Difference between revisions of "Smolke:Journal Club"

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(Voting on Papers)
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*'''Huo et al.''':
 
*'''Huo et al.''':
 
*'''Bond-Watts et al.''' and '''Shen et al.''': Joe, Stephanie
 
*'''Bond-Watts et al.''' and '''Shen et al.''': Joe, Stephanie
*'''Yim et al.''': Joe, Stephanie
+
*'''Yim et al.''': Joe, Stephanie, Ryan
*'''Schwanhäusser et al.''': DK, Megan
+
*'''Schwanhäusser et al.''': DK, Megan, Ryan
  
 
==Past Papers==
 
==Past Papers==

Revision as of 12:14, 26 May 2011

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Next Meeting

  • When: Monday, June 6, 2pm
  • Where: Y2E2 270
  • Paper: TBD
  • Moderator: TBD

Suggested Future Papers

Note: The biblio extension is broken. Suggested papers need full references.

  1. 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.
  2. O'Shaughnessy EC, Palani S, Collins JJ, Sarkar CA. Tunable Signal Processing in Synthetic MAP Kinase Cascades. Cell.144(1):119-31.
  3. Churchman LS, Weissman JS. Nascent transcript sequencing visualizes transcription at nucleotide resolution. Nature.469(7330):368-73.
  4. Wörsdörfer B, Woycechowsky KJ, and Hilvert, D. Directed Evolution of a Protein Container. Science 4 February 2011: 331 (6017), 589-592.
  5. Chen X, Denison L, Levy M, Ellington AD. Direct selection for ribozyme cleavage activity in cells. RNA 23 November 2009: 15 (11), 2035-45.
  6. 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.
  7. 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.
  8. 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
  9. 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, Van Dien S. Metabolic engineering of Escherichia coli for direct production of 1,4-butanediol. Nat Chem Biol. 2011 May 22
  10. 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.

Comments on Papers

Voting on Papers

  • Poliseno et al.:
  • O'Shaughnessy et al.:
  • Churchman and Weissman:
  • Wörsdörfer et al.:
  • Chen et al:
  • Huo et al.:
  • Bond-Watts et al. and Shen et al.: Joe, Stephanie
  • Yim et al.: Joe, Stephanie, Ryan
  • Schwanhäusser et al.: DK, Megan, Ryan

Past Papers

  1. KM, Carlson JC, Liu DR. A system for the continuous directed evolution of biomolecules. Nature. 2011. [Esvelt]
  2. 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 | PubMed ID:20671186 | HubMed [schirmer]
  3. 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 | PubMed ID:20453864 | HubMed [sinha]
  4. 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 | PubMed ID:20154731 | HubMed [neumann]
  5. 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 | PubMed ID:19745116 | HubMed [drinnenberg]
  6. 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 | PubMed ID:19648908 | HubMed [dueber]
  7. 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 | PubMed ID:19633652 | HubMed [wang]
  8. 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 | PubMed ID:19079053 | HubMed [yu]
  9. 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 | PubMed ID:19131595 | HubMed [lincoln]
  10. 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 | PubMed ID:19234448 | HubMed [lam]
  11. 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 | PubMed ID:19279212 | HubMed [nevozhay]
All Medline abstracts: PubMed | HubMed

Aged Out

  1. 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.
  2. 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.
  3. 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.
  4. 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.
  5. 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.
  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.
  7. 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.
  8. 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. A new strategy for the synthesis of glycoproteins. Science. 2004 Jan 16;303(5656):371-3. DOI:10.1126/science.1089509 | PubMed ID:14726590 | HubMed [zhang]
  2. 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 | PubMed ID:19666472 | HubMed [antonczak]
  3. 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 | PubMed ID:20175178 | HubMed [zhou]
  4. 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 | PubMed ID:20185727 | HubMed [to]
  5. 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 | PubMed ID:19265475 | HubMed [jones]
  6. 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 | PubMed ID:19377462 | HubMed [ellis]
  7. 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 | PubMed ID:19416889 | HubMed [liu]
  8. 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 | PubMed ID:19589923 | HubMed [burns]
  9. 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 | PubMed ID:19478183 | HubMed [friedland]
  10. 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 | PubMed ID:19536156 | HubMed [mitchell]
  11. 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 | PubMed ID:19359587 | HubMed [kudla]
  12. 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 | PubMed ID:19098893 | HubMed [ray]
  13. 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 | PubMed ID:19151732 | HubMed [ranguphan]
  14. 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 | PubMed ID:19135890 | HubMed [han]
  15. 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 | PubMed ID:15875027 | 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. 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 | PubMed ID:19327819 | HubMed [cantone]
  17. 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 | PubMed ID:19359021 | HubMed [kempe]
  18. 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 | PubMed ID:19494908 | HubMed [tokuriki]
  19. 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 | PubMed ID:19578359 | HubMed [eldar]
All Medline abstracts: PubMed | HubMed