Stephanopoulos:Literature Reviewed

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Revision as of 15:23, 3 May 2007


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.

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  1. Error fetching PMID 16540542: [Curt1]
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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.

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  1. Error fetching PMID 16122420: [Joel1]
  2. Error fetching PMID 16527929: [Joel2]
  3. Error fetching PMID 16319894: [Joel3]
  4. Error fetching PMID 16455487: [Joel4]
  5. Error fetching PMID 16554755: [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.

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  1. Error fetching PMID 16612386: [Jose1]
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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.

Error fetching PMID 15660163:
  1. Error fetching PMID 15660163: [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.

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  1. Error fetching PMID 16895997: [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.

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  1. Error fetching PMID 16936719: [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.

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  1. Error fetching PMID 12817086: [Christine1]
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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.

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  1. Error fetching PMID 17086191: [Jose4]

8 March 2007: Benjamin L. Wang

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

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  1. Error fetching PMID 17218526: [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.

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  1. Error fetching PMID 17435746: [Jamey2]

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