20.109(F08): Mod 2 Day 6 Journal Club I

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20.109(F08): Laboratory Fundamentals of Biological Engineering

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The list of papers below is provided as a guideline for the types of papers that might be relevant for your presentation. You will notice that the papers fall roughly into two categories--protein protein interactions and chromatin remodeling.

Journal club will be held in 16-336 from 1-5 PM on Thursday Oct 23rd/Friday Oct 24th.

You are not limited to the following list of primary research articles. The list is provided simply to give you an idea of the kinds of subjects that could make suitable presentations for the class. Search pubmed yourself to find articles of interest to you. Once you have decided on a paper for your presentation, please email it to nkuldell or astachow AT mit DOT edu, and also "reserve" it by putting your (initials/lab section/team color) next to the listing here. As you prepare your talk be sure to follow the specific guidelines for oral presentations in this class.

For visibility, please use the following format to sign up if possible, substituting in your own initials and team colour: [BE/WF/Purple]. Thanks!

Probing Protein Protein Interactions

  1. GST fusion proteins, e.g. Gueller S et al. "Adaptor protein Lnk associates with Y568 in c-Kit" Biochem J. (2008) doi:10.1042/BJ20080102
  2. Co-immunoprecipitation, e.g. Ozbay T, and Nahta R. "A novel unidirectional cross-talk from the insulin-like growth factor-I receptor to leptin receptor in human breast cancer cells" Mol Cancer Res(2008) 6:1052-8. PMID: 18515755[SL/TR/Orange]
  3. Chemical crosslinking, e.g. Wirschell M, et al. "Building a radial spoke: flagellar radial spoke protein 3 (RSP3) is a dimer" Cell Motil Cytoskeleton (2008) 65:238-48 PMID: 18157907 [HA/WF/Blue]
  4. Yeast two hybrid, e.g. Dutta S, et. al. "High-throughput Analysis of the Protein Sequence-Stability Landscape using a Quantitative Yeast Surface Two-hybrid System and Fragment Reconstitution" J Mol Biol. 2008 Jul 22.PMID: 18674545, or e.g. Fields S, and Song O."A novel genetic system to detect protein-protein interactions" Nature 1989 Jul 20;340(6230):245-6.PMID: 2547163
  5. Phage display, e.g. Lidqvist M et al. "Phage display for site-specific immunization and characterization of high-risk human papillomavirus specific E7 monoclonal antibodies"J Immunol Methods. 2008 Jul 9.PMID: 18606164 (JIL, T/R, Orange)
  6. Genetic, e.g. Kaplan CD et al. "The RNA polymerase II trigger loop functions in substrate selection and is directly targeted by alpha-amanitin" Mol Cell. 2008 Jun 6;30(5):547-56.PMID: 18538653
  7. FRET, e.g. Fretwell JF et al. "Characterization of a randomized FRET library for protease specificity determination." Mol Biosyst. 2008 Aug;4(8):862-70. [[PMID: 18633488]
  8. GFP-PRIM, e.g. De Angelis DA et al. "PRIM: proximity imaging of green fluorescent protein-tagged polypeptides." Proc Natl Acad Sci U S A. 1998 Oct 13;95(21):12312-6. PMID: 9770483 [YL/WF/Purple]
  9. Mass spec, e.g. Moser K and White FM. "Phosphoproteomic analysis of rat liver by high capacity IMAC and LC-MS/MS." J Proteome Res. 2006 Jan;5(1):98-104. PMID: 16396499
  10. TAP, e.g. Panigrahi AK et al. "Mitochondrial complexes in Trypanosoma brucei: a novel complex and a unique oxidoreductase complex." Mol Cell Proteomics. 2008 Mar;7(3):534-45.PMID: 18073385
  11. ScFV engineering, e.g. Fan CY et al."Production of multivalent protein binders using a self-trimerizing collagen-like peptide scaffold." FASEB J. 2008 PMID: 18635738 [EL/WF/GREEN]'
  12. Computational approaches, e.g. Mewes HW et al. "MIPS: analysis and annotation of genome information in 2007." Nucleic Acids Res. (2008) Database issue:D196-201. PMID: 18158298

Chromatin dynamics and remodeling complexes

  1. Ma J et al. "Unconventional Genomic Architecture in the Budding Yeast Saccharomyces cerevisiae Masks the Nested Antisense Gene NAG1" Eukaryotic Cell(2008) 7(8): 1289-1298 doi:10.1128/EC.00053-08
  2. Monahan BJ et al. "Fission yeast SWI/SNF and RSC complexes show compositional and functional differences from budding yeast" Nature Structural & Molecular Biology(2008) 15, 873 - 880 doi:10.1038/nsmb.1452
  3. Dion MF et al. "Dynamics of Replication-Independent Histone Turnover in Budding Yeast" Science (2007) 315(5817):1405 - 1408 doi: 10.1126/science.1134053 [SC/TR/Red]
  4. Laprade L et al. "Characterization of New Spt3 and TATA-Binding Protein Mutants of Saccharomyces cerevisiae: Spt3–TBP Allele-Specific Interactions and Bypass of Spt8" Genetics(2007)177: 2007-2017 doi:10.1534/genetics.107.081976
  5. Zhang L et al. "Spn1 regulates the recruitment of Spt6 and the Swi/Snf complex during transcriptional activation by RNA polymerase II."Mol Cell Biol. (2008) 28(4):1393-403. PMID: 18086892
  6. Dobi KC and Winston F. " Analysis of transcriptional activation at a distance in Saccharomyces cerevisiae." Mol Cell Biol. (2007) 27(15):5575-86. PMID: 17526727[PW/TR/Purple]
  7. Martens JA et al. "Regulation of an intergenic transcript controls adjacent gene transcription in Saccharomyces cerevisiae."Genes Dev. (2005) 19(22):2695-704. PMID: 16291644
  8. Hoke SM et al. "Systematic genetic array analysis links the Saccharomyces cerevisiae SAGA/SLIK and NuA4 component Tra1 to multiple cellular processes."BMC Genet. (2008) Jul 10;9:46.PMID: 18616809
  9. Lemieux K et al. "Variant histone H2A.Z, but not the HMG proteins Nhp6a/b, is essential for the recruitment of Swi/Snf, Mediator, and SAGA to the yeast GAL1 UAS(G)." Biochem Biophys Res Commun. (2008)369(4):1103-7. PMID: 18331823
  10. Adkins MW et al. "Chromatin disassembly from the PHO5 promoter is essential for the recruitment of the general transcription machinery and coactivators."Mol Cell Biol. (2007) 27(18):6372-82.PMID: 17620413[JW/WF/Blue]
  11. Koehler RN et al. "Activation of the ADE genes requires the chromatin remodeling complexes SAGA and SWI/SNF." Eukaryot Cell. (2007) 6(8):1474-85. PMID: 17573544
  12. Roberts GG and Hudson AP. "Transcriptome profiling of Saccharomyces cerevisiae during a transition from fermentative to glycerol-based respiratory growth reveals extensive metabolic and structural remodeling." Mol Genet Genomics. (2006) 276(2):170-86. PMID: 16741729
  13. Mujtaba S et al. "Epigenetic transcriptional repression of cellular genes by a viral SET protein" Nat Cell Biol. (2008) 10(9):1114 - 1122 doi:10.1038/ncb1772 [MY, T/R, Green]
  14. Dechassa ML et al. "Architecture of the SWI/SNF-Nucleosome Complex" Molecular and Cellular Biology (2008) 28(19):6010-6021 doi:10.1128/MCB.00693-08