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(Introduction to Synthetic Biology : Fall 2011)
(Schedule)
Line 26: Line 26:
   <td rowspan=2 class="big">1</td>
   <td rowspan=2 class="big">1</td>
   <td>9/28</td>
   <td>9/28</td>
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   <td>Introduction</td>
+
   <td>[http://depts.washington.edu/soslab/sb/1-Introduction.pdf Introduction]</td>
   <td>[http://www.sciencemag.org/site/special/syntheticbio Special Issue of Science on Synthetic Biology]: Read the introduction, news, reviews and perspectives sections. Optionally, check out [[sbf11_reading|various other reviews.]]</td>
   <td>[http://www.sciencemag.org/site/special/syntheticbio Special Issue of Science on Synthetic Biology]: Read the introduction, news, reviews and perspectives sections. Optionally, check out [[sbf11_reading|various other reviews.]]</td>
   <td>[[SBF11_A1|A1]], due 10/5</td>
   <td>[[SBF11_A1|A1]], due 10/5</td>

Revision as of 20:45, 27 September 2011

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 - 11:20, EEB M406
  • MWF 11:30-12:20
  • MOR 234

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 -
9/30 Growth - - -
2 10/3 Noise - - -
10/5 - - - -
10/7 - - - -

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