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(Schedule)
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   <td>10/12</td>
   <td>10/12</td>
   <td>[http://depts.washington.edu/soslab/sbf12/9-Synthetic-Gene-Networks.pdf Synthetic Gene Networks]</td>
   <td>[http://depts.washington.edu/soslab/sbf12/9-Synthetic-Gene-Networks.pdf Synthetic Gene Networks]</td>
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   <td>Lots of circuits this lecture: a [http://www.nature.com/nature/journal/v403/n6767/full/403339a0.html genetic toggle switch] in E. coli;
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   <td>[http://www.nature.com/news/2010/100120/full/463288a.html 5 hard truths of synthetic biology]
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[http://www.pnas.org/content/early/2012/05/14/1202344109 rewritable digital storage] in living cells;
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a [http://www.nature.com/nature/journal/v403/n6767/full/403335a0.html transciptional oscillator] in E. coli;
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another [http://www.cell.com/retrieve/pii/S0092867403003465 toggle switch/oscillator] in E. coli;
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implementation and modeling of a [http://www.nature.com/nature/journal/v456/n7221/full/nature07389.html very robust and tunable gene oscillator];
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a [http://www.nature.com/nature/journal/v457/n7227/abs/nature07616.html tunable oscillator in mammalian cells];
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induced [http://www.nature.com/nature/journal/v440/n7083/full/nature04588.html cellular differentiation].
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But how do we tune these circuits for genetic context?
 
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Yokobayashi, Weiss, and Arnold perform [http://www.pnas.org/content/99/26/16587.abstract directed evolution] on a genetic circuit;
 
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Egbert and Klavins fine-tune genetic circuits using [http://www.pnas.org/content/early/2012/08/21/1205693109.abstract simple sequence repeats];
 
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Lou, Stanton, Chen, Munsky, and Voigt suggest a method for [http://www.nature.com/nbt/journal/vaop/ncurrent/full/nbt.2401.html buffering synthetic circuits from genetic context].
 
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Finally, some [http://www.nature.com/nrm/journal/v10/n6/abs/nrm2698.html current limits] and [http://www.nature.com/news/2010/100120/full/463288a.html 5 hard truths of synthetic biology].
 
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Revision as of 15:58, 22 October 2012


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.


Schedule

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
2 10/1 Chemical Kinetics
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.
3 10/8 Gene Regulation

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 5 hard truths of synthetic biology


4 10/15 Signaling 0.gro,1.gro,2.gro,3.gro A4, due 10/22
10/17 Pattern Formation
10/19 Extra Pattern Formation Slides le_example.gro,midpoint.gro
5 10/22 A5, due 10/29
10/24
10/26
6 10/29 Review
10/31 MIDTERM
11/1
7 11/5
11/7
11/9
8 11/12 Vetrans Day
11/14
11/16
9 11/19
11/21 Guest Lecture: Rob Carlson
11/23 Thanksgiving
10 11/26 Guest Lecture: Georg Seelig
11/28 Guest Lecture: James Carothers
11/30 Grad Presentations
11 12/3 Grad Presentations
12/5 Grad Presentations
12/7 FINAL
12/12 FINAL MEETING : Simulation presentations!

Reading

1 History

2 Synthetic Biology Overviews

3 Biology Reviews

4 Chemical Kinetics

5 gro

6 iGEM

Links