Scientific Publications 2006
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2006. "Active NDH-1 complexes from the cyanobacterium Synechocystis sp. strain PCC 6803." Plant & Cell Physiology 47(10):1432-1346. doi:10.1093/pcp/pcl008 Abstract We identified eight bands by staining the native gels for NADPH-nitroblue tetrazolium oxidoreductase activity after electrophoresis of n-dodecyl-ß-maltoside-treated membranes of Synechocystis sp. strain PCC 6803. Among them, bands A, C, D and E were attributed to the activity of NADPH dehydrogenase (NDH-1). Band A is a highly active super-complex of NDH-1 (about 1,000 kDa) that was absent in ΔndhD1/D2 mutant and was suppressed under low CO2. Band C was induced under low CO2 or in ΔndhD1/D2 mutant and was converted to bands D and E. Bands A and C appear to be NDH-1L dimer and NDH-1M, respectively, with subunits essential for the activity.
2006. "Observation of a Forbidden E"-A' (1) Infrared Transition in (BF3)-B-11." Journal of Molecular Spectroscopy 238(2):135-144. Abstract The forbidden 011100-000000 E"-A1' transition of 11BF3 has been observed in absorption in the infrared near 2140 cm-1. Although weak, the entire band is observed and does not show any sign of intensity borrowing from nearby bands. The transitions obey the electric dipole allowed selection rules k = +2, l = +1. As shown by the J and K dependence of the line intensities, the band appears to derive its intensity from terms in the dipole moment operator described by Aliev and Watson [1]. That theory is further developed and it is shown that, for this particular case, the intensity comes largely from the term in the dipole moment operator that governs the intensity of the 002200-000000 transitions and to a lesser extent from terms that govern the intensity of the 001111-000000 transitions and the fundamental bands.
2006. "c-Type Cytochrome-Dependent Formation of U(IV) Nanoparticles by Shewanella oneidensis ." PloS Biology 4(8):1324-1333. Abstract Modern approaches for bioremediation of radionuclide contaminated environments are based on the ability of microorganisms to effectively catalyze changes in the oxidation states of metals that in turn influence their solubility. Although microbial metal reduction has been identified as an effective means for immobilizing highly-soluble uranium(VI) complexes in situ, the biomolecular mechanisms of U(VI) reduction are not well understood. Here, we show that c-type cytochromes of a dissimilatory metal reducing bacterium, Shewanella oneidensis MR-1 are essential for the reduction of U(VI) and formation of extracelluar UO2 nanoparticles. In particular, the outer membrane (OM) decaheme cytochrome MtrC, previously implicated in Mn(IV) and Fe(III) reduction, directly transferred electrons to U(VI). Additionally, deletions of mtrC and/or omcA significantly affected the in vivo U(VI) reduction rate relative to wild type MR-1. Similar to the wild type, the mutants accumulated UO2 nanoparticles extracellularly to high densities in association with an exopolymeric substance (EPS). In wild type cells, this UO2-EPS matrix exhibited glycocalyx-like properties, contained multiple elements of the OM, polysaccharide, and heme containing proteins. Using a novel combination of methods including synchrotron-based X-ray fluorescence microscopy and high resolution immune-electron microscopy, we demonstrate a close association of the extracellular UO2 nanoparticles with MtrC and OmcA. This is the first study to directly localize the OM-associated cytochromes with EPS, which contains biogenic UO2 nanoparticles. In the environment, such association of UO2 nanoparticles with biopolymers may exert a strong influence on subsequent behavior including susceptibility to oxidation by O2 or transport in soils and sediments.
2006. "Two-dimensional hyperfine sublevel correlation spectroscopy: Powder features for S = 1/2, I = 1." Journal of Magnetic Resonance 179(1):120-135. doi:10.1016/j.jmr.2005.11.013 Abstract The lineshapes of two-dimensional magnetic resonance spectra of disordered or partially-ordered solids are defined by ridges of singularities in the frequency plane. The positions of these ridges are described by a branch of catastrophe theory concerning the mapping of one 2-D surface onto another. The specific case of HYSCORE spectra for paramagnetic centers having electron spin S = ½ and nuclear spin I = 1 is discussed in terms of catastrophe theory using an exact solution of the nuclear spin Hamiltonian. The line shape characteristics are considered for several general cases
2006. "Synthesis and Structure of Perrhenate Sodalite." Microporous and Mesoporous Materials 91(1-3):139-144. Abstract Na8(AlSiO4)6(ReO4)2 sodalite was synthesized using a hydrothermal method, and its crystal structure was determined from Rietveld refinement of experimental X-ray powder diffraction data. The refinement showed that this compound adopts the cubic sodalite structure (Space Group , #218) with a = 9.1528 (1) Å. Raman spectroscopic measurements confirm the presence of tetrahedral ReO4- groups. Broadening of the asymmetric stretching and bending vibrational modes suggests the tetrahedra are slightly distorted from ideal Td symmetry in the sodalite lattice. MAS NMR of 29Si and 27Al nuclei showed single intense peaks at �iso = -92.4 ppm and �iso = 57.5 ppm, respectively, confirming the alternating Si, Al tetrahedral ordering in sodalite deduced from the structural data. Chemical shifts for 29Si and 27Al calculated using correlative structural parameters (56.6 ± 0.8 ppm and -92.3 ± 0.9 ppm) showed good agreement with measured data indicating the validity of data derived from the Rietveld structural refinement.
2006. "The Heats of Formation of Diazene, Hydrazine, N₂H₃ ⁺, N₂H₅ +, N₂H, and N₂H₃ and the Methyl Derivatives CH₃NNH, CH₃NNCH₃, and CH₃HNNHCH₃." Journal of Physical Chemistry A 110(33):10116-10121. doi:10.1021/jp061854u Abstract The research described in this product was performed in part in the Environmental Molecular Sciences Laboratory, a national scientific user facility sponsored by the Department of Energy's Office of Biological and Environmental Research and located at Pacific Northwest National Laboratory. The heats of formation of N2H, diazene (cis- and trans-N2H2), N2H3, and hydrazine (N2H4), as well as their protonated species (diazenium, N2H3 +, and hydrazinium, N2H5 +), have been calculated by using high level electronic structure theory. Energies were calculated by using coupled cluster theory with a perturbative treatment of the triple excitations (CCSD(T)) and employing augmented correlation consistent basis sets (aug-cc-pVnZ) up to quintuple-ú, to perform a complete basis set extrapolation for the energy. Geometries were optimized at the CCSD(T) level with the aug-cc-pVDZ and aug-cc-pVTZ basis sets. Core-valence and scalar relativistic corrections were included, as well as scaled zero point energies. We find the following heats of formation (kcal/mol) at 0 (298) K: ¢Hf(N2H) ) 60.8 (60.1); ¢Hf(cis-N2H2) ) 54.9 (53.2); ¢Hf(trans-N2H2) ) 49.9 (48.1) versus g48.8 ( 0.5 (exptl, 0 K); ¢Hf(N2H4) ) 26.6 (23.1) versus 22.8 ( 0.2 (exptl, 298 K); ¢Hf(N2H3) ) 56.2 (53.6); ¢Hf(N2H3 +) ) 231.6 (228.9); and ¢Hf(N2H5 +) ) 187.1 (182.7). In addition, we calculated the heats of formation of CH3NH2, CH3NNH, and CH3HNNHCH3 by using isodesmic reactions and at the G3(MP2) level. The calculated results for the hydrogenation reaction RNNR + H2 f RHNNHR show that substitution of an organic substituent for H improved the energetics, suggesting that these types of compounds may be possible to use in a chemical hydrogen storage system.
2006. "On the unusual stability of valence anions of thymine based on very rare tautomers. A computational study." Journal of Physical Chemistry B 110(48):24696-24707. doi:10.1021/jp065666f Abstract We characterized valence-type and dipole-bound anionic states of thymine using various electronic structure methods, with the most accurate results obtained at the CCSD(T)/aug-cc-pVDZ level of theory followed by extrapolations to complete basis set limits. We found that the most stable anion in the gas phase is related to neither the canonical 2,4-dioxo nor a rare imino-hydroxy tautomer. Instead, it is related to an imino-oxo tautomer, in which the N1H proton is transferred to the C5 atom. This valence anion, , is characterized by an electron vertical detachment energy (VDE) of 1251 meV and it is adiabatically stable with respect to the canonical neutral by 2.4 kcal/mol. It is also more stable than the dipole-bound ( ) and valence anion ( ) of the canonical tautomer. The latter is adiabatically unbound with respect to by 0.1 kcal/mol and this instability is smaller than the uncertainty of the computational model used. The VDE values for and are 55 and 457 meV, respectively. Another, anionic, low-lying imino-oxo tautomer with a VDE of 2458 meV has a proton transferred from N3H to C5 ( ). It is less stable than by 3.2 kcal/mol. The mechanism of formation of anionic tautomers with the carbons C5 or C6 protonated may involve intermolecular proton transfer or dissociative electron attachment to the canonical neutral tautomer followed by a barrier-free attachment of a hydrogen atom to C5. The six-member ring structure of anionic tautomers with carbon atoms protonated might be unstable upon an excess electron detachment. Indeed, the neutral systems resulting from electron detachment from and evolve, along barrier-free decomposition pathways, to a linear or a bicyclo structure, respectively, which might be viewed as lesions to DNA.
2006. "Substrate Changes Associated with the Chemistry of Self-Assembled Monolayers on Silicon." Langmuir 22(13):5617-5624. doi:10.1021/la060153l Abstract Alkylsiloxane self-assembled monolayers (SAMs) are used in the semi-conductor industry, and more recently as proxies for organics adsorbed on airborne mineral dust and on buildings and construction materials. A number of methods have been used for removing the SAM from the substrate after reaction or use, particularly plasmas or piranha (H2SO4:H2O2) solution. However, the impact of these cleaning methods on the chemistry of subsequently formed SAMs on the surface is not known. We report here AFM, XPS, Auger and FTIR studies of changes in the silicon substrate on repetitive deposition and removal of SAMs by these two methods. It is shown that a layer of silicon oxide is formed, and the surface becomes very irregular and roughened, particularly for the piranha treatment. This layer of silica impacts the structure of SAMs attached to it and can serve as a reservoir for trace gases that adsorb on it, potentially contributing to the subsequent reactions of the SAM. The implications for the use of such surfaces as a proxy for reactions of organics on airborne dust particles and on structures in the boundary layer are discussed.
2006. "Microscale Controls on the Fate of Contaminant Uranium in the Vadose Zone, Hanford Site, Washington." Geochimica et Cosmochimica Acta 70(8):1873-1887 . doi:10.1016/j.gca.2005.10.037 Abstract An alkaline brine containing uranyl (UO22+) leaked to the thick unsaturated zone at the Hanford Site. X-ray and electron microprobe imaging showed that the uranium was associated with a minority of clasts, specifically granitic clasts occupying less than four percent of the sediment volume. XANES analysis at micron resolution showed the uranium to be hexavalent. The uranium was precipitated in microfractures as radiating clusters of uranyl silicates, and sorbed uranium was not observed on other surfaces. Compositional determinations of the 1-3 µm precipitates were difficult, but indicated a sodium potassium uranyl silicate, likely sodium boltwoodite. Observations suggested that uranyl was removed from pore waters by diffusion and precipitation in microfractures, where dissolved silica within the granite-equilibrated solution would cause supersaturation with respect to sodium boltwoodite. This hypothesis was tested using a diffusion reaction model operating at microscale. Conditions favoring precipitation were simulated to be transient, and driven by the compositional contrast between pore and fracture space. Pore-space conditions, including alkaline pH, were eventually imposed on the microfracture environment. However, conditions favoring precipitation were prolonged within the microfracture by reaction at the silicate mineral surface to buffer pH in a solubility limiting acidic state, and to replenish dissolved silica. During this time, uranyl was additionally removed to the fracture space by diffusion from pore space. Uranyl is effectively immobilized within the microfracture environment within the presently unsaturated vadose zone.
2006. "Characterization of the Human Pancreatic Islet Proteome by Two-Dimensional LC/MS/MS." Journal of Proteome Research 5(12):3345-3354. doi: 10.1021/pr060322n Abstract Research to elucidate the pathogenesis of type 1 diabetes mellitus has traditionally focused on the genetic and immunological factors associated with the disease, and, until recently, has not considered the target cell. While there have been reports detailing proteomic analyses of established islet cell lines or isolated rodent islets, the information gained is not always easily extrapolated to humans. Therefore, extensive characterization of the human islet proteome could result in better understanding of islet biology and lead to more effective treatment strategies. We have applied a two-dimensional LC-MS/MS-based analysis to the characterization of the human islet proteome, resulting in the detection of 29,021 unique peptides corresponding to 4,925 proteins. As expected, major islet hormones (insulin, glucagon, somatostatin), beta-cell enriched secretory products (IAPP), ion channels (K-ATP channel), and transcription factors (PDX-1, Nkx 6.1, HNF-1 beta) were detected. In addition, significant proteome coverage of metabolic enzymes and cellular pathways was obtained, including the insulin signaling cascade and the MAP kinase, NF-κβ, and JAK/STAT pathways. This work represents the most extensive characterization of the human islet proteome to date and provides a peptide reference library that may be utilized in future studies of islet biology and type 1 diabetes.
2006. "Application of Magnetic Resonance (MR) Imaging for the Development and Validation of Computational Fluid Dynamic (CFD) Models of the Rat Respiratory System." Inhalation Toxicology 18(10):787-794. doi: 10.1080/08958370600748729 Abstract Computational fluid dynamic (CFD) models of the respiratory system provide a quantitative, biological basis for extrapolating the localized dosimetry of inhaled materials and improving human health risk assessments based upon inhalation studies conducted in animals. Nevertheless, model development and validation have historically been tedious and time-consuming tasks that have traditionally limited CFD’s wider utilization for inhalation research. In recognition of this we previously reported on the use of proton (1H) Magnetic Resonance (MR) imaging for visualizing nasal-sinus passages in the rat, and on the use of three-dimensional (3D) image data for speeding computational mesh generation. Here, detailed 3D 1H MR imaging of pulmonary casts is reported, mesh generation is described in more detail, simulated gas-flows in nasal-sinus airways are presented, and the feasibility of validating CFD predictions with MR is tested by imaging the dynamics of hyperpolarized 3He at physiological flow rates in a straight pipe with a diameter comparable to the rat trachea. Results show that measured laminar flow structure is significantly blurred by rapid 3He diffusion but that the degree of blurring is generally predictable from the diffusion equation. Findings therefore support the notion that MR imaging is not only useful for defining airway architecture but also rapid CFD validation, and in this context, progress towards applications involving live animals and airway models is described.
2006. "Magnetic Resonance Imaging (MRI) of PEM Dehydration and Gas Manifold Flooding During Continuous Fuel Cell Operation." Journal of Power Sources 161(2):856-863. Abstract The methods, apparatus, and results are reported for in-situ, near real time, magnetic resonance imaging (MRI) of MEA dehydration and gas manifold flooding in an operating PEM fuel cell. To acquire high-resolution, artifact-free images for visualizing water distribution, acquisition parameters for a standard, two-dimensional (2D), spin-echo sequence were first optimized for the measured magnetic field heterogeneity induced by fuel cell components. 2D images of water inside the fuel cell were then acquired every 128 seconds during 11.4 hours of continuous operation under constant load. Collected images revealed that MEA dehydration proceeded non-uniformly across its plane, starting from gas inlets and ending at gas outlets, and that upon completion of this dehydration process manifold flooding began. To understand these observations, acquired images were correlated to the current output and operating characteristics of the fuel cell. Results demonstrate the power of MRI for in-situ, near real-time imaging of water distribution and non-uniformity in operating PEM fuel cells, and highlight its utility for understanding PEM fuel cell operation, the causes of cell failure, and for developing new strategies of water management.
2006. "Electron Density Redistribution Accounts for Half the Cooperativity of Alpha Helix Formation." Journal of Physical Chemistry B 110:4503-4505. doi:10.1021/jp057161f Abstract No abstract is available at this time for this article.
