Showing papers by "Environmental Molecular Sciences Laboratory published in 2009"

Rapid and sustained nuclear–cytoplasmic ERK oscillations induced by epidermal growth factor

Abstract: Although the ERK pathway has a central role in the response of cells to growth factors, its regulatory structure and dynamics are incompletely understood. To investigate ERK activation in real time, we expressed an ERK–GFP fusion protein in human mammary epithelial cells. On EGF stimulation, we observed sustained oscillations of the ERK–GFP fusion protein between the nucleus and cytoplasm with a periodicity of ∼15 min. The oscillations were persistent (>45 cycles), independent of cell cycle phase, and were highly dependent on cell density, essentially disappearing at confluency. Oscillations occurred even at ligand doses that elicited very low levels of ERK phosphorylation, and could be detected biochemically in both transfected and nontransfected cells. Mathematical modeling revealed that negative feedback from phosphorylated ERK to the cascade input was necessary to match the robustness of the oscillation characteristics observed over a broad range of ligand concentrations. Our characterization of single-cell ERK dynamics provides a quantitative foundation for understanding the regulatory structure of this signaling cascade.

Morphology and Electronic Structure of the Oxide Shell on the Surface of Iron Nanoparticles

Abstract: An iron (Fe) nanoparticle exposed to air at room temperature will be instantly covered by an oxide shell that is typically approximately 3 nm thick. The nature of this native oxide shell, in combination with the underlying Fe(0) core, determines the physical and chemical behavior of the core-shell nanoparticle. One of the challenges of characterizing core-shell nanoparticles is determining the structure of the oxide shell, that is, whether it is FeO, Fe(3)O(4), gamma-Fe(2)O(3), alpha-Fe(2)O(3), or something else. The results of prior characterization efforts, which have mostly used X-ray diffraction and spectroscopy, electron diffraction, and transmission electron microscopic imaging, have been framed in terms of one of the known Fe-oxide structures, although it is not necessarily true that the thin layer of Fe oxide is a known Fe oxide. In this Article, we probe the structure of the oxide shell on Fe nanoparticles using electron energy loss spectroscopy (EELS) at the oxygen (O) K-edge with a spatial resolution of several nanometers (i.e., less than that of an individual particle). We studied two types of representative particles: small particles that are fully oxidized (no Fe(0) core) and larger core-shell particles that possess an Fe core. We found that O K-edge spectra collected for the oxide shell in nanoparticles show distinct differences from those of known Fe oxides. Typically, the prepeak of the spectra collected on both the core-shell and the fully oxidized particles is weaker than that collected on standard Fe(3)O(4). Given the fact that the origin of this prepeak corresponds to the transition of the O 1s electron to the unoccupied state of O 2p hybridized with Fe 3d, a weak pre-edge peak indicates a combination of the following four factors: a higher degree of occupancy of the Fe 3d orbital; a longer Fe-O bond length; a decreased covalency of the Fe-O bond; and a measure of cation vacancies. These results suggest that the coordination configuration in the oxide shell on Fe nanoparticles is defective as compared to that of their bulk counterparts. Implications of these defective structural characteristics on the properties of core-shell structured iron nanoparticles are discussed.

Molecular characterization of nitrogen-containing organic compounds in biomass burning aerosols using high-resolution mass spectrometry.

Abstract: Although nitrogen-containing organic compounds (NOC) are important components of atmospheric aerosols, little is known about their chemical composition. Here we present detailed characterization of the NOC constituents of biomass burning aerosol (BBA) samples using high-resolution electrospray ionization mass spectrometry (ESI/MS). Accurate mass measurements combined with MS/MS fragmentation experiments of selected ions were used to assign molecular structures to individual NOC species. Our results indicate that N-heterocyclic alkaloid compounds (species naturally produced by plants and living organisms) comprise a substantial fraction of NOC in BBA samples collected from test burns of five biomass fuels. High abundance of alkaloids in test burns of ponderosa pine (a widespread tree in the western U.S. areas frequently affected by large scale fires) suggests that N-heterocyclic alkaloids in BBA may play a significant role in dry and wet deposition of fixed nitrogen in this region.

Trends in covalency for d- and f-element metallocene dichlorides identified using chlorine K-edge X-ray absorption spectroscopy and time-dependent density functional theory.

Abstract: We describe the use of Cl K-edge X-ray absorption spectroscopy (XAS) and both ground-state and time-dependent hybrid density functional theory (DFT) to probe the electronic structure and determine the degree of orbital mixing in M-Cl bonds for (C(5)Me(5))(2)MCl(2) (M = Ti, 1; Zr, 2; Hf, 3; Th, 4; U, 5), where we can directly compare a class of structurally similar compounds for d- and f-elements. Pre-edge features in the Cl K-edge XAS data for the group IV transition-metals 1-3 provide direct evidence of covalent M-Cl orbital mixing. The amount of Cl 3p character was experimentally determined to be 25%, 23%, and 22% per M-Cl bond for 1-3, respectively. For actinides, we find a pre-edge shoulder for 4 (Th) and distinct and weak pre-edge features for U, 5. The amount of Cl 3p character was determined to be 9% for 5, and we were unable to make an experimental determination for 4. Using hybrid DFT calculations with relativistic effective core potentials, the electronic structures of 1-5 were calculated and used as a guide to interpret the experimental Cl K-edge XAS data. For transition-metal compounds 1-3, the pre-edge features arise due to transitions from Cl 1s electrons into the 3d-, 4d-, and 5d-orbitals, with assignments provided in the text. For Th, 4, we find that 5f- and 6d-orbitals are nearly degenerate and give rise to a single pre-edge shoulder in the XAS. For U, 5, we find the 5f- and 6d-orbitals fall into two distinct energy groupings, and Cl K-edge XAS data are interpreted in terms of Cl 1s transitions into both 5f- and 6d-orbitals. Time-dependent DFT was used to calculate the energies and intensities of Cl 1s transitions into empty metal-based orbitals containing Cl 3p character and provide simulated Cl K-edge XAS spectra for 1-4. For 5, which has two unpaired 5f electrons, simulated spectra were obtained from transition dipole calculations using ground-state Kohn-Sham orbitals. To the best of our knowledge, this represents the first application of Cl K-edge XAS to actinide systems. Overall, this study allows trends in orbital mixing within a well-characterized structural motif to be identified and compared between transition-metals and actinide elements. These results show that the orbital mixing for the d-block compounds slightly decreases in covalency with increasing principal quantum number, in the order Ti > Zr approximately = Hf, and that uranium displays approximately half the covalent orbital mixing of transition elements.

Chemical Reactivity of Reduced TiO2(110): The Dominant Role of Surface Defects in Oxygen Chemisorption

Abstract: O2 chemisorption on reduced, rutile TiO2(110) with various concentrations of oxygen vacancies (Ov) and bridging hydroxyls (OHb) is investigated with scanning tunneling microscopy, temperature-programmed desorption, and electron-stimulated desorption. On the annealed surface, two oxygen molecules can be chemisorbed per Ov. The same amount of O2 chemisorbs on surfaces where each Ov is converted to two OHb’s by exposure to water (i.e., 1 O2 per OHb). Surfaces with few or no Ov’s or OHb’s can be created by exposing the hydroxylated surface to O2 at room temperature, and the amount of O2 that chemisorbs on these surfaces at low temperatures is only ∼20% of the amount on the annealed (reduced) surface. In contrast, the amount of chemisorbed O2 increases by more than a factor of 2 when the OHb concentration is enhanced—without changing the concentration of subsurface Ti interstitials. The results indicate that the reactivity of TiO2(110) is primarily controlled by the amount of electron-donating surface species ...

Reduction in biomass burning aerosol light absorption upon humidification: roles of inorganically-induced hygroscopicity, particle collapse, and photoacoustic heat and mass transfer

Abstract: . Smoke particle emissions from the combustion of biomass fuels typical for the western and southeastern United States were studied and compared under high humidity and ambient conditions in the laboratory. The fuels used were Montana ponderosa pine (Pinus ponderosa), southern California chamise (Adenostoma fasciculatum), and Florida saw palmetto (Serenoa repens). Information on the non-refractory chemical composition of biomass burning aerosol from each fuel was obtained with an aerosol mass spectrometer and through estimation of the black carbon concentration from light absorption measurements at 870 nm. Changes in the optical and physical particle properties under high humidity conditions were observed for hygroscopic smoke particles containing substantial inorganic mass fractions that were emitted from combustion of chamise and palmetto fuels. Light scattering cross sections increased under high humidity for these particles, consistent with the hygroscopic growth measured for 100 nm particles in HTDMA measurements. Photoacoustic measurements of aerosol light absorption coefficients revealed a 20% reduction with increasing relative humidity, contrary to the expectation of light absorption enhancement by the liquid coating taken up by hygroscopic particles. This reduction is hypothesized to arise from two mechanisms: (1) shielding of inner monomers after particle consolidation or collapse with water uptake; (2) the lower case contribution of mass transfer through evaporation and condensation at high relative humidity (RH) to the usual heat transfer pathway for energy release by laser-heated particles in the photoacoustic measurement of aerosol light absorption. The mass transfer contribution is used to evaluate the fraction of aerosol surface covered with liquid water solution as a function of RH.

Global systems-level analysis of Hfq and SmpB deletion mutants in Salmonella: implications for virulence and global protein translation.

Abstract: Using sample-matched transcriptomics and proteomics measurements it is now possible to begin to understand the impact of post-transcriptional regulatory programs in Enterobacteria. In bacteria post-transcriptional regulation is mediated by relatively few identified RNA-binding protein factors including CsrA, Hfq and SmpB. A mutation in any one of these three genes, csrA, hfq, and smpB, in Salmonella is attenuated for mouse virulence and unable to survive in macrophages. CsrA has a clearly defined specificity based on binding to a specific mRNA sequence to inhibit translation. However, the proteins regulated by Hfq and SmpB are not as clearly defined. Previous work identified proteins regulated by hfq using purification of the RNA-protein complex with direct sequencing of the bound RNAs and found binding to a surprisingly large number of transcripts. In this report we have used global proteomics to directly identify proteins regulated by Hfq or SmpB by comparing protein abundance in the parent and isogenic hfq or smpB mutant. From these same samples we also prepared RNA for microarray analysis to determine if alteration of protein expression was mediated post-transcriptionally. Samples were analyzed from bacteria grown under four different conditions; two laboratory conditions and two that are thought to mimic the intracellular environment. We show that mutants of hfq and smpB directly or indirectly modulate at least 20% and 4% of all possible Salmonella proteins, respectively, with limited correlation between transcription and protein expression. These proteins represent a broad spectrum of Salmonella proteins required for many biological processes including host cell invasion, motility, central metabolism, LPS biosynthesis, two-component regulatory systems, and fatty acid metabolism. Our results represent one of the first global analyses of post-transcriptional regulons in any organism and suggest that regulation at the translational level is widespread and plays an important role in virulence regulation and environmental adaptation for Salmonella.

Size distribution and morphology of nascent soot in premixed ethylene flames with and without benzene doping

Abstract: Particle size distribution functions of nascent soot formed in four burner-stabilized, premixed ethylene–oxygen–argon flames were studied in a spatially resolved manner by online sampling/scanning mobility particle sizer. Particle morphology was analyzed by atomic force microscopy (AFM) of substrate-deposited samples. Two of the four flames were doped with benzene. An aerosol electrometer is introduced to extend the lower detection limit to around 1.5 nm in diameter. The results show that the bimodal behavior of particle size is applicable to all premixed ethylene flames studied. The variation of the size distribution from flame to flame is conclusively attributed to flame temperature variation. Under the condition of an equal carbon concentration, benzene doping leads to negligible changes in the characteristics of the size distribution. For all flames studied, AFM observations show that nascent soot is liquid-like and spreads extensively upon impact on a substrate surface.

Time-resolved molecular characterization of limonene/ozone aerosol using high-resolution electrospray ionization mass spectrometry

Abstract: Molecular composition of limonene/O3 secondary organic aerosol (SOA) was investigated using high-resolution electrospray ionization mass spectrometry (HR-ESI-MS) as a function of reaction time. SOA was generated by ozonation of D-limonene in a reaction chamber and sampled at different time intervals using a cascade impactor. The SOA samples were extracted into acetonitrile and analyzed using a HR-ESI-MS instrument with a resolving power of 100 000 (m/Δm). The resulting mass spectra provided detailed information about the extent of oxidation inferred from the O : C ratios, double bond equivalency (DBE) factors, and aromaticity index (AI) values in hundreds of identified individual SOA species. The chemical composition of SOA was approximately the same for all size-fractionated samples studied in this experiment (0.05 to 0.5 μm range). The SOA constituents quickly reached an average O : C ratio of 0.43, which grew to 0.46 after one hour of additional oxidation of particles by the excess ozone. The dominant mechanism of oligomerization, inferred from high resolution ESI-MS data, was reaction between Criegee intermediates and stable first-generation products of limonene ozonolysis. Although the SOA composition was dominated by various oxidized aliphatic compounds, a small fraction of products appeared to contain aromatic rings. SOA generation was also studied in the presence of UV radiation and at elevated relative humidity (RH). The presence of UV radiation had a negligible effect on the SOA composition. The presence of water vapor resulted in a slight redistribution of peak intensities in the mass spectrum likely arising from hydration of certain SOA constituents. The data are consistent with fast production of the first-generation SOA constituents, including oligomers, followed by very slow aging processes that have a relatively small effect on the average molecular composition on the timescale of our experiments.

Two Pathways for Water Interaction with Oxygen Adatoms on TiO2(110)

Abstract: Scanning tunneling microscopy and density functional theory studies show that oxygen adatoms (Oa), produced during O2 exposure of reduced TiO2(110) surfaces, alter the water dissociation and recombination chemistry through two distinctive pathways. Depending on whether H2O and Oa are on the same or adjacent Ti4+ rows, Oa facilitates H2O dissociation and proton transfer to form a terminal hydroxyl pair, positioned along or across the Ti4+ row, respectively. The latter process has not been reported previously, and it starts from a "pseudodissociated" state of water. In both pathways, the reverse H transfer results in H2O reformation and O scrambling, as manifested by an apparent along- or across-row motion of Oa's.

Molecular characterization of biomass burning aerosols using high-resolution mass spectrometry.

Abstract: Chemical characterization of atmospheric aerosols presents a serious analytical challenge because of the complexity of particulate matter analyte composed of a large number of compounds with a wide range of molecular structures, physico-chemical properties, and reactivity. In this study the chemical composition of the organic constituents of biomass burning aerosol (BBA) samples is characterized by high-resolution electrospray ionization mass spectrometry (ESI/MS). Accurate mass measurement combined with Kendrick analysis allows assignment of the elemental composition for hundreds of compounds in the range of m/z values of 50−1000. ESI/MS spectra of different BBA samples contain a variety of distinct, sample specific, characteristic peaks that can be used as unique markers for different types of biofuels. Our results indicate that a significant number of high-MW organic compounds in BBA samples are highly oxidized polar species that can be efficiently detected using ESI/MS but are difficult to observe usi...

Gaussian Basis Set and Planewave Relativistic Spin-Orbit Methods in NWChem.

Abstract: Relativistic spin-orbit density functional theory (DFT) methods have been implemented in the molecular Gaussian DFT and pseudopotential planewave DFT modules of the NWChem electronic-structure program. The Gaussian basis set implementation is based upon the zeroth-order regular approximation (ZORA) while the planewave implementation uses spin-orbit pseudopotentials that are directly generated from the atomic Dirac-Kohn-Sham wave functions or atomic ZORA-Kohn-Sham wave functions. Compared to solving the full Dirac equation these methods are computationally efficient but robust enough for a realistic description of relativistic effects such as spin-orbit splitting, molecular orbital hybridization, and core effects. Both methods have been applied to a variety of small molecules, including I2, IF, HI, Br2, Bi2, AuH, and Au2, using various exchange-correlation functionals. Our results are in good agreement with experiment and previously reported calculations.

Excited states of DNA base pairs using long-range corrected time-dependent density functional theory.

Abstract: In this work, we present a study of the excitation energies of adenine, cytosine, guanine, thymine, and the adenine-thymine (AT) and guanine-cytosine (GC) base pairs using long-range corrected (LC) density functional theory. We compare three recent LC functionals, BNL, CAM-B3LYP, and LC-PBE0, with B3LYP and coupled cluster results from the literature. We find that the best overall performance is for the BNL functional based on LDA. However, in order to achieve this good agreement, a smaller attenuation parameter is needed, which leads to nonoptimum performance for ground-state properties. B3LYP, on the other hand, severely underestimates the charge-transfer (CT) transitions in the base pairs. Surprisingly, we also find that the CAM-B3LYP functional also underestimates the CT excitation energy for the GC base pair but correctly describes the AT base pair. This illustrates the importance of retaining the full long-range exact exchange even at distances as short as that of the DNA base pairs. The worst overall performance is obtained with the LC-PBE0 functional, which overestimates the excitations for the individual bases as well as the base pairs. It is therefore crucial to strike a good balance between the amount of local and long-range exact exchange. Thus, this work highlights the difficulties in obtained LC functionals, which provides a good description of both ground- and excited-state properties.

Imaging Consecutive Steps of O2 Reaction with Hydroxylated TiO2(110): Identification of HO2 and Terminal OH Intermediates

Abstract: We report the results of a combined experimental and theoretical investigation of the reaction of molecular oxygen with a partially hydroxylated TiO2(110) surface. The consecutive steps of both primary and secondary site-specific reactions have been tracked with high-resolution scanning tunneling microscopy (STM). We have directly imaged stable, adsorbed hydroperoxyl (HO2) species, which is believed to be a key intermediate in many heterogeneous photochemical processes but generally metastable and “elusive” until now. We also found terminal hydroxyl groups, which are another critical but never previously directly observed intermediates. Conclusive evidence that O2 reacts spontaneously with a single bridging OH group as an initial reaction step is provided. The experimental results are supported by density functional theory (DFT) calculations that have determined the energies and configurations of these species. Reported observations provide a base for a consistent description of the elementary reaction st...

Defining Active Catalyst Structure and Reaction Pathways from ab Initio Molecular Dynamics and Operando XAFS: Dehydrogenation of Dimethylaminoborane by Rhodium Clusters

Abstract: We present the results of a detailed operando XAFS and density functional theory (DFT)-based ab initio molecular dynamics (AIMD) investigation of a proposed mechanism of the dehydrogenation of dimethylaminoborane (DMAB) by a homogeneous Rh4 cluster catalyst. Our AIMD simulations reveal that previously proposed Rh structures, based on XAFS measurements, are highly fluxional, exhibiting both metal cluster and ligand isomerizations and dissociation that can only be accounted for by examining a finite temperature ensemble. It is found that a fluxional species Rh4(H2BNMe2)82+ is fully compatible with operando XAFS measurements, suggesting that this species may be the observed catalyst resting state. On the basis of this assignment, we propose a mechanism for catalytic DMAB dehydrogenation that exhibits an energy barrier of approximately 28 kcal/mol.

Correlated substitution in paramagnetic Mn 2 + -doped ZnO epitaxial films

Abstract: Epitaxial films of ${\text{Mn}}^{2+}$-doped ZnO were deposited by pulsed laser deposition on $\ensuremath{\alpha}{\text{-Al}}_{2}{\text{O}}_{3}(0001)$ using targets created from ${\text{Mn}}^{2+}$-doped ZnO nanoparticles. Using x-ray absorption spectroscopy and x-ray magnetic circular dichroism, Mn(II) was found to substitute for Zn(II) in the w\"urtzite ZnO lattice with only a paramagnetic dichroic component from the Mn and no magnetic component from either the O or Zn. The dichroism reveals that, while substitutional, the ${\text{Mn}}^{2+}$ distribution in the ZnO lattice is not stochastic. Rather, ${\text{Mn}}^{2+}$ has a tendency to substitute with higher effective local concentrations than anticipated from a stochastic doping model.

Dynamic host energetics and cytoskeletal proteomes in human immunodeficiency virus type 1-infected human primary CD4 cells: analysis by multiplexed label-free mass spectrometry.

Abstract: We report on a proteomic analysis of ex vivo human immunodeficiency virus (HIV) type 1 infection in human primary CD4 cells by shotgun liquid chromatography-tandem mass spectrometry analysis, revealing two distinct proteomic profiles at two phases of virus replication. Relative to mock-infected cells, 168 signature proteins exhibited abundance changes at the first sign of Gag p24 production (8 h postinfection [p.i.]) or the peak of virus replication (24 h p.i.); interestingly, most of the changes were exclusive to only one phase of virus replication. Based on characterization by functional ontology and known human-HIV protein interactions, we observed the enrichment for protein abundance increases pertaining to protein synthesis and nucleasomal reorganization amid an otherwise placid cellular proteome at the first sign of HIV replication. In contrast, we observed indications of decreased protein turnover, concomitant with heightened DNA repair activities and preludes to apoptosis, in the presence of robust virus replication. We also observed hints of disruptions in protein and small molecule trafficking. Our label-free proteomic strategy allowed us to perform multiplexed comparisons-we buttressed our detection specificity with the use of a reverse transcriptase inhibitor as a counterscreen, enabling highlighting of cellular protein abundance changes unique to robust virus replication as opposed to viral entry. In conjunction with complementary high-throughput screens for cellular partners of HIV, we put forth a model pinpointing specific rerouting of cellular biosynthetic, energetic, and trafficking pathways as HIV replication accelerates in human primary CD4 cells.

An Extensive Survey of Tyrosine Phosphorylation Revealing New Sites in Human Mammary Epithelial Cells

Abstract: Protein tyrosine phosphorylation represents a central regulatory mechanism in cell signaling. Here we present an extensive survey of tyrosine phosphorylation sites in a normal-derived human mammary epithelial cell line by applying anti-phosphotyrosine peptide immunoaffinity purification coupled with high sensitivity capillary liquid chromatography tandem mass spectrometry. A total of 481 tyrosine phosphorylation sites (covered by 716 unique peptides) from 285 proteins were confidently identified in HMEC following the analysis of both the basal condition and acute stimulation with epidermal growth factor (EGF). The estimated false discovery rate was 1.0% as determined by searching against a scrambled database. Comparison of these data with existing literature showed significant agreement for previously reported sites. However, we observed 281 sites that were not previously reported for HMEC cultures and 29 of which have not been reported for any human cell or tissue system. The analysis showed that the majority of highly phosphorylated proteins were relatively low-abundance. Large differences in phosphorylation stoichiometry for sites within the same protein were also observed, raising the possibility of more important functional roles for such highly phosphorylated pTyr sites. By mapping to major signaling networks, such as the EGF receptor and insulin growth factor-1 receptor signaling pathways, many known proteins involved in these pathways were revealed to be tyrosine phosphorylated, which provides interesting targets for future hypothesis-driven and targeted quantitative studies involving tyrosine phosphorylation in HMEC or other human systems.

Excitation energies of zinc porphyrin in aqueous solution using long-range corrected time-dependent density functional theory.

Abstract: We study the low-lying excited states of the zinc porphyrin molecule in aqueous solution using long-range corrected TDDFT. We report results using the CAM-B3LYP and CAM-PBE0 functionals and compare them with previously reported excited states based on high-level coupled cluster (CC) methods. The aqueous environment is treated via a QM/MM approach.

A simple procedure for effective quenching of trypsin activity and prevention of 18O-labeling back-exchange.

Abstract: Trypsin-catalyzed stable isotope 16O/18O-labeling of the C-terminal carboxyl groups of peptides is increasingly used in shotgun proteomics for relative peptide/protein quantitation. However, precise quantitative measurements are often complicated by residual trypsin that can catalyze the back-exchange of 18O with 16O after labeling. Here, we demonstrate through a detailed evaluation that boiling the peptide sample for 10 min provides a simple means for completely quenching residual trypsin activity and preventing oxygen back-exchange in 18O-labeled samples. We also observed that the presence of organic solvents such as acetonitrile made boiling less efficient for inactivating trypsin. Finally, current 18O-labeling methods that typically employ immobilized trypsin result in significant sample losses due to nonspecific binding of peptides to the resin, making their application toward smaller biological samples increasingly impractical. We present here an improved 18O-labeling protocol that is more applicable to microscale biological samples by using solution-phase trypsin instead of immobilized trypsin. The ability to generate stably 18O-labeled samples without back-exchange should enable more effective applications of 18O-labeling toward large-scale biomarker discovery and validations where an 18O-labeled sample can be used as a common reference for quantitation.

Crystallographic dependence of visible-light photoactivity in epitaxial TiO2-xNx anatase and rutile

Abstract: Nitrogen-doped ${\text{TiO}}_{2}$ materials have been shown to exhibit visible-light photoactivity, but the operative mechanism(s) are not well understood. Here we use structurally and compositionally well-defined epitaxial films of ${\text{TiO}}_{2\ensuremath{-}x}{\text{N}}_{x}$ anatase (001) and rutile (110) $(x\ensuremath{\le}\ensuremath{\sim}0.02)$ to show a qualitative difference between the visible-light activities for the two polymorphs. Holes generated by visible light at N sites in anatase (001) readily diffuse to the surface and oxidize adsorbed trimethyl acetate while the same in rutile (110) remain trapped in the bulk. In light of the low doping densities that can be achieved in phase-pure material, conventional wisdom suggests that holes should be trapped at N sites in both polymorphs. Although the detailed mechanism is not yet understood, these results suggest that the hole hopping probability is much higher along the [001] direction in N-doped anatase than along the [110] direction in N-doped rutile.

Electron donor‐dependent radionuclide reduction and nanoparticle formation by Anaeromyxobacter dehalogenans strain 2CP‐C

Abstract: Anaeromyxobacter dehalogenans strain 2CP-C can rapidly reduce U(VI) or Tc(VII) to U(IV)O2(s) or Tc(IV)O2(S) using either acetate or H2 as an electron donor source. Kinetic studies reveal that the H2-driven reduction of either U(VI) or Tc(VII) is faster than the acetate-driven reduction. The sub-cellular localization of reduced UO2 is extracellular while TcO2 nanoparticles are both periplasmic and extracellular. While electron donor-specific differences in UO2 nanoparticle aggregate size were observed, the association of UO2 nanoparticles with an exopolymeric substance (EPS) was observed and found to be independent of electron donor source. Electron donor-specific localization differences were not observed in cells incubated with Tc(VII). These finding have direct implications on immobilization strategies for highly soluble radionuclide contaminants in subsurface waters and the development of microbially assisted biostimulation efforts.

Hygroscopic properties of CH3SO3Na, CH3SO3NH4, (CH3SO3)2Mg, and (CH3SO3)2Ca particles studied by micro-FTIR spectroscopy.

Abstract: The hygroscopic behavior of CH3SO3Na, CH3SO3NH4, (CH3SO3)2Mg, and (CH3SO3)2Ca particles as a function of relative humidity (RH) has been studied using microscopic Fourier transform infrared (micro-...

HER/ErbB receptor interactions and signaling patterns in human mammary epithelial cells

Abstract: Knowledge about signaling pathways is typically compiled based on data gathered using different cell lines. This approach implicitly assumes that the cell line dependence is not important. However, different cell lines do not always respond to a particular stimulus in the same way, and lack of coherent data collected from closely related cellular systems can be detrimental to the efforts to understand the regulation of biological processes. To address this issue, we created a clone library of human mammary epithelial (HME) cells that expresses different levels of HER2 and HER3 receptors in combination with endogenous EGFR/HER1. Using our clone library, we have quantified the receptor activation patterns and systematically tested the validity of the existing hypotheses about the interaction patterns between HER1-3 receptors. Our study identified HER2 as the dominant dimerization partner for both EGFR and HER3. Contrary to earlier suggestions, we find that lateral interactions with HER2 do not lead to strong transactivation between EGFR and HER3, i.e., EGFR activation and HER3 activation are only weakly linked in HME cells. We also find that observed weak transactivation is uni-directional where stimulation of EGFR leads to HER3 activation whereas HER3 stimulation does not activate the EGFR. Repeating our experiments at lower cell confluency established that cell confluency is not a major factor in the observed interaction patterns. We have also quantified the dependence of the kinetics of Erk and Akt activation on different HER receptors. We found that HER3 signaling makes the strongest contribution to Akt activation and that, stimulation of either EGFR or HER3 leads to significant Erk activation. Our study shows that clone cell libraries can be a powerful resource in systems biology research by making it possible to differentiate between various hypotheses in a consistent cellular background. Using our constructed clone library we profiled the cell signaling patterns to establish the role of HER2 in the crosstalk between EGFR and HER3 receptors in HME cells. Our results for HME cells show that the weak linkage between EGFR and HER3 pathways can lead to distinct downstream cellular signaling patterns in response to the ligands of these two receptors.

Bonded interactions in silica polymorphs, silicates, and siloxane molecules

Abstract: Experimental model electron density distributions obtained for the silica polymorphs coesite and stishovite are comparable with electron density distributions calculated for various silicates and siloxane molecules. The Si-O bond lengths and Si-O-Si angles calculated with first-principles density functional theory methods as a function of pressure are also comparable with the bond lengths and angles observed for coesite and quartz within the experimental error. The similarity of the topological properties of the Si-O bonded interactions and the experimental and the geometry-optimized structures for the silica polymorphs provide a basis for understanding the properties and crystal chemistry of silica. The agreement supports the argument that the bulk of the structural and physical properties of the silica polymorphs are intrinsic properties of molecular-like coordination polyhedra such that the silica polymorphs can be pictured as “supermolecules” of silica bound by virtually the same forces that bind the Si and O atoms in simple siloxane molecules. The topology of the electron density distribution is consistent with the assertion that the Si-O bonded interaction arises from the net electrostatic attraction exerted on the nuclei by the electron density accumulated between the Si and O atoms. The correlation between the Si-O bond length and Si-O-Si angle is ascribed to the progressive local concentration of the electron density in the nonbonded lone pair region of the O atom rather than to a bonded interaction that involves the d -orbitals on Si. The accumulation of deformation electron density, Δρ( r ), in the bonded and nonbonded regions of the Si-O bond, the close proximity of the bond critical point, r c, of the bond with the nodal surface of the Laplacian and the negative value of the total energy density are taken as evidence that the bond has a nontrivial component of shared character. For M-O bonded interactions for first and second row metal atoms bonded to O, ∇2ρ( r c) is positive and increases linearly as ρ( r c) and G ( r c)/ρ( r c) both increase and as the value of H ( r c) decreases; the greater the shared character of the interaction, the larger the values of both ∇2ρ( r c) and G ( r c)/ρ( r c). In addition, a mapping of ∇2ρ( r ) serves to highlight those Lewis base domains that are susceptible to electrophilic attack by H, like the O atoms in coesite involved in bent Si-O-Si angles; the narrower the angle, the greater the affinity for H. On the basis of the net charges conferred on the Si and O atoms and the bonded radii of the two atoms, the Si-O bond for stishovite, with six-coordinated Si and three-coordinated O, is indicated to be more ionic in character than that in quartz with four-coordinated Si and two-coordinated O. Unlike the conclusion reached for ionic and crystal radii, it is the bonded radius of the O atom that increases with the increasing coordination number of Si, not the radius of the Si atom. The modeling of the electron density distributions for quartz, coesite, and beryl as a function of pressure suggests that the shared character of the bonded interactions in these minerals increases slightly with increasing pressure. The insight provided by the calculations and the modeling of the electron density distributions and the structures of the silica polymorphs bodes well for future Earth materials studies that are expected to improve and clarify our understanding of the connection between properties and structure within the framework of quantum mechanical observables, to find new and improved uses for the materials and to enhance our understanding of crystal chemistry and chemical reactions of materials in their natural environment at the atomic level.

Evaluation of a High Intensity Focused Ultrasound-Immobilized Trypsin Digestion and 18O-Labeling Method for Quantitative Proteomics

Abstract: A new method that uses immobilized trypsin concomitant with ultrasonic irradiation results in ultrarapid digestion and more thorough 18O labeling for quantitative protein comparisons. The method was reproducible and provided effective digestions within <1 min with lower amounts of enzyme, compared to traditional methods. This method was demonstrated for digestion of both simple and complex protein mixtures, including bovine serum albumin, a global proteome extract from the bacteria Shewanella oneidensis, and mouse plasma, as well as 18O labeling of complex protein mixtures, validating this method for differential proteomic measurements. This approach is simple, reproducible, cost-effective, rapid, and well suited for automation.