Scientific Publications 2010
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B
2010. "Role of Extracellular Polymeric Substances in Bioflocculation of Activated Sludge Microorganisms under Glucose‐Controlled Conditions." Water Research 44(2010):4505-4516. doi:10.1016/j.watres.2010.06.024 Abstract Extracellular polymeric substances (EPS) secreted by suspended cultures of microorganisms from an activated sludge plant in the presence of glucose was characterized in detail using colorimetric analysis, X‐ray photoelectron spectroscopy (XPS) and Fourier transform infrared (FTIR) spectroscopy. EPS produced by the mixed population were similar to literature reports obtained from pure cultures in terms of functionalities with respect to C and O but differed subtly in terms of N and P. Hence, it appears that EPS produced by different microorganisms maybe similar in major chemical constituents but may differ in minor components. The role of specific EPS constituents on microbial aggregation was also determined. The weak tendency of microorganisms to bioflocculate during the exponential growth phase was attributed to electrostatic repulsion when EPS concentration was low and acidic in nature (higher fraction of uronic acids to total EPS). However, during the stationary phase, polymeric interactions overwhelmed electrostatic interactions (lower fraction of uronic acids to total EPS) resulting in greater bioflocculation. More specifically, microorganisms appeared to aggregate in the presence of protein secondary structures including aggregated strands, β−sheets, α− and 3−turn helical structures. Bioflocculation was also favored by increasing O‐acetylated carbohydrates and overall C−(O,N) and O=C–OH + O=C–OR functionalities.
2010. "Application of Surface Chemical Analysis Tools for Characterization of Nanoparticles." Analytical and Bioanalytical Chemistry 396(3):983-1002. Abstract The important role that surface chemical analysis methods can and should play in the characterization of nanoparticles is described. The types of information that can be obtained from analysis of nanoparticles using Auger electron spectroscopy (AES); X-ray photoelectron spectroscopy (XPS); time of flight secondary ion mass spectrometry (TOF-SIMS); low energy ion scattering (LEIS); and scanning probe microscopy (SPM), including scanning tunneling microscopy (STM) and atomic force microscopy (AFM), are briefly summarized. Examples describing the characterization of engineered nanoparticles are provided. Specific analysis considerations and issues associated with using surface analysis methods for the characterization of nanoparticles are discussed and summarized, along with the impact that shape instability, environmentally induced changes, deliberate and accidental coating, etc., have on nanoparticle properties.
2010. "Approaches to analyzing insulators with Auger Electron Spectroscopy: Update and Overview." Journal of Electron Spectroscopy and Related Phenomena 176(1-3, SP ISS):80-94. Abstract This paper provides an updated overview, intended to be of practical value to analysts, of methods that can be applied to minimize or control the buildup of near surface electrical charge during electron induced Auger electron spectroscopy (AES). Although well developed methods can be highly effective, dealing with insulating or ungrounded samples for which high spatial resolution is needed remains a challenge. Examples of the application of methods involving low energy ion sources and sample thinning using a focused ion beam that can allow high resolution measurements on a variety of samples are highlighted. The physical bases of newer and traditional methods are simply described along with strengths and limitations of the methods. Summary tables indicate which methods apply to almost any spectrometer, which require special instrumental capabilities, and those that require special sample preparation or mounting.
2010. "Comparison of the Sputter Rates of Oxide Films Relative to the Sputter Rate of SiO2." Journal of Vacuum Science and Technology A--Vacuum, Surfaces and Films 28(5):1060-1072. doi:10.1116/1.3456123 Abstract Because of the increasing technological importance of oxide films for a variety of applications, there is a growing interest in knowing the sputter rates for a wide variety of oxides. To support needs of users of the Environmental Molecular Sciences Laboratory (EMSL) User facility as well as our research programs, we have made a series of measurements of the sputter rates for oxide films that have been grown by oxygen plasma assisted molecular beam epitaxy (OPA-MBE), pulsed laser deposition (PLD), Atomic Layer Deposition (ALD), electrochemical oxidation, or sputter deposition. The sputter rates for these oxide films were determined in comparison to the sputter rates for thermally grown SiO2, a common sputter rate reference material. The film thicknesses and densities of these films were usually measured using x-ray reflectivity (XRR). These samples were mounted in an x-ray photoelectron spectroscopy (XPS) system or an Auger electron spectrometer for sputtering measurements using argon ion sputtering. Although the primary objective was to determine relative sputter rates at a fixed angle, the measurements were also used to determine: i) the angle dependence of the relative sputter rates; ii) the energy dependence of the relative sputter rates; and iii) the extent of ion beam reduction for the various oxides. Materials examined include: SiO2 (reference films), Al2O3, CeO2, Cr2O3, Fe2O3, HfO2, ITO (In-Sn-oxide) Ta2O5, TiO2 (anatase and rutile) and ZnO. We find that the sputter rates for the oxides can vary up to a factor of two (usually slower) from that observed for SiO2. The ratios of sputter rates to SiO2 appear to be relatively independent of ion beam energy for the range of 1kV to 4 kV and for incident angles of less than 50º. As expected, the ion beam reduction of the oxides varies with the sputter angle. These studies demonstrate that we can usually obtain sputter rate reproducibility better than 5% for similar oxide films.
2010. "Separation, Characterization and Initial Reaction Studies of Magnetite Particles from Hanford Sediments." Physics and Chemistry of the Earth 35(6-8):233-241. doi:10.1016/j.pce.2010.04.010 Abstract Magnetic and density separation methods have been applied to composite sediment sample from the Hanford formation from sediment recovered during drilling of an uncontaminated borehole located near the 200 West Area of the Hanford Site in southeastern Washington State. This paper describes the results of using those separation methods and from the characterization and initial reactivity measurements on a highly magnetic fraction isolated from that sediment. X-ray diffraction (XRD) analysis of the highly magnetic sediment fraction indicates that this material contains predominantly magnetite (Fe3O4). Particle morphology observed by scanning electron microscopy (SEM) and compositions determined energy dispersive spectroscopy (EDS) are consistent with this identification. Analyses by X-ray photoelectron spectroscopy (XPS) indicates that there is a thin coating on the particles that are likely a type of aluminosilicate. This highly magnetic fraction of material is not reactive with indigo carmine, an organic redox probe molecule that was shown to readily react with synthetic magnetite. Because of the limited amounts of material readily available, initial tests have been conducted that demonstrate the ability to complete U(VI) sorption on individual particles (nominally ~100 µm in size) of the isolated sediment and to remove and mount these individual particles for analysis of the concentration and chemical state of the sorbed U species using small area XPS.
2010. "Separation, Characterization and Initial Reaction Studies of Magnetite Particles from Hanford Sediments." Physics and Chemistry of the Earth 35(6-8):233-241. doi:10.1016/j.pce.2010.04.010 Abstract Magnetic and density separation methods have been applied to composite sediment sample from the Hanford formation from sediment recovered during drilling of an uncontaminated borehole located near the 200 West Area of the Hanford Site in southeastern Washington State. This paper describes the results of using those separation methods and from the characterization and initial reactivity measurements on a highly magnetic fraction isolated from that sediment. X-ray diffraction (XRD) analysis of the highly magnetic sediment fraction indicates that this material contains predominantly magnetite (Fe3O4). Particle morphology observed by scanning electron microscopy (SEM) and compositions determined energy dispersive spectroscopy (EDS) are consistent with this identification. Analyses by X-ray photoelectron spectroscopy (XPS) indicates that there is a thin coating on the particles that are likely a type of aluminosilicate. This highly magnetic fraction of material is not reactive with indigo carmine, an organic redox probe molecule that was shown to readily react with synthetic magnetite. Because of the limited amounts of material readily available, initial tests have been conducted that demonstrate the ability to complete U(VI) sorption on individual particles (nominally ~100 µm in size) of the isolated sediment and to remove and mount these individual particles for analysis of the concentration and chemical state of the sorbed U species using small area XPS.
2010. "XPS Analysis of Nanostructured Materials and Biological Surfaces." Journal of Electron Spectroscopy and Related Phenomena 178-179:415-432. doi:10.1016/j.elspec.2009.09.003 Abstract This paper examines the types of information that XPS can provide about a variety of nano-structured materials. Although it is sometimes not considered a “nano-scale analysis method” XPS can provide a great deal of information about elemental distributions, layer or coating structure and thicknesses, surface functionality, and even particles sizes on the 1-20 nm scale for samples types that may not be readily analyzed by other methods. This information is important for both synthetic nanostructured or nanosized materials and a variety of natural materials with nanostructure. Although the links between nanostructure materials and biological systems may not at first be obvious, many biological molecules and some organisms are the sizes of nanoparticles. The nanostructure of cells and microbes plays a significant role in how they interact with their environment. The interaction of biomolecules with nanoparticles is important for medical and toxicity studies. The interaction of biomolecules is important for sensor function and many nanomaterials are now the active elements in sensors. This paper first discusses how nanostructures influences XPS data as part of understanding how simple models of sample structure and data analysis can be used to extract information about the physical and chemical structure of the materials being analyzed. Equally important, aspects of sample and analysis limitations and challenges associated with understanding nanostructured materials are indicated. Examples of the application of XPS to nanostructured and biological systems and materials are provided.
2010. "Proteomic and Physiological Responses of Kineococcus radiotolerans to Copper." PLoS One 5(8):Article No. e12427. doi:10.1371/journal.pone.0012427 Abstract Copper is a highly reactive, toxic metal whose transport into the cell is tightly regulated. Kineococcus radiotolerans was previously shown to specifically accumulate soluble copper in the cytoplasm and cell growth was significantly enhanced by copper during chronic irradiation. This study provides a systematic investigation of copper accumulation, toxicity, and homeostasis in K. radiotolerans through combined physiological experimentation and quantitative shot-gun proteomics. Aerobic growth rates and biomass yields were similar over a range of Cu(II) concentrations, though intracellular metal accumulation was positively correlated with Cu(II) concentration in the growth medium (R2 = 0.7). Global proteomics analysis revealed a significant positive correlation between the total number of response proteins and their abundance with copper concentration and culture age. Approximately 40% of the K. radiotolerans genome was differentially expressed in response to the copper treatments imposed. Copper accumulation coincided with increased abundance of proteins involved in oxidative stress and defense, DNA stabilization and repair, and protein turnover. Concomitant production of antioxidants and protective osmolytes signifies an important adaptation for maintenance of cellular redox; few known metal binding proteins were detected. This study offers a first glimpse into the complexity of coordinated biochemical response pathways in K. radiotolerans invoked by sub-lethal copper concentrations that may be pertinent for new biotechnologies in metal recovery and sequestration, and environmental restoration.
2010. "An LC-IMS-MS Platform Providing Increased Dynamic Range for High-Throughput Proteomic Studies." Journal of Proteome Research 9(2):997-1006. doi:10.1021/pr900888b Abstract A high-throughput approach and platform using 15 minute reversed-phase capillary liquid chromatography (RPLC) separations in conjunction with ion mobility spectrometry-mass spectrometry (IMS-MS) measurements was evaluated for the rapid analysis of complex proteomics samples. To test the separation quality of the short LC gradient, a sample was prepared by spiking twenty reference peptides at varying concentrations from 1 ng/mL to 10 µg/mL into a tryptic digest of mouse blood plasma and analyzed with both a LC-Linear Ion Trap Fourier Transform (FT) MS and LC-IMS-TOF MS. The LC-FT MS detected thirteen out of the twenty spiked peptides that had concentrations ≥100 ng/mL. In contrast, the drift time selected mass spectra from the LC-IMS-TOF MS analyses yielded identifications for nineteen of the twenty peptides with all spiking level present. The greater dynamic range of the LC-IMS-TOF MS system could be attributed to two factors. First, the LC-IMS-TOF MS system enabled drift time separation of the low concentration spiked peptides from the high concentration mouse peptide matrix components, reducing signal interference and background, and allowing species to be resolved that would otherwise be obscured by other components. Second, the automatic gain control (AGC) in the linear ion trap of the hybrid FT MS instrument limits the number of ions that are accumulated to reduce space charge effects, but in turn limits the achievable dynamic range compared to the TOF detector.
2010. "The Critical Role of Surfactants in the Growth of Cobalt Nanoparticles." Langmuir 26(1):478–483. doi:10.1021/la902120e Abstract We report a combined experimental and computational study on the critical role of surfactants in the nucleation and growth of Co nanoparticles synthesized by chemical routes. By varying the surfactant species, Co nanoparticles of different morphologies under similar reaction conditions (e.g., temperature and Co-precursor concentration) were produced. Depending on the surfactant species, the growth of Co nanoparticles followed three different growth pathways. For example, with surfactants oleic acid (OA) and trioctylphosphine oxide (TOPO) used in combination, Co nanoparticles followed a diffusional growth pathway, leading to single crystalline nanoparticles. Multiple-grained nanoparticles, through an aggregation process, were formed with the combination of surfactants OA and dioctylamine (DOA). Further, an Ostwald ripening process was observed in the case of TOPO alone. Complementary electronic structure calculations were used to predict the optimized Co-surfactant complex structures and to quantify the binding energy between the surfactants (ligands) and the Co atoms. These calculations were further applied to predict the Co nanoparticle nucleation and growth processes based on the stability of Co-surfactant complexes.
2010. "High-Resolution Electrospray Ionization Mass Spectrometry Analysis of Water- Soluble Organic Aerosols Collected with a Particle into Liquid Sampler ." Analytical Chemistry 82(19):8010-8016. doi:10.1021/ac1014386 Abstract This work demonstrates the utility of a particle-into-liquid sampler (PILS) a technique traditionally used for identification of inorganic ions present in ambient or laboratory aerosols for the analysis of water soluble organic aerosol (OA) using high resolution electrospray ionization mass spectrometry (HR ESI-MS). Secondary organic aerosol (SOA) was produced from 0.5 ppm mixing ratios of limonene and ozone in a 5 m3 Teflon chamber. SOA was collected simultaneously using a traditional filter sampler and a PILS. The filter samples were later extracted with either water or acetonitrile, while the aqueous PILS samples were analyzed directly. In terms of peak intensities, types of detectable compounds, average O:C ratios, and organic mass to organic carbon ratios, the resulting high resolution mass spectra were essentially identical for the PILS and filter based samples. SOA compounds extracted from both filter/acetonitrile extraction and PILS/water extraction accounted for >95% of the total ion current in ESI mass spectra. This similarity was attributed to high solubility of limonene SOA in water. In contrast, significant differences in detected ions and peak abundances were observed for pine needle biomass burning organic aerosol (BBOA) collected with PILS and filter sampling. The water soluble fraction of BBOA is considerably smaller than for SOA, and a number of unique peaks were detectable only by the filter/acetonitrile method. The combination of PILS collection with HR-ESI-MS analysis offers a new approach for molecular analysis of the water-soluble organic fraction in biogenic SOA, aged photochemical smog, and BBOA.
2010. "Effect of Surface Charge on Laser-induced Neutral Atom Desorption." Applied Physics A, Materials Science and Processing 101(1):61-64. doi:10.1007/s00339-010-5758-1 Abstract When an ionic metal oxide crystal is cleaved, inhomogeneous electrical charging of the surface can be a result. Such an effect has been well-documented in magnesium oxide (100). For example, recent rigorous AFM studies indicate that nanoscale charged clusters of MgO are created during cleavage, with high concentrations often located at terrace step edges.[1] In addition, ablation processes of freshly cleaved magnesium oxide crystals may be effected by remnant surface charging and microstructures.[2] We report here that such surface charging strongly impacts even neutral atom desorption, even under conditions of extremely mild excitation of surface terrace features. In our experiments, single crystal MgO (100) is cleaved in air and placed in an ultra-high vacuum chamber (UHV). We irradiate the crystal at 6.4 eV, photon energy resonant with five-coordinated (5-C) terrace sites and probe desorbing neutral oxygen atoms. It is found that a significant fraction of desorbed neutral oxygen atoms from the charged surface possess kinetic energies in excess of 0.7 eV. This is in contrast to uncharged samples (discharged in vacuo over 24 hours) that display a near-thermal oxygen atom distribution.
2010. "Adiabatic Tip-Plasmon Focusing for Nano-Raman Spectroscopy." The Journal of Physical Chemistry Letters 1(24):3427–3432. doi:10.1021/jz101289z Abstract True nanoscale optical spectroscopy requires the efficient delivery of light for a spatially nanoconfined excitation.We utilize adiabatic plasmon focusing to concentrate an optical field into the apex of a scanning probe tip of ∼10 nm in radius. The conical tips with the ability for two-stage optical mode matching of the surface plasmon polariton (SPP) grating-coupling and the adiabatic propagating SPP conversion into a localized SPP at the tip apex represent a special optical antenna concept for far-field transduction into nanoscale excitation. The resulting high nanofocusing efficiency and the spatial separation of the plasmonic gratingcoupling element on the tip shaft from the near-field apex probe region allows for true background-free nanospectroscopy. As an application, we demonstrate tip-enhanced Raman spectroscopy (TERS) of surface molecules with enhanced contrast and its extension into the near-IR with 800 nm excitation.
2010. "Bioavailability of Fe(III) in Loess Sediments: An Important Source of Electron Acceptors." Clays and Clay Minerals 58(4):542-557. doi:10.1346/CCMN.2010.0580409 Abstract A quantitative study was conducted to understand if Fe (III) in loess sediments is available for microbial respiration by using a common metal reducing bacterium, Shewanella putrefaciens, CN32. The loess samples were collected from three different sites: St. Louis (Peoria), Missouri, USA; Huanxia (HX) and Yanchang (YCH), Shanxi Province of China. Wet chemical analyses indicated that the total Fe concentration for the three samples was 1.69%, 2.76%, and 3.29%, respectively, of which 0.48%, 0.67%, and 1.27% was Fe(III). All unreduced loess sediments contained iron oxides and phyllosilicates (smectite, illite, chlorite, vermiculite), in addition to common minerals such as quartz, feldspar, plagioclase, calcite, and dolomite. Bioreduction experiments were performed at a loess concentration of 20 mg/mL using lactate as the sole electron donor, Fe(III) in loess as the sole electron acceptor in the presence and absence of anthraquinone-2, 6-disulfonate (AQDS) as an electron shuttle. Experiments were performed in non-growth (bicarbonate buffer) and growth (M1) media with a cell concentration of ~2.8 x 107 and 2.1 x 107 cells/mL, respectively. The unreduced and bioreduced solids were analyzed by X-ray diffraction (XRD), Mössbauer spectroscopy, diffuse reflection spectroscopy (DRS), and scanning electron microscopy/energy dispersive spectroscopy (SEM/EDS) methods. Despite many similarities among the three loess samples, the extent and rate of Fe (III) reduction varied significantly. For example, in presence of AQDS the extent of reduction in the non-growth experiment was 25% in HX, 34% in Peoria, and 38% in YCH. The extent of reduction in the growth experiment was 72% in HX, 94% in Peoria, and 56% in YCH. The extent of bioreduction was lower in absence of AQDS. Overall, AQDS and the M1 growth medium significantly enhanced the rate and extent of bioreduction. Fe(III) in iron oxides and Fe(III)-containing phyllosilicates was bioreduced. Biogenic illite, siderite, and vivianite formed. The results of this study suggest that Fe (III) in loess sediments represents a potentially important source of electron acceptors to support microbial activity in dry environments.
2010. "First Principles Simulation of the Bonding, Vibrational, and Electronic Properties of the Hydration Shells of the High-Spin Fe3+ Ion in Aqueous Solutions." Journal of Physical Chemistry A 114(5):2189-2200. doi:10.1021/jp904967n Abstract Results of parameter-free first principles simulations of a spin up 3d5 Fe3+ ion hydrated in an aqueous solution (64 waters, 30 ps, 300 K) are reported. The first hydration shell associated with the first maximum of the radial distribution function, gFeO(r), at d(Fe−OI) = 2.11−2.15 Å, contains 6 waters with average d(OH) = 0.99 Å, in good agreement with observations. A second shell with average coordination number 13.3 can be identified with average shell radius of d(Fe−OII) = 4.21−4.32 Å. The waters in this hydration shell are coordinated to the first shell via a trigonal H-bond network with d(OI−OII) = 2.7−2.9 Å, also in agreement with experimental measurements. The first shell tilt angle average is 33.4° as compared to the reported value of 41°. Wannier−Boys orbitals (WBO) show an interaction between the unoccupied 3d orbitals of the Fe3+ valence (spin up, 3d5) and the occupied spin down lone pair orbitals of first shell waters. The effect of the spin ordering of the Fe3+ ion on the WBO is not observed beyond the first shell. From this local bond analysis and consistent with other observations, the electronic structure of waters in the second shell is similar to that of a bulk water even in this strongly interacting system. H-bond decomposition shows significant bulk-like structure within the second shell for Fe3+. The vibrational density of states shows a first shell red shift of 230 cm−1 for the v1,2v2,v3 overtone, in reasonable agreement with experimental estimates for trivalent cations (300 cm−1). No exchanges between first and second shell were observed. Waters in the second shell exchanged with bulk waters via dissociative and associative mechanisms. Results are compared with an AIMD study of Al3+ and 64 waters. For Fe3+ the average first shell tilt angle is larger and the tilt angle distribution wider. H-bond decomposition shows that second shell to second shell H-bonding is enhanced in Fe3+ suggesting an earlier onset of bulk-like water structure.
2010. "The diammoniate of diborane: Crystal structure and hydrogen release." Chemical Communications 46(45):8564-8566. doi:10.1039/C0CC03249B Abstract [(NH3)2BH2]+[BH4]- is formed from the room temperature decomposition of NH4+BH4-, via a NH3BH3 intermediate. Its crystal structure has been determined and contains disordered BH4- ions in 2 distinct sites. Hydrogen release is similar to that from NH3BH3 but with faster kinetics.
2010. "On the Roles of Substrate Binding and Hinge Unfolding in Conformational Changes of Adenylate Kinase." Biophysical Journal 99(10):3420-3429. doi:10.1016/j.bpj.2010.09.040 Abstract We characterized the conformational change of adenylate kinase (AK) between open and closed forms by conducting five all-atom molecular-dynamics simulations, each of 100 ns duration. Different initial structures and substrate binding configurations were used to probe the pathways of AK conformational change in explicit solvent, and no bias potential was applied. A complete closed-to-open and a partial open-to-closed transition were observed, demonstrating the direct impact of substrate-mediated interactions on shifting protein conformation. The sampled configurations suggest two possible pathways for connecting the open and closed structures of AK, affirming the prediction made based on available x-ray structures and earlier works of coarse-grained modeling. The trajectories of the all-atom molecular-dynamics simulations revealed the complexity of protein dynamics and the coupling between different domains during conformational change. Calculations of solvent density and density fluctuations surrounding AK did not show prominent variation during the transition between closed and open forms. Finally, we characterized the effects of local unfolding of an important hinge near Pro177 on the closed-to-open transition of AK and identified a novel mechanism by which hinge unfolding modulates protein conformational change. The local unfolding of Pro177 hinge induces alternative tertiary contacts that stabilize the closed structure and prevent the opening transition.
2010. "CHARACTERIZATION OF MACAQUE PULMONARY FLUID PROTEOME DURING MONKEYPOX INFECTION: DYNAMICS OF HOST RESPONSE." Molecular & Cellular Proteomics. MCP 9(12):2760-2771. doi:10.1074/mcp.M110.001875 Abstract Understanding viral pathogenesis is challenging due to confounding factors, including nonabrasive access to infected tissues and high abundance of inflammatory mediators that may mask mechanistic details. In diseases such as influenza and smallpox, where the primary cause of mortality results from complications in the lung, the characterization of lung fluid offers a unique opportunity to study host-pathogen interactions with minimal affect on infected animals. This investigation characterizes the global proteome response in the pulmonary fluid, broncheoalveolar lavage fluid (BALF), of macaques during upper respiratory infection by Monkeypox virus (MPXV), a close relative of the causative agent of smallpox, Variola virus. These results are compared and contrasted against Vaccinia virus (VV) infections, a low pathogenic relative of MPXV, and with extracellular fluid from MPXV-infected HeLa cells. To identify changes in the pulmonary protein compartment, macaque lung fluid was sampled twice prior to infection, serving as baseline, and up to 6 times following intrabronchial infection with either MPXV or VV. Increased expression of inflammatory proteins was observed in response to both viruses. While the increased expression resolved for a subset of proteins, such as C-reactive protein, S100A8, and S100A9, high expression levels persisted for other proteins, including Vitamin-D-binding protein and fibrinogen gamma. Structural and metabolic proteins were substantially decreased in lung fluid exclusively during MPXV, and not VV infection. Decreases in structural and metabolic proteins were similarly observed in the extracellular fluid of MPXV-infected HeLa cells. Results from this study suggest the host inflammatory response may not be the only facilitator of viral pathogenesis, but rather maintaining pulmonary structural integrity could be a key factor influencing disease progression and mortality.
2010. "Macaque Proteome Response to Highly Pathogenic Avian Influenza and 1918 Reassortant Influenza Virus Infections." Journal of Virology 84(22):12058-12068. Abstract The host proteome response and molecular mechanisms that drive disease in vivo during infection by a human isolate of the highly pathogenic avian influenza (HPAI) and 1918 pandemic influenza virus remains poorly understood. This study presents a comprehensive characterization of the proteome response in cynomolgus macaque (Macaca fascicularis) lung tissue over 7 days of infection with HPAI (most virulent), a reassortant virus containing 1918 hemagglutinin (HA) and neuraminidase (NA) surface proteins (intermediate virulence), or a human seasonal strain (least virulent). A high sensitivity two-dimensional LC-MS/MS strategy and functional network analysis were implemented to gain insight into response pathways activated in macaques during influenza infection. A macaque protein database was assembled and used in the identification of 35,239 unique peptide sequences corresponding to approximately 4,259 proteins. Quantitative analysis identified an increase in expression of 400 proteins during viral infection. The abundance levels of a subset of these 400 proteins produced strong correlations with disease progression observed in the macaques, distinguishing a "core" response to viral infection from a :high" response specific to severe disease. Proteome expression profiles revealed distinct temporal response kinetics between viral strains, with HPAI inducing the most rapid response. While proteins involved in immune response, metabolism, and transport were increased rapidly in the lung by HPAI, the other viruses produced a delayed response, characterized by an increase in proteins involved in oxidative phosphorylation, RNA processing, and translation. Proteomic results were integrated with previous genomic and pathologic analysis to characterize the dynamic nature of the influenza viral infection process.
2010. "Mapping the Subcellular Proteome of Shewanella oneidensis MR-1 using Sarkosyl-based fractionation and LC-MS/MS protein identification." Journal of Proteome Research 9(9):4454-4463. doi:10.1021/pr100215h Abstract A simple and effective subcellular proteomic method for fractionation and analysis of gram-negative bacterial cytoplasm, periplasm, inner, and outer membranes was applied to Shewanella oneidensis to gain insight into its subcellular architecture. A combination of differential centrifugation, Sarkosyl solubilization, and osmotic lysis was used to prepare subcellular fractions. Global differences in protein fractions were observed by SDS PAGE and heme staining, and tryptic peptides were analyzed using high-resolution LC-MS/MS. Compared to crude cell lysates, the fractionation method achieved a significant enrichment (average ~2-fold) in proteins predicted to be localized to each subcellular fraction. Compared to other detergent, organic solvent, and density-based methods previously reported, Sarkosyl most effectively facilitated separation of the inner and outer membranes and was amenable to mass spectrometry, making this procedure ideal for probing the subcellular proteome of gram-negative bacteria via LC-MS/MS. With 40% of the observable proteome represented, this study has provided extensive information on both subcellular architecture and relative abundance of proteins in S. oneidensis and provides a foundation for future work on subcellular organization and protein-membrane interactions in other gram-negative bacteria.
2010. "Comparison of FTIR and Particle Mass Spectrometry for the Measurement of Paticulate Organic Nitrates." Environmental Science & Technology 44(3):1056-1061. doi:10.1021/es9029864 Abstract While multifunctional organic nitrates are formed during the atmospheric oxidation of volatile organic compounds, relatively little is known about their signatures in particle mass spectrometers. High resolution time-of-flight aerosol mass spectrometry (HR-ToF-AMS) was applied to NH4NO3, NaNO3 and isosorbide 5-mononitrate (IMN) particles, and to secondary organic aerosol (SOA) from NO3 radical reactions at 22 C and 1 atm in air with and pinene, 3-carene, limonene and isoprene. For comparison, single particle laser ablation mass spectra (SPLAT II) were also obtained for IMN and SOA from the pinene reaction. The mass spectra of all particles exhibit significant intensity at m/z 30, and for the SOA, weak peaks corresponding to various organic fragments containing nitrogen [CxHyNzOa]+ were identified using HR-ToF-AMS. The NO+/NO2+ ratios from HR-ToF-AMS were 10-15 for IMN and the SOA from the and pinene, 3-carene and limonene reactions, ~5 for the isoprene reaction, 2.4 for NH4NO3 and 80 for NaNO3. The N/H ratios from HR-ToF-AMS for the SOA were smaller by a factor of 2 to 4 than the -ONO2/C-H ratios measured using FTIR on particles impacted on ZnSe windows. While the NO+/NO2+ ratio may provide a generic indication of organic nitrates under some conditions, specific identification of particulate organic nitrates awaits further development of particle mass spectrometry techniques.
2010. "A multi-pronged search for a common structural motif in the secretion signal of Salmonella enterica serovar Typhimurium type III effector proteins." Molecular Biosystems 6(12):2448-2458. doi:10.1039/c0mb00097c Abstract Many pathogenic Gram-negative bacteria use a type III secretion system (T3SS) to deliver effector proteins into the host cell where they reprogram host defenses and facilitate pathogenesis. While it has been determined that the first 20 - 30 N-terminal residues usually contain the ‘secretion signal’ that targets effector proteins for translocation, the molecular basis for recognition of this signal is not understood. Recent machine-learning approaches, such as SVM-based Identification and Evaluation of Virulence Effectors (SIEVE), have improved the ability to identify effector proteins from genomics sequence information. While these methods all suggest that the T3SS secretion signal has a characteristic amino acid composition bias, it is still unclear if the amino acid pattern is important and if there are any unifying structural properties that direct recognition. To address these issues a peptide corresponding to the secretion signal for Salmonella enterica serovar Typhimurium effector SseJ was synthesized (residues 1-30, SseJ) along with scrambled peptides of the same amino acid composition that produced high (SseJ-H) and low (SseJ-L) SIEVE scores. The secretion properties of these three peptides were tested using a secretion signal-CyaA fusion assay and their structures systematically probed using circular dichroism, nuclear magnetic resonance, and ion mobility spectrometry-mass spectrometry. The signal-CyaA fusion assay showed that the native and SseJ-H fusion constructs were secreted into J774 macrophage at similar levels via the SPI-2 secretion pathway while secretion of the SseJ-L fusion construct was substantially retarded, suggesting that the SseJ secretion signal was sequence order dependent. The structural studies showed that the SseJ, SseJ-H, and SseJ-L peptides were intrinsically disordered in aqueous solution with only a small predisposition to adopt nascent helical structure in the presence of the powerful structure stabilizing agent, 1,1,1,3,3,3-hexafluoroisopropanol (HFIP). Intrinsic disorder may be a universal feature of effector secretion signals as analogous conclusions were reached following a similar structural characterization of peptides corresponding to the N-terminal regions of the S. Typhimurium effectors SptP, SopD-2, GtgE, and the Yersinia pestis effector YopH.
2010. "A Solution NMR Investigation into the Murine Amelogenin Splice-Variant LRAP (Leucine-Rich Amelogenin Protein)." Biochimica et Biophysica Acta--Proteins and Proteomics 1804(9):1768-1774. Abstract Amelogenins are the dominant proteins present in ameloblasts during the early stages of enamel biomineralization, making up >90% of the matrix protein. Along with the full-length protein there are several splice-variant isoforms of amelogenin present including LRAP (Leucine-Rich Amelogenin Protein), a protein that consists of the first 33 and the last 26 residues of full-length amelogenin. Using solution-state NMR spectroscopy we have assigned the 1H-15N HSQC spectrum of murine LRAP (rp(H)LRAP) in 2% acetic acid at pH 3.0 by making extensive use of previous chemical shift assignments for full-length murine amelogenin (rp(H)M180). This correlation was possible because LRAP, like the full-length protein, is intrinsically disordered under these solution conditions. The major difference between the 1H-15N HSQC spectra of rp(H)M180 and rp(H)LRAP was an additional set of amide resonances for each of the seven non-proline residues between S12* and Y12 at the N-terminus of rp(H)LRAP indicating that the N-terminal region of LRAP exists in two different conformations. Analysis of the proline carbon chemical shifts suggest that the molecular basis for the two states is not a cis-trans isomerization of one or more of the proline residues in the N-terminal region and is likely due to a slow exchange process. As observed with rp(H)M180, residue specific changes in molecular dynamics, manifested by the reduction in intensity and disappearance of 1H-15N HSQC cross peaks, were observed with the addition of NaCl to rp(H)LRAP. These perturbations may signal early events governing supramolecular self-assembly of rp(H)LRAP into nanospheres. However, the different pattern of 1H-15N HSQC cross peak perturbation between rp(H)LRAP and rp(H)M180 in high salt suggest that the termini may behave differently in their respective nanospheres, and perhaps, these differences account for the cell signaling properties attributable to LRAP but not the full-length protein.
2010. "Circular Dichrosim Studies on the Deinococcus Radiodurans Nudix Hydrolase DR_0079: an Atypical Thermal Melt." Protein and Peptide Letters 17(7):831-835. Abstract We have recently determined the solution structure of the hypothetical Deinococcus radiodurans Nudix protein DR0079 [Proteins 56:28-39]. The protein is a monomer and contains the fundamental fold common to the Nudix family, a large mixed b-sheet sandwiched between a-helices. The protein¹s physical properties were further characterized by circular dichroism (CD) spectroscopy. A CD thermal melt indicates an inflection point at ~52ºC. However, unlike typical CD thermal melts, the ellipticity at 220 nm decreases upon passing through the inflection point suggesting that the amount of secondary structure in the protein has increased after heating. NMR spectroscopy and size exclusion chromatography indicates that heating effects the irreversible formation of a large molecular weight complex. After cooling, the ellipiticity at 220 nm increases further, and overall, the CD spectrum at 25ºC shows that heat-treated DR0079 has more ³structure² than non-heat treated DR0079.
2010. "Solution Structure of Rv2377c-Founding Member of the MbtH-Like Protein Family." Tuberculosis 90(4):245-251. Abstract The Mycobacterium tuberculosis protein Rv2377c (71 residues, MW = 8.4 kDa) has been characterized using nuclear magnetic resonance (NMR) and circular dichroism (CD) spectroscopy. Rv2377c was the first identified member of the MbtH-like family of proteins. MbtH-like proteins have been implicated in siderophore biosynthesis, however, their precise biochemical function remain unknown. Size exclusion chromatography and NMR spectroscopy show that Rv2377c is a monomer in solution. Circular dichroism spectroscopy indicates that Rv2377c unfolds upon heating and will reversible fold into its native conformation upon cooling. Using NMR-based methods the solution structure of Rv2377c was determined and some of the dynamic properties of the protein studied. The protein contains a three-strand, anti-parallel β-sheet (β3:β1:β2) nestled against one C-terminal α-helix (S48-N55). Weak or absent amide cross peaks in the 1H-15N HSQC spectrum for many of the β1 and β2 residues suggest intermediate motion on the ms to μs timescale at the β1:β2 interface. Amide cross peaks in the 1H-15N HSQC spectrum are absent for all but one residue at the C-terminus (W56 - D71), a region that includes a highly conserved sequence WXDXR, suggesting this region is intrinsically disordered. The latter observation differs with the crystal structure of another MbtH-like protein, PA2412 from Pseudomonas aeruginosa, where a second ordered α-helix was observed at the extreme C-terminus.
2010. "Structural characterization of Burkholderia pseudomallei adenylate kinase (Adk): Profound asymmetry in the crystal structure of the ‘open’ state ." Biochemical and Biophysical Research Communications 394(4):1012-1017. Abstract In all organisms adenylate kinases (Adks) play a vital role in cellular energy metabolism and nucleic acid synthesis. Due to differences in catalytic properties between the Adks found in prokayotes and in the cytoplasm of eukaryotes, there is interest in targeting this enzyme for new drugs therapies against infectious bacterial agents. Here we report the 2.1 Å resolution crystal structure for the 220-residue Adk from Burkholderia pseudomallei (BpAdk), the etiological agent responsible for the infectious disease meliodosis. The general structure of apo BpAdk is similar to other Adk structures, composed of a CORE subdomain with peripheral ATP-binding (ATPbd) and LID subdomains. The two molecules in the asymmetric unit have significantly different conformations, with a backbone RMSD of 1.46 Å. These two BpAdk conformations may represent ‘open’ Adk sub-states along the preferential pathway to the ‘closed’ substrate-bound state.
2010. "Verifying the Presence of Low Levels of Neptunium in a Uranium Matrix with Electron Energy-Loss Spectroscopy ." Micron 41(1):65-70. Abstract This paper examines the problems associated with the analysis of low levels of neptunium (Np) in a uranium (U) matrix with electron energy-loss spectroscopy (EELS) on the transmission electron microscope (TEM). The detection of Np in a matrix of uranium (U) can be impeded by the occurrence of a plural scattering event from U (U-M5 + U-O4,5) that results in severe overlap on the Np-M5 edge at 3665 eV. Low levels (1600 - 6300 ppm) of Np can be detected in U solids by confirming the energy gap between the Np-M5 and Np-M4 edges is at 184 eV and showing that the M4/M5 ratio for the Np is smaller than that for U. The Richardson-Lucy deconvolution method was applied to energy-loss spectral images and was shown to increase the signal to noise. This method also improves the limits of detection for Np in a U matrix.
2010. "Free Energies for Degradation Reactions of 1,2,3-Trichloropropane from ab initio Electronic Structure Theory." Journal of Physical Chemistry A 114(46):12269-12282. doi:10.1021/jp105726u Abstract Electronic structure methods were used to calculate the gas-phase and aqueous phase reaction energies for reductive dechlorination (i.e. hydrogenolysis), reductive Beta-elimination, dehydrochlorination, and nucleophilic substitution by OH- of 1,2,3-trichloropropane. The thermochemical properties Delta Hof(298.15K), So(298.15K,1 bar), and Delta GS(298.15K, 1 bar) were calculated by using ab initio electronic structure calculations, isodesmic reactions schemes, gas-phase entropy estimates, and continuum solvation models for 1,2,3-trichloropropane and several likely metabolites. On the basis of these thermochemical estimates, together with a Fe(II)/Fe(III) chemical equilibrium model for natural reducing environments, all of the reactions studied were predicted to be very favorable in the standard state and under a wide range of pH conditions. The most favorable reaction was reductive Beta-elimination (Delta Gorxn ≈ -32 kcal/mol), followed closely by reductive dechlorination (Delta Gorxn ≈ -27 kcal/mol), dehydrochlorination (Delta Gorxn ≈ -27kcal/mol), and nucleophilic substitution by OH- (Delta Gorxn ≈ -25 kcal/mol). For both reduction reactions studied, it was found that the first electron-transfer step, yielding the intermediate CH2-CHCl-CH2Cl , and CH2Cl-CH-CH2Cl species, was not favorable in the standard state (Delta Gorxn ≈ +15 kcal/mol) and was predicted to occur only at relatively high pH values. This result suggests that reduction by natural attenuation is unlikely.
2010. "Hard scaling challenges for ab initio molecular dynamics capabilities in NWChem: Using 100,000 CPUs per second." Journal of Physics: Conference Series 180(1):, doi:10.1088/1742-6596/180/1/012028 Abstract An overview of the parallel algorithms for ab initio molecular dynamics (AIMD) used in the NWChem program package is presented, including recent developments for computing exact exchange. These algorithms make use of a two-dimensional processor geometry proposed by Gygi et al for use in AIMD algorithms. Using this strategy, a highly scalable algorithm for exact exchange has been developed and incorporated it into AIMD. This new algorithm for exact exchange employs an incomplete butterfly to overcome the bottleneck associated with exact exchange term, and it makes judicious use of data replication. Initial testing has shown that this algorithm can scale to over 20,000 CPUs even for modest size simulation.
