Smolke:Journal Club

=Next Meeting=
 * When: July 11, 2011, 2pm
 * Where: Y2E2 270
 * Paper: Saito H, Fujita Y, Kashida S, Hayashi K, Inoue T. Synthetic human cell fate regulation by protein-driven RNA switches. Nat Commun. 2011 Jan 18;2:160.
 * Moderator: Ryan

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


 * 1) 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.
 * 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) 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
 * 4) 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.
 * 5) The arsenic bacteria paper, the 8 technical comments, and the authors' reply.
 * 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
 * 7) 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
 * 8) 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.
 * 9) Xie Z., Liu S.J., Bleris L. and Benenson Y. Logic integration of mRNA signals by an RNAi-based molecular computer. Nucleic Acids Research 2010 38, 2692-2701. and Leisner M., Bleris L., Lohmueller J., Xie Z. and Benenson Y. Rationally designed logic integration of regulatory signals in mammalian cells. Nature Nanotechnology 2010 5(9), 666-670.

Voting on Papers

 * Huo et al.:
 * Bond-Watts et al. and Shen et al.:
 * Schwanhäusser et al.:
 * Arsenic + comments:
 * Fisher et al.:
 * Marliere et al.:

Past Papers

 * 1) 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
 * 2) Esvelt KM, Carlson JC, Liu DR. A system for the continuous directed evolution of biomolecules. Nature. 2011.
 * 3) schirmer pmid=20671186
 * 4) sinha pmid=20453864
 * 5) neumann pmid=20154731
 * 6) drinnenberg pmid=19745116
 * 7) dueber pmid=19648908
 * 8) wang pmid=19633652
 * 9) yu pmid=19079053
 * 10) lincoln pmid=19131595
 * 11) lam pmid=19234448
 * 12) nevozhay pmid=19279212

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 pmid=14726590
 * 2) antonczak pmid=19666472
 * 3) zhou pmid=20175178
 * 4) to pmid=20185727
 * 5) jones pmid=19265475
 * 6) ellis pmid=19377462
 * 7) liu pmid=19416889
 * 8) burns pmid=19589923
 * 9) friedland pmid=19478183
 * 10) mitchell pmid=19536156
 * 11) kudla pmid=19359587
 * 12) ray pmid=19098893
 * 13) ranguphan pmid=19151732
 * 14) han pmid=19135890
 * 15) fung pmid=15875027
 * 16) cantone pmid=19327819
 * 17) kempe pmid=19359021
 * 18) tokuriki pmid=19494908
 * 19) eldar pmid=19578359