Individual Publication List for Ames Research Center
Organized by project

Chemical Building Blocks Early Metabolic Pathways Early Microbial Ecosystems: Modern Analogs Habitable Planets

Chemical Building Blocks top

Allamandola, L.J., Bernstein, M.P., Sandford, S.A., & Walker, R. (1999). Evolution of interstellar ices. Space Science Reviews, 90: 219-232. Allamandola, L.J., Bernstein, M.P., Sandford, S.A., & Walker R.M. (1999). Evolution of interstellar ices. In: K. Altwegg, P. Ehrenfreund, J. Geiss, & H. Rickman, (Eds.). Composition and Origin of Cometary Material, International Space Science Institute Book Series, Vol 8, (pp. 219-232). Dordrecht: Kluwer Academic Publishers. Allamandola, L.J., Hudgins, D.M., & Sandford, S.A. (1999). Modeling the unidentified infrared emission with combinations of polycyclic aromatic hydrocarbons. Astrophysical Journal (Letters), 511: L115-L119. Becker, L., Bunch, T.E., & Allamandola, L.J. (1999). C60, C70 and the higher fullerenes (C100 to C400) in the Allende meteorite. Nature, 400: 227-228. Bernstein, M.P., & Sandford, S.A. (1999). Variations in the strength of the infrared forbidden 2328.2 cm-1 fundamental of solid N2 in binary mixtures. Spectrochimica Acta. Part A, 55: 2455-2466. Bernstein, M.P., Sandford, S.A., & Allamandola, L.J. (1999). Life's far-flung raw materials. Scientific American, 281(1): 42-49. Bernstein, M.P., Sandford, S.A., Allamandola, L.J., Gillette, J.S., Clemett, S.J., & Zare, R.N. (1999). UV irradiation of polycyclic aromatic hydrocarbons in ices: Production of alcohols, quinones, and ethers. Science, 283: 1135-1138. Dworkin, J.P., Sandford, S.A., Allamandola, L.J., Deamer, D.W., Gilette, J.S., & Zare, R.N. (2000). Large molecule and membrane production from simulations of cometary ice [Abstract]. First Astrobiology Science Conference, NASA Ames Research Center, Moffett Field, CA.

Early Metabolic Pathways top

Brown, L.S., Needleman, R., & Lanyi, J.K. (2000). Origins of deuterium kinetic isotope effects on the proton transfers of the bacteriorhodopsin photocycle. Biochemistry, 39: 938-945. Chipot, C., Maigret, B., & Pohorille, A. (1999). Early events in the folding of an amphipatic peptide: a multinanosecond molecular dynamics study. Proteins: Structure, Function, and Genetics, 36: 383-399. Cho, G., Wilson, D.W., Keefe, A.D., Liu, R., & Szostak, J.W. (2000). Constructing high complexity synthetic libraries of long ORFs using in vitro selection. Journal of Molecular Biology, 297: 309-319. Chon, Y.-S., Kandori, H., Sasaki, J., Lanyi, J. K., Needleman, R., & Maeda, A. (1999). Existence of two L photointermediates of halorhodopsin from Halobacterium salinarum, differing in their protein and water FTIR bands. Biochemistry, 38(29): 9449-9455. Colombano, S.P., New, M.H., Pohorille, A., Scargle, J., Stassinopoulos, D., Pearson, M., & J. Warren. (2000, February). Evolutionary cell computing: From protocells to self-organized computing [Abstract]. Proceedings of the Computational Aerosciences Workshop, NASA Ames Research Center, Moffett Field, CA. Deamer, D.W., & Chakrabarti, A. (1999). The first living organisms: In the light or in the dark? ChemTracts, 12(6): 453-467. Des Marais, D.J., Walter, M.R., Fautin, D.G., Futuyma, D.J., & James, F.C. (1999). Astrobiology: Exploring the origins, evolution and distribution of life in the universe. Annual Review of Ecology and Systematics, 30: 397-420. Dioumaev, A.K., Brown, L.S., Needleman R., & Lanyi, J.K. (1999). Fourier transform infrared spectra of a late intermediate of the bacteriorhodopsin photocycle suggest transient protonation of Asp-212. Biochemistry, 38(31): 10,070-10,078. Haith, G.L., Colombano, S.P., Lohn, J.D., Stassinopoulos, D. (1999). Coevolution for problem simplification. In: W. Banzhaf, et al. (Eds.), Proceedings of the Genetic and Evolutionary Computation Conference (pp. 244-251). San Francisco, CA: Morgan Kaufmann Publishers. Kandori, H., Kinoshita, N., Yamazaki, Y., Maeda, A., Shichida, Y., Needleman, R., Lanyi, J.K., Bizounok, M., Herzfeld, J., Raap, J., & Lugtenburg, J. (1999). Structural change of threonine 89 upon photoisomerization in bacteriorhodopsin as revealed by polarized FTIR spectroscopy. Biochemistry, 38: 9676-9683. Kandori, H., Kinoshita, N., Yamazaki, Y., Maeda, A., Shichida, Y., Needleman, R., Lanyi, J.K., Bizounok, M., Herzfeld, J., Raap, J., & Lugtenburg, J. (2000). Local and distant protein structural changes on photoisomerization of the retinal in bacteriorhodopsin. Proceedings of the National Academy of Sciences of the United States of America, 97: 4643-4648. Keefe, A.D., Szostak, J.W. (In Press, 2000). Protein selection using mRNA display. Current Protocols in Molecular Biology. Lanyi, J. K. (1999). Progress toward an explicit mechanistic model for the light-driven pump, bacteriorhodopsin. FEBS Letters, 464: 103-107. Lohn, J. D., Colombano, S. P., Haith, G. L., & Stassinopoulos, D. (2000). A parallel genetic algorithm for automated electronic circuit design [Abstract]. Proceedings of the Computational Aerosciences Workshop, NASA Ames Research Center, Moffett Field, CA. Lohn, J.D., Haith, G.L., Colombano, S.P., & Stassinopoulos, D. (1999). A comparison of dynamic fitness schedules for evolutionary design of amplifiers. In: A. Stoica, D. Keymeulen, & J. Lohn (Eds.), Proceedings of the First NASA/DoD Workshop on Evolvable Hardware (pp. 87-92). Los Alamitos, CA: IEEE Computer Society Press. Lohn, J.D., Haith, G.L., Colombano, S.P., & Stassinopoulos, D. (2000). Towards evolving electronic circuits for autonomous space applications [Abstract]. Proceedings of the 2000 IEEE Aerospace Conference, Big Sky, MT. Luecke, H., Schobert, B., Richter, J., Cartailler, P., & Lanyi, J.K. (1999). Structure of bacteriorhodopsin at 1.55 angstrom resolution. Journal of Molecular Biology, 291(4): 899-911. Luecke, H., Schobert, B., Richter, J., Cartailler P., & Lanyi, J.K. (1999). Structural changes in bacteriorhodopsin at 2 angstrom resolution. Science, 286: 255-260. Monnard, P-A., & Deamer, D.W. (1999, July). Transcription of liposome encapsulated DNA: A model for prebiotic replication of genetic material [Abstract]. International Society for the Study of the Origin of Life (ISSOL) Congress. Monnard, P.A., & Deamer, D. (In Press, 2000). Nutrient uptake by protocells: A liposome model system. Origins of Life and Evolution of the Biosphere. New, M.H., & Pohorille, A. (2000). An inherited efficiencies model of non-genomic evolution. Simulation Practice and Theory, 8(1-2): 99-108. Paula, S., Akeson, M., Deamer, D. (1999). Water transport by the bacterial channel alpha hemolysis. Biochimica Biophysica Acta, 1418: 117-126. Pohorille, A. (1999). Non-genomic evolution of catalytic peptides in protocells [Abstract]. Seventh International Conference on Intelligent Systems in Molecular Biology, Heidelberg, Germany. Pohorille, A. (1999, October). Towards the creation of simple, functional, cell-like structures. [Abstract]. 1999 Foresight Conference in Molecular Nanotechnology, Santa Clara, CA. Pohorille, A. (2000, March). Computer modeling of the earliest cellular structures and functions [Abstract]. Abstracts of the American Physical Society Meeting, Minneapolis, MN. Pohorille, A. (2000). Models of the protocellular structures, functions and evolution [Abstract]. Frontiers of Life Conference, Blois, France. Pohorille, A. (2000). Molecular simulations in astrobiology [Abstract]. The 2000 HPCC/CAS Workshop, NASA Ames Research Center, Moffett Field, CA. Pohorille, A., Chipot, C., New, M.H., Schweighofer, K., Stassinopoulos, D., & Wilson, M.A. (2000, April). Computer modeling of the protocellular structures, functions and evolution [Abstract]. First Astrobiology Science Conference, (p. 154), NASA Ames Research Center, Moffett Field, CA. Pohorille, A., Wilson, M.A., Chipot, C., New, M.H., & Schweighofer, K. (1999). Interactions of small moleculaes and peptides with membranes. In: J. Leszczynski (Ed.), Computational Molecular Biology (pp. 485-535). Amsterdam: Elsevier. Pohorille, A., Wilson, M.A., & Schweighofer, K. (1999). Electrostatic properties of aqueous interfaces. In: L.R. Pratt, & G. Hummer (Eds.), Simulation and Theory of Electrostatic Interactions in Solution (pp. 492-508). New York: American Institute of Physics. Pohorille, A., New, M. H., Schweighofer, K., & Wilson, M.A. (1999). Insights from computer simulations into the interactions of small molecules with lipid membranes. Current Topics in Membranes, 48: 50-76. Pohorille, A., Wilson, M.A., Schweighofer, K., Chipot, C., & New, M.H. (1999). Molecular simulations of protocellular membrane functions [Abstract]. 1999 Meeting of the International Society for Studies of the Origin of Life (ISSOL), La Jolla, CA. Schweighofer, K., & Pohorille, A. (2000). Computer simulations of ion channel gating: The M2 channel of Influenza A virus. Biophysical Journal, 78: 150-163. Segre, D., Deamer, D., & Lancet, D. (In Press, 2000). The Lipid World. Origins of Life and Evolution of the Biosphere. Stassinopoulos, D., Colombano, S.P., Lohn J.D., Haith, G.L.. Scargle, J., & Liang, S. (In Press, 2000). Spatial autocatalytic dynamics: An approach to modelling Prebiotic evolution. In: Proceedings Of the Second International Conference of Complex Systems. Perseus Books. Subramaniam, S., Lindahl, M., Bullogh, P., Faruqi, W., Tittor, J., Oesterhelt, D., Brown, L.S., Lanyi, J.K., & Henderson, R. (1999). Electron crystallographic analysis of protein conformational changes in the late stages of the bacteriorhodopsin photocycle. Journal of Molecular Biology, 287: 145-161. Szostak, J.W. (1999). Constraints on the sizes of the earliest cells. In: Steering Group on Astrobiology of the Space Studies Board, National Research Council. Size Limits of Very Small Microorganisms: Proceedings of a Workshop. Washington, DC: National Academy of Sciences Press. Szostak, J.W. (2000). Directed evolution: A vehicle for the exploration of sequence space [Abstract]. Keystone Millennium Symposium, Howard Hughes Medical Institute and Department of Molecular Biology, Boston, MA. Szostak, J.W. (2000). Directed protein evolution and functional genomics using RNA-protein fusions [Abstract]. American Society for Microbiology Meeting. Szostak, J.W. (2000). Prospects for the synthesis of a molecular ensemble capable of growth, replication and evolution, i.e., a cell [Abstract]. Les Treilles Symposium. Váró, G., Brown, L.S., Needleman, R., & Lanyi, J.K. (1999). Binding of calcium ions to bacteriorhodopsin. Biophysical Journal, 76: 3219-3226. Wilson, D.S., & Keefe, A.D. (In Press, 2000). Random mutagenesis by PCR. Current Protocols in Molecular Biology.

Early Microbial Ecosystems: Modern Analogs top

Albert, D., Hoehler, T.M., Des Marais, D.J., & Bebout, B.M. (2000, April). Fluxes of organic acids from hypersaline mcrobial mats [Abstract]. First Astrobiology Science Conference (p. 317), NASA Ames Reasearch Center, Moffett Field, CA. Bebout, B.M., Hoehler, T.M., Visscher, P.T., & Des Marais, D.J. (2000, April). Measurements of methane production in microbial mats [Abstract]. First Astrobiology Science Conference, NASA Ames Research Center, Moffett Field, CA. Beaumont, V.I., Jahnke, L.L. & Des Marais, D.J. (In Press, 2000). Nitrogen isotopic fractionation in the synthesis of photosynthetic pigments in Rhodobacter capsulatus and Anabaena cylindrica. Organic Geochemistry. Borowski, W., Hoehler, T., Alperin, M., Rodriguez, N., & Paull, C. (2000). Significance of anaerobic methane oxidation in methane-rich sediments overlying the Blake Ridge gas hydrates. In: Paull, Matsumoto, Wallace, & Dillon (Eds.), Proceedings of the Oil Drilling Program, Science Results, Vol. 164 (pp. 87-99). College Station, TX: Ocean Drilling Program. Caroff, L.I., & Des Marais, D.J. (Eds.). (2000). Pale Blue Dot 2 Workshop: Habitable and Inhabited Worlds Beyond Our Solar System. (NASA Conference Publication 2000-209595). Moffett Field, CA: NASA Ames Research Center. Condie, K. and Des Marais, D.J. (1999) Black shales and paleoweathering: Response to mantle plume events and the supercontinent cycle. [Abstract]. Geological Society of America, Abstracts with Programs, 1999 Annual Meeting, (p. A-325), Denver, CO. Condie, K. and Des Marais, D.J. (1999). Response of near-Earth-surface systems to a superplume/supercontinent event at 1.9 Ga. [Abstract]. Eos, Transactions of the American Geophysical Union, 1999 Fall Meeting, 80 (46): F1144, San Francisco, CA . Dehler, C.M., Des Marais, D.J., Bowring, S.A., Sharp, Z.D., Karlstrom, K.E., & Elrick, M.B. (1999). Chuar Group (1.1-0.74 Ga), Grand Canyon: Carbon isotope systematics at the onset of Sturtian glaciation [Abstract]. Geological Society of America, Abstracts with Programs. Des Marais, D.J. (2000, June). Long-term evolution of the sun and our biosphere: Causes and effects? [Abstract]. Solar Physics Division Meeting, Lake Tahoe, CA. Des Marais, D.J. (1999). Coevolution of our biosphere and planet [Abstract]. Bioastronomy 1999: A New Era in the Search for Life in the Universe, (p. 50), Kona, HI. Des Marais, D.J. (1999). Living versus lifeless habitable planets: Learning to distinguish the difference [Abstract]. Geological Society of America, Abstracts with Programs, 1999 Annual Meeting, (p. A-303), Denver, CO . Des Marais, D.J. (1999). Searching for pale blue dots in the universe: Understanding microbial contributions to planetary atmospheres [Abstract]. Eos, Transactions of the American Geophysical Union, 1999 Fall Meeting, 80(46): F67-F68, San Francisco, CA, Des Marais, D.J. (2000). Evolution of Earth's early biosphere and amosphere. In: L.I. Caroff, & D.J. Des Marais (Eds.), Pale Blue Dot 2 Workshop: Habitable and Inhabited Worlds Beyond Our Own Solar System (pp.188-202). (NASA Conference Publication 2000-209595). Moffett Field, CA: NASA Ames Research Center. Des Marais, D.J. (2000). Modern microbial ecosystems are a key to understanding our biosphere's early evolution and its contributions to the atmosphere and rock record [Abstract]. First Astrobiology Science Conference, (p. 374), NASA Ames Reasearch Center, Moffett Field, CA. Des Marais, D.J. (2000). Searching for pale blue dots in the universe: Understanding microbial contributions to planetary atmospheres [Abstract]. First Astrobiology Science Conference (p. 175), NASA Ames Reasearch Center, Moffett Field, CA Farmer, J.D., & Des Marais, D.J. (1999). Exploring for a record of ancient Martian life. Journal of Geophysical Research: Planets, 104 (E11): 26,977-26,995. Fouke, B.W., Farmer, J.D., Des Marais, D.J., Pratt, L., Sturchio, N.C., Burns, P.C., & Discipulo, M. (2000). Depositional facies and aqueous-solid geochemistry of travertine-depositing hot springs (Angel Terrace, Mammoth Hot Springs, Yellowstone National Park). Journal of Sedimentary Research, 70(3): 565-585. Hoehler, T., Albert, D., Alperin, M., & Martens, C. (1999). Acetogenesis from CO2 in an anoxic marine sediment. Limnology & Oceanography, 44(3): 662-667. Hoehler, T., Alperin, M., Albert, D., & Martens, C. (1999). Thermodynamics of molecular hydrogen in anaerobic microbial ecosystems [Abstract]. Ninth Annual V.M. Goldschmidt Conference. Hoehler, T., Bebout, B., Albert, D., Visscher, P.T., & Des Marais, D. (2000). Dynamics of molecular hydrogen in hypersaline microbial mats [Abstract]. First Astrobiology Science Conference, NASA Ames Research Center, Moffett Field, CA. Hoehler, T., Bebout, B., Visscher, P., & Des Marais, D. (1999). Hydrogen concentrations in microbial mat ecosystems [Abstract]. Eos, Transactions of the American Geophysical Union, 1999 Fall Meeting, 80(46): F82-83. Hoehler, T., Borowski, W., Alperin, M., Rodriguez, N., & Paull, C. (2000). Model, stable isotope, and radio-tracer characterization of anaerobic methane oxidation in gas hydrate-bearing sediments of the Blake Ridge. In: Paull, Matsumoto, Wallace, and Dillon (Eds.), Proceedings of the Oil Drilling Program, Science Results, Vol. 164 (pp. 79-85). College Station, TX: Ocean Drilling Program. Jahnke, L.L., Summons, R.E., Farmer, J.D., & Klein, H.P. (2000). Hopanoid biomarker preservation in coniform (Phormidium) stromatolites in siliceous thermal springs, Yellowstone National Park [Abstract]. First Astrobiology Science Conference, NASA Ames Research Center, Moffett Field, CA. Jahnke, L.L., Summons, R.E., Farmer, J.D., Klein, H.P. (1999). Organic biomarker preservation in coniform (Phormidium) stromatolites in siliceous thermal springs, Yellowstone National Park [Abstract]. Geological Society of America, Abstracts with Programs, 1999 Annual Meeting, 31(7): A-433. Karlstrom, K.E., Bowring, S.A., Dehler, C.M., Knoll, A.H., Porter, S.M., Sharp, Z.D., Des Marais, D.J., Weil, A.B., Geissman, J.W., Elrick, M.B., Timmons, J.M., Keefe, K., & Crossey, L.J. (In Press, 2000). The Chuar Group of the Grand Canyon. Geology. Londry, K.L. and Des Marais, D.J. (1999) Sulfate-reducing bacteria: Carbon isotopic discrimination during heterotrophic and autotrophic growth [Abstract]. Geological Society of America, Abstracts with Programs, 1999 Annual Meeting, A-489. MacIntyre, I.G., Prufert-Bebout, L. and Reid, P.R. (In Press, 2000). The role of endolithic cyanobacteria in the formation of lithified laminae in Bahamian stromatolites. Sedimentology. Prufert-Bebout, L., MacIntyre, I., & Reid, P. (Submitted, 2000). The role of endolithic cyanobacteria in the formation of lithified laminae in Bahamian stromatolites. Sedimentology. Reid, R.P., Bebout, B.M., Pufert-Bebout, L., Decho, A.W., Macintyre, I.G., Paerl, H., Steppe, T., Pinckney, J., Stolz, J., & Visscher, P.T. (1999). Stromatolite formation in a microbialite/algal ridge fringing reef complex [Abstract]. Geological Society of America, Abstracts with Programs, 1999 Annual Meeting, Denver, CO. Reid, R.P., Bebout, B.M., Prufert-Bebout, L., Decho, A.W., Macintyre, I.G., Steppe, T., Pinckney, J., Stolz, J., & Visscher, P.T. (2000). Microbial lithification in modern marine stromatolites [Abstract]. Meeting in Highborne Cay, Bahamas. Reid, R.P., Visscher, P., Decho, A., Stolz, J., Bebout, B., Macintyre, I.G., Dupraz, C., Pinckney, J., Paerl, H., Prufert-Bebout, L., Steppe, T., & Des Marais, D. (In Press, 2000). Microbial lithification in modern marine stromatolites. Nature. Sessions, A., Des Marais, D.J., Londry, K., Jahnke, L., & Hayes, J. (2000). Distribution of deuterium in biologic lipids -- Current progress [Abstract]. First Astrobiology Science Conference (p. 273), NASA Ames Reasearch Center, Moffett Field, CA. Sessions, A., Jahnke, L., Londry, K., Des Marais, D.J., & Hayes, J. (1999). Hydrogen isotope fractionation in microorganisms [Abstract]. Eos, Transactions of the American Geophysical Union, 1999 Fall Meeting, 80(46): F82, San Francisco, CA. Summons, R.E., Jahnke, L.L., Hope, J.M., & Logan G.A. (1999). 2-methylhopanoids as biomarkers for cyanobacterial oxygenic photosynthesis. Nature, 400: 554-557. Visscher, P.T. (1999, May). Biogeochemistry of anaerobic systems. In: L.I. Caroff, & D.J. Des Marais (Eds.), Pale Blue Dot 2 Workshop: Habitable and Inhabited Worlds Beyond Our Own Solar System, (pp. 161-174). (NASA Conference Publication 2000-209595). Moffett Field, CA: NASA Ames Research Center. Visscher, P.T., Gritzer, R.F., & Leadbetter, E.R. (1999). Low-molecular weight sulfonates, a major substrate for sulfate reducers in marine microbial mats. Applied and Environmental Microbiology, 65: 3272-3278. Visscher, P.T, Reid, R.P., & Bebout, B.M. (1999). Microscale investigation of biogeochemical processes in modern marine stromatolites [Abstract]. Geological Society of America, Abstracts with Programs, 1999 Annual Meeting, Denver, CO. Visscher, P.T, Reid, R.P., & Bebout, B.M. (1999). Microscale investigation of biogeochemical processes in modern marine stromatolites [Abstract]. Geological Society of America, Abstracts with Programs, 1999 Annual Meeting, Denver, CO. Visscher, P.T., Rogers, D.R., Bebout, B.M., Hoehler, T.M., Des Marais, D.J. (2000). Organosulfur fluxes in sedimentary systems: Useful biogenic indicators? [Abstract]. First Astrobiology Science Conference, NASA Ames Research Center, Moffett Field, CA.

Habitable Planets top

Anbar, A., Arnold, G., Mojzsis, S.J., & Zahnle, K. (In Press, 2000). Extraterrestrial iridium and sediment accumulation on the Hadean Earth. Journal of Geophysical Research. Catling, D.C., McKay, C.P., & Zahnle, K.J. (2000). The timescale to develop oxygen atmospheres on habitable extrasolar planets and the consequences for extraterrestrial life [Abstract]. First Astrobiology Science Conference, (p. 173), NASA Ames Research Center, Moffett Field, CA. Haberle, R.M., Zent, A.P., McKay, C.P., & Quinn, R.C. (2000). On the stability of liquid water on present day Mars [Abstract]. First Astrobiology Science Conference (p. 8), NASA Ames Research Center, Moffett Field, CA. Kasting, J.F. (1999, October). Runaway greenhouses and runaway glaciation: How stable is Earth's climate? [Abstract]. Cess Climate Symposium, San Diego, CA. Kasting, J.F. (In Press, 2000). Planets. In: Encyclopedia of Global Change. Mischna, M., & Kasting, J.F. (In Press, 2000). CO2 clouds and the climate of early Mars: Effect of cloud height and optical depth. Icarus. 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(E5): 11,981-11,990. Rabbette, M., McKay, C., Pilewskie, P., & Young, R. (2000). The runaway greenhouse effect on earth and other planets [Abstract]. First Astrobiology Science Conference (p. 186), NASA Ames Research Center, Moffett Field, CA. Rosenberg, N.D., Cuzzi, J.N., Bourcier, W.L., Travis, B.J., & Browning, L.B. (2000). Modeling aqueous processes in primitive bodies [Abstract]. First Astrobiology Science Conference (p. 169), NASA Ames Research Center, Moffett Field, CA. Schindler, T.L., & Kasting, J.F. (In Press, 2000). Synthetic spectra of simulated terrestrial atmospheres. Icarus. Zahnle, K. (2000). Life and death on Mars and Earth [Abstract]. First Astrobiology Science Conference, (p. 220), NASA Ames Research Center, Moffett Field, CA.