Stephanopoulos:Literature Reviewed

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(14 Sep 2006: José O. Alemán)
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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.
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.
 +
== 2006 ==
=== 27 April 2006: Curt Fischer ===
=== 27 April 2006: Curt Fischer ===
Curt presented a recent PNAS article <cite>Curt1</cite> 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 <cite>Curt2</cite>, and the other presents laborious and careful analysis carbon utilization of non-thermophilic archaea living in medium-depth oceanic waters<cite>Curt3</cite>.  These bacteria fix inorganic carbon and oxidize nitrogen, and are probably major players in the global nitrogen cycle.
Curt presented a recent PNAS article <cite>Curt1</cite> 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 <cite>Curt2</cite>, and the other presents laborious and careful analysis carbon utilization of non-thermophilic archaea living in medium-depth oceanic waters<cite>Curt3</cite>.  These bacteria fix inorganic carbon and oxidize nitrogen, and are probably major players in the global nitrogen cycle.
Line 40: Line 41:
#Jose3 pmid=15660163
#Jose3 pmid=15660163
</biblio>
</biblio>
 +
=== 21 Sep 2006: Jamey D. Young ===
=== 21 Sep 2006: Jamey D. Young ===
Line 46: Line 48:
<biblio>
<biblio>
#Jamey1 pmid=16895997
#Jamey1 pmid=16895997
 +
</biblio>
 +
 +
 +
=== 12 Oct 2006: Curt Fischer ===
 +
 +
Curt presented a very recent paper from Nature Chemical Biology about isotopically instationary analysis of nitrogen assimilation in E. coli.  Two notable things about this paper were 1) the invention of a technique for rapid metabolome quenching of E. coli while still obtaining some degree of intracellular/extracellular separation, and 2) the agreement of the measured net fluxes with net fluxes predicted by FBA.
 +
<biblio>
 +
#Curt4 pmid=16936719
 +
</biblio>
 +
 +
 +
=== 26 Oct 2006: Christine Santos ===
 +
 +
Christine presented two papers on cannibalism in Bacillus subtilis.  In an effort to delay sporulation under conditions of extreme nutrient deprivation, B. subtilis cells with an activated sporulation regulatory protein, Spo0A, make use of two modes of killing to bring about the cell lysis of genetically identical sister cells and the subsequent release of nutrients.
 +
<biblio>
 +
#Christine1 pmid=12817086
 +
#Christine2 pmid=16469701
 +
</biblio>
 +
 +
 +
=== 30 Nov 2006: José O. Alemán ===
 +
 +
José presented a paper documenting the effects of resveratrol, one of the active compounds in red wine and an effector of caloric restriction, in preventing disease progression associated with a high-calorie diet in mice.
 +
 +
<biblio>
 +
#Jose4 pmid=17086191
 +
</biblio>
 +
 +
== 2007 ==
 +
=== 8 March 2007: Benjamin L. Wang ===
 +
 +
Ben presented a paper describing the use of a microfluidic device to measure transcription factor binding.
 +
 +
<biblio>
 +
#Ben1 pmid=17218526
 +
</biblio>
 +
 +
 +
=== 3 May 2007: Jamey D. Young ===
 +
 +
Jamey presented a paper on reducing photorespiration and improving growth in C<math>_3</math> plants. This was accomplished by introducing the glycolate catabolic pathway from ''E. coli'' into ''A. thaliana''.
 +
 +
<biblio>
 +
#Jamey2 pmid=17435746
 +
</biblio>
 +
 +
 +
=== 13 December 2007: Benjamin L. Wang ===
 +
 +
Ben presented a paper describing a model relating mRNA, protein, enzymatic activity, and flux levels.  The model system used was the glycolytic pathway in Saccharomyces cerevisiae.
 +
 +
<biblio>
 +
#Ben2 pmid=17898166
 +
</biblio>
 +
 +
==2008==
 +
=== 7 February 2008: Curt R. Fischer===
 +
 +
Curt discussed the two high-profile papers from the J. Craig Venter Institute on genome transplantation and genome synthesis.  The lab debated if the popular press's treatment of the two articles was consistent with their actual scientific impact.
 +
<biblio>
 +
#Curt4 pmid=18218864
 +
#Curt5 pmid=17600181
 +
</biblio>
 +
 +
 +
 +
=== 20 March 2008: Mitchell Tai===
 +
 +
Mitchell presented a paper on a method for genome-scale analysis and tracking of library population under selective pressure. The technique, named SCALEs, utilizes microarrays to determine distribution of gene fragements in plasmids in a population. It is useful for determining genes which have beneficial (or deleterious) effects on cell fitness.
 +
 +
<biblio>
 +
#Mitch1 pmid=18093856
 +
#Mitch2 pmid=11997466
 +
</biblio>
 +
 +
=== 11 September 2008: Mitchell Tai===
 +
 +
Mitchell presented two papers relating to future metabolic engineering tasks for biodiesel production: conversion of fatty acids to fatty acid alkyl esters, and secretion of fatty acids/triglycerides. The former is performed using a wax ester synthase/diglyceride acyltransferase enzyme from ''Acinetobacter'' sp. which transesterifies alcohols with acyl-coA. The latter has been found from a knockout of the FAA (acyl-CoA synthetase) enzymes in S. cerevisiae.
 +
 +
<biblio>
 +
#Mitch3 pmid=16946248
 +
#Mitch4 pmid=12501395
</biblio>
</biblio>
<big>'''''back to the [[Stephanopoulos Lab]] home page'''''</big>
<big>'''''back to the [[Stephanopoulos Lab]] home page'''''</big>

Current revision

Contents

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.

2006

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. . pmid:16540542. PubMed HubMed [Curt1]
  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. . pmid:16598256. PubMed HubMed [Curt2]
  3. Ingalls AE, Shah SR, Hansman RL, Aluwihare LI, Santos GM, Druffel ER, and Pearson A. . pmid:16614070. PubMed HubMed [Curt3]
All Medline abstracts: PubMed HubMed


4 May 2006: Joel Forrest 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.

  1. 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. . pmid:16122420. PubMed HubMed [Joel1]
  2. Gresham D, Ruderfer DM, Pratt SC, Schacherer J, Dunham MJ, Botstein D, and Kruglyak L. . pmid:16527929. PubMed HubMed [Joel2]
  3. 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. . pmid:16319894. PubMed HubMed [Joel3]
  4. 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. . pmid:16455487. PubMed HubMed [Joel4]
  5. 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. . pmid:16554755. PubMed HubMed [Joel5]
All Medline abstracts: PubMed HubMed


18 May 2006: José O. Alemán

José gave a brief overview of two papers looking at insulin resistance from a perspective of cellular and animal experiments. The first uses cellular and animal experiments addressing reactive oxygen species' role in insulin resistance, while the second carefully dissects insulin signaling in the liver to tease divergent metabolic control of glucose and lipid metabolism.

  1. Houstis N, Rosen ED, and Lander ES. . pmid:16612386. PubMed HubMed [Jose1]
  2. Taniguchi CM, Kondo T, Sajan M, Luo J, Bronson R, Asano T, Farese R, Cantley LC, and Kahn CR. . pmid:16679292. PubMed HubMed [Jose2]
All Medline abstracts: PubMed HubMed


14 Sep 2006: José O. Alemán

José presented a paper using deuterium and carbon labeling to elucidate the function of a redundant metabolic module for formaldehyde metabolism in Methylobacterium extorquens AM1.

  1. Marx CJ, Van Dien SJ, and Lidstrom ME. . pmid:15660163. PubMed HubMed [Jose3]


21 Sep 2006: Jamey D. Young

Jamey presented a paper from the Nicholson group describing the effects of gut microbes on choline metabolism in the development of fatty liver disease.

  1. Dumas ME, Barton RH, Toye A, Cloarec O, Blancher C, Rothwell A, Fearnside J, Tatoud R, Blanc V, Lindon JC, Mitchell SC, Holmes E, McCarthy MI, Scott J, Gauguier D, and Nicholson JK. . pmid:16895997. PubMed HubMed [Jamey1]


12 Oct 2006: Curt Fischer

Curt presented a very recent paper from Nature Chemical Biology about isotopically instationary analysis of nitrogen assimilation in E. coli. Two notable things about this paper were 1) the invention of a technique for rapid metabolome quenching of E. coli while still obtaining some degree of intracellular/extracellular separation, and 2) the agreement of the measured net fluxes with net fluxes predicted by FBA.

  1. Yuan J, Fowler WU, Kimball E, Lu W, and Rabinowitz JD. . pmid:16936719. PubMed HubMed [Curt4]


26 Oct 2006: Christine Santos

Christine presented two papers on cannibalism in Bacillus subtilis. In an effort to delay sporulation under conditions of extreme nutrient deprivation, B. subtilis cells with an activated sporulation regulatory protein, Spo0A, make use of two modes of killing to bring about the cell lysis of genetically identical sister cells and the subsequent release of nutrients.

  1. González-Pastor JE, Hobbs EC, and Losick R. . pmid:12817086. PubMed HubMed [Christine1]
  2. Ellermeier CD, Hobbs EC, Gonzalez-Pastor JE, and Losick R. . pmid:16469701. PubMed HubMed [Christine2]
All Medline abstracts: PubMed HubMed


30 Nov 2006: José O. Alemán

José presented a paper documenting the effects of resveratrol, one of the active compounds in red wine and an effector of caloric restriction, in preventing disease progression associated with a high-calorie diet in mice.

  1. Baur JA, Pearson KJ, Price NL, Jamieson HA, Lerin C, Kalra A, Prabhu VV, Allard JS, Lopez-Lluch G, Lewis K, Pistell PJ, Poosala S, Becker KG, Boss O, Gwinn D, Wang M, Ramaswamy S, Fishbein KW, Spencer RG, Lakatta EG, Le Couteur D, Shaw RJ, Navas P, Puigserver P, Ingram DK, de Cabo R, and Sinclair DA. . pmid:17086191. PubMed HubMed [Jose4]

2007

8 March 2007: Benjamin L. Wang

Ben presented a paper describing the use of a microfluidic device to measure transcription factor binding.

  1. Maerkl SJ and Quake SR. . pmid:17218526. PubMed HubMed [Ben1]


3 May 2007: Jamey D. Young

Jamey presented a paper on reducing photorespiration and improving growth in C3 plants. This was accomplished by introducing the glycolate catabolic pathway from E. coli into A. thaliana.

  1. Kebeish R, Niessen M, Thiruveedhi K, Bari R, Hirsch HJ, Rosenkranz R, Stäbler N, Schönfeld B, Kreuzaler F, and Peterhänsel C. . pmid:17435746. PubMed HubMed [Jamey2]


13 December 2007: Benjamin L. Wang

Ben presented a paper describing a model relating mRNA, protein, enzymatic activity, and flux levels. The model system used was the glycolytic pathway in Saccharomyces cerevisiae.

  1. Daran-Lapujade P, Rossell S, van Gulik WM, Luttik MA, de Groot MJ, Slijper M, Heck AJ, Daran JM, de Winde JH, Westerhoff HV, Pronk JT, and Bakker BM. . pmid:17898166. PubMed HubMed [Ben2]

2008

7 February 2008: Curt R. Fischer

Curt discussed the two high-profile papers from the J. Craig Venter Institute on genome transplantation and genome synthesis. The lab debated if the popular press's treatment of the two articles was consistent with their actual scientific impact.

  1. Gibson DG, Benders GA, Andrews-Pfannkoch C, Denisova EA, Baden-Tillson H, Zaveri J, Stockwell TB, Brownley A, Thomas DW, Algire MA, Merryman C, Young L, Noskov VN, Glass JI, Venter JC, Hutchison CA 3rd, and Smith HO. . pmid:18218864. PubMed HubMed [Curt4]
  2. Lartigue C, Glass JI, Alperovich N, Pieper R, Parmar PP, Hutchison CA 3rd, Smith HO, and Venter JC. . pmid:17600181. PubMed HubMed [Curt5]
All Medline abstracts: PubMed HubMed


20 March 2008: Mitchell Tai

Mitchell presented a paper on a method for genome-scale analysis and tracking of library population under selective pressure. The technique, named SCALEs, utilizes microarrays to determine distribution of gene fragements in plasmids in a population. It is useful for determining genes which have beneficial (or deleterious) effects on cell fitness.

  1. Bonomo J, Lynch MD, Warnecke T, Price JV, and Gill RT. . pmid:18093856. PubMed HubMed [Mitch1]
  2. Gill RT, Wildt S, Yang YT, Ziesman S, and Stephanopoulos G. . pmid:11997466. PubMed HubMed [Mitch2]
All Medline abstracts: PubMed HubMed

11 September 2008: Mitchell Tai

Mitchell presented two papers relating to future metabolic engineering tasks for biodiesel production: conversion of fatty acids to fatty acid alkyl esters, and secretion of fatty acids/triglycerides. The former is performed using a wax ester synthase/diglyceride acyltransferase enzyme from Acinetobacter sp. which transesterifies alcohols with acyl-coA. The latter has been found from a knockout of the FAA (acyl-CoA synthetase) enzymes in S. cerevisiae.

  1. Kalscheuer R, Stölting T, and Steinbüchel A. . pmid:16946248. PubMed HubMed [Mitch3]
  2. Nojima Y, Kibayashi A, Matsuzaki H, Hatano T, and Fukui S. . pmid:12501395. PubMed HubMed [Mitch4]
All Medline abstracts: PubMed HubMed

back to the Stephanopoulos Lab home page

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