Smolke:Journal Club: Difference between revisions
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{{Smolke_Top}} | {{Smolke_Top}} | ||
=Next Meeting= | =Next Meeting= | ||
*When: | *When: 8/6 2pm | ||
*Where: TBD | *Where: TBD | ||
*Paper: | *Paper: 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, 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. | ||
*Moderator: TBD | *Moderator: TBD | ||
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Note: The biblio extension is broken. Suggested papers need full references. | Note: The biblio extension is broken. Suggested papers need full references. | ||
#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. | #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. | ||
#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 | #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 | ||
#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. | #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. | ||
#The arsenic bacteria paper, the 8 technical comments, and the authors' reply. | #The arsenic bacteria paper, the 8 technical comments, and the authors' reply. | ||
#Isaacs, F.J., et al. Precise Manipulation of Chromosomes in Vivo Enables Genome-Wide Codon Replacement. Science 15 July 2011: 333 (6040), 348-353. | #Isaacs, F.J., et al. Precise Manipulation of Chromosomes in Vivo Enables Genome-Wide Codon Replacement. Science 15 July 2011: 333 (6040), 348-353. | ||
#Paige, J.S., et al. RNA Mimics of Green Fluorescent Protein. Science 29 July 2011: 333, 642-646. | #Paige, J.S., et al. RNA Mimics of Green Fluorescent Protein. Science 29 July 2011: 333, 642-646. | ||
#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. | #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 | #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 | ||
#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. | #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. | ||
#Dellomonaco C, Clomburg JM, Miller EN, Gonzalez R. Engineered reversal of the β-oxidation cycle for the synthesis of fuels and chemicals. Nature. 2011 Aug 10. | #Dellomonaco C, Clomburg JM, Miller EN, Gonzalez R. Engineered reversal of the β-oxidation cycle for the synthesis of fuels and chemicals. Nature. 2011 Aug 10. | ||
==Comments on Papers== | ==Comments on Papers== | ||
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==Voting on Papers== | ==Voting on Papers== | ||
*'''Huo et al.''': | *'''Huo et al.''': | ||
*'''Bond-Watts et al.''' and '''Shen et al.''': | *'''Bond-Watts et al.''' and '''Shen et al.''': | ||
*'''Schwanhäusser et al.''': | *'''Schwanhäusser et al.''': | ||
*'''Arsenic + comments''': | *'''Arsenic + comments''': | ||
*'''Grigorya et al.''': | *'''Grigorya et al.''': | ||
*'''Fisher et al.''': | *'''Fisher et al.''': | ||
*'''Marliere et al.''': | *'''Marliere et al.''': | ||
*'''Isaacs et al.''': | *'''Isaacs et al.''': | ||
*'''Paige et al.''': | *'''Paige et al.''': | ||
*'''Poliseno et al.''' and '''Salmena et al''': | *'''Poliseno et al.''' and '''Salmena et al''': | ||
*'''Greiss and Chin''': | *'''Greiss and Chin''': | ||
*'''Porter et al.''': | *'''Porter et al.''': | ||
*'''Poelwijk et al.''': | *'''Poelwijk et al.''': | ||
*'''Dellomonaco et al.''': | *'''Dellomonaco et al.''': | ||
*'''Wang et al.''': | *'''Wang et al.''': | ||
==Past Papers== | ==Past Papers== | ||
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==Aged Out== | ==Aged Out== | ||
#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. Computational Design of Virus-Like Protein Assemblies on Carbon Nanotube Surfaces. Science 332, 1071 (2011);DOI: 10.1126/science.1198841 | |||
#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 | |||
#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. | |||
#Greiss S, and Chin JW. Expanding the Genetic Code of an Animal. J Am Chem Soc. 2011 Aug 8 | |||
#Poelwijk FJ, de Vos MG, Tans SJ. Tradeoffs and Optimality in the Evolution of Gene Regulation. Cell, 5 August 2011 | |||
#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 | |||
#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. | #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. | ||
#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. | #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. |
Revision as of 14:18, 30 September 2011
Next Meeting
Suggested Future PapersNote: The biblio extension is broken. Suggested papers need full references.
Comments on PapersVoting on Papers
Past Papers
Aged Out
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