CH391L/S12/Assignments

Other topic ideas

• Riboswitches (synthetic and natural) - OPEN
• Directed evolution (plasmid-based in vivo evolution of thermostability, altered substrate specificity, etc) and/or phage display. - OPEN
  • Possible reference [1]

1. Gupta RD, Goldsmith M, Ashani Y, Simo Y, Mullokandov G, Bar H, Ben-David M, Leader H, Margalit R, Silman I, Sussman JL, and Tawfik DS. Directed evolution of hydrolases for prevention of G-type nerve agent intoxication. Nat Chem Biol. 2011 Feb;7(2):120-5. DOI:10.1038/nchembio.510 |

• Computer-Aided Design (CAD) systems for synthetic biology - OPEN

Final Project Groups

Project	Group
Caffeine	Erik, Brian, Midhat, Peter
Spinach	Mike, Jon, Logan, Jeremy
Snow Globe	Adam, Yi, Razan, Ben, (Jeff)
Zombie Apocalypse	David, Joe, Jared

For Monday, April 30, 2012

Final project presentations!

For Monday, April 23, 2012

As a group we will all read these three papers and discuss them in class on April 23 in detail.

Papers to Read

2. Sinha J, Reyes SJ, and Gallivan JP. Reprogramming bacteria to seek and destroy an herbicide. Nat Chem Biol. 2010 Jun;6(6):464-70. DOI:10.1038/nchembio.369 |

   Atrazine seek and destroy Votes: Barrick, Meyer, Truong, Yi, Bachman

3. Neumann H, Wang K, Davis L, Garcia-Alai M, and Chin JW. Encoding multiple unnatural amino acids via evolution of a quadruplet-decoding ribosome. Nature. 2010 Mar 18;464(7287):441-4. DOI:10.1038/nature08817 |

   Encoding multiple unnatural amino acids via evolution of a quadruplet-decoding ribosome Votes: Meyer, Truong, Yi, Barrick

4. Saeidi N, Wong CK, Lo TM, Nguyen HX, Ling H, Leong SS, Poh CL, and Chang MW. Engineering microbes to sense and eradicate Pseudomonas aeruginosa, a human pathogen. Mol Syst Biol. 2011 Aug 16;7:521. DOI:10.1038/msb.2011.55 |

   Engineering microbes to sense and eradicate Pseudomonas aeruginosa, a human pathogen Votes: Meyer, Truong, Patel

Other Nominated Papers

(Vote by placing your name in the comments after a paper. You can vote for as many as you would like). Voting is over --April 16'

5. Tabor JJ, Levskaya A, and Voigt CA. Multichromatic control of gene expression in Escherichia coli. J Mol Biol. 2011 Jan 14;405(2):315-24. DOI:10.1016/j.jmb.2010.10.038 |

   Multichromatic Control of Gene Expression in Escherichia coli Votes: Meyer (vote retracted, Jared covered this)

6. Danino T, Mondragón-Palomino O, Tsimring L, and Hasty J. A synchronized quorum of genetic clocks. Nature. 2010 Jan 21;463(7279):326-30. DOI:10.1038/nature08753 |

   A synchronized quorum of genetic clocks. This is a very nice paper featuring logic circuits, oscillators, and quorum sensing. Votes: Meyer

For Monday, April 16, 2012

Smell (or maybe magnetic yeast? Huh?) - Joe Hanson

• Guest topic (2 PM) - Dr. Hal Alper (Chemical Engineering)

Paper discussions.

For Monday, April 9, 2012

New Topics: Systems II

• Artemisinic acid engineering- Peter Otoupal
• MAGE lycopene production, CAGE "Amberless" E. coli - Logan Bachman
• Synthetic Cooperation - Jeremy McLain

For Monday, April 2, 2012

• Comment on or add to old topics.

New Topics: Systems I

• Repressilator, counter, toggle swtich - Razan Alnahhas
• Edge detection E. coli - Jared Ellefson
• Refactored T7 and yeast - Jon Laurent

For Monday, March 26, 2012

• Comment on or add to old topics.

New Topics: Complex Parts

• Quorum sensing - Brian Renda
• Locomotion - Erik Quandt
• Unnatural amino acids - Michael Hammerling

For Monday, March 19, 2012

• Comment on or add to old topics.

New Topics: Reporter Genes

• Guest topic (2 PM) - Dr. Andy Ellington (Chemistry and Biochemistry)
• Fluorescent/luminescent proteins (GFP, lux, variants) - Midhat Patel
• Pigments - Yi Kou

For Monday, March 5, 2012

• Comment on or add to old topics.

New Topics: Gene Regulation

• Origins of Replication - Adam Meyer
• Protein regulators of transcription (Lac, Ara, etc) - Ben Slater
• Light sensing. Two-component systems - David Truong

For Monday, February 27, 2012

• Comment on or add to old topics.

New Topics: Basic Gene Construction

• Transcription: initiation and termination - Logan Bachman
• Spinach RNA - Jon Laurent
• Translation. Ribosome binding sites and codon optimization - Jeremy McLain

For Monday, February 20, 2012

• Comment on or add to old topics.

New Topics: Chassis and Backbones

• Selectable genetic markers (Ab resistance, etc.) - Peter Otoupal
• Toxin/anti-toxins, plasmid addiction systems - Brian Renda
• Counter-selectable genetic markers - Erik Quandt

For Monday, February 13, 2012

• Comment on or add to old topics.

New Topics: Optimizing Parts and their Interactions

• Gene/genome synthesis/Gibson assembly - Joe Hanson
• Host organisms (general properties of common ones, new ones that are being developed) - Michael Hammerling
• Metabolic engineering - Razan Alnahhas

For Monday, February 6, 2012

• Add a link to your user page to the CH391L Users Page.
• Add something to your user page.
• Comment on or add to old topics.

New Topics: Assembling Biological Parts

• Restriction enzyme cloning & BioBricks/BglBricks assembly - Ben Slater
• Advanced PCR techniques - Yi Kou

For Monday, January 30, 2012

• Register to use the OpenWetWare Wiki.
• Learn how to edit pages.
• Play around in the WIki sandbox.
• Leave at least one comment on the Talk page or make at least one addition to Introduction to Synthetic Biology
• Read the review article:
  7. 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 |

New Topics: Finding Biological Parts

• iGEM registry - Midhat Patel
• bioprospecting / metagenomics - David Truong
• directed evolution / in vitro selection - Adam Meyer
• ancestral protein construction - Jared Ellefson