Scientific Publications 2010
2010. "In Vivo MRI of Altered Proton Signal Intensity and T2 Relaxation in a Bleomycin Model of Pulmonary Inflammation and Fibrosis." Journal of Magnetic Resonance Imaging 31(5):1091-1099. doi:10.1002/jmri.22166 Abstract Purpose: The ability to distinguish lung inflammation and fibrosis using signal intensity (S0) and T2 relaxation measured with magnetic resonance imaging (MRI) was investigated. Materials and Methods: Three groups of rats (n=5) were instilled intratracheally with bleomycin (2.5 U/kg or 3.5 U/kg) in saline or with saline only. Rats were imaged before dosing and 1, 2, 4, and 7 weeks after. Imaging was performed at 2.0 T using a multi-echo pulse sequence (TE=6 ms). S0 and T2 of dosed animals were calculated on a pixel-by-pixel basis and compared to controls. At week 7, rats were sacrificed, left lungs were prepared for histological analysis, and right lungs were used to measure water and hydroxyproline (collagen) content. Results: Results show that S0xT2 is significantly correlated with water and collagen content in HD rats (p<0.05), and that MRI is sensitive to temporal changes in the lung. Conclusion: MRI can be used to confidently localize diseased lung regions using bivariate statistical analysis (p<0.05) but may lack the specificity required to distinguish mild inflammation from fibrosis. MRI may be particularly well suited for repeated follow-up imaging during therapeutic intervention when disease type is known or for evaluating animals in pre-clinical drug studies.
2010. "Electronic and defect structure of CuSCN." Journal of Physical Chemistry C 114(19):9111-9117. doi:10.1021/jp101586q Abstract We calculate the band structure, bonding characteristics and basic native defect configurations of hexagonal copper thiocyanate, -CuSCN, for the first time. -CuSCN is predicted to be an indirect-gap semiconductor with an unusual orbital character: While the highest valence bands have the expected character of Cu 3d levels hybridized with S 3p states, the conduction band minimum (at the K point of the hexagonal Brillouin zone) has mostly cyanide antibonding character. This quasi-molecular character results in some unusual properties, including that the electron effective masses are comparable or even larger than the hole effective masses. However, optical absorption measurements on polycrystalline films do not support the predicted indirect nature of the lowest transitions, though they also do not clearly contradict it. The dominant p-type character of this material is explained in terms of copper vacancies, possibly augmented by CN unit vacancies, which are expected to be acceptors. By contrast, a vacancy of a complete SCN unit would be a donor, but is not expected to occur at significant concentrations in this material.
2010. "Defect studies in ion irradiated AlGaN." Nuclear Instruments and Methods in Physics Research. Section B, Beam Interactions with Materials and Atoms 268(11-12):2056-2059. doi:10.1016/j.nimb.2010.02.055 Abstract Defects created in Al0.4Ga0.6N crystals by 320 keV Ar ion irradiation were studied by using RBS/C and TEM techniques. One of the main aims of the work was to use a new version of McChasy, a Monte – Carlo simulation code of backscattering spectra, for the analysis of experimental results obtained for a dislocations-containing crystal. Transmission Electron Microscopy technique was used to get a better insight into dislocation and dislocation loop geometries in order to restrict the range of parameters used in simulations. RBS/C analysis was performed in a 1.5 MeV – 3 MeV energy range in order to check if MC simulations correctly reproduce backscattering spectra at different energies.
2010. "Fractionation of Oxygen Isotopes in Phosphate during its Interactions with Iron Oxides." Geochimica et Cosmochimica Acta 74(4):1309-1319. doi:10.1016/j.gca.2009.11.010 Abstract Iron (III) oxides are ubiquitous in near-surface soils and sediments and interact strongly with dissolved phosphates via sorption, co-precipitation, mineral transformation and redox-cycling reactions. Iron oxide phases are thus, an important reservoir for dissolved phosphate, and phosphate bound to iron oxides should reflect dissolved sources as well as carry a history of the biogeochemical cycling of phosphorus (P). It has recently been demonstrated that dissolved inorganic phosphate (DIP) in rivers, lakes, estuaries and the open ocean can be used to distinguish different P sources and biological reaction pathways in the ratio of 18O/16O (18OP) in PO43-. Here we present results of experimental studies aimed at determining whether non-biological interactions between dissolved inorganic phosphate and solid iron-oxides involve fractionation of oxygen isotopes in PO4. Determination of such fractionations is critical to any interpretation of 18OP values of modern (e.g. hydrothermal iron oxide deposits, marine sediments, soils, groundwater systems) to ancient and extraterrestrial samples (e.g., BIF’s, Martian soils). Batch sorption experiments were performed using varied concentrations of synthetic ferrihydrite and isotopically- labeled dissolved ortho-phosphate at temperatures ranging from 4 to 95 oC. Mineral transformations and morphological changes were determined by X-Ray, Mössbauer spectroscopy and SEM image analyses. Our results reveal that isotopic fractionation between sorbed and aqueous phosphate occurs during the early phase of sorption with isotopically light phosphate preferentially incorporated into sorbed/solid phases. This fractionation showed negligible temperature-dependence and gradually decreased as a result of O-isotopic exchange between sorbed and aqueous phase phosphate, to become insignificant at greater than ~100 hours of reaction. In high-temperature experiments, this exchange was very rapid resulting in negligible fractionation between sorbed and aqueous-phase phosphate at much shorter reaction times. Mineral transformation resulted in initial preferential desorption/loss of light phosphate (P16O4) to solution. However, the continual exchange between sorbed and aqueous PO4, concomitant with this mineralogical transformation resulted again in negligible fractionation between aqueous and sorbed PO4 at long reaction times (> 2000 hrs). This finding is consistent with results obtained from natural ocean samples. This finding is important to the interpretation of PO4 O-isotope values in natural systems where iron-oxides are present and to studies of the biogeochemical cycling of P and PO4 biomarkers.
2010. "Amorphization of nanocrystalline 3C-SiC irradiated with Si+ ions." Journal of Materials Research 25(12):2341-2348. doi:10.1557/JMR.2010.0311 Abstract Irradiation induced amorphization in nanocrystalline and single crystal 3C-SiC has been studied using 1 MeV Si+ ions under the identical irradiation conditions at room temperature and 400 K. The disordering behavior has been characterized using in-situ ion channeling and ex-situ x-ray diffraction methods. The results show that, compared to single crystal 3C-SiC, full amorphization of small 3C-SiC grains (~3.8 nm in size) occurs at a slightly lower dose at room temperature. For grains with sizes of 3.0 - 3.8 nm, the amorphization dose is lower at room temperature than 400 K. A significantly lower dose for amorphization of smaller grains (2.0 nm in size) is observed at 400 K. The behavior has been interpreted based on the competition between the interface and interior amorphization.
2010. "Antibody Microarrays for High-Throughput, Multianalyte Analysis." Cancer Biomarkers 6(5-6):281-290. doi:10.3233/CBM-2009-0140 Abstract Enzyme-linked immunosorbent assay (ELISA) microarray technology promises to be a powerful tool for detecting and validating protein biomarkers, especially panels of biomarkers. ELISA microarrays are capable of high-throughput analysis of multiple proteins using small sample volumes. In this chapter we review the literature on the use of antibody microarrays for biomarker discovery and validation. We also described the methodologies we employ to obtain high-quality data through protocol optimization and data calibration.
2010. "Comparison of Aromatic Hydrocarbon Measurements made by PTR-MS, DOAS and GC-FID during the MCMA 2003 Field Experiment." Atmospheric Chemistry and Physics 10(4):1989-2005. Abstract A comparison of aromatic hydrocarbon measurements is reported for the CENICA upersite in the district of Iztapalapa during the Mexico City Metropolitan Area field experiment in April 2003 (MCMA 2003). Data from three different measurement methods were compared: a Proton Transfer Reaction Mass Spectrometer (PTR-MS), long path measurements using a UV Differential Optical Absorption Spectrometer (DOAS), and Gas Chromatography-Flame Ionization analysis (GC-FID) of canister samples. The principle focus was on the comparison between PTR-MS and DOAS data. Lab tests established that the PTR-MS and DOAS calibrations were consistent for a suite of aromatic compounds including benzene, toluene, p-xylene, ethylbenzene, 1,2,4-trimethylbenzene, phenol and styrene. The point sampling measurements by the PTR-MS and GC-FID showed good correlations (r=0.6), and were in reasonable agreement for toluene, C₂-alkylbenzenes and C3-alkylbenzenes. The PTR-MS benzene data were consistently high, indicating interference from ethylbenzene fragmentation for the 145 Td drift field intensity used in the experiment. Correlations between the open-path data measured at 16-m height over a 860-m path length (retroreflector in 430m distance), and the point measurements collected at 37-m sampling height were best for benzene (r=0.61), and reasonably good for toluene, C2-alkylbenzenes, naphthalene, styrene, cresols and phenol (r>0.5). There was good agreement between DOAS and PTR-MS measurements of benzene after correction for the PTR-MS ethylbenzene interference. Mixing ratios easured by DOAS were on average a factor of 1.7 times greater than the PTR-MS data for toluene, C2-alkylbenzenes, naphthalene and styrene. The level of agreement for the toluene data displayed a modest dependence on wind direction, establishing that spatial gradients - horizontal, vertical, or both – in toluene mixing ratios were significant, and up to a factor of 2 despite the fact that all measurements were conducted above roof level. Our analysis highlights a potential problem in defining a VOC sampling strategy that is meaningful for the comparison with photochemical transport models: meaningful measurements require a spatial fetch that is comparable to the grid cell size of models, which is typically a few 10 km2. Long-path DOAS measurements inherently average over a larger spatial scale than point measurements. The spatial representativeness can be further increased if observations are conducted outside the surface roughness sublayer, which might require measurements at altitudes as high as 10s of metres above roof level.
2010. "Mid-Gap Electronic States in Zn1 xMnxO." Physical Review. B, Condensed Matter 82(11):Art. No. 115202. Abstract Electronic absorption, magnetic circular dichroism, photoconductivity, and valence-band X-ray photoelectron (XPS) spectroscopic measurements were performed on epitaxial Zn1 xMnxO films to investigate the origin of the new mid-gap band that appears upon introduction of Mn2+ into the ZnO lattice. Absorption and MCD spectroscopies reveal Mn2+-related intensity at energies below the first excitonic transition of ZnO, tailing well into the visible energy region, with an onset at ~2.2 eV. Photoconductivity measurements show that excitation into this visible band generates mobile charge carriers, consistent with assignment as a Mn2+/3+ photoionization transition. XPS measurements reveal the presence of occupied Mn2+ levels just above the valence-band edge, supporting this assignment. Magnetic circular dichroism measurements additionally show a change in sign and large increase in magnitude of the excitonic Zeeman splitting in Zn1 xMnxO relative to ZnO, suggesting that sp-d exchange in Zn1 xMnxO is not as qualitatively different from those in other II-VI diluted magnetic semiconductors as has been suggested. The singular electronic structure feature of Zn1 xMnxO is its Mn2+/3+ ionization level within the gap, and the influence of this level on other physical properties of Zn1 xMnxO is discussed.
2010. "In Situ Reactivity and TOF SIMS Analysis of Surfaces Prepared by Soft and Reactive Landing of Mass Selected Ions." Analytical Chemistry 82(13):5718-5727. doi:10.1021/ac100734g Abstract An instrument has been designed and constructed that enables in situ reactivity and time of flight secondary ion mass spectrometry (TOF-SIMS) analysis of surfaces prepared or modified through soft- and reactive landing of mass-selected polyatomic cations and anions. The apparatus employs an electrospray ion source coupled to a high transmission electrodynamic ion funnel, two focusing collision quadrupoles, a large 19 mm diameter quadrupole mass filter, and a quadrupole bender that deflects the ion beam, thereby preventing neutral contaminants from impinging on the deposition surface. The ion soft landing apparatus is coupled to a commercial TOF-SIMS instrument permitting the introduction of surfaces into vacuum and SIMS analysis before and after ion deposition without breaking vacuum. To facilitate a comparison of the current TOF-SIMS instrument with the in situ Fourier transform ion cyclotron resonance (FT-ICR-SIMS) deposition apparatus constructed previously, dications of the cyclic peptide Gramicidin S (GS) and the photoactive organonometallic complex ruthenium tris-bipyridine (Ru(bpy)3) were soft landed onto fluorinated self-assembled monolayer (FSAM) on gold surfaces. In both cases similarities and differences were observed in the secondary ion mass spectra, with the TOF-SIMS results, in general, characterized by greater sensitivity, larger dynamic range, less fragmentation, and fewer in-plume reactions than the corresponding FT-ICR-SIMS spectra. The charge reduction kinetics of both the doubly and singly protonated GS cations on the FSAM surface were also examined as was the influence of the primary gallium ion (Ga+) flux on the efficiency of these processes. In addition, we demonstrate that the new instrument enables detailed studies of the reactivity of catalytically active species immobilized by soft- and reactive landing towards gaseous reagents.
2010. "Preparation of Surface Organometallic Catalysts by Gas-Phase Ligand Stripping and Reactive Landing of Mass-Selected Ions." Chemistry - A European Journal 16(48):14433-14438. doi:10.1002/chem.201002292 Abstract Organometallic complexes immobilized on surfaces combine the high selectivity of homogeneous catalysts with the ease of separation of catalyst from products of heterogeneous materials. Here we report a novel approach for the highly controlled preparation of surface organometallic catalysts by gas-phase ligand stripping combined with reactive landing of mass-selected ions onto self assembled monolayer surfaces. Collision induced dissociation is used to generate highly reactive undercoordinated metal complexes in the gas-phase for subsequent surface immobilization. Complexes with an open coordination shell around the metal center are demonstrated to show enhanced activity towards reactive landing in comparison to fully ligated species. In situ TOF-SIMS analysis indicates that the immobilized complexes exhibit behaviour consistent with catalytic activity when exposed to gaseous reagents.
2010. "Transition Metal Dopants Essential for Producing Ferromagnetism in Metal Oxide Nanoparticles." Physical Review. B, Condensed Matter 82(5):Art. No. 054419. doi:10.1103/PhysRevB.82.054419 Abstract Recent claims that ferromagnetism can be produced in nanoparticles of metal oxides without the presence of transition metal dopants has been refuted in this work by investigating 62 high quality well-characterized nanoparticle samples of both undoped and Fe doped (0-10% Fe) ZnO. The undoped ZnO nanoparticles showed zero or negligible magnetization, without any dependence on the nanoparticle size. However, chemically synthesized Zn₁₋xFexO nanoparticles showed clear ferromagnetism, varying systematically with Fe concentration. Furthermore, the magnetic properties of Zn₁₋xFexO nanoparticles showed strong dependence on the reaction media used to prepare the samples. The zeta potentials of the Zn₁₋xFexO nanoparticles prepared using different reaction media were significantly different, indicating strong differences in the surface structure. Electron paramagnetic resonance studies clearly showed that the difference in the ferromagnetic properties of Zn₁₋xFexO nanoparticles with different surface structures originate from differences in the fraction of the doped Fe³⁺ ions that are coupled ferromagnetically.
2010. "An Infrared Spectral Database for Detection of Gases Emitted by Biomass Burning." Vibrational Spectroscopy 53(1):97-102. doi:10.1016/j.vibspec.2010.02.010 Abstract We report the construction of a database of infrared spectra aimed at detecting the gases emitted by biomass burning (BB). The project uses many of the methods of the Pacific Northwest National Laboratory (PNNL) infrared database, but the selection of the species and special experimental considerations are optimized. Each spectrum is a weighted average derived from 10 or more individual measurements. Each composite has a spectral range from ≤ 600 cm-1 to ≥ 6500 cm-1 with an instrumental apodized resolution of 0.11 cm-1. The resolution was chosen to bring out all spectral features, but recognizing that pressure broadening at 760 Torr results in essentially all ro-vibrational lines having these or greater linewidths.
2010. "Characterization of the Decaheme c-Type Cytochrome OmcA in Solution and on Hematite Surfaces by Small Angle X-Ray Scattering and Neutron Reflectometry." Biophysical Journal 98(12):3035-3043. Abstract The outer membrane protein OmcA is an 85 kDa decaheme c-type cytochrome located on the surface of the dissimilatory metal-reducing bacterium Shewanella oneidensis MR-1. It is assumed to mediate shuttling of electrons to extracellular acceptors that include solid metal oxides such as hematite (a-Fe2O3). No information is yet available concerning OmcA structure in physiologically relevant conditions such as aqueous environments. We purified OmcA and characterized its solution structure by small angle x-ray scattering (SAXS), and its interaction at the hematite-water interface by neutron reflectometry. SAXS showed that OmcA is a monomer that adopts a flat ellipsoidal shape with an overall dimension of 34 x 90 x 65A˚ 3. To our knowledge, we obtained the first direct evidence that OmcA undergoes a redox state-dependent conformational change in solution whereby reduction decreases the overall length of OmcA by ~7 A˚ (the maximum dimension was 96 A˚ for oxidized OmcA, and 89 A˚ for NADH and dithionite-reduced OmcA). OmcA was also found to physically interact with electron shuttle molecules such as flavin mononucleotide, resulting in the formation of high-molecular-weight assemblies. Neutron reflectometry showed that OmcA forms a well-defined monomolecular layer on hematite surfaces, where it assumes an orientation that maximizes its contact area with the mineral surface. These novel insights into the molecular structure of OmcA in solution, and its interaction with insoluble hematite and small organic ligands, demonstrate the fundamental structural bases underlying OmcA’s role in mediating redox processes.
2010. "Electrochemically Controlled Atom by Atom Deposition of Gold to Polyaniline." Journal of the Electrochemical Society 157(10):P83-P87. doi:10.1149/1.3474932 Abstract Plyaniline (PANI) has been shown to be an effective matrix for hosting metal nanoclusters. In the case of gold, the tetrachloroaurate anion (AuCl₄) has a high affinity for the imine sites of polyaniline. Upon contract with PANI, AuCl₄ is spontaneously reduced to metallic gold, but the size of the formed Au clusters can not be precisely controlled. Herein, we report on electrochemical method of controlled deposition of one atom by one atom of gold per one imine site of PANI. By controlling the potential, we keep PANI in an oxidized state while exposing it to a solution of AuCl₄ to form a PANI*AuCl₄ complex. The AuCl₄ is reduced to atomic gold by sweeping the potential negative. That frees up the imine sites of PANI again and makes them accessible for the next Au deposition cycle. The repeated deposition of Au atoms follows a cyclic pathway. The amount of gold deposited using this method is consistent for each repeated cycle.
2010. "An investigation into the reactions of biochar in soil." Australian Journal of Soil Research 48(7):501-515. doi:10.1071/SR10009 Abstract Interactions between biochar, soil, microbes and plant roots may occur within a short period of time after application to the soil. The extent, rates and implications of these interactions, however, are far from being understood. This review includes a description of the properties of biochars and suggests possible reactions that may occur after the addition of biochars to soil. These include dissolution-precipitation, adsorption-desorption, acid-base and redox reactions. Special attention is given to reactions occurring within pores, and to interactions with roots, microorganisms and soil fauna. The examination of biochars (from chicken litter, greenwaste and paper mill sludges) weathered for one and two years in an Australian Ferrosol provides evidence for some of the mechanisms described in this review and offers an insight to reactions at a molecular scale. These interactions are biochar- and site-specific. Therefore, suitable experimental trials combining biochar types and different pedoclimatic conditions are needed to determine the extent to which these reactions influence the potential of biochar as a soil amendment and C-sequestration tool.
2010. "Trypsin coatings on electrospun and alcohol-dispersed polymer nanofibers for trypsin digestion column." Analytical Chemistry 82(18):7828 - 7834. doi:10.1021/ac101633e Abstract The construction of a trypsin reactor in a chromatography column for rapid and efficient protein digestion in proteomics is described. Electrospun and alcohol-dispersed polymer nanofibers were used for the fabrication of highly stable trypsin coating, which was prepared by a two-step process of covalent attachment and enzyme crosslinking. In a comparative study with the trypsin coatings on asspun and non-dispersed nanofibers, it has been observed that a simple step of alcohol dispersion improved not only the enzyme loading but also the performance of protein digestion. In-column digestion of enolase was successfully performed in less than twenty minutes. By applying the alcohol dispersion of polymer nanofibers, the bypass of samples was reduced by filling up the column with well-dispersed nanofibers, and subsequently, interactions between the protein and the enzymes were improved yielding more complete and reproducible digestions. Regardless of alcohol-dispersion or not, trypsin coating showed better digestion performance and improved performance stability under recycled uses than covalently-attached trypsin. The combination of highly stable trypsin coating and alcoholdispersion of polymer nanofibers has opened up a new potential to develop a trypsin column for on-line and automated protein digestion.
2010. "Integrated Post-Experiment Monoisotopic Mass Refinement: An Integrated Approach to Accurately Assign Monoisotopic Precursor Masses to Tandem Mass Spectrometric Data." Analytical Chemistry 82(20):8510-8518. doi:10.1021/ac101388b Abstract Accurate assignment of monoisotopic precursor masses to tandem mass spectrometric (MS/MS) data is a fundamental and critically important step for successful peptide identifications in mass spectrometry based proteomics. Here we describe an integrated approach that combines three previously reported methods of treating MS/MS data for precursor mass refinement. This combined method, “integrated Post-Experiment Monoisotopic Mass Refinement” (iPE MMR), integrates steps: 1) generation of refined MS/MS data by DeconMSn, 2) additional refinement of the resultant MS/MS data by a modified version of PE-MMR, and 3) elimination of systematic errors of precursor masses using DtaRefinery. iPE-MMR is the first method that utilizes all MS information from multiple MS scans of a precursor ion and multiple charge states of it in an MS scan to determine precursor mass. By combining the synergistic features of each of method, iPE MMR increases sensitivity in peptide identification and provides increased accuracy when applied to complex high-throughput proteomics data. iPE MMR also allows incorporating additional data processing step(s) or skipping step(s), if necessary, to enable new developments or applications of the tools, as each step of iPE MMR produces output data in a common and conventional format used in proteomics data processing.