Smolke:Journal Club

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Next Meeting When: Friday Nov. 30 2:00pm Where: 1st floor green atrium conference room (I will get more chairs this time) Paper: Spitale Moderator: Andy Suggested Future Papers without pmid link here: Spitale RNA Shape analysis in living cells link suggestions with pmid links. Click on an author name to go to the paper OR click on the HubMed link at the bottom of the page to see all abstracts. Salmena L, Poliseno L, Tay Y, Kats L, and Pandolfi PP. A ceRNA hypothesis: the Rosetta Stone of a hidden RNA language?. Cell. 2011 Aug 5;146(3):353-8. DOI:10.1016/j.cell.2011.07.014 | Mutalik VK, Qi L, Guimaraes JC, Lucks JB, and Arkin AP. Rationally designed families of orthogonal RNA regulators of translation. Nat Chem Biol. 2012 Mar 25;8(5):447-54. DOI:10.1038/nchembio.919 | Qi L, Lucks JB, Liu CC, Mutalik VK, and Arkin AP. Engineering naturally occurring trans-acting non-coding RNAs to sense molecular signals. Nucleic Acids Res. 2012 Jul;40(12):5775-86. DOI:10.1093/nar/gks168 | Li GW, Oh E, and Weissman JS. The anti-Shine-Dalgarno sequence drives translational pausing and codon choice in bacteria. Nature. 2012 Mar 28;484(7395):538-41. DOI:10.1038/nature10965 | Li H, Opgenorth PH, Wernick DG, Rogers S, Wu TY, Higashide W, Malati P, Huo YX, Cho KM, and Liao JC. Integrated electromicrobial conversion of CO2 to higher alcohols. Science. 2012 Mar 30;335(6076):1596. DOI:10.1126/science.1217643 | Low JT, Knoepfel SA, Watts JM, ter Brake O, Berkhout B, and Weeks KM. SHAPE-directed discovery of potent shRNA inhibitors of HIV-1. Mol Ther. 2012 Apr;20(4):820-8. DOI:10.1038/mt.2011.299 | Ausländer S, Ausländer D, Müller M, Wieland M, and Fussenegger M. Programmable single-cell mammalian biocomputers. Nature. 2012 Jul 5;487(7405):123-7. DOI:10.1038/nature11149 | Sandoval NR, Kim JY, Glebes TY, Reeder PJ, Aucoin HR, Warner JR, and Gill RT. Strategy for directing combinatorial genome engineering in Escherichia coli. Proc Natl Acad Sci U S A. 2012 Jun 26;109(26):10540-5. DOI:10.1073/pnas.1206299109 | Douglas SM, Bachelet I, and Church GM. A logic-gated nanorobot for targeted transport of molecular payloads. Science. 2012 Feb 17;335(6070):831-4. DOI:10.1126/science.1214081 | Fu J, Bian X, Hu S, Wang H, Huang F, Seibert PM, Plaza A, Xia L, Müller R, Stewart AF, and Zhang Y. Full-length RecE enhances linear-linear homologous recombination and facilitates direct cloning for bioprospecting. Nat Biotechnol. 2012 May;30(5):440-6. DOI:10.1038/nbt.2183 | Paige JS, Wu KY, and Jaffrey SR. RNA mimics of green fluorescent protein. Science. 2011 Jul 29;333(6042):642-6. DOI:10.1126/science.1207339 | Paige JS, Nguyen-Duc T, Song W, and Jaffrey SR. Fluorescence imaging of cellular metabolites with RNA. Science. 2012 Mar 9;335(6073):1194. DOI:10.1126/science.1218298 | Pinheiro VB, Taylor AI, Cozens C, Abramov M, Renders M, Zhang S, Chaput JC, Wengel J, Peak-Chew SY, McLaughlin SH, Herdewijn P, and Holliger P. Synthetic genetic polymers capable of heredity and evolution. Science. 2012 Apr 20;336(6079):341-4. DOI:10.1126/science.1217622 | Sharon E, Kalma Y, Sharp A, Raveh-Sadka T, Levo M, Zeevi D, Keren L, Yakhini Z, Weinberger A, and Segal E. Inferring gene regulatory logic from high-throughput measurements of thousands of systematically designed promoters. Nat Biotechnol. 2012 May 20;30(6):521-30. DOI:10.1038/nbt.2205 | Regot S, Macia J, Conde N, Furukawa K, Kjellén J, Peeters T, Hohmann S, de Nadal E, Posas F, and Solé R. Distributed biological computation with multicellular engineered networks. Nature. 2011 Jan 13;469(7329):207-11. DOI:10.1038/nature09679 | Karr JR, Sanghvi JC, Macklin DN, Gutschow MV, Jacobs JM, Bolival B Jr, Assad-Garcia N, Glass JI, and Covert MW. A whole-cell computational model predicts phenotype from genotype. Cell. 2012 Jul 20;150(2):389-401. DOI:10.1016/j.cell.2012.05.044 | Jinek M, Chylinski K, Fonfara I, Hauer M, Doudna JA, and Charpentier E. A programmable dual-RNA-guided DNA endonuclease in adaptive bacterial immunity. Science. 2012 Aug 17;337(6096):816-21. DOI:10.1126/science.1225829 | Qi L, Haurwitz RE, Shao W, Doudna JA, and Arkin AP. RNA processing enables predictable programming of gene expression. Nat Biotechnol. 2012 Oct;30(10):1002-6. DOI:10.1038/nbt.2355 | Moss-Racusin CA, Dovidio JF, Brescoll VL, Graham MJ, and Handelsman J. Science faculty's subtle gender biases favor male students. Proc Natl Acad Sci U S A. 2012 Oct 9;109(41):16474-9. DOI:10.1073/pnas.1211286109 | Coelho PS, Brustad EM, Kannan A, and Arnold FH. Olefin cyclopropanation via carbene transfer catalyzed by engineered cytochrome P450 enzymes. Science. 2013 Jan 18;339(6117):307-10. DOI:10.1126/science.1231434 | This last HubMed link seems to work. Click on it to bring up all the abstracts. This should facilitate voting. To add your paper this way, get the pmid from pubmed, and follow the format when editing. The PubMed link doesn't seem to work. Anyone know why? Comments on Papers Voting on Papers RUN OFF Spitale: Eric, Kathy, Jay, Yen-Hsiang, CDS, Andy Sandoval: Isis, Mike, Kate Spitale et al.: Andy, CDS, Yen-Hsiang, Jay Sandoval et al.: Eric, SG, Isis, Kate Poliseno et al. and Salmena et al: Paige et al. and Paige et. al.: Ryan Douglas et al.: Maureen, Kathy Mutalik et al. and Qi et al.: Eric, Jay, Yen-Hsiang G. Li et al.: H. Li et al.: SG, Mike, Kate Fu et al.: Andy Pinheiro et al.: Mike Sharon et al.: Isis Auslander S, et al.: Maureen, Kathy Jinek et al.: Qi et al.: CDS, remus Karr et al: Ryan Moss-Racusin et al.: Freida and Block: Past Papers Past papers Frieda KL and Block SM. Direct observation of cotranscriptional folding in an adenine riboswitch. Science. 2012 Oct 19;338(6105):397-400. DOI:10.1126/science.1225722 | Wargacki AJ, Leonard E, Win MN, Regitsky DD, Santos CN, Kim PB, Cooper SR, Raisner RM, Herman A, Sivitz AB, Lakshmanaswamy A, Kashiyama Y, Baker D, and Yoshikuni Y. An engineered microbial platform for direct biofuel production from brown macroalgae. Science. 2012 Jan 20;335(6066):308-13. DOI:10.1126/science.1214547 | Bonacci W, Teng PK, Afonso B, Niederholtmeyer H, Grob P, Silver PA, and Savage DF. Modularity of a carbon-fixing protein organelle. Proc Natl Acad Sci U S A. 2012 Jan 10;109(2):478-83. DOI:10.1073/pnas.1108557109 | Carothers JM, Goler JA, Juminaga D, and Keasling JD. Model-driven engineering of RNA devices to quantitatively program gene expression. Science. 2011 Dec 23;334(6063):1716-9. DOI:10.1126/science.1212209 | Conrado RJ, Wu GC, Boock JT, Xu H, Chen SY, Lebar T, Turnšek J, Tomšič N, Avbelj M, Gaber R, Koprivnjak T, Mori J, Glavnik V, Vovk I, Benčina M, Hodnik V, Anderluh G, Dueber JE, Jerala R, and DeLisa MP. DNA-guided assembly of biosynthetic pathways promotes improved catalytic efficiency. Nucleic Acids Res. 2012 Feb;40(4):1879-89. DOI:10.1093/nar/gkr888 | Dellomonaco C, Clomburg JM, Miller EN, and Gonzalez R. Engineered reversal of the β-oxidation cycle for the synthesis of fuels and chemicals. Nature. 2011 Aug 10;476(7360):355-9. DOI:10.1038/nature10333 | Dymond JS, Richardson SM, Coombes CE, Babatz T, Muller H, Annaluru N, Blake WJ, Schwerzmann JW, Dai J, Lindstrom DL, Boeke AC, Gottschling DE, Chandrasegaran S, Bader JS, and Boeke JD. Synthetic chromosome arms function in yeast and generate phenotypic diversity by design. Nature. 2011 Sep 14;477(7365):471-6. DOI:10.1038/nature10403 | Xie Z, Liu SJ, Bleris L, and Benenson Y. Logic integration of mRNA signals by an RNAi-based molecular computer. Nucleic Acids Res. 2010 May;38(8):2692-701. DOI:10.1093/nar/gkq117 | Leisner M, Bleris L, Lohmueller J, Xie Z, and Benenson Y. Rationally designed logic integration of regulatory signals in mammalian cells. Nat Nanotechnol. 2010 Sep;5(9):666-70. DOI:10.1038/nnano.2010.135 | Saito H, Fujita Y, Kashida S, Hayashi K, and Inoue T. Synthetic human cell fate regulation by protein-driven RNA switches. Nat Commun. 2011 Jan 18;2:160. DOI:10.1038/ncomms1157 | Yim H, Haselbeck R, Niu W, Pujol-Baxley C, Burgard A, Boldt J, Khandurina J, Trawick JD, Osterhout RE, Stephen R, Estadilla J, Teisan S, Schreyer HB, Andrae S, Yang TH, Lee SY, Burk MJ, and Van Dien S. Metabolic engineering of Escherichia coli for direct production of 1,4-butanediol. Nat Chem Biol. 2011 May 22;7(7):445-52. DOI:10.1038/nchembio.580 | Esvelt KM, Carlson JC, and Liu DR. A system for the continuous directed evolution of biomolecules. Nature. 2011 Apr 28;472(7344):499-503. DOI:10.1038/nature09929 | 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 | Imai M, Watanabe T, Hatta M, Das SC, Ozawa M, Shinya K, Zhong G, Hanson A, Katsura H, Watanabe S, Li C, Kawakami E, Yamada S, Kiso M, Suzuki Y, Maher EA, Neumann G, and Kawaoka Y. Experimental adaptation of an influenza H5 HA confers respiratory droplet transmission to a reassortant H5 HA/H1N1 virus in ferrets. Nature. 2012 May 2;486(7403):420-8. DOI:10.1038/nature10831 | Zhang F, Carothers J, Keasling JD. Design of a dynamic sensor-regulator system for production of chemicals and fuels derived from fatty acids. Nature Biotechnology 2012, doi:10.1038/nbt.2149 Aged Out Valderrama-Rincon JD, et al. An engineered eukaryotic protein glycosylation pathway in Escherichia coli. Nature Chemical Biology 2012, doi:10.1038/nchembio.921 The arsenic bacteria paper, the 8 technical comments, and the authors' reply. Shen, Claire R., Lan, Ethan I., Dekishima, Yasumasa, Baez, Antonino, Cho, Kwang Myung, Liao, James C. High titer anaerobic 1-butanol synthesis in Escherichia coli enabled by driving forces. Appl. Environ. Microbiol. 2011 0: AEM.03034-10 Bond-Watts BB, Bellerose RJ and Chang MC. Enzyme mechanism as a kinetic control element for designing synthetic biofuel pathways. Nature Chemical Biology. April 2011. 222-227. Paige, J.S., et al. RNA Mimics of Green Fluorescent Protein. Science 29 July 2011: 333, 642-646. Wochner A, Attwater J, Coulson A, Holliger P. Ribozyme-catalyzed transcription of an active ribozyme. Science. 2011 Apr 8;332(6026):209-12. baker pmid=22194412 Brown ME, Walker MC, Nakashige TG, Iavarone AT, Chang MC. Discovery and characterization of heme enzymes from unsequenced bacteria: Application to microbial lignin degradation. JACS 2011, 133, 18006-18009. dx.doi.org/10.1021/ja203972q Porter DL, Levine BL, Kalos M, Bagg A, June CH. Chimeric Antigen Receptor-Modified T Cells in Chronic Lymphoid Leukemia. N Engl J Med. 2011 Aug 10. Milias-Argeitis A, Summers S, Stewart-Ornstein J, Zuleta I, Pincus D, El-Samad H, Khammash M, Lygeros J. In silico feedback for in vivo regulation of a gene expression circuit. Nature Biotechnology. November 2011. Schwanhäusser B, Busse D, Li N, Dittmar G, Schuchhardt J, Wolf J, Chen W, Selbach M. Global quantification of mammalian gene expression control. Nature. 2011 May 19;473(7347):337-42. Isaacs, F.J., et al. Precise Manipulation of Chromosomes in Vivo Enables Genome-Wide Codon Replacement. Science 15 July 2011: 333 (6040), 348-353. Huo YX, Cho KM, Rivera JG, Monte E, Shen CR, Yan Y, Liao JC. Conversion of proteins into biofuels by engineering nitrogen flux. Nat Biotechnol. 2011 Mar 6. Gevorg Grigorya, Yong Ho Kim, Rudresh Acharya, Kevin Axelrod, Rishabh M. Jain, Lauren Willis, Marija Drndic, James M. Kikkawa, William F. DeGrado. Computational Design of Virus-Like Protein Assemblies on Carbon Nanotube Surfaces. Science 332, 1071 (2011);DOI: 10.1126/science.1198841 Fisher MA, McKinley KL, Bradley LH, Viola SR, Hecht MH. De novo designed proteins from a library of artificial sequences function in Escherichia coli and enable cell growth. PLoS One. 2011 Jan 4; 6(1). PMID: 21245923 Marlière P, Patrouix J, Döring V, Herdewijn P, Tricot S, Cruveiller S, Bouzon M, Mutzel R. Chemical Evolution of a Bacterium's Genome. Angew Chem Int Ed Engl. 2011 Jun 27. doi: 10.1002/anie.201100535. Greiss S, and Chin JW. Expanding the Genetic Code of an Animal. J Am Chem Soc. 2011 Aug 8 Poelwijk FJ, de Vos MG, Tans SJ. Tradeoffs and Optimality in the Evolution of Gene Regulation. Cell, 5 August 2011 Wang, H, Claveau, D, Vaillancourt, JP, Roemer, T, Meredith, TC. High-frequency transposition for determining antibacterial mode of action. Nat Chem Biol. 2011 Sept 04. doi:10.1038/nchembio.643 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. 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. Peter Y Watson and Martha J Fedor. The glmS riboswitch integrates signals from activating and inhibitory metabolites in vivo. Nature Structural & Molecular Biology March 2011: 18 (3), 359-363. 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 |