Difference between revisions of "Smolke:Journal Club"

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(Next Meeting)
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==Next Meeting==
 
==Next Meeting==
 
*When: ?
 
*When: ?
**November 5th - Jay, CDS, Joe, Isis
+
**November 5th - Jay, CDS, Joe, Isis, Ying
 
**other suggested dates?
 
**other suggested dates?
 
*Where: ?
 
*Where: ?

Revision as of 12:01, 22 October 2009

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Next Meeting

  • When: ?
    • November 5th - Jay, CDS, Joe, Isis, Ying
    • other suggested dates?
  • Where: ?
  • Paper:
  1. 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]
  • Moderator: Michael

Suggested Future Papers

  1. Bayer TS, Widmaier DM, Temme K, Mirsky EA, Santi DV, and Voigt CA. Synthesis of methyl halides from biomass using engineered microbes. J Am Chem Soc. 2009 May 13;131(18):6508-15. DOI:10.1021/ja809461u | PubMed ID:19378995 | HubMed [bayer]
  2. 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]
  3. 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]
  4. Lartigue C, Vashee S, Algire MA, Chuang RY, Benders GA, Ma L, Noskov VN, Denisova EA, Gibson DG, Assad-Garcia N, Alperovich N, Thomas DW, Merryman C, Hutchison CA 3rd, Smith HO, Venter JC, and Glass JI. Creating bacterial strains from genomes that have been cloned and engineered in yeast. Science. 2009 Sep 25;325(5948):1693-6. DOI:10.1126/science.1173759 | PubMed ID:19696314 | HubMed [lartigue]
  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. 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]
  7. 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]
  8. Schreier B, Stumpp C, Wiesner S, and Höcker B. Computational design of ligand binding is not a solved problem. Proc Natl Acad Sci U S A. 2009 Nov 3;106(44):18491-6. DOI:10.1073/pnas.0907950106 | PubMed ID:19833875 | HubMed [schreier]
All Medline abstracts: PubMed | HubMed

Comments on Papers

  • Bayer et al. - Travis's paper! ~MSS
  • Schreier et al. - Homme Hellinga goes down again... [1] -Josh

Voting on Papers

  • Bayer et al.:
  • Ellis et al.:
  • Kowtoniuk et al.:
  • Lartigue et al.:
  • Drinnenberg et al.:
  • Burns et al.:
  • Jones et al.:
  • Schreier et al.: Josh

Past Papers

  1. 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]
  2. 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]
  3. 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]
  4. 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]
  5. 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. 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]
  2. 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]
  3. 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]
  4. 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]
  5. 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]
  6. 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]
  7. 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]
  8. 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]
  9. 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]
  10. 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]
  11. 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