Smolke:Journal Club

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*Low JT, Knoepfel SA, Watts JM, Ter Brake O, Berkhout B, Weeks KM. SHAPE-directed Discovery of Potent shRNA Inhibitors of HIV-1. Mol Ther. 2012 Feb 7 (pmid=22314289)
*Low JT, Knoepfel SA, Watts JM, Ter Brake O, Berkhout B, Weeks KM. SHAPE-directed Discovery of Potent shRNA Inhibitors of HIV-1. Mol Ther. 2012 Feb 7 (pmid=22314289)
*Auslander S, et al. Programmable single-cell mammalian biocomputers. 2012 Nature.
*Auslander S, et al. Programmable single-cell mammalian biocomputers. 2012 Nature.
 +
*Sandoval NR, et al. Strategy for directing combinatorial genome engineering in E. coli. PNAS 2012 109(26):10540-5. PMID: 22689973
<biblio>
<biblio>

Revision as of 18:34, 2 July 2012

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Contents

Next Meeting

  • When: 1pm 5/24/12
  • Where: 3rd floor green atrium
  • Paper: TBD
  • Moderator: TBD

Suggested Future Papers

Feel free to use PMID for new paper suggestions

  • 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. 2010 Jun 24;465(7301):1033-8.
  • Salmena L, Poliseno L, Tay Y, Kats L, Pandolfi PP. A ceRNA Hypothesis: The Rosetta Stone of a Hidden RNA Language? Cell. 2011 Jul 27
  • Wargacki AJ, et al. An Engineered Microbial Platform for Direct Biofuel Production from Brown Macroalgae. Science. 2012 Jan 20;335(6066):308-13.
  • Imai M, et al. Experimental adaptation of an influenza H5 HA confers respiratory droplet transmission to a reassortant H5 HA/H1N1 virus in ferrets. Nature 2012, doi:10.1038/nature10831
  • Mutalik VK, et al. Rationally designed families of orthogonal RNA regulators of translation. Nature Chemical Biology 2012, doi:10.1038/NChemBio.919
  • Qi L, et al. Engineering naturally occurring trans-acting non-coding RNAs to sense molecular signals. Nucl. Acids Res. (2012) doi: 10.1093/nar/gks168
  • Li G, et al. The anti-Shine-Dalgarno sequence drives translational pausing and codon choice in bacteria. Nature, doi:10.1038/nature10965
  • Li H, et al. Integrated Electromicrobial Conversion of CO2 to Higher Alcohols. Science 30 March 2012: Vol. 335 no. 6076 p. 1596 DOI: 10.1126/science.1217643
  • Low JT, Knoepfel SA, Watts JM, Ter Brake O, Berkhout B, Weeks KM. SHAPE-directed Discovery of Potent shRNA Inhibitors of HIV-1. Mol Ther. 2012 Feb 7 (pmid=22314289)
  • Auslander S, et al. Programmable single-cell mammalian biocomputers. 2012 Nature.
  • Sandoval NR, et al. Strategy for directing combinatorial genome engineering in E. coli. PNAS 2012 109(26):10540-5. PMID: 22689973
  1. Paige JS, Wu KY, and Jaffrey SR. . pmid:21798953. PubMed HubMed [paige]
  2. Paige JS, Nguyen-Duc T, Song W, and Jaffrey SR. . pmid:22403384. PubMed HubMed [paige]
  3. Douglas SM, Bachelet I, and Church GM. . pmid:22344439. PubMed HubMed [douglas]
  4. Fu J, Bian X, Hu S, Wang H, Huang F, Seibert PM, Plaza A, Xia L, Müller R, Stewart AF, and Zhang Y. . pmid:22544021. PubMed HubMed [fu]
  5. 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. . pmid:22517858. PubMed HubMed [pinheiro]
  6. Sharon E, Kalma Y, Sharp A, Raveh-Sadka T, Levo M, Zeevi D, Keren L, Yakhini Z, Weinberger A, and Segal E. . pmid:22609971. PubMed HubMed [sharon]
All Medline abstracts: PubMed HubMed

Comments on Papers

Voting on Papers

  • Poliseno et al. and Salmena et al: Jay
  • Wargacki et al.: Kate
  • Paige et al. and Paige et. al.: Kathy
  • Douglas et al.:
  • Mutalik et al. and Qi et al.: Jay, Kathy
  • G. Li et al.: Josh
  • H. Li et al.:
  • Fu et al.:
  • Imai et al.: Andy, CDS
  • Pinheiro et al.: Andy, Yen-Hsiang

Past Papers

  1. 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 [sensor]
  2. Bonacci W, Teng PK, Afonso B, Niederholtmeyer H, Grob P, Silver PA, and Savage DF. . pmid:22184212. PubMed HubMed [bonacci]
  3. Carothers JM, Goler JA, Juminaga D, and Keasling JD. . pmid:22194579. PubMed HubMed [carothers]
  4. 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. . pmid:22021385. PubMed HubMed [conrado]
  5. Dellomonaco C, Clomburg JM, Miller EN, and Gonzalez R. . pmid:21832992. PubMed HubMed [dellomonaco]
  6. 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. . pmid:21918511. PubMed HubMed [dymond]
  7. Xie Z, Liu SJ, Bleris L, and Benenson Y. . pmid:20194121. PubMed HubMed [xie]
  8. Leisner M, Bleris L, Lohmueller J, Xie Z, and Benenson Y. . pmid:20622866. PubMed HubMed [leisner]
  9. Saito H, Fujita Y, Kashida S, Hayashi K, and Inoue T. . pmid:21245841. PubMed HubMed [saito]
  10. 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. . pmid:21602812. PubMed HubMed [yim]
  11. Esvelt KM, Carlson JC, and Liu DR. . pmid:21478873. PubMed HubMed [esvelt]
  12. Schirmer A, Rude MA, Li X, Popova E, and del Cardayre SB. . pmid:20671186. PubMed HubMed [schirmer]
  13. Sinha J, Reyes SJ, and Gallivan JP. . pmid:20453864. PubMed HubMed [sinha]
  14. Neumann H, Wang K, Davis L, Garcia-Alai M, and Chin JW. . pmid:20154731. PubMed HubMed [neumann]
  15. Drinnenberg IA, Weinberg DE, Xie KT, Mower JP, Wolfe KH, Fink GR, and Bartel DP. . pmid:19745116. PubMed HubMed [drinnenberg]
  16. Dueber JE, Wu GC, Malmirchegini GR, Moon TS, Petzold CJ, Ullal AV, Prather KL, and Keasling JD. . pmid:19648908. PubMed HubMed [dueber]
  17. Wang HH, Isaacs FJ, Carr PA, Sun ZZ, Xu G, Forest CR, and Church GM. . pmid:19633652. PubMed HubMed [wang]
  18. Yu RC, Pesce CG, Colman-Lerner A, Lok L, Pincus D, Serra E, Holl M, Benjamin K, Gordon A, and Brent R. . pmid:19079053. PubMed HubMed [yu]
  19. Lincoln TA and Joyce GF. . pmid:19131595. PubMed HubMed [lincoln]
  20. Lam BJ and Joyce GF. . pmid:19234448. PubMed HubMed [lam]
  21. Nevozhay D, Adams RM, Murphy KF, Josic K, and Balázsi G. . pmid:19279212. PubMed HubMed [nevozhay]
All Medline abstracts: PubMed HubMed

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.
  1. 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
  2. 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.
  3. Paige, J.S., et al. RNA Mimics of Green Fluorescent Protein. Science 29 July 2011: 333, 642-646.
  4. Wochner A, Attwater J, Coulson A, Holliger P. Ribozyme-catalyzed transcription of an active ribozyme. Science. 2011 Apr 8;332(6026):209-12.
  5. baker pmid=22194412
  6. 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
  7. 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.
  8. 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.
  9. 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.
  10. Isaacs, F.J., et al. Precise Manipulation of Chromosomes in Vivo Enables Genome-Wide Codon Replacement. Science 15 July 2011: 333 (6040), 348-353.
  11. 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.
  12. 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
  13. 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
  14. 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.
  15. Greiss S, and Chin JW. Expanding the Genetic Code of an Animal. J Am Chem Soc. 2011 Aug 8
  16. Poelwijk FJ, de Vos MG, Tans SJ. Tradeoffs and Optimality in the Evolution of Gene Regulation. Cell, 5 August 2011
  17. 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
  18. 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.
  19. 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.
  20. 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.
  21. 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.
  22. 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.
  23. 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.
  24. 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.
  25. 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.
  1. Zhang Z, Gildersleeve J, Yang YY, Xu R, Loo JA, Uryu S, Wong CH, and Schultz PG. . pmid:14726590. PubMed HubMed [zhang]
  2. Antonczak AK, Simova Z, and Tippmann EM. . pmid:19666472. PubMed HubMed [antonczak]
  3. Zhou M, Liang X, Mochizuki T, and Asanuma H. . pmid:20175178. PubMed HubMed [zhou]
  4. To TL and Maheshri N. . pmid:20185727. PubMed HubMed [to]
  5. Jones S, Peng PD, Yang S, Hsu C, Cohen CJ, Zhao Y, Abad J, Zheng Z, Rosenberg SA, and Morgan RA. . pmid:19265475. PubMed HubMed [jones]
  6. Ellis T, Wang X, and Collins JJ. . pmid:19377462. PubMed HubMed [ellis]
  7. Kowtoniuk WE, Shen Y, Heemstra JM, Agarwal I, and Liu DR. . pmid:19416889. PubMed HubMed [liu]
  8. Burns WR, Zheng Z, Rosenberg SA, and Morgan RA. . pmid:19589923. PubMed HubMed [burns]
  9. Friedland AE, Lu TK, Wang X, Shi D, Church G, and Collins JJ. . pmid:19478183. PubMed HubMed [friedland]
  10. Mitchell A, Romano GH, Groisman B, Yona A, Dekel E, Kupiec M, Dahan O, and Pilpel Y. . pmid:19536156. PubMed HubMed [mitchell]
  11. Kudla G, Murray AW, Tollervey D, and Plotkin JB. . pmid:19359587. PubMed HubMed [kudla]
  12. Ray PS, Jia J, Yao P, Majumder M, Hatzoglou M, and Fox PL. . pmid:19098893. PubMed HubMed [ray]
  13. Runguphan W and O'Connor SE. . pmid:19151732. PubMed HubMed [ranguphan]
  14. Han J, Pedersen JS, Kwon SC, Belair CD, Kim YK, Yeom KH, Yang WY, Haussler D, Blelloch R, and Kim VN. . pmid:19135890. PubMed HubMed [han]
  15. Fung E, Wong WW, Suen JK, Bulter T, Lee SG, and Liao JC. . pmid:15875027. PubMed HubMed [fung]
  16. Cantone I, Marucci L, Iorio F, Ricci MA, Belcastro V, Bansal M, Santini S, di Bernardo M, di Bernardo D, and Cosma MP. . pmid:19327819. PubMed HubMed [cantone]
  17. Kempe K, Higashi Y, Frick S, Sabarna K, and Kutchan TM. . pmid:19359021. PubMed HubMed [kempe]
  18. Tokuriki N and Tawfik DS. . pmid:19494908. PubMed HubMed [tokuriki]
  19. Eldar A, Chary VK, Xenopoulos P, Fontes ME, Losón OC, Dworkin J, Piggot PJ, and Elowitz MB. . pmid:19578359. PubMed HubMed [eldar]
All Medline abstracts: PubMed HubMed
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