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2014 Spring Date Time Location Paper Moderator 21-Apr 11:00 am Spilker 143 Enquist-Newman Kate 19-May 11:00 am Spilker 143 16-Jun 11:00 am Spilker 143 Suggested Future Papers 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. Wang X, Lu Z, Gomez A, Hon GC, Yue Y, Han D, Fu Y, Parisien M, Dai Q, Jia G, Ren B, Pan T, and He C. N6-methyladenosine-dependent regulation of messenger RNA stability. Nature. 2014 Jan 2;505(7481):117-20. DOI:10.1038/nature12730 | Wang BL, Ghaderi A, Zhou H, Agresti J, Weitz DA, Fink GR, and Stephanopoulos G. Microfluidic high-throughput culturing of single cells for selection based on extracellular metabolite production or consumption. Nat Biotechnol. 2014 May;32(5):473-8. DOI:10.1038/nbt.2857 | ña-Meyer pmid=24696455 Liu Y, Samuel BS, Breen PC, and Ruvkun G. Caenorhabditis elegans pathways that surveil and defend mitochondria. Nature. 2014 Apr 17;508(7496):406-10. DOI:10.1038/nature13204 | Cao J, Arha M, Sudrik C, Schaffer DV, and Kane RS. Bidirectional regulation of mRNA translation in mammalian cells by using PUF domains. Angew Chem Int Ed Engl. 2014 May 5;53(19):4900-4. DOI:10.1002/anie.201402095 | Kotula JW, Kerns SJ, Shaket LA, Siraj L, Collins JJ, Way JC, and Silver PA. Programmable bacteria detect and record an environmental signal in the mammalian gut. Proc Natl Acad Sci U S A. 2014 Apr 1;111(13):4838-43. DOI:10.1073/pnas.1321321111 | Creasey KM, Zhai J, Borges F, Van Ex F, Regulski M, Meyers BC, and Martienssen RA. miRNAs trigger widespread epigenetically activated siRNAs from transposons in Arabidopsis. Nature. 2014 Apr 17;508(7496):411-5. DOI:10.1038/nature13069 | Church GM, Elowitz MB, Smolke CD, Voigt CA, and Weiss R. Realizing the potential of synthetic biology. Nat Rev Mol Cell Biol. 2014 Apr;15(4):289-94. DOI:10.1038/nrm3767 | Olson EJ, Hartsough LA, Landry BP, Shroff R, and Tabor JJ. Characterizing bacterial gene circuit dynamics with optically programmed gene expression signals. Nat Methods. 2014 Apr;11(4):449-55. DOI:10.1038/nmeth.2884 | Karas BJ, Jablanovic J, Irvine E, Sun L, Ma L, Weyman PD, Gibson DG, Glass JI, Venter JC, Hutchison CA 3rd, Smith HO, and Suzuki Y. Transferring whole genomes from bacteria to yeast spheroplasts using entire bacterial cells to reduce DNA shearing. Nat Protoc. 2014 Apr;9(4):743-50. DOI:10.1038/nprot.2014.045 | Lee JH, Daugharthy ER, Scheiman J, Kalhor R, Yang JL, Ferrante TC, Terry R, Jeanty SS, Li C, Amamoto R, Peters DT, Turczyk BM, Marblestone AH, Inverso SA, Bernard A, Mali P, Rios X, Aach J, and Church GM. Highly multiplexed subcellular RNA sequencing in situ. Science. 2014 Mar 21;343(6177):1360-3. DOI:10.1126/science.1250212 | Ding BJ, Hofvander P, Wang HL, Durrett TP, Stymne S, and Löfstedt C. A plant factory for moth pheromone production. Nat Commun. 2014 Feb 25;5:3353. DOI:10.1038/ncomms4353 | Fossati E, Ekins A, Narcross L, Zhu Y, Falgueyret JP, Beaudoin GA, Facchini PJ, and Martin VJ. Reconstitution of a 10-gene pathway for synthesis of the plant alkaloid dihydrosanguinarine in Saccharomyces cerevisiae. Nat Commun. 2014;5:3283. DOI:10.1038/ncomms4283 | Velagapudi SP, Gallo SM, and Disney MD. Sequence-based design of bioactive small molecules that target precursor microRNAs. Nat Chem Biol. 2014 Apr;10(4):291-7. DOI:10.1038/nchembio.1452 | Blazeck J, Hill A, Liu L, Knight R, Miller J, Pan A, Otoupal P, and Alper HS. Harnessing Yarrowia lipolytica lipogenesis to create a platform for lipid and biofuel production. Nat Commun. 2014;5:3131. DOI:10.1038/ncomms4131 | Lienert F, Lohmueller JJ, Garg A, and Silver PA. Synthetic biology in mammalian cells: next generation research tools and therapeutics. Nat Rev Mol Cell Biol. 2014 Feb;15(2):95-107. DOI:10.1038/nrm3738 | Enquist-Newman M, Faust AM, Bravo DD, Santos CN, Raisner RM, Hanel A, Sarvabhowman P, Le C, Regitsky DD, Cooper SR, Peereboom L, Clark A, Martinez Y, Goldsmith J, Cho MY, Donohoue PD, Luo L, Lamberson B, Tamrakar P, Kim EJ, Villari JL, Gill A, Tripathi SA, Karamchedu P, Paredes CJ, Rajgarhia V, Kotlar HK, Bailey RB, Miller DJ, Ohler NL, Swimmer C, and Yoshikuni Y. Efficient ethanol production from brown macroalgae sugars by a synthetic yeast platform. Nature. 2014 Jan 9;505(7482):239-43. DOI:10.1038/nature12771 | Avendaño MS, Leidy C, and Pedraza JM. Tuning the range and stability of multiple phenotypic states with coupled positive-negative feedback loops. Nat Commun. 2013;4:2605. DOI:10.1038/ncomms3605 | Bogorad IW, Lin TS, and Liao JC. Synthetic non-oxidative glycolysis enables complete carbon conservation. Nature. 2013 Oct 31;502(7473):693-7. DOI:10.1038/nature12575 | 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 | 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 | Birmingham WR, Starbird CA, Panosian TD, Nannemann DP, Iverson TM, and Bachmann BO. Bioretrosynthetic construction of a didanosine biosynthetic pathway. Nat Chem Biol. 2014 May;10(5):392-9. DOI:10.1038/nchembio.1494 | Matthews ML, Chang WC, Layne AP, Miles LA, Krebs C, and Bollinger JM Jr. Direct nitration and azidation of aliphatic carbons by an iron-dependent halogenase. Nat Chem Biol. 2014 Mar;10(3):209-15. DOI:10.1038/nchembio.1438 | Alberts B, Kirschner MW, Tilghman S, and Varmus H. Rescuing US biomedical research from its systemic flaws. Proc Natl Acad Sci U S A. 2014 Apr 22;111(16):5773-7. DOI:10.1073/pnas.1404402111 | 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 Vote for Apr. 21st, 2014 Creasey et al: Church et al:KYW Olson et al: Karas et al: KT Lee et al: MHM, MM Ding et al: YL Fossati et al: Velagapudi et al:KYW Blazeck et al: KT, MS Lienert et al: Enquist-Newman et al: YL, MS, RW, SG Wang et al: Avendaño et al: MHM Bogorad et al: Qi & Arkin et al: MM Ausländer et al: Birmingham et al: SG Matthews et al: Vote for Mar 17th, 2014 Ding et al: KT Nishimasu et al: Fossati et al: YHW, MSS, IJT Velagapudi et al:KYW, MHM Hammerling: Lienert:KYW, JVV Moses et al: YL, KT, SG, IJT Enquist-Newman et al: YL, YHW, MSS Avendaño et al: MHM Bogorad et al: SG Mutalic et al: Qi & Arkin et al: JVV Ausländer et al: RW Past Papers Past papers Ding Y, Tang Y, Kwok CK, Zhang Y, Bevilacqua PC, and Assmann SM. In vivo genome-wide profiling of RNA secondary structure reveals novel regulatory features. Nature. 2014 Jan 30;505(7485):696-700. DOI:10.1038/nature12756 | Nishimasu H, Ran FA, Hsu PD, Konermann S, Shehata SI, Dohmae N, Ishitani R, Zhang F, and Nureki O. Crystal structure of Cas9 in complex with guide RNA and target DNA. Cell. 2014 Feb 27;156(5):935-49. DOI:10.1016/j.cell.2014.02.001 | Hammerling MJ, Ellefson JW, Boutz DR, Marcotte EM, Ellington AD, and Barrick JE. Bacteriophages use an expanded genetic code on evolutionary paths to higher fitness. Nat Chem Biol. 2014 Mar;10(3):178-80. DOI:10.1038/nchembio.1450 | Moses T, Pollier J, Almagro L, Buyst D, Van Montagu M, Pedreño MA, Martins JC, Thevelein JM, and Goossens A. Combinatorial biosynthesis of sapogenins and saponins in Saccharomyces cerevisiae using a C-16α hydroxylase from Bupleurum falcatum. Proc Natl Acad Sci U S A. 2014 Jan 28;111(4):1634-9. DOI:10.1073/pnas.1323369111 | 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 | Carter GT. NP/MS since 1970: from the basement to the bench top. Nat Prod Rep. 2014 Jun;31(6):711-7. DOI:10.1039/c3np70085b | Fica SM, Tuttle N, Novak T, Li NS, Lu J, Koodathingal P, Dai Q, Staley JP, and Piccirilli JA. RNA catalyses nuclear pre-mRNA splicing. Nature. 2013 Nov 14;503(7475):229-34. DOI:10.1038/nature12734 | 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 | Paddon CJ, Westfall PJ, Pitera DJ, Benjamin K, Fisher K, McPhee D, Leavell MD, Tai A, Main A, Eng D, Polichuk DR, Teoh KH, Reed DW, Treynor T, Lenihan J, Fleck M, Bajad S, Dang G, Dengrove D, Diola D, Dorin G, Ellens KW, Fickes S, Galazzo J, Gaucher SP, Geistlinger T, Henry R, Hepp M, Horning T, Iqbal T, Jiang H, Kizer L, Lieu B, Melis D, Moss N, Regentin R, Secrest S, Tsuruta H, Vazquez R, Westblade LF, Xu L, Yu M, Zhang Y, Zhao L, Lievense J, Covello PS, Keasling JD, Reiling KK, Renninger NS, and Newman JD. High-level semi-synthetic production of the potent antimalarial artemisinin. Nature. 2013 Apr 25;496(7446):528-32. DOI:10.1038/nature12051 | 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 | 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 | Choi YJ and Lee SY. Microbial production of short-chain alkanes. Nature. 2013 Oct 24;502(7472):571-4. DOI:10.1038/nature12536 | 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 | Cong L, Ran FA, Cox D, Lin S, Barretto R, Habib N, Hsu PD, Wu X, Jiang W, Marraffini LA, and Zhang F. Multiplex genome engineering using CRISPR/Cas systems. Science. 2013 Feb 15;339(6121):819-23. DOI:10.1126/science.1231143 | Mali P, Yang L, Esvelt KM, Aach J, Guell M, DiCarlo JE, Norville JE, and Church GM. RNA-guided human genome engineering via Cas9. Science. 2013 Feb 15;339(6121):823-6. DOI:10.1126/science.1232033 | Hwang WY, Fu Y, Reyon D, Maeder ML, Tsai SQ, Sander JD, Peterson RT, Yeh JR, and Joung JK. Efficient genome editing in zebrafish using a CRISPR-Cas system. Nat Biotechnol. 2013 Mar;31(3):227-9. DOI:10.1038/nbt.2501 | 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 | Cho SW, Kim S, Kim JM, and Kim JS. Targeted genome engineering in human cells with the Cas9 RNA-guided endonuclease. Nat Biotechnol. 2013 Mar;31(3):230-2. DOI:10.1038/nbt.2507 | 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 | Spitale RC, Crisalli P, Flynn RA, Torre EA, Kool ET, and Chang HY. RNA SHAPE analysis in living cells. Nat Chem Biol. 2013 Jan;9(1):18-20. DOI:10.1038/nchembio.1131 | 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. 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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. 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