Individual Publication List for Pennsylvania State University
Organized by project

Biochemistry of Psychrophilic Organisms The Environment of Prebiotic Earth: Theoretical Approach Enzymes of Ancient Metabolic Pathways Evolution of Atmospheric O2, Climate and the Terrestrial Biosphere: Approaches from Field-Oriented Geochemical Investigations Evolution of Atmospheric O2, Climate, and the Terrestrial Biosphere: Causes and Consequences of the Diversification and Extinction of Metazoans Microbe-Mineral Interactions Neoproterozoic Variations in Carbon and Sulfur Cycling Paleomicrobiology and the evolution of metabolic pathways in the Archean environment. The Prebiotic Chemistry of Hydrogen Cyanide Timescale for the Early Evolution of Life on Earth: Molecular Evolutionary Approach Whole Genome-Based Phylogenetic Analysis of Free-Living Microorganisms

Biochemistry of Psychrophilic Organisms top

Brenchley, J., & Sheridan, P. (In Press, 2000). Psychrophilic bacteria (Antarctica meltpond) cloning and characterization. Applied and Environmental Microbiology. Sheridan, P.P., & Brenchley, J.E. (2000). Characterization of a salt-tolerant family 42 b-galactosidase from a psychrophilic Antarctic Planococcus isolate. Applied and Environmental Microbiology, 66(6): 2438-2444.

The Environment of Prebiotic Earth: Theoretical Approach top

Kasting J.F., & others. (1999). Signposts of life: Detection of life via remote sensing. In: TPF Report (Terrestrial Planet Finder Report), Chapter 4, (JPL/Caltech/IPAC, MS 100-22). Pasadena, CA: JPL/Caltech/Infrared Processing and Analysis Center. Pavlov, A.A., Kasting, J.F., Brown, L.L., Rages, K.A., & Freedman, R. (2000). Greenhouse warming by CH4 in the atmosphere of early Earth. Journal of Geophysical Research: Planets, 105(5): 11,981-11,990. Pavlov, A.A., Pavlov, A.K., & Kasting, J.F. (1999). Irradiated interplanetary dust particles as a possible solution for the deuterium/hydrogen paradox of Earth's oceans. Journal of Geophysical Research: Planets, 104(12): 30,725-30,728. Schindler, T.L., & Kasting, J.F. (2000). Synthetic spectra of simulated terrestrial atmospheres. Icarus, 145(1): 262-271.

Enzymes of Ancient Metabolic Pathways top

Borup, B, & Ferry. J.G. (2000). O-acetylserine sulfhydrylase from Methanosarcina thermophila. Journal of Bacteriology, 182: 45-50. Smith, K.S., & Ferry, J.G. (1999). A plant-type (b-class) carbonic anhydrase in the thermophilic methanoarchaeon Methanobacterium thermoautotrophicum. Journal of Bacteriology, 181: 6247-6253. Smith, K.S., & Ferry, J.G. (2000). Prokaryotic carbonic anhydrases. FEMS Microbiology Reviews, 682: 1-32. Smith, K.S., Jakubzick, C., Whittam, T.S., & and Ferry, J.G. (1999). Carbonic anhydrase is an ancient enzyme widespread in prokaryotes. Proceedings of the National Academy of Sciences of the United States of America, 96: 15,184-15,189.

Evolution of Atmospheric O2, Climate and the Terrestrial Biosphere: Approaches from Field-Oriented Geochemical Investigations top

Bau, M., Romer, R.L., Lüders, V., & Buekes, N.J. 1999. Pb, O, and C isotopes in silicified Mooidraai dolomite (Transvaal Supergroup, South Africa): Implications for the composition of Paleoproterozoic seawater and 'dating' the increase of oxygen in the Precambrian atmosphere. Earth and Planetary Science Letters 174: 43-57. Bestland, E.A., Hammond, P.E., Blackwell, D.L.S., Retallack, G.J. & Stimac, J. (1999). Geologic framework of the Clarno Unit, John Day Fossil Beds National Monument, central Oregon. Oregon Geology, 61(1): 3-19. Hein, J.R., Koschinsky, A., Bau, M., Manheim, F.T., Kang, J-K., & Roberts, L. 2000. Cobalt-rich ferromanganese crusts in the Pacific. In: Handbook of Marine Mineral Deposits (pp. 239-279). CRC Press. Hurtgen, M.T., Lyons, T.W., Ingall, E.D., & Cruse, A.M. 1999. Anomalous enrichments of iron monosulfide in euxinic marine sediments and the role of H2S in iron sulfide transformations: examples from Effingham Inlet, Orca Basin, and the Black Sea. American Journal of Science, 299: 556-588. Isbell, J.I., Askin, R.A., & Retallack, G.J. (1999). Search for evidence of impact at the Permian-Triassic boundary in Antarctica and Australia: Comment and reply. Geology, 27: 859-860. Kakegawa, T., & Ohmoto, H. 1999. Sulfur isotope evidence for the origin of 3.4 to 3.1 Ga pyrite at the Princeton gold mine, Barberton Greenstone Belt, South Africa. Precambrian Research, 96: 209-224. Kakegawa, T., Kasahara, Y., Hayashi, K-I., & Ohmoto, H. 2000. Sulfur and carbon isotope analyses of the 2.7 Ga Jeerinah Formation, Fortescue Group, Australia. Geochemical Journal, 34: 121-133. Knappe, A., Jarmersted, C.S., Pekdeger, A., Bau, M., & Dulski, P. 1999. Gadolinium in aquatic systems as indicator for sewage water contamination. In: Armannsson (Ed.), Geochemistry of the Earth's Surface. ISBN 90 5809 073 6. Rotterdam: Balkerna. Ohmoto, H., Rasmussen, B., Buick, R. & Holland, H.D. 1999. Redox state of the Archean atmosphere: Evidence from detrital heavy minerals in ca. 3250-2750 Ma sandstones from the Pilbara Craton, Australia: Discussion and reply. Geology, 27(12): 1151-1152. Retallack, G.J. (1999). A Jurassic prehnite vein intruding the Permian-Triassic boundary at Graphite Peak, Antarctica. Antarctic Journal of the United States, 32(5): 5-7. Retallack, G.J. (1999). Carboniferous fossil plants and soils of an early tundra ecosystem. Palaios, 14: 324-336. Retallack, G.J. (1999). Cenozoic spread of grasslands in East Africa. Proceedings of the Oregon Academy of Sciences, 35: 44. Retallack, G.J. (1999). Chemoassays, bioassays and pedoassays of environmental acidification as a selective extinction mechanism at the Cretaceous-Tertiary boundary. Geological Society of America, Abstracts with Programs, 31(7): A-240. Retallack, G.J. (1999). Evolutionary and ecological polarities in Miocene apes. Journal of Vertebrate Paleontology, 19(3): 70A. Retallack, G.J. (1999). Evolutionary polarities [Abstract]. In: Life Patterns (A Workshop on the "biology of form" and its application to our understanding of evolution and the fossil record). Seminar and Workshop of the Colorado University Denver Trackers Research Group, (pp. 117-130). Retallack, G.J. (1999). Mass extinctions: Life's revolutions. In: J.H. Anderson (Ed.), Towards Gondwana Alive (pp. 40-41). Pretoria, South Africa: Gondwana Alive Society. Retallack, G.J. (1999). Paleosols. In: T.P. Jones, & N.P. Rowe (Eds.), Fossil Plants and Spores: Modern Techniques (pp. 214-219). London: The Geological Society. Retallack, G.J. (1999). Paleosols: Traces of past vegetation. In: J.H. Anderson (Ed.), Towards Gondwana Alive (pp. 42-43). Pretoria, South Africa: Gondwana Alive Society. Retallack, G.J. (1999). Permafrost palaeoclimate of Permian palaeosols in the Gerringong volcanics of New South Wales. Australian Journal of Earth Sciences, 46: 11-22. Retallack, G.J. (1999). Post-apocalyptic greenhouse paleoclimate revealed by earliest Triassic paleosols in the Sydney Basin, Australia. Bulletin of the Geological Society of America, 111: 52-70. Retallack, G.J. (2000). Acid rain and the differential survival of birds and dinosaurs at the Cretaceous-Tertiary boundary [Abstract]. Abstracts of the Symposium on Birds and Dinosaurs, Publications in Paleontology, Graves Museum, Florida, 2: 23. Retallack, G.J. (Submitted, 2000). Soils of the Past: An Introduction to Paleopedology (2nd ed.). Oxford: Blackwells. Retallack, G.J., Bestland, E.A., & Fremd, T.J. (2000). Eocene and Oligocene paleosols and environmental change in central Oregon. Geological Society of America, Special Paper, 344: 1-192. Retallack, G.J., & Krull, E.S. (1999). Landscape ecological shift at the Permian-Triassic boundary in Antarctica. Australian Journal of Earth Sciences, 46(4): 786-812. Retallack, G.J., & Krull, E.S. (1999). Neogene paleosols from the Sirius Group, Dominion Range, Antarctica. Antarctic Journal of the United States, 32(5): 10-14. Retallack, G.J., & Krull, E.S. (1999). Permian coprolites from Graphite Peak, Antarctica. Antarctic Journal of the United States, 32(5): 7-9. Retallack, G.J., & Storaasli, M. (1999). Problematic impressions from the Precambrian of Montana [Abstract]. Geological Society of America, Abstracts with Programs, 31(7): A-362.

Evolution of Atmospheric O2, Climate, and the Terrestrial Biosphere: Causes and Consequences of the Diversification and Extinction of Metazoans top

Capo, R.C., & Chadwick, O.A. (1999). Sources of strontium and calcium in desert soil and calcrete. Earth and Planetary Science Letters, 170: 61-72. Capo R.C., Whipkey, C.E., Blachère, J., & Chadwick, O.A. (2000). Pedogenic origin of dolomite in a basaltic weathering profile, Kohala Peninsula, Hawaii. Geology, 28: 271-274. Lasaga, A.C., & Ohmoto, H. (2000). Modeling the evolution of oxygen in the Earth atmosphere [Abstract]. First Astrobiology Science Conference (p. 303), NASA Ames Research Center, Moffett Field, CA. Ohmoto, H. (1999). Lower oxygen limit given by survival of uraninite is as high as 100 PAL [Abstract]. First General Astrobiology Meeting, NASA Ames Research Center, Moffett Field, CA. Ohmoto, H., Rasmussen, B., Buick, R., & Holland, H.D. (1999). Redox state of the Archean atmosphere: Evidence from detrital heavy minerals in ca. 3250-2750 Ma sandstones from the Pilbara Craton, Australia: Discussion and reply. Geology, 27(12): 1151-1152. Ohmoto, H., Watanabe, Y., Yamaguchi, K., Ono, S., Kakegawa, T., Hyashi, K. Naraoka, H., Nedachi, M., & Nedachi, Y. (2000). Geochemical evidence for the early development of an oxygenated atmosphere and terrestrial biomass [Abstract]. First Astrobiology Science Conference (p. 291), NASA Ames Research Center, Moffett Field, CA. Pretti, V.A., Stewart, B.W., & Capo, R.C. (1999). Hydrologic sources for the Owens River system, eastern California: Chemistry and strontium isotope composition of eastern Sierra Nevada stream water [Abstract]. Eos, Transactions of the American Geophysical Union, 80. Retallack, G.J. (1999). Post-apocalyptic greenhouse paleoclimate revealed by earliest Triassic paleosols in the Sydney Basin, Australia. Bulletin of the Geological Society of America, 111: 52-70. Stafford, S.L., Capo, R.C., Stewart, B.W., Macpherson, G.L., & Ohmoto, H. (1999). Micromorphology and geochemistry of an apparent Archean weathering profile, Ontario, Canada [Abstract]. Eos, Transactions of the American Geophysical Union, 80. Stewart, B.W., Capo, R.C., Watanabe, Y., & Ohmoto, H. (1999). Provenance of a 2.6 Ga terrestrial carbonate sequence from the eastern Transvaal region, South Africa [Abstract]. Eos, Transactions of the American Geophysical Union, 80.

Microbe-Mineral Interactions top

Kalinowski, B.E., Liermann, L.J., Brantley, S.L., & Pantano, C.G. (2000). X-ray photoelectron evidence for bacteria-enhanced dissolution of hornblende. Geochimica Cosmochimica Acta, 64: 1331-1343.

Neoproterozoic Variations in Carbon and Sulfur Cycling top

Arthur, M.A. 2000. Volcanic contributions to the carbon and sulfur geochemical cycles and global change. In: Encyclopedia of Volcanoes, (pp. 1045-1056). Academic Press. Kump, L.R., & Arthur, M.A. 1999. Interpreting carbon-isotope excursions: carbonates and organic matter. Chemical Geology, 161: 181-198.

Paleomicrobiology and the evolution of metabolic pathways in the Archean environment. top

House, C.H., Schopf, J.W., McKeegan, K.D., Coath, C.D., Harrison, T.M., & Stetter, K.O. (2000). Carbon isotopic composition of individual Precambrian microfossils. Geology, 28(8): 707-710.

The Prebiotic Chemistry of Hydrogen Cyanide top

Minard, R.D., Hatcher, P.G., Stauffer, E., Kahle, K., & Matthews, C.N. (In Preparation, 2000). Titan N2/CH4 tholin contains HCN polymers: Evidence from TMAH thermochemolysis/GC-MS Analysis. [Will be submitted to: Geochemistry]. Minard, R.D., Hatcher, P.G., Gourley, C.R., & Matthews, C.N. (1998). Structural investigations of hydrogen cyanide polymers: New insights using TMAH thermochemolysis/GC-MS. Origins of Life and Evolution of the Biosphere, 28(4-6): 461-473.

Timescale for the Early Evolution of Life on Earth: Molecular Evolutionary Approach top

Hedges, S.B. (1999). Caught in the act: Forest life encapsulated in amber 20 million years ago can be reassembled. [Review of the book, The Amber Forest: A Reconstruction of a Vanished World]. Nature, 402: 459. Hedges, S.B. (2000). Molecular evidence for the early history of living vertebrates. In: E. Albert (Ed.), Major Events in Early Evolution: Palaeontology, Phylogeny, and Development. London: Taylor & Francis. Hedges, S.B., & Kumar, S. (1999). Divergence times of eutherian mammals. Science, 285: 2031a. Hedges, S.B., & Schweitzer, M.H. (1999). Molecular paleontology. In: Encyclopedia of Paleontology, (pp. 752-754). O'Brien, S.J., Eisenberg, J.F., Miyamoto, M., Hedges, S.B., Kumar, S., Wilson, D.E., et al. (1999). Genome maps 10. Comparative genomics. Mammalian radiations. Wall chart (phylogenetic tree). Science, 286: 463-478. Takahashi, K., & Nei, M. (In Press, 2000). Efficiencies of fast algorithms of phylogenetic inference under the criteria of maximum parsimony, minimum evolution, and maximum likelihood when a large number of sequences are used. Molecular Biology and Evolution. Van Tuinen, M., Sibley, C.G., & Hedges, S.B. (2000). The early history of modern birds inferred from DNA sequences of nuclear and mitochondrial ribosomal genes. Molecular Biology and Evolution, 17: 451-457.

Whole Genome-Based Phylogenetic Analysis of Free-Living Microorganisms top

Fitz-Gibbon, S.T., & House, C.H. (1999). Whole genome-based phylogenetic analysis of free-living microorganisms. Nucleic Acids Research, 27(21): 4218-4222.