Harvard:Synthetic Biology Nanocourse/2007

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(Synthetic Biology: Cellular and Molecular Engineering)
Current revision (16:54, 20 October 2007) (view source)
 
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==Course Project==
==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.
+
*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.
-
*Registered students and instructors will read the proposals and meet on Friday, 2007 October 26 at noon to critique the proposals (see above).
+
*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).
-
*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):
+
*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://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/2007/Brainstorming
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<br>
<br>
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==Reading List (Recommended)==
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==Reading List==
 +
===Lecture 1 (Silver)===
 +
*Recommended review articles
 +
<biblio>
 +
# pas1 pmid=17289915
 +
# pas2 pmid=16978856
 +
# pas3 pmid=16738572
 +
</biblio>
<br>
<br>
-
Lecture 1 (Silver)
+
*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>
-
Drubin DA, Way JC, Silver PA.  Designing biological systems. Genes Dev. 2007 Feb 1;21(3):242-54.
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===Lecture 2 (Shih)===
 +
*Recommended review articles
 +
<biblio>
 +
# wms1 pmid=17710092
 +
# wms2 pmid=17269482
 +
# wms3 pmid=15602549
 +
# wms4 pmid=12540916
 +
</biblio>
 +
<br>
-
Voigt CA.Genetic parts to program bacteria.Curr Opin Biotechnol. 2006 Oct;17(5):548-57. Epub 2006 Sep 15.
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*Additional papers of interest in the field
 +
<biblio>
 +
# wms5 pmid=14631033
 +
# wms6 pmid=15218149
 +
#
 +
#
 +
# wms7 pmid=16541064
 +
# wms8 pmid=17404217
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Chang MC, Keasling JD.Production of isoprenoid pharmaceuticals by engineered microbes. Nat Chem Biol. 2006 Dec;2(12):674-81
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</biblio>
 +
<br>
-
Anderson JC, Clarke EJ, Arkin AP, Voigt CA.Environmentally controlled invasion of cancer cells by engineered bacteria. J Mol Biol. 2006 Jan 27;355(4):619-27. Epub 2005 Nov 14.
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===Lecture 3 (Church)===
 +
*Recommended review articles
 +
<biblio>
 +
# gmc1 pmid=17151344
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# gmc2 pmid=17557094
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</biblio>
 +
<br>
-
Andrianantoandro E, Basu S, Karig DK, Weiss R. Synthetic biology: new engineering rules for an emerging discipline. Mol Syst Biol. 2006;2:2006.0028. Epub 2006 May 16
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*Additional papers of interest in the field
-
 
+
<biblio>
-
Deans TL, Cantor CR, 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.
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# gmc3 pmid=17600181
-
 
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# gmc4 pmid=17086184
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Ajo-Franklin CM, Drubin DA, Eskin JA, Gee EP, Landgraf D, Phillips I, Silver PA. Rational design of memory in eukaryotic cells. Genes Dev. 2007 Sep 15;21(18):2271-6.
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</biblio>
-
 
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<br>
-
Basu S, Gerchman Y, Collins CH, Arnold FH, Weiss R. A synthetic multicellular system for programmed pattern formation. Nature. 2005 Apr 28;434(7037):1130-4.
+
-
 
+
-
Elowitz MB, Leibler S.A synthetic oscillatory network of transcriptional regulators. Nature. 2000 Jan 20;403(6767):335-8.
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==Uploaded Proposals==
==Uploaded Proposals==
<br>
<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.

Current revision

Intellectual Unit: Experimental Tools for Biological Discovery

Contents

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
Error fetching PMID 17289915:
Error fetching PMID 16978856:
Error fetching PMID 16738572:
  1. Error fetching PMID 17289915: [pas1]
  2. Error fetching PMID 16978856: [pas2]
  3. Error fetching PMID 16738572: [pas3]
All Medline abstracts: PubMed HubMed


  • Additional papers of interest in the field
Error fetching PMID 17108985:
Error fetching PMID 16330045:
Error fetching PMID 17662949:
Error fetching PMID 17875664:
Error fetching PMID 15858574:
Error fetching PMID 10659856:
  1. Error fetching PMID 17108985: [pas4]
  2. Error fetching PMID 16330045: [pas5]
  3. Error fetching PMID 17662949: [pas6]
  4. Error fetching PMID 17875664: [pas7]
  5. Error fetching PMID 15858574: [pas8]
  6. Error fetching PMID 10659856: [pas9]
All Medline abstracts: PubMed HubMed


Lecture 2 (Shih)

  • Recommended review articles
Error fetching PMID 17710092:
Error fetching PMID 17269482:
Error fetching PMID 15602549:
Error fetching PMID 12540916:
  1. Error fetching PMID 17710092: [wms1]
  2. Error fetching PMID 17269482: [wms2]
  3. Error fetching PMID 15602549: [wms3]
  4. Error fetching PMID 12540916: [wms4]
All Medline abstracts: PubMed HubMed


  • Additional papers of interest in the field
Error fetching PMID 14631033:
Error fetching PMID 15218149:
Error fetching PMID 16541064:
Error fetching PMID 17404217:
  1. Error fetching PMID 14631033: [wms5]
  2. Error fetching PMID 15218149: [wms6]
  3. Error fetching PMID 16541064: [wms7]
  4. Error fetching PMID 17404217: [wms8]
All Medline abstracts: PubMed HubMed


Lecture 3 (Church)

  • Recommended review articles
Error fetching PMID 17151344:
Error fetching PMID 17557094:
  1. Error fetching PMID 17151344: [gmc1]
  2. Error fetching PMID 17557094: [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.

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