 30%, Final : 30%, Project : 10%
- Grading (Grads): Homework : 30%, Midterm : 25%, Final : 25%, Project : 10%, Review : 10%
- Homework policies: The lowest homework grade will be dropped. Extra credit will be recorded and used subjectively when determining letter grades. Homework must be turned in on time. Late homeworks are not accepted except for prearranged travel or unexpected illness.
|Date||Topic||Readings and Other Materials||Assignment||Solution|
|1||9/24||History||A variety of option readings are listed below.||A1, due 10/1||A1 Solution|
|9/26||Synthetic Biology||Special Issue of Science on Synthetic Biology
and optional overviews of synthetic biology.
|9/28||Gene Expression||Find a tutorial that speaks to you|
ODEs in Matlab
|For more on chemical reactions, check out Lecture 2 of Feinberg's notes. The notation is a bit different, but the ideas are the same.||A2, due 10/8||A2 Solution|
|10/3||Introduction to gro||Read the paper on gro. A few other papers are listed below.|
|10/5||iGEM!||Check out UW's iGEM wiki page and also read about other teams.|
Cox, Surrette, and Ellowitz describe engineered promoters. Isaacs, Swyer, and Collins discuss engineered riboregulators in RNA synthetic biology. Bayer and Smolke build riboregulators with RNA aptamers and ribozymes in Eukaryotes.
|A3, due 10/15|
|10/10||Modeling Gene Regulation||
Kauffman (1969) introduces the Boolean network as a model of genetic regulatory networks. And here's a more recent paper on identifying gene networks based on expression patterns using boolean networks.
|10/12||Synthetic Gene Networks||Lots of circuits this lecture: a genetic toggle switch in E. coli;
rewritable digital storage in living cells; a transciptional oscillator in E. coli; another toggle switch/oscillator in E. coli; implementation and modeling of a very robust and tunable gene oscillator; a tunable oscillator in mammalian cells; induced cellular differentiation.
But how do we tune these circuits for genetic context? Yokobayashi, Weiss, and Arnold perform directed evolution on a genetic circuit; Egbert and Klavins fine-tune genetic circuits using simple sequence repeats; Lou, Stanton, Chen, Munsky, and Voigt suggest a method for buffering synthetic circuits from genetic context.
|4||10/15||Signaling||0.gro,1.gro,2.gro,3.gro||A4, due 10/22|
|10/19||Extra Pattern Formation Slides||le_example.gro,midpoint.gro|
|5||10/22||A5, due 10/29|
|11/21||Guest Lecture: Rob Carlson|
|10||11/26||Guest Lecture: Georg Seelig|
|11/28||Guest Lecture: James Carothers|
|12/12||FINAL MEETING : Simulation presentations!|
- DNA Science, A First Course has a great history in it.
- Biology is Technology covers the economics of the coming biotechnological age.
- Carslon, The changing economics of DNA synthesis, Nature, 2009.
2 Synthetic Biology Overviews
- Special Issue of Science on Synthetic Biology: Read the introduction, news, reviews and perspectives sections.
- Five hard truths: http://www.nature.com/news/2010/100120/pdf/463288a.pdf
- Adventures in Synthetic Biology
- Andrianantoandro, Basu, Karig and Ron Weiss, Synthetic biology: new engineering rules for an emerging discipline. Molecular Systems Biology 2, 2006.
- Arkin and Fletcher, Fast, Cheap and Somewhat in Control. Genome Biology 7(8), 114, 2006.
- Basu, Karig and Weiss, Synthetic biology: new engineering rules for an emerging discipline. Molecular Systems Biology 2, 2006.
- Caleb J. Bashor, Andrew A. Horwitz, Sergio G. Peisajovich, and Wendell A. Lim, Rewiring cells: synthetic biology as a tool to interrogate the organizational principles of living systems. Annual Review of Biophysics 39, 515-537 (2010).
- Guillaume, Mutalik, and Arkin, Toward rational design of bacterial genomes. Current Opinion in Microbiology, 2011.
3 Biology Reviews
- A good text on biochemistry is essential. We like Lehninger Principles of Biochemistry, Fourth Edition, 2004.
- A Youtube video on transcription and translation.
- The Inner Life of the Cell
- Transcribe and translate a gene -- interactive! (somewhat misleading in the translation step, as the code seems not complimented like it should be).
- Lots of other online tutorials are available. Try googling "Gene Expression Tutorial". For example, this one.
- Raser and O'Shea, Noise in Gene Expression: Origins, Consequences, and Control, Science 2005.
- McAdams and Arkin. Stochastic mechanisms in gene expression, PNAS, 1997.
4 Chemical Kinetics
- Feinberg's Notes. Read the first two chapters.
- S.S. Jang, K.T. Oishi, R.G. Egbert, and E. Klavins, Specification and simulation of multicelled behaviors, ACS Synthetic Biology, Vol. 1, No. 8, pp. 365--374. 2012.
- E.W. Dijkstra, Guarded Commands, Nondeterminacy and Formal Derivation of Programs, CACM, 1975.
- PRISM is a stochastic guarded command language like gro, except super formal and accompanied by a model-checker.
- Library proxy information: http://www.lib.washington.edu/help/connect.html
- Last Year's Wiki
- Assignment Dropbox: https://catalyst.uw.edu/collectit/dropbox/koishi/23996
- Class GoPost: https://catalyst.uw.edu/gopost/board/koishi/30230/