Smolke:Journal Club

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Next Meeting When: Where: Paper: Moderator: Suggested Future Papers Ray PS, Jia J, Yao P, Majumder M, Hatzoglou M, and Fox PL. A stress-responsive RNA switch regulates VEGFA expression. Nature. 2009 Feb 12;457(7231):915-9. DOI:10.1038/nature07598 | Runguphan W and O'Connor SE. Metabolic reprogramming of periwinkle plant culture. Nat Chem Biol. 2009 Mar;5(3):151-3. DOI:10.1038/nchembio.141 | Ham TS, Lee SK, Keasling JD, and Arkin AP. Design and construction of a double inversion recombination switch for heritable sequential genetic memory. PLoS One. 2008 Jul 30;3(7):e2815. DOI:10.1371/journal.pone.0002815 | Yu RC, Pesce CG, Colman-Lerner A, Lok L, Pincus D, Serra E, Holl M, Benjamin K, Gordon A, and Brent R. Negative feedback that improves information transmission in yeast signalling. Nature. 2008 Dec 11;456(7223):755-61. DOI:10.1038/nature07513 | Han J, Pedersen JS, Kwon SC, Belair CD, Kim YK, Yeom KH, Yang WY, Haussler D, Blelloch R, and Kim VN. Posttranscriptional crossregulation between Drosha and DGCR8. Cell. 2009 Jan 9;136(1):75-84. DOI:10.1016/j.cell.2008.10.053 | Fung E, Wong WW, Suen JK, Bulter T, Lee SG, and Liao JC. A synthetic gene-metabolic oscillator. Nature. 2005 May 5;435(7038):118-22. DOI:10.1038/nature03508 | Lincoln TA and Joyce GF. Self-sustained replication of an RNA enzyme. Science. 2009 Feb 27;323(5918):1229-32. DOI:10.1126/science.1167856 | Lam BJ and Joyce GF. Autocatalytic aptazymes enable ligand-dependent exponential amplification of RNA. Nat Biotechnol. 2009 Mar;27(3):288-92. DOI:10.1038/nbt.1528 | Comments on Papers I found the Ham et al. [3] paper extremely disappointing. If you want an example of what not to do, it's a good one. But otherwise I'd skip it. -Josh I suggested the Ham et al. [3] mostly to throw out a paper about synthetic information processing in cells. It is outside my area of familiarity, but I think it could be interesting, especially since that is what the Endy lab is gearing up to attack. So if anyone else has a good recent paper on some synthetic biology approach to information processing, I think that might be cool for us to read and critique. -Mike 7 and 8 can be reviewed together if anyone is interested. It's amazing that they resulted in two different high-profile publications. -Win Voting on Papers Paper 1. Midori Paper 2. Paper 3. Paper 4. Paper 5. Paper 6. Paper 7. Paper 8. Joe