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 Curt1 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 Curt2, and the other presents laborious and careful analysis carbon utilization of non-thermophilic archaea living in medium-depth oceanic waters Curt3. These bacteria fix inorganic carbon and oxidize nitrogen, and are probably major players in the global nitrogen cycle.


 * 1) Curt1 pmid=16540542
 * 2) Curt2 pmid=16598256
 * 3) Curt3 pmid=16614070

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) Joel1 pmid=16122420
 * 2) Joel2 pmid=16527929
 * 3) Joel3 pmid=16319894
 * 4) Joel4 pmid=16455487
 * 5) Joel5 pmid=16554755

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) Jose1 pmid=16612386
 * 2) Jose2 pmid=16679292

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) Jose3 pmid=15660163

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) Jamey1 pmid=16895997

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) Curt4 pmid=16936719

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) Christine1 pmid=12817086
 * 2) Christine2 pmid=16469701

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) Jose4 pmid=17086191

8 March 2007: Benjamin L. Wang
Ben presented a paper describing the use of a microfluidic device to measure transcription factor binding.


 * 1) Ben1 pmid=17218526

3 May 2007: Jamey D. Young
Jamey presented a paper on reducing photorespiration and improving growth in C$$_3$$ plants. This was accomplished by introducing the glycolate catabolic pathway from E. coli into A. thaliana.


 * 1) Jamey2 pmid=17435746

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) Ben2 pmid=17898166

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) Curt4 pmid=18218864
 * 2) Curt5 pmid=17600181

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) Mitch1 pmid=18093856
 * 2) Mitch2 pmid=11997466

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) Mitch3 pmid=16946248
 * 2) Mitch4 pmid=12501395

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