Smolke:Journal Club

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2014-2015 Journal Club Date Time Location Paper Moderator 21-Apr 11:00 am Spilker 143 Enquist-Newman Kate 19-May 11:00 am Spilker 143 Lee & Church Joy 16-Jun 11:00 am Spilker 143 Xiong Yanran 21- Jul 11:00am SC 262 Hansen, et al. Kathy 25-Aug 11:00am SC 262 Xu, et al. Isis Sep Remus Oct Yen-Hsiang Nov Melina Dec Kate Jan Peter Feb Maureen Mar Michale Apr Stephanie May Shireen Jun Ben Jul Joy Paper to be discussed Xiong M, Schneiderman DK, Bates FS, Hillmyer MA, and Zhang K. Scalable production of mechanically tunable block polymers from sugar. Proc Natl Acad Sci U S A. 2014 Jun 10;111(23):8357-62. DOI:10.1073/pnas.1404596111 | Interesting 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. Duss O, Michel E, Yulikov M, Schubert M, Jeschke G, and Allain FH. Structural basis of the non-coding RNA RsmZ acting as a protein sponge. Nature. 2014 May 29;509(7502):588-92. DOI:10.1038/nature13271 | 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 | Annaluru N, Muller H, Mitchell LA, Ramalingam S, Stracquadanio G, Richardson SM, Dymond JS, Kuang Z, Scheifele LZ, Cooper EM, Cai Y, Zeller K, Agmon N, Han JS, Hadjithomas M, Tullman J, Caravelli K, Cirelli K, Guo Z, London V, Yeluru A, Murugan S, Kandavelou K, Agier N, Fischer G, Yang K, Martin JA, Bilgel M, Bohutski P, Boulier KM, Capaldo BJ, Chang J, Charoen K, Choi WJ, Deng P, DiCarlo JE, Doong J, Dunn J, Feinberg JI, Fernandez C, Floria CE, Gladowski D, Hadidi P, Ishizuka I, Jabbari J, Lau CY, Lee PA, Li S, Lin D, Linder ME, Ling J, Liu J, Liu J, London M, Ma H, Mao J, McDade JE, McMillan A, Moore AM, Oh WC, Ouyang Y, Patel R, Paul M, Paulsen LC, Qiu J, Rhee A, Rubashkin MG, Soh IY, Sotuyo NE, Srinivas V, Suarez A, Wong A, Wong R, Xie WR, Xu Y, Yu AT, Koszul R, Bader JS, Boeke JD, and Chandrasegaran S. Total synthesis of a functional designer eukaryotic chromosome. Science. 2014 Apr 4;344(6179):55-8. DOI:10.1126/science.1249252 | 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 | 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 | Lian J, Si T, Nair NU, and Zhao H. Design and construction of acetyl-CoA overproducing Saccharomyces cerevisiae strains. Metab Eng. 2014 Jul;24:139-49. DOI:10.1016/j.ymben.2014.05.010 | 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? Past Papers Past papers Error fetching PMID 24744377: Error fetching PMID 24696455: Error fetching PMID 24677733: Error fetching PMID 24603933: Error fetching PMID 24578530: Error fetching PMID 24445655: Error fetching PMID 22383579: Error fetching PMID 24733905: Error fetching PMID 24670663: Error fetching PMID 24608181: Error fetching PMID 24513861: Error fetching PMID 24284625: Error fetching PMID 24463698: Error fetching PMID 24529477: Error fetching PMID 24487692: Error fetching PMID 24434554: Error fetching PMID 22446835: Error fetching PMID 24270811: Error fetching PMID 24196718: Error fetching PMID 22461604: Error fetching PMID 22689973: Error fetching PMID 22544021: Error fetching PMID 22517858: Error fetching PMID 22609971: Error fetching PMID 22817898: Error fetching PMID 22745249: Error fetching PMID 21802130: Error fetching PMID 23287718: Error fetching PMID 23287722: Error fetching PMID 23360964: Error fetching PMID 23258409: Error fetching PMID 22267807: Error fetching PMID 22194579: Fica SM, Mefford MA, Piccirilli JA, and Staley JP. Evidence for a group II intron-like catalytic triplex in the spliceosome. Nat Struct Mol Biol. 2014 May;21(5):464-471. DOI:10.1038/nsmb.2815 | Lee K, Cui Y, Lee LP, and Irudayaraj J. Quantitative imaging of single mRNA splice variants in living cells. Nat Nanotechnol. 2014 Jun;9(6):474-80. DOI:10.1038/nnano.2014.73 | 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 | 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 | 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 | 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 | 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 | 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 | 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 | 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 | 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 | 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 | 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 | 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 | 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 | 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 | 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 | 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 | 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