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Revision as of 19:45, 20 February 2013 (view source) Jeffrey E. Barrick (Talk | contribs) m (→For Monday, February 25th, 2013) ← Previous diff		Revision as of 17:36, 25 February 2013 (view source) Jeffrey E. Barrick (Talk | contribs) (→For Monday, March 4th, 2013) Next diff →
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	* Biocontainment (Thomas)		* Biocontainment (Thomas)
	* New Marker Genes  (Ben)		* New Marker Genes  (Ben)
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		+	= For Monday, March 18th, 2013 =
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		+	Brainstorm ideas for final projects.
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		+	= For Monday, March 25th, 2013 =
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		+	Topics and groups for final projects due.
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		+	= For Monday, April 1st, 2013 =
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		+	= For Monday, April 8th, 2013 =
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		+	= For Monday, April 15th, 2013 =
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		+	= For Monday, April 22nd, 2013 =

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Revision as of 17:36, 25 February 2013

Contents 1 For Monday, January 28th, 2013 1.1 New Topics: 2 For Monday, February 4th, 2013 2.1 Topic Updates 2.2 Papers for Discussion 2.3 New Topics 3 For Monday, February 11th, 2013 3.1 Topic Updates 3.2 Papers for Discussion 3.3 New Topics 4 For Monday, February 18th, 2013 4.1 Topic Updates 4.2 Papers for Discussion 4.3 New Topics 5 For Monday, February 25th, 2013 5.1 Papers for Discussion 5.2 New Topics 6 For Monday, March 4th, 2013 7 For Monday, March 18th, 2013 8 For Monday, March 25th, 2013 9 For Monday, April 1st, 2013 10 For Monday, April 8th, 2013 11 For Monday, April 15th, 2013 12 For Monday, April 22nd, 2013

For Monday, January 28th, 2013

• Register to use the OpenWetWare Wiki.
• Learn how to edit pages.
• Play around in the WIki sandbox.
• Add your name to the CH391L Users page.
• Leave at least one comment on the Talk page or make at least one addition to either Introduction to Synthetic Biology or Ethics of synthetic biology.
• Add at least one event to the "Timeline of Synthetic Biology" in the Introduction to Synthetic Biology with a link or citation.
• Read articles for discussion:
  • Synthetic biology: new engineering rules for an emerging discipline
  • The promise and perils of synthetic biology

New Topics:

• Ethics of synthetic biology (Neil)
• DIY Biology Movement (John)
• BioBricks and the iGEM registry (Tyler)

For Monday, February 4th, 2013

Topic Updates

• Ethics of synthetic biology [1]
• DIY Biology[2]
• BioBricks and the iGEM registry [3]

Papers for Discussion

1. Playing God in Frankenstein's Footsteps: Synthetic Biology and the Meaning of Life [ethics]

   For Bioethics

2. Outlaw, hackers, victorian amateurs: diagnosing public participation in the life sciences today pdf [Kelty2010]

   For DIY Biology

3. Kelly JR, Rubin AJ, Davis JH, Ajo-Franklin CM, Cumbers J, Czar MJ, de Mora K, Glieberman AL, Monie DD, and Endy D. . pmid:19298678. PubMed HubMed [Endy2009]

   For BioBricks

New Topics

• CAD for Synthetic Biology (Kevin)
• DNA Assembly: From Genes to Genomes (Gabe) [4]

For Monday, February 11th, 2013

Topic Updates

• CAD for Synthetic Biology (Kevin)
• Chris Yellman and Randy Hughes will discuss the paper for DNA Assembly: From Genes to Genomes[4]

Papers for Discussion

4. Gibson DG, Benders GA, Andrews-Pfannkoch C, Denisova EA, Baden-Tillson H, Zaveri J, Stockwell TB, Brownley A, Thomas DW, Algire MA, Merryman C, Young L, Noskov VN, Glass JI, Venter JC, Hutchison CA 3rd, and Smith HO. . pmid:18218864. PubMed HubMed [Gibson2008]

   Complete chemical synthesis, assembly, and cloning of a Mycoplasma genitalium genome. For DNA synthesis and assembly

5. http://igem.synbioreview.com/ [iGEMSoftware]
6. http://2011.igem.org/Jamboree/Team_Abstracts [iGEMAbstracts]

   Find a useful or neat tool from a past iGEM software competition using one of these links. Test drive it if possible. Be able to briefly describe what it does to class. For CAD

New Topics

• Minimal / "clean" genomes (Evan)
• Functional Nucleic Acids --Alvaro E. Rodriguez M. 21:50, 27 January 2013 (EST)

For Monday, February 18th, 2013

Topic Updates

• Minimal / "clean" genomes (Evan)
• Functional Nucleic Acids (Alvaro)

Papers for Discussion

7. Pósfai G, Plunkett G 3rd, Fehér T, Frisch D, Keil GM, Umenhoffer K, Kolisnychenko V, Stahl B, Sharma SS, de Arruda M, Burland V, Harcum SW, and Blattner FR. . pmid:16645050. PubMed HubMed [Posfai2006]

   Emergent properties of reduced-genome Escherichia coli. For minimal genomes.

8. Ohuchi M, Murakami H, and Suga H. . pmid:17884697. PubMed HubMed [Ohuchi2007]

   The flexizyme system: a highly flexible tRNA aminoacylation tool for the translation apparatus. For in vitro selection.

9. Murakami H, Ohta A, Goto Y, Sako Y, and Suga H. . pmid:17150804. PubMed HubMed [Murakami2006]

   Flexizyme as a versatile tRNA acylation catalyst and the application for translation. For in vitro selection.

All Medline abstracts: PubMed HubMed

New Topics

• Ancestral sequence reconstruction (Aurko)
• Bioprospecting / Metagenomics (Andre)

For Monday, February 25th, 2013

Papers for Discussion

10. Risso VA, Gavira JA, Mejia-Carmona DF, Gaucher EA, and Sanchez-Ruiz JM. . pmid:23394108. PubMed HubMed [Risso2013]

    Hyperstability and substrate promiscuity in laboratory resurrections of Precambrian β-lactamases. For Ancestral protein reconstruction.

11. Béjà O, Aravind L, Koonin EV, Suzuki MT, Hadd A, Nguyen LP, Jovanovich SB, Gates CM, Feldman RA, Spudich JL, Spudich EN, and DeLong EF. . pmid:10988064. PubMed HubMed [Beja2000]

    Bacterial rhodopsin: evidence for a new type of phototrophy in the sea. For Metagenomic bioprospecting.

All Medline abstracts: PubMed HubMed

New Topics

• Directed protein evolution (Max)
• Riboswitches (Kate)
• Optogenetics (Sid)

For Monday, March 4th, 2013

• TBD (Jeremy)
• Biological material assembly and patterning - Belcher virus work (Marco)
• Quorum Sensing (Larry)
• Biocontainment (Thomas)
• New Marker Genes (Ben)

For Monday, March 18th, 2013

Brainstorm ideas for final projects.

For Monday, March 25th, 2013

Topics and groups for final projects due.

For Monday, April 1st, 2013

For Monday, April 8th, 2013

For Monday, April 15th, 2013

For Monday, April 22nd, 2013