CH391L/S13/Assignments

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

   For Bioethics

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

   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. Measuring the activity of BioBrick promoters using an in vivo reference standard. J Biol Eng. 2009 Mar 20;3:4. DOI:10.1186/1754-1611-3-4 |

   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. Complete chemical synthesis, assembly, and cloning of a Mycoplasma genitalium genome. Science. 2008 Feb 29;319(5867):1215-20. DOI:10.1126/science.1151721 |

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

5. http://igem.synbioreview.com/

6. http://2011.igem.org/Jamboree/Team_Abstracts

   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. Emergent properties of reduced-genome Escherichia coli. Science. 2006 May 19;312(5776):1044-6. DOI:10.1126/science.1126439 |

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

8. Ohuchi M, Murakami H, and Suga H. The flexizyme system: a highly flexible tRNA aminoacylation tool for the translation apparatus. Curr Opin Chem Biol. 2007 Oct;11(5):537-42. DOI:10.1016/j.cbpa.2007.08.011 |

   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. Flexizyme as a versatile tRNA acylation catalyst and the application for translation. Nucleic Acids Symp Ser (Oxf). 2006(50):35-6. DOI:10.1093/nass/nrl018 |

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

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. Hyperstability and substrate promiscuity in laboratory resurrections of Precambrian β-lactamases. J Am Chem Soc. 2013 Feb 27;135(8):2899-902. DOI:10.1021/ja311630a |

    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. Bacterial rhodopsin: evidence for a new type of phototrophy in the sea. Science. 2000 Sep 15;289(5486):1902-6. DOI:10.1126/science.289.5486.1902 |

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

New Topics

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

For Monday, March 4th, 2013

Papers for Discussion

12. Giver L, Gershenson A, Freskgard PO, and Arnold FH. Directed evolution of a thermostable esterase. Proc Natl Acad Sci U S A. 1998 Oct 27;95(22):12809-13. DOI:10.1073/pnas.95.22.12809 |

    Directed evolution of a thermostable esterase. For directed protein evolution.

13. Davidson ME, Harbaugh SV, Chushak YG, Stone MO, and Kelley-Loughnane N. Development of a 2,4-dinitrotoluene-responsive synthetic riboswitch in E. coli cells. ACS Chem Biol. 2013 Jan 18;8(1):234-41. DOI:10.1021/cb300274g |

    Development of a 2,4-dinitrotoluene-responsive synthetic riboswitch in E. coli cells. For riboswitches.

New Topics

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

For Monday, March 18th, 2013

Brainstorm ideas for final projects.

For Monday, March 25th, 2013

Topics and groups for final projects due.