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

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=Synthetic Biology: Cellular and Molecular Engineering=
 
=Synthetic Biology: Cellular and Molecular Engineering=
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*[http://idb.med.harvard.edu/content/category/6/88/27/ link to idb website for this nanocourse]
 +
<br>
 +
 
 
==Instructors==
 
==Instructors==
*Nanocourse Director: Pam Silver
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*Nanocourse Lecturers: [[User:Geochurch|George Church]] ([http://arep.med.harvard.edu/gmc/email.html talk]), [[User:wmshih|William Shih]] ([[User_talk:wmshih|talk]]) (co-director), and [[User:PamSilver|Pamela Silver]] ([[User_talk:PamSilver|talk]]) (co-director)
*Nanocourse Lecturers: George Church, William Shih and Pam Silver  
 
 
<br>
 
<br>
  
 
==Course Description==  
 
==Course Description==  
*Synthetic biology explores the design rules for building artificial behavior of biomolecular systems through cycles of construction and comparison of intended versus  
+
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  
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.  
 
engineering cellular and molecular systems and will explore current and future applications for synthetic biology approaches.  
 
<br>
 
<br>
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==Meeting Times==  
 
==Meeting Times==  
*First Meeting: Monday, October 22nd, 1:30-4:30pm  
+
*First Meeting: Monday, 2007 October 22nd, 1:30pm&ndash;4:30pm  
 
**Location: Goldenson 122 (on the HMS quad)  
 
**Location: Goldenson 122 (on the HMS quad)  
 
   
 
   
*Second Meeting: Friday, October 26th, 12-2pm  
+
*Second Meeting: Friday, 2007 October 26th, 12pm&ndash;2pm  
**Location: TBD
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**Location: Warren Alpert Building 436
 +
<br>
 +
 
 +
==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
 +
<br>
 +
 
 +
==Reading List==
 +
===Lecture 1 (Silver)===
 +
*Recommended review articles
 +
<biblio>
 +
# pas1 pmid=17289915
 +
# pas2 pmid=16978856
 +
# pas3 pmid=16738572
 +
</biblio>
 +
<br>
 +
 
 +
*Additional papers of interest in the field
 +
<biblio>
 +
# pas4 pmid=17108985
 +
# pas5 pmid=16330045
 +
# pas6 pmid=17662949
 +
# pas7 pmid=17875664
 +
# pas8 pmid=15858574
 +
# pas9 pmid=10659856
 +
</biblio>
 +
<br>
 +
 
 +
===Lecture 2 (Shih)===
 +
*Recommended review articles
 +
<biblio>
 +
# wms1 pmid=17710092
 +
# wms2 pmid=17269482
 +
# wms3 pmid=15602549
 +
# wms4 pmid=12540916
 +
</biblio>
 +
<br>
 +
 
 +
*Additional papers of interest in the field
 +
<biblio>
 +
# wms5 pmid=14631033
 +
# wms6 pmid=15218149
 +
#
 +
#
 +
# wms7 pmid=16541064
 +
# wms8 pmid=17404217
 +
 
 +
</biblio>
 +
<br>
 +
 
 +
===Lecture 3 (Church)===
 +
*Recommended review articles
 +
<biblio>
 +
# gmc1 pmid=17151344
 +
# gmc2 pmid=17557094
 +
</biblio>
 +
<br>
 +
 
 +
*Additional papers of interest in the field
 +
<biblio>
 +
# gmc3 pmid=17600181
 +
# gmc4 pmid=17086184
 +
</biblio>
 +
<br>
 +
 
 +
==Uploaded Proposals==
 +
<br>
 +
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.

Latest revision as of 14:54, 20 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. 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 | PubMed ID:17710092 | HubMed [wms1]
  2. Alvizo O, Allen BD, and Mayo SL. Computational protein design promises to revolutionize protein engineering. Biotechniques. 2007 Jan;42(1):31, 33, 35 passim. PubMed ID:17269482 | HubMed [wms2]
  3. Breaker RR. Natural and engineered nucleic acids as tools to explore biology. Nature. 2004 Dec 16;432(7019):838-45. DOI:10.1038/nature03195 | PubMed ID:15602549 | HubMed [wms3]
  4. Seeman NC. DNA in a material world. Nature. 2003 Jan 23;421(6921):427-31. DOI:10.1038/nature01406 | PubMed ID:12540916 | HubMed [wms4]
All Medline abstracts: PubMed | HubMed


  • Additional papers of interest in the field
  1. 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 | PubMed ID:14631033 | HubMed [wms5]
  2. 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 | PubMed ID:15218149 | HubMed [wms6]
  3. Rothemund PW. Folding DNA to create nanoscale shapes and patterns. Nature. 2006 Mar 16;440(7082):297-302. DOI:10.1038/nature04586 | PubMed ID:16541064 | HubMed [wms7]
  4. 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 | PubMed ID:17404217 | HubMed [wms8]
All Medline abstracts: PubMed | HubMed


Lecture 3 (Church)

  • Recommended review articles
  1. Forster AC and Church GM. Synthetic biology projects in vitro. Genome Res. 2007 Jan;17(1):1-6. DOI:10.1101/gr.5776007 | PubMed ID:17151344 | HubMed [gmc1]
  2. 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 | PubMed ID:17557094 | HubMed [gmc2]
All Medline abstracts: PubMed | HubMed


  • Additional papers of interest in the field
Error fetching PMID 17600181:
Error fetching PMID 17086184:
  1. Error fetching PMID 17600181: [gmc3]
  2. Error fetching PMID 17086184: [gmc4]
All Medline abstracts: PubMed | HubMed


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.