Stephanopoulos:Literature Reviewed

Literature Reviewed

The purpose of this page is to post the recent articles that we in the Stephanopoulos group review in our nearly-weekly literature review presentations. Sometimes the presenter focuses on a particular paper, and sometimes the roughly one-hour talk gives a brief overview of an important series of related papers.

27 April 2006: Curt Fischer

Curt presented a recent PNAS article [1] which explicated a newly-discovered operon in E. coli. This operon encodes a previously unreported pathway for uracil degradation, which ends in the excretion of 3-hydroxypropionic acid in the medium. He also briefly mentioned two other recent high-profile papers on nitrogen metabolism--one reported the genome sequence of a anaerobic ammonium oxidizing bacterium and hypthesized the full structure of this metabolic pathway [2], and the other presents laborious and careful analysis carbon utilization of non-thermophilic archaea living in medium-depth oceanic waters[3]. These bacteria fix inorganic carbon and oxidize nitrogen, and are probably major players in the global nitrogen cycle.

1. Loh KD, Gyaneshwar P, Markenscoff Papadimitriou E, Fong R, Kim KS, Parales R, Zhou Z, Inwood W, and Kustu S. A previously undescribed pathway for pyrimidine catabolism. Proc Natl Acad Sci U S A. 2006 Mar 28;103(13):5114-9. DOI:10.1073/pnas.0600521103 |
2. Strous M, Pelletier E, Mangenot S, Rattei T, Lehner A, Taylor MW, Horn M, Daims H, Bartol-Mavel D, Wincker P, Barbe V, Fonknechten N, Vallenet D, Segurens B, Schenowitz-Truong C, Médigue C, Collingro A, Snel B, Dutilh BE, Op den Camp HJ, van der Drift C, Cirpus I, van de Pas-Schoonen KT, Harhangi HR, van Niftrik L, Schmid M, Keltjens J, van de Vossenberg J, Kartal B, Meier H, Frishman D, Huynen MA, Mewes HW, Weissenbach J, Jetten MS, Wagner M, and Le Paslier D. Deciphering the evolution and metabolism of an anammox bacterium from a community genome. Nature. 2006 Apr 6;440(7085):790-4. DOI:10.1038/nature04647 |
3. Ingalls AE, Shah SR, Hansman RL, Aluwihare LI, Santos GM, Druffel ER, and Pearson A. Quantifying archaeal community autotrophy in the mesopelagic ocean using natural radiocarbon. Proc Natl Acad Sci U S A. 2006 Apr 25;103(17):6442-7. DOI:10.1073/pnas.0510157103 |

4 May 2006: Joel Moxley

Joel gave an excellent overview of several landmark papers about new tools for high-throughput data collection in systems biology. The papers were made possible by advances in tiling DNA microarrays, protein arrays, and automated yeast transformation and colony characterization.

4. Pokholok DK, Harbison CT, Levine S, Cole M, Hannett NM, Lee TI, Bell GW, Walker K, Rolfe PA, Herbolsheimer E, Zeitlinger J, Lewitter F, Gifford DK, and Young RA. Genome-wide map of nucleosome acetylation and methylation in yeast. Cell. 2005 Aug 26;122(4):517-27. DOI:10.1016/j.cell.2005.06.026 |
5. Gresham D, Ruderfer DM, Pratt SC, Schacherer J, Dunham MJ, Botstein D, and Kruglyak L. Genome-wide detection of polymorphisms at nucleotide resolution with a single DNA microarray. Science. 2006 Mar 31;311(5769):1932-6. DOI:10.1126/science.1123726 |
6. Ptacek J, Devgan G, Michaud G, Zhu H, Zhu X, Fasolo J, Guo H, Jona G, Breitkreutz A, Sopko R, McCartney RR, Schmidt MC, Rachidi N, Lee SJ, Mah AS, Meng L, Stark MJ, Stern DF, De Virgilio C, Tyers M, Andrews B, Gerstein M, Schweitzer B, Predki PF, and Snyder M. Global analysis of protein phosphorylation in yeast. Nature. 2005 Dec 1;438(7068):679-84. DOI:10.1038/nature04187 |
7. Sopko R, Huang D, Preston N, Chua G, Papp B, Kafadar K, Snyder M, Oliver SG, Cyert M, Hughes TR, Boone C, and Andrews B. Mapping pathways and phenotypes by systematic gene overexpression. Mol Cell. 2006 Feb 3;21(3):319-30. DOI:10.1016/j.molcel.2005.12.011 |
8. Krogan NJ, Cagney G, Yu H, Zhong G, Guo X, Ignatchenko A, Li J, Pu S, Datta N, Tikuisis AP, Punna T, Peregrín-Alvarez JM, Shales M, Zhang X, Davey M, Robinson MD, Paccanaro A, Bray JE, Sheung A, Beattie B, Richards DP, Canadien V, Lalev A, Mena F, Wong P, Starostine A, Canete MM, Vlasblom J, Wu S, Orsi C, Collins SR, Chandran S, Haw R, Rilstone JJ, Gandi K, Thompson NJ, Musso G, St Onge P, Ghanny S, Lam MH, Butland G, Altaf-Ul AM, Kanaya S, Shilatifard A, O'Shea E, Weissman JS, Ingles CJ, Hughes TR, Parkinson J, Gerstein M, Wodak SJ, Emili A, and Greenblatt JF. Global landscape of protein complexes in the yeast Saccharomyces cerevisiae. Nature. 2006 Mar 30;440(7084):637-43. DOI:10.1038/nature04670 |

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