ABRC TEAM PUBLICATIONS
2012
T.L. Hamilton, K. Vogl, D.A. Bryant, E.S. Boyd, J.W. Peters, “Environmental constraints defining the distribution, composition, and evolution of chlorophototrophs in thermal features of Yellowstone National Park,” Geobiology, 2012 May;10(3):236-49
J.W. Peters, JB Borderick, “Emergineg Paradigms for Complex Iron-Sulfur Cofactor Assembly and Insertion,” Annu Rev Biochem, 2012, Apr, Epub ahead of print
B.R. Duffus, T.L. Hamilton, E.M. Shepard, E.S. Boyd, J.W. Peters, J.B. Broderick, “Radical AdoMet enzymes in complex metal cluster biosynthesis,” Biochim Biophys Acta, 2012, Jan, Epub ahead of print
de Melo-Martín, I; Intemann, K. (2012). Interpreting evidence: Why values can matter as much as science. Perspectives in Biology and Medicine, 55 (1):59-70.
W. A. Alexander, T. K. Minton, J. P. Wiens, and G. M. Nathanson, “Reactions of Solvated Electrons Initiated by Sodium Atom Ionization at the Vacuum-Liquid Interface” Science, in revision, January 2012.
Minton TK, Wright ME, Tomczak SJ, Marquez SA, Shen L, Brunsvold AL, Cooper R, Zhang J, Vij V, Guenthner AJ, Petteys BJ, “Atomic oxygen effects on POSS polyimides in low earth orbit,” ACS Appl Mater Interfaces. 2012 Feb;4(2):492-502
Ceballos R.M., Marceau C.D., Morales C.T., Lucas D.D., Clore A.J. 3, and Stedman K.M. (2012) “Unique Features of Infection Emerge from Sulfolobus Spindle Virus Host-Range Study,” [J.Virology, under review],
Ceballos R.M., Marceau J.O., Benn D., and Kinnersley M. (2012) “Two New Members of the Genus Sulfolobus Isolated from Central American Hot Springs: S. salvadorensis sp. nov. and S. costariquensis sp.nov.,” [under review IJSEM].
2011
T.L. Hamilton, E.S. Boyd, and J.W. Peters "Geochemical controls on the phylogenetic structure and composition of NifH in Yellowstone National Park" Microbial. Ecol,. 2011 61:860–870.
I.I. Brown, D.A. Bryant, D. Casamatta, K.L. Thomas-Keprta, S.A. Sarkisova, G. Shen, J.E. Graham, E.S. Boyd, J.W. Peters, D.H. Garrison, and D.S. McKay "Polyphasic characterization of a thermotolerant siderophilic filamentous cyanobacterium that produces intracellular iron deposits" Appl. Environ. Microbiol. 2010 76:6664-6672
E.S. Boyd, T.L. Hamilton, J.R. Spear, M. Lavin, J.W. Peters "[FeFe]-hydrogenase in Yellowstone National Park: evidence for dispersal limitation and phylogenetic niche conservatism." ISME J. 2010 4:1485-1495
T.L. Hamilton, R.K. Lange, E.S. Boyd, J.W. Peters "Biological nitrogen fixation in acidic high temperature geothermal springs in Yellowstone National Park, Wyoming" Environ. Microbiol. 2011 10.1111/j.1462-2920
E.S. Boyd, A.D. Andbar, S. Miller, T.L. Hamilton, M. Lavin, J.W. Peters "A late methanogen origin for molybdenum-dependent nitrogenase" Geobiology 2011 May;9(3):221-32 T.L.
E.S. Boyd, R.K. Lange, A.C. Mitchell, J.R. Havig, T.L. Hamilton, E.L. Shock, J.W. Peters, and M. Skidmore "Diversity, abundance, and potential activity of nitrifying and denitrifying microbial assemblages in a subglacial ecosystem" Appl. Environ. Microbiol. 2011
77(14):4778-87
Hamilton, T.L., E.S. Boyd, and J.W. Peters. 2011. Environmental constraints underpin the distribution and phylogenetic diversity of nifH in the Yellowstone geothermal complex. Microbiol. Ecol. 61:860–870.
Hamilton,T.L., K. Vogl, D.A. Bryant, E.S. Boyd, and J.W. Peters. 2011. Environmental constraints defining the distribution, composition, and evolution of chlorophototrophs in thermal features of Yellowstone National Park. Geobiology. 10.1111/j.1472-4669.2011.00296.x.
Schut, G.J., E.S. Boyd, J.W. Peters, and Michael W. W. Adams. 2011. The unique respiratory complexes involved in hydrogen and sulfur metabolism by heterotrophic hyperthermophilic Archaea and their evolutionary implications. Submitted
Boyd, E.S., T.L. Hamilton, and J.W. Peters. 2011. An alternative path for the evolution of biological nitrogen fixation. Front. Microbio. 2:205. 10.3389/fmicb.2011.00205.
Waller, S., 2011 "Introduction to Cognitive Science" in The Lincoln Library of Essential Information, Cleveland: Lincoln Library Press.
David W. Mulder, Eric M. Shepard, JE Meuser, Neelambari Joshi, PW King, MC Posewitz, Joan B. Broderick, John W. Peters, "Insights into [FeFe]-hydrogenase Structure, Mechanism, and Maturation," Structure, 2011 19(8):1038-52.
Eric M. Shepard, Eric S. Boyd, Joan B. Broderick, John W. Peters, "Biosynthesis of complex iron-sulfur enzymes," Curr Opin Chem Biol., 2011 (2):319-27
Intemann, K. and de Melo-Martín, I. (2011). Bias, impartiality, and conflicts of interest in biomedical sciences. In Science At The Frontiers: Perspectives on the History & Philosophy of Science, William Krieger (ed.), Landham: Roman & Littlefield. 170-193.
T. K. Minton, M. E. Wright, S. J. Tomczak, S. A. Marquez, L. Shen, A. L. Brunsvold, R. Cooper, J. Zhang, V. Vij, A. J. Guenthner, and B. J. Petteys, “Atomic Oxygen Effects on POSS Polyimides in Low Earth Orbit, ACS Appl. Mater. Interfaces,” DOI: 10.1021/am201509n (2011).
L. Y. Yeung, M. Okumura, J. Zhang, T. K. Minton, J. T. Paci, A. Karton, J. M. L. Martin, J. P. Camden, and G. C. Schatz, “O(3P) + CO2 Collisions at Hyperthermal Energies: Dynamics of Non-Reactive Scattering, Oxygen Isotope Exchange, and Oxygen-Atom Abstraction,” J. Phys. Chem. A, DOI: 10.1021/jp2080379 (2011).
J. Zhang, S. A. Lahankar, D. J. Garton, T. K. Minton, W. Zhang, and X. Yang, “Crossed-Beams Studies of the Dynamics of the H-atom Abstraction Reaction, O(3P) + CH4 ⇒ OH + CH3, at Hyperthermal Collision Energies,” J. Phys. Chem. A 115, 10894-10902, 2011.
J. T. Paci, G. C. Schatz, T. K. Minton, “Theoretical Studies of the Erosion of (100) and (111) Diamond Surfaces by Hyperthermal O(3P),” J. Phys. Chem. C 115, 14770-14777 (2011).
L. Che, D. J. Gardenghi, R. K. Szilagyi, and T. K. Minton, “Production of a Biomimetic Fe(I)-S Phase on Pyrite by Atomic Hydrogen Beam Surface Reactive Scattering, “ Langmuir 27, 6814-6821 (2011).
Usselman, R.J., Walter, E.D., Willits, D., Douglas, T., Young, M., Singel, D.J., 2011. Monitoring Structural Transitions in Icosahedral Virus Protein Cages by Site-Directed Spin Labeling. Journal of the American Chemical Society 133, 4156-4159
Che Li, Gardenghi D.J., Szilagyi R.K., Minton T.K.: Production of a Biomimetic Fe(I)-S Phase on Pyrite by Atomic Hydrogen Beam Surface Reactive Scattering Langmuir, 2011, 27(11), 6814-6821
Grigoropoulos A., Szilagyi R.K: In silico Evaluation of Proposed Biosynthetic Pathways for the Unique Dithiolate Ligand of the H-cluster of [FeFe]-hydrogenase J. Comp. Chem., 2011, 32(15), 3194-3206
Harris T.V., Szilagyi R.K.: Comparative Assessment of the Composition and Charge State of Nitrogenase FeMo-Cofactor Inorg. Chem., 2011, 50(11), 4811-4824
Harris T.V., Szilagyi R.K.: Nitrogenase Structure and Function Relationships by Density Functional Theory in Methods in Molecular Biology: Nitrogen Fixation, 2011, 766(5), 267-291
VanEngelen M.R., Szilagyi R.K., Gerlach R., Lee B.D., Apel W.A., Peyton B.M.: Uranium Exerts Acute Toxicity by Binding to Pyrroloquinoline Quinone Cofactor Environ. Sci. Techn., 2011, 45(3), 937-942
Bhandari, N., Reeder, R.J., Strongin, D.R., "Photoinduced oxidation of arsenite to arsenate on ferrihydrite," Environmental Science & Technology (2011), 45(7), 2783-2789.
Bandyopadhyay, P., "The Logic of Simpson's Paradox," Synthese, 2011, Fall (With Nelson, Greenwood, Brittan, and Berwald)
Bandyopadhyay, P., "Elementary Probability & Statistics: A Primer." In P.S. Bandyopadhyay & M. Forster (eds.) Handbook of Philosophy of Statistics. Elsevier; 2011. (With Steve Cheery)
Bandyopadhyay, P., "Philosophy of Statistics: An Introduction to the Volume" to Handbook of Philosophy of Statistics. (With Malcolm Forster). Elsevier, 2011.
2010
D.W. Mulder, E.S. Boyd, R. Sarma, R.K. Lange, J.A. Endrizzi, J.B. Broderick, and J.W. Peters "Stepwise [FeFe]-hydrogenase H-cluster assembly revealed in the structure of HydAΔEFG" Nature 2010 465:248-251
E.S. Boyd, M. Skidmore, A.C. Mitchell, C. Bakermans, and J. W. Peters "Methanogenesis in Subglacial Sediments" Environ. Microbiol. Reports 2010 2:685-692 B. Soboh, E.S. Boyd, D. Zhao, J.W. Peters, and L.M. Rubio "Substrate specificity and evolutionary implications of a NifDK enzyme carrying NifB-co at its active site" FEBS Lett. 2010 584:1487-1492
Soboh, B., E.S. Boyd, D. Zhao, J.W. Peters, and L.M. Rubio. 2010. Substrate specificity and evolutionary implications of a NifDK enzyme carrying NifB-co at its active site. FEBS Lett. 584(8): 1487-1492.
Yi Peng, Susan E. Veneziano, Gregory D. Gillispie, and Joan B. Broderick, "Pyruvate formatelyase: Evidence for an open conformation favored in the presence of its activating enzyme," J. Biol. Chem. 2010 285, 27224-27231.
Eric M. Shepard, Benjamin R. Duffus, Simon J. George, Shawn E. McGlynn, Martin R. Challand, Kevin D. Swanson, Peter L. Roach, Stephen P. Cramer, John W. Peters, and Joan B. Broderick, "[FeFe]-Hydrogenase Maturation: HydG-Catalyzed Synthesis of Carbon
Monoxide," J. Am. Chem. Soc. 2010 132(27), 9247-9249.
Eric M. Shepard, Shawn E. McGlynn, Alexandra L. Bueling, Celestine S. Grady-Smith, Simon J. George, Mark A. Winslow, Stephen P. Cramer, John W. Peters, and Joan B. Broderick, "Synthesis of the 2Fe subcluster of the [FeFe]-hydrogenase H cluster on the HydF scaffold," Proc. Natl. Acad. Sci. U.S.A. 2010, 107(23), 10448-10453.
Kaitlin S. Duschene and Joan B. Broderick, "The Antiviral Protein Viperin is a Radical SAM Enzyme," FEBS Lett. 2010 584(6), 1263-1267.
Sunshine C. Silver, Tilak Chandra, Egidijus Zilinskas, Shourjo Ghose, William E. Broderick, Joan B. Broderick, "Complete stereospecific repair of a synthetic dinucleoside spore photoproduct by spore photoproduct lyase," J. Biol. Inorg. Chem. 2010, 15(6), 943-955.
Intemann, K. and de Melo-Martín, I. (2010). Social values and evidentiary standards: The case of the HPV vaccine. Biology and Philosophy 25(2): 203-213.
Waller, S., 2010 "Neuro-Enhancement: Warning, Autonomax may be Necessary" Journal of Ethics in Mental Health with Carmela Epright. Vol. 5 number 1
R.C. Driesener, M.R. Challand, S.E. McGlynn, E.M. Shepard, E.S. Boyd, J.B. Broderick, J.W. Peters, and P.L. Roach, "[FeFe]-hydrogenase cyanide ligands derived From S adenosylmethionine-dependent cleavage of tyrosine" Angew Chem. Int. Ed. Engl. 2010
49:1687-1690
S.E. McGlynn, E.S. Boyd, E.M. Shepard, R.K. Lange, R. Gerlach, J.B. Broderick, and J.W. Peters, "Identification and characterization of a novel member of the radical AdoMet enzyme superfamily and implications for the biosynthesis of the Hmd hydrogenase active site cofactor" J. Bacteriol. 2010 192:595-598
E.S. Boyd, J.R. Spear, and J.W. Peters, "[FeFe]-hydrogenase genetic diversity provides insight into molecular adaptation in a saline microbial mat community" Appl. Environ. Microbiol 2010 75:4620-4623
Inskeep, W.P., Rusch, D.B., Jay, Z.J., Herrgard, M.J., Kozubal, M.A., Richardson, T.H., Macur, R.E., Hamamura, N., Jennings, R.D., Fouke, B.W., Reysenbach, A.L., Roberto, F., Young, M., Schwartz, A., Boyd, E.S., Badger, J.H., Mathur, E.J., Ortmann, A.C., Bateson, M., Geesey, G., Frazier, M., 2010. Metagenomes from High-Temperature Chemotrophic Systems Reveal Geochemical Controls on Microbial Community Structure and Function. Plos One 5.
Khayat, R., Fu, C.Y., Ortmann, A.C., Young, M.J., Johnson, J.E., 2010. The Architecture and Chemical Stability of the Archaeal Sulfolobus Turreted Icosahedral Virus. Journal of Virology 84, 9575-9583.
Menon, S.K., Eilers, B.J., Young, M.J., Lawrence, C.M., 2010. The Crystal Structure of D212 from Sulfolobus Spindle-Shaped Virus Ragged Hills Reveals a New Member of the PD-(D/E)XK Nuclease Superfamily. Journal of Virology 84, 5890-5897.
Snyder, J.C., Bateson, M.M., Lavin, M., Young, M.J., 2010. Use of Cellular CRISPR (Clusters of Regularly Interspaced Short Palindromic Repeats) Spacer-Based Microarrays for Detection of Viruses in Environmental Samples. Applied and Environmental Microbiology 76, 7251-7258.
Usselman, R.J., Klem, M.T., Russek, S.E., Young, M., Douglas, T., Goldfarb, R.B., 2010. Two-component magnetic structure of iron oxide nanoparticles mineralized in Listeria innocua protein cages. Journal of Applied Physics 107.
Schoonen, M.A.A., Harrington, A., Laffers, R., Strongin, D.R., "Role of Hydrogen Peroxide and Hydroxyl Radical in Pyrite Oxidation by Molecular Oxygen," (2010) Geochimica et Cosmochimica Acta 74, 4971- 4987.
F.M. Michel, H. Hosein, D.B. Hausner, S. Debnath, and D.R. Strongin, "Reactivity and Structure of Ferritin," Biochimica et Biophysica Acta (2010), 1800, 871 –885
Cohn, C., Fisher, S., Brownawell, B., and Schoonen, M., 2010. Adenine oxidation by pyrite-generated hydroxyl radicals. Geochemical Transactions 11, 2.
Bandyopadhyay, P., "Two Dogmas of Strong Objective Bayesianism," In International Studies in the Philosophy of Science, 2010, March. (With Gordon Brittan)
Bandyopadhyay, P., "How to Undermine Underdetermination?" Foundations of Sciences. 2010. Jan. (With John Bennett) (The paper has been accepted for publication. However, we need to revise some parts of the paper in light of the referee reports.)
R.C. Driesener, M.R. Challand, S.E. McGlynn, E.M. Shepard, E.S. Boyd, J.B. Broderick, J.W. Peters, and P.L. Roach, "[FeFe]-hydrogenase cyanide ligands derived From S adenosylmethionine-dependent cleavage of tyrosine" Angew Chem. Int. Ed. Engl. 2010
49:1687-1690
2009
Boyd, E.S., W.D. Leavitt, and G.G. Geesey. 2009. CO2 uptake and fixation by a thermoacidophilic microbial community attached to sulfur flocs in a geothermal spring. Appl. Environ. Microbiol. 75 (13): 4289-4296.
Intemann, K. (2009). Why diversity matters: Understanding and applying the diversity component of the NSF's broader impacts criterion. Social Epistemology 23, 3-4: 249-266.
de Melo-Martín, I. and Intemann, K. (2009). How do disclosure policies fail? Let us count the ways. Federation of American Societies for Experimental Biology Journal 23:1638-1642.
Banfield, J.F., Young, M., 2009. Variety-the Splice of Life-in Microbial Communities. Science 326, 1198-1199.
Waller, S. 2009 "Psychological Investigations: The Private Language Argument and Inferences in Contemporary Cognitive Science." With C.D. Meyers. Synthese 171:135-156.
Szilagyi R.K.: Structural Origins of Noninnocent Coordination Chemistry in Encyclopedia of Inorganic Chemistry , Wiley, 2009
Murphy, R., Strongin, D. R., "Surface reactivity of pyrite and related sulfides,", Surface Science Reports (2009) 64, (1), 1-45.
S.E. McGlynn, D.M. Mulder, E.M. Shepard, J.B. Broderick, and J.W. Peters, "Hydrogenase cluster biosynthesis: Organometallic chemistry nature's way" Dalton Trans. 2009 22:4274- 4285
J.W. Peters, "Carbon monoxide and cyanide lignads in the active site of [FeFe]-hydrogenase. In Metal ions in life sciences" 2009 Sigel, A; Sigel, H; Sigel, RKO; Eds. RSC Pub: 6, pp. 179-218
2008
R. Sarma, B.M. Barney, T.L. Hamilton, A. Jones, L.C. Seefeldt, and J.W. Peters JW. "Crystal structure of the L protein of Rhodobacter sphaeroides light-independent protochlorophyllide reductase with MgADP bound: A homologue of the Nitrogenase Fe protein" Biochemistry
2008 47:13004-13015
S.E. McGlynn, E.M. Shepard, M.A. Winslow, AV. Naumov, K.S. Duschene, M.C. Posewitz, W.E. Broderick, J.B. Broderick, and J.W. Peters "HydF as a scaffold in [FeFe]-hydrogenase H cluster biosynthesis" FEBS Lett. 2008 582:2183-2187
A. Pandey, T. Harris, L. Giles, J.W. Peters, R.K. Szilagyi, “Dithiomethylether as a ligand in the hydrogenase H cluster,” J. Amer. Chem. Soc. 2008 103:4533-4540
A.S. Steunou, S.I. Jensen, E. Brecht, M.M. Bateson, O. Killian, D. Bhaya, D.M. Ward, J.W. Peters, A.R. Grossman, M. Kuhl, “Regulation of nif gene expression and the energetic of cyanobacterial N2 fixation over the diel cycle in a hot spring micorbioal mat,” ISME J. 2008
M. Parker, B. Ramsay, M. Allen, M. Klem, M. Young, T. Douglas "Expanding the Temperature Range of Biomimetic Synthesis Using a Ferritin from the Hyperthermophile Pyrococcus furiosus" Chem. Mater. (2008) 20, 1541-1547.
M. Klem, J. Mosolf, M. Young, T. Douglas “Synthesis of Protein Encapsulated Nanomaterials by Photoreduction” Inorg Chem (2008) 47, 2237-2239.
M. Klem, M. Young, T. Douglas“Biomimetic Synthesis of b-TiO2 Inside a Viral Capsid” J. Materials Chem (2008) 18, 3821-3823.
M.C.F. Wander, J.D. Kubicki, M.A.A. Schoonen, Reduction of N2 by Fe2+ via homogeneous and heterogeneous reactions Part 2: The role of metal binding in activating N2 for reduction; a requirement for both pre-biotic and biological mechanisms, Origins of Life and Evolution of Biospheres 38(2008) 195-209.
Sebyung Kang, Janice Lucon, Zachary B. Varpness, Lars Liepold, Masaki Uchida, Debbie Willits, Mark J. Young, and Trevor Douglas “Monitoring Biomimetic Platinum Nanocluster Formation using Non-covalent Mass Spectrometry and Cluster Dependent H2 Production” Angewandte Chemie (2008) 47, 7845–7848.
Lars O. Liepold, Luke M. Oltrogge, Peter Suci, Trevor Douglas, Mark J. Young ” Accurate Mass Assignment of Noncovalent Complexes by Electrospray Mass Spectrometry” J. Amer. Society for Mass Spec. (2008)
Intemann, K. and de Melo-Martín, I. (2008). Regulating science: Should scientists be left alone? Federation of American Societies for Experimental Biology (FASEB) Journal, 22: 654-658.
Pandey A.S., Harris T.V., Giles L.J., Peters J.W., Szilagyi R.K.: Dithiomethylether as a Ligand in the Hydrogenase H-Cluster J. Am. Chem. Soc., 2008, 130(13), 4533-4540
Rokhsana D., Dooley D.M., Szilagyi R.K.: Systematic development of computational models for the catalytic site in galactose oxidase: impact of outer-sphere residues on the geometric and electronic structures J. Biol. Inorg. Chem., 2008, 13(3), 371-383
Waller, S., 2008 "Dolphin Words and Wolf Worlds: Ethology, Philosophy, Mind and Language" in LACUS: Linguistic Association of Canada & the United States Forum #34.
Smirnov A, Hausner D, Laffers R, Strongin DR, Schoonen MAA., "Abiotic ammonium formation in the presence of Ni-Fe metals and alloys and its implications for the Hadean nitrogen cycle," Geochemical Transactions (2008) 9, 1.
