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

Paper for Discussion

14. Prindle A, Samayoa P, Razinkov I, Danino T, Tsimring LS, and Hasty J. A sensing array of radically coupled genetic 'biopixels'. Nature. 2011 Dec 18;481(7379):39-44. DOI:10.1038/nature10722 |

    A sensing array of radically coupled genetic 'biopixels'.

New Topics

• Algal Biofuels (Aurko)
• Probiotics (Alvaro)
• Brainstorm ideas for final projects!

For Monday, March 25th, 2013

Discuss preliminary research into topics for final projects. Decide on topics and groups.

Papers for Discussion

15. Hillman JD. Genetically modified Streptococcus mutans for the prevention of dental caries. Antonie Van Leeuwenhoek. 2002 Aug;82(1-4):361-6.

    Genetically modified Streptococcus mutans for the prevention of dental caries.

16. Tran M, Van C, Barrera DJ, Pettersson PL, Peinado CD, Bui J, and Mayfield SP. Production of unique immunotoxin cancer therapeutics in algal chloroplasts. Proc Natl Acad Sci U S A. 2013 Jan 2;110(1):E15-22. DOI:10.1073/pnas.1214638110 |

    Production of unique immunotoxin cancer therapeutics in algal chloroplasts

New Topics

• Synthetic Meat/Organs (Sid)
• Phage Therapy (Neil)

For Monday, April 1st, 2013

Papers for Discussion

17. Ott HC, Matthiesen TS, Goh SK, Black LD, Kren SM, Netoff TI, and Taylor DA. Perfusion-decellularized matrix: using nature's platform to engineer a bioartificial heart. Nat Med. 2008 Feb;14(2):213-21. DOI:10.1038/nm1684 |

    Perfusion-decellularized matrix: using nature's platform to engineer a bioartificial heart.

18. Lu TK and Collins JJ. Engineered bacteriophage targeting gene networks as adjuvants for antibiotic therapy. Proc Natl Acad Sci U S A. 2009 Mar 24;106(12):4629-34. DOI:10.1073/pnas.0800442106 |

    Engineered bacteriophage targeting gene networks as adjuvants for antibiotic therapy.

New Topics

• Gas Vesicles (Larry)
• DNA Computation (Tyler)
• Operon Refactoring (Max)

For Monday, April 8th, 2013

Papers for Discussion

19. Bonnet J, Yin P, Ortiz ME, Subsoontorn P, and Endy D. Amplifying genetic logic gates. Science. 2013 May 3;340(6132):599-603. DOI:10.1126/science.1232758 |

    Amplifying genetic logic gates

20. Temme K, Zhao D, and Voigt CA. Refactoring the nitrogen fixation gene cluster from Klebsiella oxytoca. Proc Natl Acad Sci U S A. 2012 May 1;109(18):7085-90. DOI:10.1073/pnas.1120788109 |

    Refactoring the nitrogen fixation gene cluster from Klebsiella oxytoca.

New Topics

• Biomaterials (Gabe)
• Cell Printing / Scaffolding (Evan)
• Genome Editing (Ben)

For Monday, April 15th, 2013

Papers for Discussion

21. Lazaris A, Arcidiacono S, Huang Y, Zhou JF, Duguay F, Chretien N, Welsh EA, Soares JW, and Karatzas CN. Spider silk fibers spun from soluble recombinant silk produced in mammalian cells. Science. 2002 Jan 18;295(5554):472-6. DOI:10.1126/science.1065780 |

    Spider silk fibers spun from soluble recombinant silk produced in mammalian cells

22. Jiang W, Bikard D, Cox D, Zhang F, and Marraffini LA. RNA-guided editing of bacterial genomes using CRISPR-Cas systems. Nat Biotechnol. 2013 Mar;31(3):233-9. DOI:10.1038/nbt.2508 |

    RNA-guided editing of bacterial genomes using CRISPR-Cas systems

New Topics

• Metabolic Engineering (Thomas)
• Genetic Circuits / Single-Molecule / Single-Cell / something (Andre)

For Monday, April 22nd, 2013

Papers for Discussion

23. Keller MW, Schut GJ, Lipscomb GL, Menon AL, Iwuchukwu IJ, Leuko TT, Thorgersen MP, Nixon WJ, Hawkins AS, Kelly RM, and Adams MW. Exploiting microbial hyperthermophilicity to produce an industrial chemical, using hydrogen and carbon dioxide. Proc Natl Acad Sci U S A. 2013 Apr 9;110(15):5840-5. DOI:10.1073/pnas.1222607110 |

    Exploiting microbial hyperthermophilicity to produce an industrial chemical, using hydrogen and carbon dioxide

24. Elowitz MB and Leibler S. A synthetic oscillatory network of transcriptional regulators. Nature. 2000 Jan 20;403(6767):335-8. DOI:10.1038/35002125 |

    A synthetic oscillatory network of transcriptional regulators

New Topics

• Molecular Gastronomie (Kate)
• Mechanosensing (Kevin)

For Monday, April 29th, 2013

Papers for Discussion

25. Boyle PM, Burrill DR, Inniss MC, Agapakis CM, Deardon A, DeWerd JG, Gedeon MA, Quinn JY, Paull ML, Raman AM, Theilmann MR, Wang L, Winn JC, Medvedik O, Schellenberg K, Haynes KA, Viel A, Brenner TJ, Church GM, Shah JV, and Silver PA. A BioBrick compatible strategy for genetic modification of plants. J Biol Eng. 2012 Jun 20;6(1):8. DOI:10.1186/1754-1611-6-8 |

    A BioBrick compatible strategy for genetic modification of plants

26. Assadi-Porter FM, Patry S, and Markley JL. Efficient and rapid protein expression and purification of small high disulfide containing sweet protein brazzein in E. coli. Protein Expr Purif. 2008 Apr;58(2):263-8. DOI:10.1016/j.pep.2007.11.009 |

    Efficient and rapid protein expression and purification of small high disulfide containing sweet protein brazzein in E. coli

27. Follonier S, Panke S, and Zinn M. Pressure to kill or pressure to boost: a review on the various effects and applications of hydrostatic pressure in bacterial biotechnology. Appl Microbiol Biotechnol. 2012 Mar;93(5):1805-15. DOI:10.1007/s00253-011-3854-6 |

    Pressure to kill or pressure to boost: a review on the various effects and applications of hydrostatic pressure in bacterial biotechnology