Difference between revisions of "Harvard:Synthetic Biology Nanocourse/2007"

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Revision as of 13:09, 17 October 2007

Intellectual Unit: Experimental Tools for Biological Discovery

Synthetic Biology: Cellular and Molecular Engineering


Instructors


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):


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 | PubMed ID:17289915 | HubMed [pas1]
  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 | PubMed ID:16978856 | HubMed [pas2]
  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 | PubMed ID:16738572 | HubMed [pas3]
All Medline abstracts: PubMed | HubMed


  • Additional papers of interest in the field
  1. 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 | PubMed ID:17108985 | HubMed [pas4]
  2. 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 | PubMed ID:16330045 | HubMed [pas5]
  3. 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 | PubMed ID:17662949 | HubMed [pas6]
  4. 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 | PubMed ID:17875664 | HubMed [pas7]
  5. 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 | PubMed ID:15858574 | HubMed [pas8]
  6. Elowitz MB and Leibler S. A synthetic oscillatory network of transcriptional regulators. Nature. 2000 Jan 20;403(6767):335-8. DOI:10.1038/35002125 | PubMed ID:10659856 | HubMed [pas9]
All Medline abstracts: PubMed | HubMed


Lecture 2 (Shih)

  • Recommended review articles
  1. []


  • Additional papers of interest in the field
  1. []


Lecture 3 (Church)

  • Recommended review articles
  1. []


  • Additional papers of interest in the field
  1. []


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.