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Caltech Geobiology

A weekly group discussing geobiology-related journal articles.

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  • Discussion Papers (23)
  • Related Papers (14)
  • Suggested Papers for Discussion (40)

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Anne Dekas
Rachel Poretsky
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  • Woody Fischer (Caltech) is following 3 new articles in Suggested Papers for Discussion
    Geodynamo, Solar Wind, and Magnetopause 3.4 to 3.45 Billion Years Ago. Tarduno J. A. (2010) Science.
    Energized outer membrane and spatial separation of metabolic processes in the hyperthermophilic Archaeon Ignicoccus hospitalis. Kuper U. (2010) Proceedings of the National Academy of Sciences.
    The Chicxulub Asteroid Impact and Mass Extinction at the Cretaceous-Paleogene Boundary. Schulte P. (2010) Science.
    March 7, 2010
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  • Woody Fischer (Caltech) is following 1 new article in Suggested Papers for Discussion
    EPR, ENDOR, and HYSCORE Study of the Structure and the Stability of Vanadyl−Porphyrin Complexes Encapsulated in Silica: Potential Paramagnetic Biomarkers for the Origin of Life. Gourier Didier (2010) J. Phys. Chem. B.
    February 28, 2010
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  • Woody Fischer (Caltech) is following 1 new article in Discussion Papers
    Redox Stabilization of the Atmosphere and Oceans by Phosphorus-Limited Marine Productivity. Van Cappellen P. (1996) Science.
    February 26, 2010
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  • Anne Dekas (Caltech)

    FYI, the first author of a paper we read several weeks ago is giving a talk in the Biology department about that study today. Here are the details: Thursday, February 25, 2010, General Biology Seminar, 4:00 PM, Norman Davidson Hall, 119 Kerckhoff, Jeffrey Barrick ,Department of Microbiology and Molecular Genetics
    Michigan State University "Genome dynamics during a 20-year Evolution Experiment with E. coli"

    February 25, 2010
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  • Woody Fischer (Caltech) is following 1 new article in Discussion Papers
    A new model for Proterozoic ocean chemistry. Canfield D. E. (1998) Nature.
    February 24, 2010
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  • Woody Fischer (Caltech) is following 1 new article in Discussion Papers
    Flow enhances photosynthesis in marine benthic autotrophs by increasing the efflux of oxygen from the organism to the water. Mass T. (2010) Proceedings of the National Academy of Sciences.
    February 14, 2010
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  • Woody Fischer (Caltech) is following 2 new articles in Suggested Papers for Discussion
    Darwinian Evolution of Prions in Cell Culture. Li J. (2010) Science.
    Predicting the reaction coordinates of millisecond light-induced conformational changes in photoactive yellow protein. Vreede J. (2010) Proceedings of the National Academy of Sciences.
    February 14, 2010
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  • Jonathan Wilson (Caltech) is following 1 new article in Suggested Papers for Discussion
    Common functions for diverse small RNAs of land plants. Axtell MJ (2007) Plant Cell.
    February 5, 2010
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  • Anne Dekas (Caltech) is following 1 new article in Discussion Papers
    Respiratory Mechanisms and the Metazoan Fossil Record. RAFF RUDOLF A. (1970) Nature.
    February 3, 2010
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  • Anne Dekas (Caltech) is following 1 new article in Discussion Papers
    Was the Archaean biosphere upside down?. Walker James C. G. (1987) Nature.
    January 27, 2010
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  • Anne Dekas (Caltech) created an event
    Journal Article Discussion
    Thursday, December 17, 2009 - 8:00am at Chandler Dining Hall

    Sorry for the late notice, but yes, there will be breakfast tomorrow at journal club! We have a special pre-winter break breakfast, so be there a few minutes early to take advantage.

    A "silent" polymorphism in the MDR1 gene changes substrate specificity. Kimchi-Sarfaty C (2007) Science.
    December 16, 2009
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  • Woody Fischer (Caltech) is following 1 new article in Discussion Papers
    A "silent" polymorphism in the MDR1 gene changes substrate specificity. Kimchi-Sarfaty C (2007) Science.
    December 14, 2009
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  • Anne Dekas (Caltech) created an event
    Journal Article Discussion
    Thursday, December 10, 2009 - 8:00am at Chandler Dining Hall
    Did an ancient chlamydial endosymbiosis facilitate the establishment of primary plastids?. Huang Jinling (2007) Genome Biol.
    December 7, 2009
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  • Jonathan Wilson (Caltech) is following 1 new article in Suggested Papers for Discussion
    Contrasting evolutionary dynamics between angiosperm and mammalian genomes. Kejnovsky Eduard (2009) Trends in Ecology & Evolution.
    December 3, 2009
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  • Anne Dekas (Caltech) created an event
    Journal Article Discussion
    Thursday, December 3, 2009 - 8:00am at Chandler Dining Hall

    We will have breakfast this week.

    Gene Transfer and Diversification of Microbial Eukaryotes. Andersson Jan O. (2009) Annu. Rev. Microbiol..
    November 29, 2009
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  • Woody Fischer (Caltech) is following 1 new article in Discussion Papers
    Gene Transfer and Diversification of Microbial Eukaryotes. Andersson Jan O. (2009) Annu. Rev. Microbiol..
    November 29, 2009
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  • Jonathan Wilson (Caltech) is following 1 new article in Suggested Papers for Discussion
    Mutation load and rapid adaptation favour outcrossing over self-fertilization. Morran Levi T (2009) Nature.
    November 23, 2009
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  • Woody Fischer (Caltech) is following 1 new article in Discussion Papers
    Redox Redux. LYONS T. W. (2009) Geobiology.
    November 17, 2009
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  • Woody Fischer (Caltech) is following 1 new article in Suggested Papers for Discussion
    Photosynthesis in the Open Ocean. Zehr J. P. (2009) Science.
    November 17, 2009
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  • Woody Fischer (Caltech) is following 1 new article in Suggested Papers for Discussion
    Coupled predator-prey oscillations in a chaotic food web. Benincà Elisa (2009) Ecology Letters.
    November 12, 2009
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  • Anne Dekas (Caltech) created an event
    Journal Article Discussion
    Thursday, November 12, 2009 - 8:00am at Chandler Dining Hall

    No breakfast this week.

    Experimental evolution of bet hedging. Beaumont HJ (2009) Nature.
    November 9, 2009
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  • Woody Fischer (Caltech) is following 1 new article in Discussion Papers
    Experimental evolution of bet hedging. Beaumont HJ (2009) Nature.
    November 9, 2009
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  • Anne Dekas (Caltech)

    I'm still thinking about how fitness was measured in the paper we discussed morning (Barrick et al 2009). I still haven't found an explanation for how they did it, but I did read an interesting approach for measuring fitness in the paper from Chris Marx's lab I just posted. They actually pitted two strains against each other in the same culture to see which could out compete the other: "Briefly, after one round of acclimation, test strains and a reference strain expressing the yellow fluorescent protein Venus were mixed by a 1:1 volume ratio, diluted 1:64 into 9.6 ml of fresh media which were incubated under the conditions described above. The ratios of non-fluorescent cells in mixed populations were measured by passing population sample ... read more

    November 5, 2009
    How much variance exists in the kinetic parameters for growth curves? - Woody Fischer (Caltech) November 9, 2009 Comment deleted
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  • Jonathan Wilson (Caltech) is following 1 new article in Related Papers
    Evolution of Animal Pollination. Ollerton J. (2009) Science.
    November 6, 2009
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  • Jonathan Wilson (Caltech) is following 1 new article in Suggested Papers for Discussion
    A Probable Pollination Mode Before Angiosperms: Eurasian, Long-Proboscid Scorpionflies. Ren D. (2009) Science.
    November 6, 2009
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  • Abigail Green (Caltech) is following 1 new article in Suggested Papers for Discussion
    Experimental evolution of bet hedging. Beaumont HJ (2009) Nature.
    November 5, 2009
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  • Anne Dekas (Caltech) is following 1 new article in Related Papers
    Fast Growth Increases the Selective Advantage of a Mutation Arising Recurrently during Evolution under Metal Limitation. Chou Hsin-Hung (2009) PLoS Genet.
    November 5, 2009
    From the author's summary: "Effects of mutations can change under different genetic backgrounds or environmental factors, also known as epistasis and genotype-by-environment interactions (G×E), respectively. Though epistasis and G×E are traditionally treated as distinct phenomena, our study of a beneficial mutation highlights their commonality." - Anne Dekas (Caltech) November 5, 2009 Comment deleted
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  • Jonathan Wilson (Caltech) is following 1 new article in Related Papers
    A "silent" polymorphism in the MDR1 gene changes substrate specificity. Kimchi-Sarfaty C (2007) Science.
    November 5, 2009
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  • Anne Dekas (Caltech) created an event
    Journal Article Discussion
    Thursday, November 5, 2009 - 8:00am at Chandler Dining Hall

    This week we will discuss a paper comparing six E. coli genomes sampled during a 40,000 generation (20 year!) laboratory culture, offering a unique opportunity to investigate genomic evolution and organismal adaptation.

    We will have bagels for breakfast courtesy of the GSC.

    Genome evolution and adaptation in a long-term experiment with Escherichia coli. Barrick Jeffrey E (2009) Nature.
    October 30, 2009
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  • Anne Dekas (Caltech) is following 1 new article in Discussion Papers
    Genome evolution and adaptation in a long-term experiment with Escherichia coli. Barrick Jeffrey E (2009) Nature.
    October 30, 2009
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