Smolke:Journal Club

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Next Meeting When: Where: Paper: Moderator: Suggested Future Papers Note: The biblio extension is broken. Suggested papers need full references. Leonard E, Ajikumar PK, Thayer K, Xiao WH, Mo JD, Tidor B, et al. Combining metabolic and protein engineering of a terpenoid biosynthetic pathway for overproduction and selectivity control. Proc Natl Acad Sci U S A.107(31):13654-9. PMCID: 2922259. Poliseno L, Salmena L, Zhang J, Carver B, Haveman WJ, Pandolfi PP. A coding-independent function of gene and pseudogene mRNAs regulates tumour biology. Nature.465(7301):1033-8. O'Shaughnessy EC, Palani S, Collins JJ, Sarkar CA. Tunable Signal Processing in Synthetic MAP Kinase Cascades. Cell.144(1):119-31. Matzas M, Stahler PF, Kefer N, Siebelt N, Boisguerin V, Leonard JT, et al. High-fidelity gene synthesis by retrieval of sequence-verified DNA identified using high-throughput pyrosequencing. Nat Biotechnol.28(12):1291-4. Kosuri S, Eroshenko N, Leproust EM, Super M, Way J, Li JB, et al. Scalable gene synthesis by selective amplification of DNA pools from high-fidelity microchips. Nat Biotechnol.28(12):1295-9. Wolfe-Simon F, Blum JS, Kulp TR, Gordon GW, Hoeft SE, Pett-Ridge J, Stolz JF, Webb SM, Weber PK, Davies PC, Anbar AD, Oremland RS. A Bacterium That Can Grow by Using Arsenic Instead of Phosphorus. Science. 2010 Dec 2. Churchman LS, Weissman JS. Nascent transcript sequencing visualizes transcription at nucleotide resolution. Nature.469(7330):368-73. Tamsir, A, Tabor, JJ, Voigt, CA. Robust multicellular computing using genetically encoded NOR gates and chemical ‘wires’. Nature 469,212–215(13 January 2011) Regot S, Macia J. et. al. Distributed biological computation with multicellular engineered networks. Nature. 2011 Jan 13;469(7329):207-11 Comments on Papers Voting on Papers Leonard et al.:Mike, Josh, Stephanie Poliseno et al.:Kathy, Yen-Hsiang, Joe, Jay O'Shaughnessy et al.: PDJ, Joe Matzas et al. and Kosuri et al.:Mike Wolfe-Simon et al.: Churchman and Weissman: Josh, PDJ, Megan, Andy Tamsir et. al. and Regot et. al.:Kathy, Yen-Hsiang, Megan, Andy Past Papers Schirmer A, Rude MA, Li X, Popova E, and del Cardayre SB. Microbial biosynthesis of alkanes. Science. 2010 Jul 30;329(5991):559-62. DOI:10.1126/science.1187936 | 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 | 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 | Drinnenberg IA, Weinberg DE, Xie KT, Mower JP, Wolfe KH, Fink GR, and Bartel DP. RNAi in budding yeast. Science. 2009 Oct 23;326(5952):544-550. DOI:10.1126/science.1176945 | Dueber JE, Wu GC, Malmirchegini GR, Moon TS, Petzold CJ, Ullal AV, Prather KL, and Keasling JD. Synthetic protein scaffolds provide modular control over metabolic flux. Nat Biotechnol. 2009 Aug;27(8):753-9. DOI:10.1038/nbt.1557 | Wang HH, Isaacs FJ, Carr PA, Sun ZZ, Xu G, Forest CR, and Church GM. Programming cells by multiplex genome engineering and accelerated evolution. Nature. 2009 Aug 13;460(7257):894-898. DOI:10.1038/nature08187 | 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 | 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 | Nevozhay D, Adams RM, Murphy KF, Josic K, and Balázsi G. Negative autoregulation linearizes the dose-response and suppresses the heterogeneity of gene expression. Proc Natl Acad Sci U S A. 2009 Mar 31;106(13):5123-8. DOI:10.1073/pnas.0809901106 | Aged Out Lartigue C, Vashee S, Algire MA, Chuang RY, Benders GA, Ma L, et al. Creating bacterial strains from genomes that have been cloned and engineered in yeast. Science. 2009;325(5948):1693-6. Iliopoulos D, Hirsch HA, Struhl K. An epigenetic switch involving NF-kappaB, Lin28, Let-7 MicroRNA, and IL6 links inflammation to cell transformation. Cell. 2009;139(4):693-706. PMCID: 2783826. Agresti JJ, Antipov E, Abate AR, Ahn K, Rowat AC, Baret JC, et al. Ultrahigh-throughput screening in drop-based microfluidics for directed evolution. Proc Natl Acad Sci U S A.107(9):4004-9. PMCID: 2840095. Verhounig A, Karcher D, Bock R. Inducible gene expression from the plastid genome by a synthetic riboswitch. Proc Natl Acad Sci U S A.107(14):6204-9. PMCID: 2852001. Zhang Z, Gildersleeve J, Yang YY, Xu R, Loo JA, Uryu S, Wong CH, and Schultz PG. A new strategy for the synthesis of glycoproteins. Science. 2004 Jan 16;303(5656):371-3. DOI:10.1126/science.1089509 | Antonczak AK, Simova Z, and Tippmann EM. A critical examination of Escherichia coli esterase activity. J Biol Chem. 2009 Oct 16;284(42):28795-800. DOI:10.1074/jbc.M109.027409 | Zhou M, Liang X, Mochizuki T, and Asanuma H. A light-driven DNA nanomachine for the efficient photoswitching of RNA digestion. Angew Chem Int Ed Engl. 2010 Mar 15;49(12):2167-70. DOI:10.1002/anie.200907082 | To TL and Maheshri N. Noise can induce bimodality in positive transcriptional feedback loops without bistability. Science. 2010 Feb 26;327(5969):1142-5. DOI:10.1126/science.1178962 | Jones S, Peng PD, Yang S, Hsu C, Cohen CJ, Zhao Y, Abad J, Zheng Z, Rosenberg SA, and Morgan RA. Lentiviral vector design for optimal T cell receptor gene expression in the transduction of peripheral blood lymphocytes and tumor-infiltrating lymphocytes. Hum Gene Ther. 2009 Jun;20(6):630-40. DOI:10.1089/hum.2008.048 | Ellis T, Wang X, and Collins JJ. Diversity-based, model-guided construction of synthetic gene networks with predicted functions. Nat Biotechnol. 2009 May;27(5):465-71. DOI:10.1038/nbt.1536 | Kowtoniuk WE, Shen Y, Heemstra JM, Agarwal I, and Liu DR. A chemical screen for biological small molecule-RNA conjugates reveals CoA-linked RNA. Proc Natl Acad Sci U S A. 2009 May 12;106(19):7768-73. DOI:10.1073/pnas.0900528106 | Burns WR, Zheng Z, Rosenberg SA, and Morgan RA. Lack of specific gamma-retroviral vector long terminal repeat promoter silencing in patients receiving genetically engineered lymphocytes and activation upon lymphocyte restimulation. Blood. 2009 Oct 1;114(14):2888-99. DOI:10.1182/blood-2009-01-199216 | Friedland AE, Lu TK, Wang X, Shi D, Church G, and Collins JJ. Synthetic gene networks that count. Science. 2009 May 29;324(5931):1199-202. DOI:10.1126/science.1172005 | Mitchell A, Romano GH, Groisman B, Yona A, Dekel E, Kupiec M, Dahan O, and Pilpel Y. Adaptive prediction of environmental changes by microorganisms. Nature. 2009 Jul 9;460(7252):220-4. DOI:10.1038/nature08112 | Kudla G, Murray AW, Tollervey D, and Plotkin JB. Coding-sequence determinants of gene expression in Escherichia coli. Science. 2009 Apr 10;324(5924):255-8. DOI:10.1126/science.1170160 | 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 | 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 | Cantone I, Marucci L, Iorio F, Ricci MA, Belcastro V, Bansal M, Santini S, di Bernardo M, di Bernardo D, and Cosma MP. A yeast synthetic network for in vivo assessment of reverse-engineering and modeling approaches. Cell. 2009 Apr 3;137(1):172-81. DOI:10.1016/j.cell.2009.01.055 | Kempe K, Higashi Y, Frick S, Sabarna K, and Kutchan TM. RNAi suppression of the morphine biosynthetic gene salAT and evidence of association of pathway enzymes. Phytochemistry. 2009 Mar;70(5):579-89. DOI:10.1016/j.phytochem.2009.03.002 | Tokuriki N and Tawfik DS. Chaperonin overexpression promotes genetic variation and enzyme evolution. Nature. 2009 Jun 4;459(7247):668-73. DOI:10.1038/nature08009 | Eldar A, Chary VK, Xenopoulos P, Fontes ME, Losón OC, Dworkin J, Piggot PJ, and Elowitz MB. Partial penetrance facilitates developmental evolution in bacteria. Nature. 2009 Jul 23;460(7254):510-4. DOI:10.1038/nature08150 |