From SOSwiki
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
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 |
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| 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.