Scientific Publications 2008
2008. "Binding and Direct Electrochemistry of OmcA, an Outer-Membrane Cytochrome from an Iron Reducing Bacterium, with Oxide Electrodes: A Candidate Biofuel Cell System." Inorganica Chimica Acta 361(3):769-777. doi:10.1016/j.ica.2007.07.015 Abstract Dissimilatory iron-reducing bacteria transfer electrons to solid ferric respiratory electron acceptors. Outer-membrane cytochromes expressed by these organisms are of interest in both microbial fuel cells and biofuel cells. We use optical waveguide lightmode spectroscopy (OWLS) to show that OmcA, an 85 kDa decaheme outer-membrane c-type cytochrome from Shewanella oneidensis MR-1, adsorbs to isostructural Al2O3 and Fe2O3 in similar amounts. Adsorption is ionic-strength and pH dependent (peak adsorption at pH 6.5–7.0). The thickness of the OmcA layer on Al2O3 at pH 7.0 [5.8 ± 1.1 (2r) nm] from OWLS is similar, within error, to that observed using atomic force microscopy (4.8 ± 2 nm). The highest adsorption density observed was 334 ng cm 2 (2.4 · 1012 molecules cm 2), corresponding to a monolayer or 9.9 nm diameter spheres or submonolayer coverage by smaller molecules. Direct electrochemistry of OmcA on Fe2O3 electrodes was observed using cyclic voltammetry, with cathodic peak potentials of 380 to 320 mV versus Ag/AgCl. Variations in the cathodic peak positions are speculatively attributed to redox-linked conformation change or changes in molecular orientation. OmcA can exchange electrons with ITO electrodes at higher current densities than with Fe2O3. Overall, OmcA can bind to and exchange electrons with several oxides, and thus its utility in fuel cells is not restricted to Fe2O3.
2008. "An Automated Self-similarity Analysis of the Pulmonary Tree of the Sprague-Dawley Rat." The Anatomical Record 291(12):1628-1648. doi:10.1002/ar.20771 Abstract Abstract In this study, we present an automated method for tabulating geometric information of biological trees, based on magnetic resonance imaging data of silicone casts of the pulmonary airway trees of Sprague Dawley rats. From a segmentation of the airway tree, we construct a scale-invariant triangulated surface that is subsequently distilled into a connected graph, representing the airway centerline. Segment statistics are derived from this graph. To validate the method, these statistics are compared to manual measurements of a single lung cast. Subsequently, we analyze the morphometry of the airway tree by assembling individual airway segments into structures that span multiple generations, which we call branches. We show that branches not segments are the fundamental repeating unit in the rat lung and develop a parameterization of these structures for the entire lung. Our analysis shows that airway diameters and lengths have both a deterministic and stochastic character and can be described by a simple set of equations.
2008. "The Influence of Cultivation Methods on Shewanella oneidensis Physiology and Proteome Expression ." Archives of Microbiology 189(4):313-324. doi:10.1007/s00203-007-0321-y Abstract High-throughput analyses that are central to microbial systems biology and ecophysiology research benefit from highly homogeneous and physiologically well-defined cell cultures. While attention has focused on the technical variation associated with high-throughput technologies, biological variation introduced as a function of cell cultivation methods has been overlooked. This study evaluated the impact of cultivation methods, controlled batch or continuous culture in bioreactors versus shake flasks, on the reproducibility of global proteome measurements in Shewanella oneidensis MR-1. Variability in dissolved oxygen concentration and consumption rate, metabolite profiles, and proteome was greater in shake flask than controlled batch or chemostat cultures. Proteins indicative of suboxic and anaerobic growth (e.g., fumarate reductase and decaheme c-type cytochromes) were more abundant in cells from shake flasks compared to bioreactor cultures, a finding consistent with data demonstrating that “aerobic” flask cultures were O2 deficient due to poor mass transfer kinetics. The work described herein establishes the necessity of controlled cultivation for ensuring highly reproducible and homogenous microbial cultures. By decreasing cell to cell metabolic variability, higher quality samples will allow for the interpretive accuracy necessary for drawing conclusions relevant to microbial systems biology research.
2008. "Electrodeposition of Technetium on Platinum for Thermal Ionization Mass Spectrometry (TIMS)." Journal of Radioanalytical and Nuclear Chemistry 276(2):493-498. doi:10.1007/s10967-008-0532-y Abstract A novel device has been fabricated for the electrodeposition of technetium metal onto platinum filaments for thermal ionization mass spectrometric (TIMS) measurements. The ability of the device to focus the deposition to diameters of hundreds of micrometers on pre-mounted TIMS filaments coupled with the ease of use and simplicity of design permit for an extremely sensitive yet economical TIMS filament loading technique. Electrodeposition parameters were varied in order to maximize deposition efficiency. X-ray photoelectron spectroscopy (XPS) was used to confirm and characterize the technetium deposit. The technetium is deposited in the metallic state, although surface oxides in the 4+ and 7+ state form readily. Initial TIMS measurements of the electrodeposited technetium in the presence of a barium sulfate ionization enhancer show potential for excellent sensitivity.
2008. "Carbonate Formation and Stability on a Pt/BaO/γ-Al2O3 NOx Storage/Reduction Catalyst." Journal of Physical Chemistry C 112(29):10952-10959. doi:10.1021/jp712180q Abstract There has been recent debate regarding the role or influence of BaCO3 species on the performance or operation of Pt/BaO/Al2O3 model NOx storage/reduction (NSR) catalysts. This influence is primarily regarded as negative, but the extent of its impact is not clear. For this reason, the formation and stability of barium carbonate species on a Pt/BaO/Al2O3 model NSR catalyst were characterized using Fourier transform infra-red (FTIR) spectroscopy. The catalyst sample was exposed to CO2, CO and CO + O2 at various temperatures, from 300K to >500K. Bidentate carbonate species readily form under all conditions while, at higher temperatures, unidentate species were also observed and likely formed from bidentate species as a result of a change in their coordination to the oxide surface. Reaction of COx species with residual hydroxide species on the catalyst led to the formation of bicarbonates, and when the sample was exposed to CO at low temperature, formate species were also formed. These formate species decomposed at elevated temperatures and contributed to the formation of carbonates. H2O exposure resulted in the agglomeration of various COx-containing phases to larger particles.
2008. "Role of the global transcriptional regulator PrrA in Rhodobacter sphaeroides 2.4.1: combined transcriptome and proteome analysis." Journal of Bacteriology 190(14):4831-4848. doi:10.1128/JB.00301-08 Abstract The PrrBA two-component regulatory system is a major global regulator in Rhodobacter sphaeroides 2.4.1. In this study we have compared the transcriptome and proteome profiles of the wild type (WT) and mutant PrrA2 cells grown anaerobically, in the dark, with DMSO as electron acceptor. Approximately 25% of the genes present in the genome are PrrA-regulated, at the transcriptional level, either directly or indirectly, by ≥ 2-fold relative to wild type. The genes affected are widespread throughout all COG functional categories, with previously unsuspected “metabolic” genes affected when in the PrrA mutant background. PrrA was found to act both as an activator and a repressor of transcription, with more genes being repressed in the presence of PrrA (9:5 ratio). An analysis of the genes encoding the 1,536 peptides detected through our chromatographic study, which corresponds to 36% coverage of the genome, revealed that approximately 20% of the genes encoding these proteins were positively regulated, whereas approximately 32% were negatively regulated by PrrA, which is in excellent agreement with the percentages obtained for the whole genomic transcriptome profile. In addition, comparison of the transcriptome and proteome mean parameter values chosen between WT and PrrA2 showed good qualitative agreement, indicating that transcript regulation paralleled the corresponding protein abundance, although not one for one. The microarray analysis was validated by direct mRNA measurement of randomly selected, both positively and negatively regulated genes. lacZ transcriptional and kan translational fusions enabled us to map putative PrrA binding sites, as well as revealing potential gene targets for indirect regulation by PrrA.
2008. "Electron-Driven Acid-Base Chemistry: Proton Transfer from Hydrogen Chloride to Ammonia." Science 319(5865):936-939. doi:10.1126/science.1151614 Abstract It is well established that NH3 and HCl form in isolation a hydrogen bonded complex NH3…HCl rather than an ionic salt, NH4+Cl-. This experimental and theoretical study utilized anion photoelectron spectroscopy and ab initio theory to investigate the effect of an excess electron on the hydrogen bonded complex NH3 …HCl. Our results indicate that one electron is sufficient to drive the hydrogen bonded complex to form the ionic salt. We propose a stepwise mechanism for this process involving an initial dipole-bound state, followed by the formation of a distorted Rydberg species, NH40.