Harvard:Synthetic Biology Nanocourse/2007

Intellectual Unit: Experimental Tools for Biological Discovery

Synthetic Biology: Cellular and Molecular Engineering

• link to idb website for this nanocourse

Instructors

• Nanocourse Lecturers: George Church (talk), William Shih (talk) (co-director), and Pamela Silver (talk) (co-director)

Course Description

Synthetic biology explores the design rules for building artificial behavior of biomolecular systems through cycles of construction and comparison of intended versus observed behaviors. The ability to synthesize biomimetic behavior is an important benchmark for biological understanding. This course will introduce strategies for engineering cellular and molecular systems and will explore current and future applications for synthetic biology approaches.

Meeting Times

• First Meeting: Monday, 2007 October 22nd, 1:30pm–4:30pm
  • Location: Goldenson 122 (on the HMS quad)

• Second Meeting: Friday, 2007 October 26th, 12pm–2pm
  • Location: Warren Alpert Building 436

Course Project

• For those enrolled in the nanocourse, the course project will be a short proposal (800–1000 words plus figures) describing a synthetic biology project that can be completed by a graduate student in three years or less. The proposals, in Adobe PDF form, must be posted on this wiki page by noon on Thursday, 2007 October 25.
• Registered students and instructors will read the proposals and meet on Friday, 2007 October 26 at noon to critique the proposals (see above).
• To see some potential project ideas, please browse through the project and brainstorming pages of former iGEM teams. If you decide to adopt one of those ideas, you need to propose a significant improvement or alteration that represents value added to the original idea. Be sure to credit the sources for your inspirations. Here are some example links (everyone, please feel free to add more or to reorganize):
  • http://parts.mit.edu/wiki/index.php/Schools_Participating_in_iGEM_2006
  • http://openwetware.org/wiki/IGEM:Harvard/2007/Brainstorming
  • http://openwetware.org/wiki/IGEM:Harvard/2006/Brainstorming
  • http://openwetware.org/wiki/IGEM:MIT/2007
  • http://openwetware.org/wiki/IGEM:MIT/2006/System_brainstorming

Reading List (Recommended)

Lecture 1 (Silver)

The first 3 papers are reviews and are highly recommended as introductory readings. The other papers are examples of designing systems that may be useful background for those taking the course and for further background in the field.

1. Drubin DA, Way JC, and Silver PA. Designing biological systems. Genes Dev. 2007 Feb 1;21(3):242-54. DOI:10.1101/gad.1507207 |
2. Voigt CA. Genetic parts to program bacteria. Curr Opin Biotechnol. 2006 Oct;17(5):548-57. DOI:10.1016/j.copbio.2006.09.001 |
3. Andrianantoandro E, Basu S, Karig DK, and Weiss R. Synthetic biology: new engineering rules for an emerging discipline. Mol Syst Biol. 2006;2:2006.0028. DOI:10.1038/msb4100073 |
4. Chang MC and Keasling JD. Production of isoprenoid pharmaceuticals by engineered microbes. Nat Chem Biol. 2006 Dec;2(12):674-81. DOI:10.1038/nchembio836 |
5. Anderson JC, Clarke EJ, Arkin AP, and Voigt CA. Environmentally controlled invasion of cancer cells by engineered bacteria. J Mol Biol. 2006 Jan 27;355(4):619-27. DOI:10.1016/j.jmb.2005.10.076 |
6. Deans TL, Cantor CR, and Collins JJ. A tunable genetic switch based on RNAi and repressor proteins for regulating gene expression in mammalian cells. Cell. 2007 Jul 27;130(2):363-72. DOI:10.1016/j.cell.2007.05.045 |
7. Ajo-Franklin CM, Drubin DA, Eskin JA, Gee EP, Landgraf D, Phillips I, and Silver PA. Rational design of memory in eukaryotic cells. Genes Dev. 2007 Sep 15;21(18):2271-6. DOI:10.1101/gad.1586107 |
8. Basu S, Gerchman Y, Collins CH, Arnold FH, and Weiss R. A synthetic multicellular system for programmed pattern formation. Nature. 2005 Apr 28;434(7037):1130-4. DOI:10.1038/nature03461 |
9. Elowitz MB and Leibler S. A synthetic oscillatory network of transcriptional regulators. Nature. 2000 Jan 20;403(6767):335-8. DOI:10.1038/35002125 |

Uploaded Proposals

Remember to upload a PDF of your file by Thursday, October 25th by noon. Uploading your file on time means that your fellow classmates and instructors can spend more time reading and considering your proposal. Please name your files something meaningful. I suggest the following format... NameofStudent_syntheticbiology2007.