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

• The course project will be a 1-2 page proposal describing a synthetic biology project. Feel free to use figures in your proposal if it can clarify critical concepts for your readers. You should use the course lectures, course readings and your own experience to come up with a proposal. Your grade in this nanocourse will not be based on the validity of this proposal. Rather, we just ask that you make a best effort to propose a set of experiments to address an important problem. We will discuss these proposals during the discussion section of the course.
• All students should post their proposal, in Adobe PDF form, to this wiki page by noon on Thursday, 2007 October 25. (This is the day before the discussion section).
• Students and instructors should do their best to read each proposal before class on Friday. On Friday, 2007 October 26, each student will have a chance to informally present their proposed experiments to the entire class. Currently there are 8 students registered to participate on the second day, so we should be able to get through every student proposal.
• 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 should 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

Lecture 1 (Silver)

• Recommended review articles

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 |

• Additional papers of interest in the field

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 |

Lecture 2 (Shih)

• Recommended review articles

10. Yeh BJ and Lim WA. Synthetic biology: lessons from the history of synthetic organic chemistry. Nat Chem Biol. 2007 Sep;3(9):521-5. DOI:10.1038/nchembio0907-521 |
11. Alvizo O, Allen BD, and Mayo SL. Computational protein design promises to revolutionize protein engineering. Biotechniques. 2007 Jan;42(1):31, 33, 35 passim. DOI:10.2144/000112336 |
12. Breaker RR. Natural and engineered nucleic acids as tools to explore biology. Nature. 2004 Dec 16;432(7019):838-45. DOI:10.1038/nature03195 |
13. Seeman NC. DNA in a material world. Nature. 2003 Jan 23;421(6921):427-31. DOI:10.1038/nature01406 |

• Additional papers of interest in the field

14. Kuhlman B, Dantas G, Ireton GC, Varani G, Stoddard BL, and Baker D. Design of a novel globular protein fold with atomic-level accuracy. Science. 2003 Nov 21;302(5649):1364-8. DOI:10.1126/science.1089427 |
15. Dwyer MA, Looger LL, and Hellinga HW. Computational design of a biologically active enzyme. Science. 2004 Jun 25;304(5679):1967-71. DOI:10.1126/science.1098432 |
16. Rothemund PW. Folding DNA to create nanoscale shapes and patterns. Nature. 2006 Mar 16;440(7082):297-302. DOI:10.1038/nature04586 |
17. Douglas SM, Chou JJ, and Shih WM. DNA-nanotube-induced alignment of membrane proteins for NMR structure determination. Proc Natl Acad Sci U S A. 2007 Apr 17;104(16):6644-8. DOI:10.1073/pnas.0700930104 |

Lecture 3 (Church)

• Recommended review articles

18. Forster AC and Church GM. Synthetic biology projects in vitro. Genome Res. 2007 Jan;17(1):1-6. DOI:10.1101/gr.5776007 |
19. Bügl H, Danner JP, Molinari RJ, Mulligan JT, Park HO, Reichert B, Roth DA, Wagner R, Budowle B, Scripp RM, Smith JA, Steele SJ, Church G, and Endy D. DNA synthesis and biological security. Nat Biotechnol. 2007 Jun;25(6):627-9. DOI:10.1038/nbt0607-627 |

• Additional papers of interest in the field

20. Lartigue C, Glass JI, Alperovich N, Pieper R, Parmar PP, Hutchison CA 3rd, Smith HO, and Venter JC. Genome transplantation in bacteria: changing one species to another. Science. 2007 Aug 3;317(5838):632-8. DOI:10.1126/science.1144622 |
21. Herring CD, Raghunathan A, Honisch C, Patel T, Applebee MK, Joyce AR, Albert TJ, Blattner FR, van den Boom D, Cantor CR, and Palsson BØ. Comparative genome sequencing of Escherichia coli allows observation of bacterial evolution on a laboratory timescale. Nat Genet. 2006 Dec;38(12):1406-12. DOI:10.1038/ng1906 |

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 will have ample time to carefully read all of the proposals. Please name your files something meaningful. I suggest the following format... NameofStudent_syntheticbiology2007.