Scientific Publications 2007
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2007. "Uranium Removal from Groundwater via In Situ Biostimulation: Field-Scale Modeling of Transport and Biological Processes." Journal of Contaminant Hydrology 93(2007):216-235. doi:10.1016/j.jconhyd.2007.02.005 Abstract During 2002 and 2003, bioremediation experiments in the unconfined aquifer of the Old Rifle UMTRA field site in western Colorado provided evidence for the immobilization of hexavalent uranium in groundwater by iron-reducing Geobacter sp. stimulated by acetate amendment. As the bioavailable Fe(III) terminal electron acceptor was depleted in the zone just downgradient of the acetate injection gallery, sulfate-reducing organisms came to dominate the microbial community. In the present study, we use multicomponent reactive transport modeling to analyze data from the 2002 field experiment to 1) identify the dominant transport and biological processes controlling uranium mobility during biostimulation, 2) determine field-scale parameters for these modeled processes, and 3) apply the calibrated process models to history match observations during the 2003 field experiment. In spite of temporally and spatially variable observations during the field-scale biostimulation experiments, the coupled process simulation approach was able to establish a quantitative characterization of the principal flow, transport, and reaction processes that could be applied without modification to describe the 2003 field experiment. Insights gained from this analysis include field-scale estimates of bioavailable Fe(III) mineral, and the magnitude of uranium bioreduction during biostimulated growth of the iron-reducing and sulfate-reducing microorganisms.
2007. "Driving Force for the WO3(001) Surface Relaxation." Surface Science 601(6):1481-1488. doi:doi:10.1016/j.susc.2007.01.013 Abstract The optimized structure of the WO3(001) surface with various types of termination ((1x1)O, (1x1) WO2, and c(2x2)O) has been simulated using density functional theory with the Perdew-Wang 91 gradient-corrected exchange correlation functional. While energy of bulk WO3 depends weakly on the distortions and tilting of the WO6 octahedra, relaxation the (001) surface results in a significant decrease of surface energy (from 10.2x10-2 eV/Å2 for bulk-extracted, ReO3-like, c(2x2)O-terminated surface to 2.2x10-2 eV/Å2 for the relaxed surface). This feature illustrates important role of surface in formation of crystalline nano-size clusters of WO3. The surface relaxation is accompanied by a dramatic redistribution of density of states near the Fermi level, in particular the transformations of surface electronic states. This redistribution is responsible for the decrease of electronic energy and therefore is suggested to be the driving force for surface relaxation of the WO3(001) surface and, presumably, similar surfaces of other transition metal oxides. Battelle operates PNNL for the USDOE.
2007. " Identification of a novel mitotic phosphorylation motif associated with protein localization to the mitotic apparatus." Journal of Cell Science 120(22):4060-70. doi:10.1242/jcs.014795 Abstract The chromosomal passenger complex (CPC) is a critical regulator of chromosome, cytoskeleton and membrane dynamics during mitosis. Here, we identified phosphopeptides and phosphoprotein complexes recognized by a phosphorylation specific antibody that labels the CPC using liquid chromatography coupled to mass spectrometry. A mitotic phosphorylation motif (PX{G/T/S}{L/M}[pS]P or WGL[pS]P) was identified in 11 proteins including Fzr/Cdh1 and RIC-8, two proteins with potential links to the CPC. Phosphoprotein complexes contained known CPC components INCENP, Aurora-B and TD-60, as well as SMAD2, 14-3-3 proteins, PP2A, and Cdk1, a likely kinase for this motif. Protein sequence analysis identified phosphorylation motifs in additional proteins including SMAD2, Plk3 and INCENP. Mitotic SMAD2 and Plk3 phosphorylation was confirmed using phosphorylation specific antibodies, and in the case of Plk3, phosphorylation correlates with its localization to the mitotic apparatus. A mutagenesis approach was used to show INCENP phosphorylation is required for midbody localization. These results provide evidence for a shared phosphorylation event that regulates localization of critical proteins during mitosis.
2007. "Applying a Targeted Label-free Approach using LC-MS AMT Tags to Evaluate Changes in Protein Phosphorylation Following Phosphatase Inhibition." Journal of Proteome Research 6(11):4489-4497. doi:10.1021/pr070068e Abstract To identify phosphoproteins regulated by the phosphoprotein phosphatase (PPP) family of S/T phosphatases, we performed a large-scale characterization of changes in protein phosphorylation on extracts from HeLa cells treated with or without calyculin A, a potent PPP enzyme inhibitor. A label-free comparative Phosphoproteomics approach using immobilized metal ion affinity chromatography and targeted tandem mass spectrometry was employed to discover and identify signatures based upon distinctive changes in abundance. Overall, 232 proteins were identified as either direct or indirect targets for PPP enzyme regulation. Most of the present identifications represent novel PPP enzyme targets at the level of both phosphorylation site and protein. These include phosphorylation sites within signaling proteins such as p120 Catenin, A Kinase Anchoring Protein 8, JunB, and Type II Phosphatidyl Inositol 4 Kinase. These data can be used to define underlying signaling pathways and events regulated by the PPP family of S/T phosphatases.
2007. "A Complete NMR Spectral Assignment of the Lipid-free Mouse Apolipoprotein A-I (ApoAI) C-terminal Truncation Mutant, ApoAI(1-216)." Biomolecular NMR Assignments 1(1):109-111. doi:10.1007/s12104-007-9031-2 Abstract Apolipoprotein A-I (apoAI) is the major protein component of the high-density lipoprotein (HDL) that has been a hot subject of interests because of its anti-atherogenic properties. Upon lipid-binding, apoAI undergoes conformational changes from lipid-free to several different HDL-associated states (1). These different conformational states regulate HDL formation, maturation and transportation. Recent crystal structure of lipid-free human apoAI represents a major progress of structural study of lipid-free apoAI (2). However, no structural is available for lipid-free mouse apoAI (240-residues). Since mouse HDL is homogenous with only HDL2-like size, whereas human HDL is heterogeneous, containing HDL2/HDL3 as its main species, a structural comparison between human and mouse apoAI may allow us to identify structure basis of HDL size distribution difference between human and mouse. We carried out an NMR structure determination of lipid-free mouse apoAI (1-216) and completely assigned backbone atoms (except backbone amide proton and nitrogen atoms for residues D1, N48, W107, K108, K132, E135, F147, R148, M169 and K203). Secondary structure prediction using backbone NMR parameters indicates that lipid-free mouse apoAI consists of a four helical segments in the N-terminal domain, residues 1-180. In addition, two short helices are also observed between residues 190-195 and 210-215. The helix locations are significantly different from those in the crystal structure of human apoAI, suggesting that mouse apoAI may have a different conformational adaptation upon lipid-binding. BMRB deposit with accession number: 15091.
2007. "Effect of the Surface Morphology on the Energy Transfer in Ion-Surface Collisions." International Journal of Mass Spectrometry 265(1):124-129. doi:10.1016/j.ijms.2007.01.018 Abstract Time- and energy-resolved surface-induced dissociation (SID) of singly protonated des-Arg1-bradykinin (PPGFSPFR) combined with RRKM modeling was used to explore the effect of surface morphology on the energy transfer in collisions of large ions with surfaces. Experiments were performed in a Fourier Transform ion cyclotron resonance mass spectrometer (FT-ICR MS) specially configured for SID studies. Massselected and vibrationally relaxed ions were collided with three diamond surfaces of varying degree of roughness. The results demonstrate that internal energy distributions resulting from collisions of large ions with surfaces are rather independent of the surface morphology: the translational to vibrational (T→V) energy transfer efficiency is 19.5±0.5% for all three diamond surfaces. However, the scattered ion signal increases with decrease in the degree of roughness of the SID target suggesting that smooth diamond surfaces are better targets for analytical applications.
2007. "Microanalyzer for Biomonitoring of Lead (Pb) in Blood and Urine ." Analytical and Bioanalytical Chemistry 387(1):335-341. doi:10.1007/s00216-006-0940-1 Abstract Biomonitoring of lead (Pb) in blood and urine enables quantitative evaluation of human occupational and environmental exposures to Pb. The state-of-the-art ICP-MS instruments analyze metals in laboratories, resulting in lengthy turn around time, and are expensive. In response to the growing need for metal analyzer for on-site, real-time monitoring of trace metals in individuals, we developed a portable microanalyzer based on flow-injection / adsorptive stripping voltammetry and used it to analyze Pb in rat blood and urine. Fouling of electrodes by proteins often prevents the effective use of electrochemical sensors in biological matrices. Minimization of such fouling was accomplished with the suitable sample pretreatment and the turbulent flowing of Pb contained blood and urine onto the glassy electrode inside the microanalyzer, which resulted in no apparent electrode fouling even when the samples contained 50% urine or 10% blood by volume. There was no matrix effect on the voltammetric Pb signals even when the samples contained 10% blood or 10% urine. The microanalyzer offered linear concentration range relevant to Pb exposure levels in human (0-20 ppb in 10%-blood samples, 0-50 ppb in 50%-urine samples). The device had excellent sensitivity and reproducibility; Pb detection limits were 0.54 ppb and 0.42 ppb, and % RSDs were 4.9 and 2.4 in 50%-urine and 10%-blood samples, respectively. It offered a high throughput (3 min per sample) and had economical use of samples (60 µL per measurement), making the collection of blood being less invasive especially to children, and had low reagent consumption (1 µg of Hg per measurement), thus minimizing the health concerns of mercury use. Being miniaturized in size, the microanalyzer is portable and field-deployable. Thus, it has a great potential to be the next-generation analyzer for biomonitoring of toxic metals.
2007. "Removal of Heavy Metals from Aqueous Systems with Thiol Functionalized Superparamagnetic Nanoparticles." Environmental Science & Technology 41(14):p.5114-5119. doi:10.1021/es0705238 Abstract We have shown that superparamagnetic iron oxide (Fe3O4) nanoparticles with a surface functionalization of dimercaptosuccinic acid is an effective, magnetic, sorbent material for toxic metals such as Hg, Ag, Pb, Cd and other soft cations. The chemical affinity, stability, capacity and kinetics of the functionalized nanoparticles has been explored and compared to conventional resin based sorbents and nanoporous silica materials with similar surface chemistries.
2007. "Electrochemical Sensors for the Detection of Lead and Other Toxic Heavy Metals: The Next Generation of Personal Exposure Biomonitors." Environmental Health Perspectives 115(12):1683-1690. Abstract To support the development and implementation of biological monitoring programs, accurate and quantitative technologies for measuring xenobiotic exposure are needed. Micro-analytical based sensors that work with complex biomatrices such as blood, urine or saliva are being developed and validated. These sensor platforms will improve our ability to make definitive associations between chemical exposures and disease. Among toxic heavy metals, lead (Pb) continues to be one of the most problematic. Despite a considerable effort to identify and eliminate Pb exposure sources, this metal still remains a significant health concern, particularly for young children. Ongoing research is focused on the development and validation of portable metal analyzers that have many advantages over current available technologies, thus having the potential to become the next-generation of toxic metal analyzers. This review will highlight the development and validation of two classes of metal analyzers for the voltammetric detection of Pb, this includes: (1) a metal analyzer based on flow injection analysis and anodic stripping voltammetry (ASV) at a Hg-film electrode, and (2) mercury-free metal analyzers employing adsorptive stripping voltammetry (AdSV) and novel nanostructure materials which include the self-assembled monolayers on mesoporous supports (SAMMS) and carbon nanotubes (CNTs). These sensors have been optimized to detect Pb in urine, blood, and saliva as accurately as the state-of-the-art-ICP-MS with high reproducibility, and sensitivity, while being much more portable, field-deployable and less expensive than conventional analytical methods. It is anticipated that these improved and portable analytical sensor platforms will facilitate our ability to conduct a meaningful biological monitoring program that will enable us to have a greater understanding of the relationship between chemical exposure assessment and disease outcomes. Keywords: biomonitoring, lead (Pb), sensors, dosimetry technology, exposure assessment
2007. "D2O Adsorption on an Ultrathin Alumina Film on NiAl(110)." Journal of Physical Chemistry C 111(47):17597-17602. doi:10.1021/jp074459s Abstract The structure of an ordered, ultra-thin Al2O3 film grown on a NiAl(110) single-crystal surface and its interaction with D2O were studied by low energy ion scattering spectroscopy (LEISS), X-ray photoelectron spectroscopy (XPS), temperature programmed desorption (TPD) and infrared reflection absorption spectroscopy (IRAS). LEISS demonstrated that the surface was terminated by an oxygen layer, and TPD data of adsorbed D2O revealed that most of the water molecularly adsorbed onto Al2O3/NiAl(110). However, we observed that a small amount of water molecules dissociated during adsorption and/or TPD measurements, and as a consequence the alumina film thickness increased after water adsorption/desorption. These results suggest that atomic oxygen and/or hydroxyl species, which are formed by dissociation of water, interact with sub-surface aluminum atoms through defects sites and cause the increase in the alumina film thickness. In addition, due to the weak interaction between adsorbed water molecules and the alumina film, a few monolayer of water can be transformed from amorphous solid water (ASW) to crystalline ice (CI) phase, as it was seen by IRAS.
2007. "The interaction of NO2 with BaO: from cooperative adsorption to Ba(NO3)2 formation." Journal of Physical Chemistry C 111(42):15299-15305. doi:10.1021/jp074179c Abstract The effect of water on the morphology of BaO/Al2O3-based NOx storage materials was investigated using Fourier transform infrared spectroscopy, temperature programmed desorption, and time-resolved synchrotron X-ray diffraction techniques. The results of this multi-spectroscopy study reveal that, in the presence of water, surface Ba-nitrates convert to bulk nitrates, and water facilitates the formation of large Ba(NO3)2 particles. The conversion of surface to bulk Ba-nitrates is completely reversible, i.e. after the removal of water from the storage material a significant fraction of the bulk nitrates re-convert to surface nitrates. NO2 exposure of a H2O-containing (wet) BaO/Al2O3 sample results in the formation of nitrites and bulk nitrates exclusively, i.e. no surface nitrates form. After further exposure to NO2, the nitrites completely convert to bulk nitrates. The amount of NOx taken up by the storage material is, however, essentially unaffected by the presence of water, regardless of whether the water was dosed prior to or after NO2 exposure. Based on the results of this study we are now able to explain most of the observations reported in the literature on the effect of water on NOx uptake on similar storage materials.
2007. "Understanding Practical Catalysts Using a Surface Science Approach: The Importance of Strong Interaction between BaO and Al2O3 in NOx Storage Materials." Journal of Physical Chemistry C 111(41):14942-14944. doi:10.1021/jp0763376 Abstract Modern surface science techniques have been commonly applied to understand issues arising from practical catalytic systems.[1-4] However, the applicability of most of the results obtained from model systems has been limited, due, primarily, to the vastly different conditions studies on model and practical systems are carried out (catalyst composition, reaction conditions etc.).[5, 6] Therefore, the need to conduct experiments on compositionally similar systems (model and practical) is necessary to obtain valuable information on the workings of real catalysts. In this communication we demonstrate the utility of surface science studies on model catalysts in understanding the properties of high surface area, BaO-based NOx storage-reduction (NSR) catalysts.[7] We present evidence for the facile formation of surface barium aluminate-like species even at very low coverages of BaO. This Ba-aluminate layer, however, can react with NO2 resulting in the formation of a bulk-like Ba(NO3)2 phase. In order to construct model catalysts that are representative of the practical NOx storage systems, we first needed to estimate the BaO covareges on the high surface area catalysts. Since the publication of the work by Fanson et al.[8], BaO loadings of 8 – 10 wt.% on a γ-alumina support (200 m2/g) have been regarded as corresponding to one monolayer (ML) coverage, based on the unit cell size of bulk BaO. The coverage equivalent of one ML, however, was significantly underestimated. Assuming complete spreading of the BaO layer and using a Ba–O distance of ~ 2.77 Å (one unit of BaO occupies 1.53 × 10-19 m2), 10 wt.% loading of BaO would cover only about 1/3 of the alumina surface. Table 1 shows our calculated estimates of two-dimensional BaO coverages as a function of loading on a -Al2O3 surface (200 m2/g) based on the lattice parameters of bulk BaO[9] (5.54 Å). Based on these values, for our model system studies we prepared BaO/Al2O3/NiAl(110) materials in which the BaO coverages were very close to those of 4, 8, and 20 wt.% BaO/γ-Al2O3 high surface area catalysts used in prior studies.
2007. "Correlation between fundamental binding forces and clinical prognosis of Staphylococcus aureus infections of medical implants." Langmuir 23(5):2289-2292. Abstract Implanted medical devices (e.g., prosthetic heart valves, permanent pacemakers) significantly improve the quality of life for many humans. However, a common clinical observation is that such devices become colonized with potentially life-threatening Staphylococcus aureus biofilms, which are difficult to combat with host defenses or antibiotics. This study attempts to draw a correlation between the clinical outcome of patients with implanted cardiac devices and the fundamental binding forces ultimately responsible for the initiation of an S. aureus biofilm in-situ. Atomic force microscopy was used to measure forces between a fibronectin-coated probe (simulating a prosthetic implant) and 15 different strains of S. aureus isolated from either patients with infected cardiac devices (invasive population) or healthy human subjects (control population). The fibronectin-coated probe was repeatedly brought into and out of contact with a bacterium’s surface, “fishing” for a reaction with the cell’s fibronectin-binding proteins. More than 40,000 force profiles were measured on 5-10 different cells for each of the 15 clinical strains. A unique force-signature was observed for a binding event between the fibronectin-coated probe and the bacteria. When grouped by the frequency of this force-signature, there was a strong distinction (p=0.01) between the invasive and control populations of S. aureus. This discovery suggests that biofilm forming bacteria may be classified according to their “force taxonomy”, which could have a positive effect on health care as it bridges the long-standing disconnect between macroscopic, clinical investigations and nanometer-scale forces ultimately responsible for a bond between S. aureus and the surface of a prosthetic device.
2007. "Correlation between fundamental binding forces and clinical prognosis of Staphylococcus aureus infections of medical implants." Langmuir 23:2289-2292. Abstract Atomic force microscopy was used to “fish” for binding reactions between a fibronectin-coated probe (i.e., substrate simulating an implant device) and each of 15 different strains of S. aureus isolated from either patients with infected cardiac prosthesis (invasive group) or healthy human subjects (control group). There is a strong distinction (p=0.01) in the binding force-signature observed for the invasive vs. control populations. This observation suggests that a microorganism’s “force taxonomy” may provide a fundamental and practical indicator of the risk that bacterial infections pose to patients with implanted medical devices.
2007. "Epitaxial Growth and Microstructure of Cu2O Nanoparticle/thin Films on SrTiO3(100)." Nanotechnology 18:Art. No. 115601. doi:10.1088/0957-4484/18/11/115601 Abstract Cuprous oxide (Cu2O) was grown on SrTiO3 (STO)(100) by oxygen plasma assisted molecular beam epitaxy. Microstructure of the grown layer and Cu valence state were analyzed using x-ray diffraction (XRD), x-ray photo-electron spectroscopy (XPS), atomic force microscopy (AFM), and cross-sectional transmission electron microscopy (TEM) as well as electron diffractions. The grown layer was dominated by Cu2O phase, possessing an epitaxial orientation with the substrate such that: Cu2O[001]//STO[001] and Cu2O(100)//STO(100). Cu2O film morphologically shows dependence on the growth rate. Typically, a fast growth will lead to the formation of a thin film with a relatively smooth surface. A slow growth will lead to the development of nanoparticles, featuring the formation of Cu2O pyramid. The pyramids are invariantly defined by the Cu2O {111} planes. Given the fact that the {111} planes correspond to the lowest surface energy of Cu2O, a slow growth will lend the system enough time to allow it to adopt the pyramid configuration by which the overall energy of the system was minimized.
2007. "Synthesis and Characterization of Compositionally Graded Si1-xGex Layers on Si substrate." Nuclear Instruments and Methods in Physics Research. Section B, Beam Interactions with Materials and Atoms 261(1-2):723-726. Abstract Thin film of silicon germanium (Si1-xGex) with tailored composition was grown on Si (100) substrate at 650oC in an ultrahigh vacuum molecular beam epitaxy system. The nominal x-value is ranged from 0 to 0.14. The quality of the film was investigated by Rutherford backscattering spectrometry (RBS) in random and channeling geometries, glancing angle x-ray diffraction (XRD), x-ray photoelectron spectroscopy (XPS), high resolution transmission electron microscopy (HRTEM), energy dispersive x-ray spectroscopy (EDX), and atomic force microscopy (AFM). RBS/Channeling measurements indicate that the strain associated with lattice mismatch is compressive in the film. Both RBS and EDX analyses indicate the compositional graded incorporation of Ge in the film with x ranging from 0 to 0.14. The film shows island growth with each island centering around an interface dislocation.
