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   <td>[[sbf11_reading|Various Optional Reading on Growth.]]</td>

Revision as of 23:13, 28 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


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 Various Optional Reading on Growth. - -
2 10/3 Noise - - -
10/5 - - - -
10/7 - - - -


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.