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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

Schedule

Date Topic Readings Assignment Solution
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. - -
6 10/31 Review
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
8 11/14 Cascades Suggested readings
11/16 Cellular Automata Suggested readings
11/18 Metabolism 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
11/25 Thanksgiving
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
Project Guidelines
11 12/5 Project Presentations - - -
12/7 Project Presentations - - -
12/9 Project Presentations - - -
12 12/14 FINAL (Comprehensive) 2:30-4:20 PM - -

Topics

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.

Software