Changes In Chemical Environment Research Articles

Preparation and microstructures of BaTi1−xZrxO3 hetero-epitaxial thin films on SrTiO3 substrates

Zr-substituted BaTiO3 thin films (BaTi1−xZrxO3: BTZ) were prepared by rf-sputtering on SrTiO3 (STO) substrates or STO substrates buffered by pulsed laser deposited SrRuO3 (SRO) electrodes. The epitaxial growth of BTZ was monitored in situ by reflective high energy electron diffraction. X-ray reflectivity measurement demonstrated that a smooth surface with a roughness of 0.5 nm could be achieved under optimized deposition parameters. Film composition and the change in chemical environment due to Zr substitution are discussed based on electron energy-loss spectroscopy. The high quality of the interfaces was confirmed by transmission electron microscopy. The epitaxial relation between BTZ/SRO and SRO/STO was studied by selected area diffraction and high resolution transmission electron microscopy. All the results show that high quality epitaxial BTZ thin films were successfully deposited and ready for further electrical studies.

Inferring long-term changes in the physical chemical environment of the shallow, enriched Lake Nero from statistical and functional analyses of its phytoplankton

The qualitative and quantitative studies of the phytoplankton, concentration of inorganic nitrogen and phosphate and chlorophyll a in the water column and its seasonal and spatial variation have been studied in the open water of the large, shallow and highly eutrophic Lake Nero over periods representing more than one decade (1988-1989 and 1999-2003). The average qualitative characteristics of phytoplankton have remained stable over the period of observations; however, structural and functional characteristics have been highly unstable in the short term. This is controversial but may be due to the high robustness of the ecosystem to the environmental stresses. The frequencies of species within seasonal-abundance parameters have been used, together with additional data on the dominance of the community expressed in terms of evaluated Species of the Functional Groups (SFG). Correlation and factor analyses were used to estimate the strength of selected environmental factors on the development of SFG. In the periods covered by our analyses, the selected parameters were always strongly correlated with first principal components, which were dominated by properties relating to the underwater light field. According to our investigation, the phytoplankton of Lake Nero supports a commonly occurring combination S1 filamentous cyanobacteria with C diatoms and participation J greens, M and H1 dinitrogen-fixing types. It is typical of shallow, nutrient-rich lakes, comprising species that perform well under conditions of poor light. Individual species dominance caries but strictly among species making up the S1 association. Full accord with the two hypotheses of the PROTECH (Phytoplankton RespOnses To Environmental CHange) model has been demonstrated.

NMR Structural Studies of the ItchWW3 Domain Reveal that Phosphorylation at T30 Inhibits the Interaction with PPxY-Containing Ligands

In this work, we study the role of phosphorylation as a regulatory mechanism for the interaction between the E3 ubiquitin ligase ItchWW3 domain and two PPxY motifs of one of its targets, the Epstein-Barr virus latent membrane protein 2A. Whereas ligand phosphorylation only diminishes binding, domain phosphorylation at residue T30 abrogates it. We show that two ItchWW domains can be phosphorylated at this position, using CK2 and PKA kinases and/or with stimulated T lymphocyte lysates. To better understand the regulation process, we determined the NMR structures of the ItchWW3-PPxY complex and of the phosphoT30-ItchWW3 variant. The peptide binds the domain using both XP and tyrosine grooves. A hydrogen bond from T30 to the ligand is also detected. This hydrogen-bond formation is precluded in the variant, explaining the inhibition upon phosphorylation. Our results suggest that phosphorylation at position 30 in ItchWW domains can be a mechanism to inhibit target recognition in vivo.

Probing Structural Differences in Prion Protein Isoforms by Tyrosine Nitration

Two conformational isomers of recombinant hamster prion protein (residues 90-232) have been probed by reaction with two tyrosine nitration reagents, peroxynitrite and tetranitromethane. Two conserved tyrosine residues (tyrosines 149 and 150) are not labeled by either reagent in the normal cellular form of the prion protein. These residues become reactive after the protein has been converted to the beta-oligomeric isoform, which is used as a model of the fibrillar form that causes disease. After conversion, a decrease in reactivity is noted for two other conserved residues, tyrosine 225 and tyrosine 226, whereas little to no effect was observed for other tyrosines. Thus, tyrosine nitration has identified two specific regions of the normal prion protein isoform that undergo a change in chemical environment upon conversion to a structure that is enriched in beta-sheet.

Effects of Changed Soil Conditions on the Mobility of Trace Metals in Moderately Contaminated Urban Soils

Changes in the soil chemical environment can be expected to increase the leaching of trace metals bound in soils. In this study the mobility of trace metals was monitored in a column experiment for two contaminated urban soils. Four different treatments were used (i.e. rain, acid rain, salt and bark). Leachates were analysed for pH, dissolved organic carbon (DOC) and for seven trace metals (cadmium (Cd), chromium (Cr), copper (Cu), mercury (Hg), nickel (Ni), lead (Pb) and zinc (Zn)). The salt treatment produced the lowest pH values (between 5 and 6) in the effluent whereas the DOC concentration was largest in the bark treatment (40–140 mg L−1) and smallest in the salt and acid treatments (7–40 mg L−1). Cadmium, Ni and Zn were mainly mobilised in the salt treatment, whereas the bark treatments produced the highest concentrations of Cu and Pb. The concentrations of Cu, Cr, and Hg were strongly correlated with DOC (r2 = 0.90, 0.91 and 0.96, respectively). A multi-surface geochemical model (SHM-DLM) produced values for metal dissolution that were usually of the correct magnitude. For Pb, however, the model was not successful indicating that the retention of this metal was stronger than assumed in the model. For all metals, the SHM-DLM model predicted that soil organic matter was the most important sorbent, although for Pb and Cr(III) ferrihydrite was also important and accounted for between 15 and 50% of the binding. The results confirm the central role of DOC for the mobilization of Cu, Cr, Hg and Pb in contaminated soils.

Ancient chemoreceptors retain their flexibility

Bacterial and archaeal microbes possess a wide array of surface-deployed receptors for monitoring their chemical and physical surroundings. Particularly prominent among microbial chemoreceptors are the so-called methyl-accepting chemotaxis proteins (MCPs), which sense changes in the cell's chemical environment and generate intracellular signals that control the organism's pattern of locomotion or gene expression. MCPs have long been known to mediate attractant-seeking and repellent-avoiding behaviors in Escherichia coli and other motile microbes, but more recently, MCPs have also been shown to regulate complex developmental programs, such as fruiting body formation (1). The sequenced microbial genomes contain thousands of MCP genes, so it seems likely that evolution has put these versatile chemical sensors to other uses as well. In this issue of PNAS, Alexander and Zhulin (2) describe an insightful structure-guided analysis of MCP sequences that reveals common architectural features conserved over the long evolutionary history of these chemoreceptors. Their work provides important new clues to the molecular signaling mechanism(s) of these remarkable molecules.

Single Asperity Wear and Stress-Assisted Dissolution of Copper

AbstractThe focus of this paper is to investigate the synergistic influence of contact loads, surface stress state and chemical environment on material removal during mechanical stimulation of copper surface. A unique setup is used to generate well characterized stress states on a polished copper specimen. Stressed surface of copper specimen is stimulated using tip of the atomic force microscope (AFM) and material removed during stimulation is measured as a function of contact loads, surface stress state and chemical environment. Measured material removal rates display a complex dependence on contact pressures and in-plane stress state which changes as the pH of chemical environment changes from acidic to basic. A surface material removal mechanism based on a single asperity wear and stress-assisted dissolution is proposed to explain the experimental observations

Experimental study of limestone micro-fracturing under a coupled stress, fluid flow and changing chemical environment

Experimental study of limestone micro-fracturing under a coupled stress, fluid flow and changing chemical environment

Nitroxidative, Nitrosative, and Nitrative Stress: Kinetic Predictions of Reactive Nitrogen Species Chemistry Under Biological Conditions

A freely available Windows-based program, RNSim1A, is utilized to predict metal-independent reactive nitrogen species (RNS) chemistry (oxidation, nitrosation, and nitration) under simulated biological conditions and make the following specific predictions. (1) The peak in oxidative reactions that occurs in vitro with 1:1 fluxes of (*)NO and O(2)(*)(-) does not occur under biological conditions. (2) By far, the quantitatively dominant (92-99.6%) process in vivo is oxidation, compared to nitrosation and nitration. (3) Only five of the many possible RNS reactions involving thiol (glutathione, GSH) and tyrosine are quantitatively important biologically. (4) Under inflammatory conditions, approximately 1% of O(2)(*)(-) reacts with (*)NO to produce ONOO(-), with the remainder reacting with SOD. (5) The dominant reaction of tyrosyl radical is a radical swap with GSH, producing the glutathiyl radical and regenerating tyrosine. (6) Nitrosothiol is formed virtually exclusively via radical recombination (RS(*) + (*)NO) as opposed to reaction with nitrous anhydride (N(2)O(3)). (7) Nitrosothiol is an intermediate, not an endproduct, and responds dynamically to changes in the immediate chemical environment. (8) The formation of a nitroso group on a particular thiol can be considered a marker of increased reactivity of that thiol, and it is likely that other modifications of that thiol (oxidation, glutathiolation) are more abundant than nitrosation and may be the functionally significant modification. (9) Specific chemical mechanisms are proposed for posttranslational protein modification via nitrosation, nitration, glutathiolation, and also dithiol/disulfide exchange, with important roles for the thiolate anion and O(2) (suggesting possible mechanisms for O(2) sensing) and variable degrees of exposure of cysteine thiol and tyrosine phenolate. (10) Patterns of reactivity are similar for low (20 nM) and high (500 nM) steady-state levels of NO. (11) The dominant reactions are those involving reactants at the highest concentrations (CO(2), thiol, O(2)). Because of the dominance of oxidative processes caused by RNS, the term nitroxidative stress is proposed, emphasizing the oxidative (as opposed to nitrosative or nitrative) stress that dominates RNS actions under biological conditions.

Solution NMR of Acetylcholine Binding Protein Reveals Agonist-Mediated Conformational Change of the C-Loop

Previous X-ray crystallography, molecular dynamics simulation, fluorescence spectroscopy, and deuterium-hydrogen exchange of acetylcholine binding protein (AChBP) suggest that after binding of the agonist, the C-loop at the periphery of the binding site draws inward to cap the site and envelop the agonist. In this study, we use high-resolution solution NMR to monitor changes in the chemical environment of the C-loop without and with acetylcholine (ACh) bound. Substitution of [15N]cysteine for the native cysteines 123, 136, 187, and 188 provided intrinsic monitors of the chemical environments of the Cys- and C-loops, respectively. Two-dimensional transverse relaxation-optimized spectroscopy 15N-1H HSQC spectroscopy of apo-AChBP revealed seven well resolved cross-peaks for the group of cysteines. The spectrum of AChBP with Ser substituted for Cys 187 and 188 shows only two main cross-peaks, corresponding to Cys 123 and 136 from the Cys-loop, enabling resonance assignments. After binding of ACh, the five cross-peaks associated with cysteines from the C-loop condense into two predominant cross-peaks not observed in the spectrum from the apo protein, indicating a restricted range of conformations and change in chemical environment of the C-loop. The results show that isotopic cysteine can be incorporated into specified positions of AChBP expressed from a eukaryotic source, that the C-loop assumes multiple conformations without ACh, but that its conformation becomes restricted with ACh bound. The collective findings suggest a structural mechanism for agonist recognition in AChBP and related Cys-loop receptors.

Observation of Room-Temperature 5D1 Luminescence of an Organoeuropium Complex Encapsulated in Sol-Gel Glass

In comparing emissions of the inorganic Eu3+ salts (chloride or nitrate) to organoeuropium complexes doped into optically transparent sol-gel glass, previous studies have indicated that changes in the local chemical environment by chelation or variation of the ligand or gel matrix compositions were found to leave the main spectral features of Eu3+ essentially unchanged; complexation just increases the emission intensity of europium and leads to broadening and splitting of the peaks. In all cases studied and irrespective of the excitation energy, the observable emission peaks result only from relaxations out of the 5D0 excited state of Eu3+ to the first five levels of the 7F ground manifold. The present research examines the luminescence behavior of EuCl3 and Eu-TETA (TETA is the macro cycle, 1,4,8,11-tetraazacyclotetradecane-1,4,8,11-tetraaceticacid) doped into a sol-gel host; in addition to emissions from the 5D0, emission from the 5D1 excited state of Eu3+ is observed for the first time.

Yttrium segregation and intergranular defects in alumina

Intergranular segregation of yttrium is investigated in a rhombohedral twin grain boundary of alumina. The deviation from the twin orientation is compensated by a periodic arrangement of intergranular dislocations. TEM tools (CTEM and HREM, EDXS, EFTEM and EELS/ELNES) have been used to characterize changes in chemical and electronic environments along this twin. Within the experimental limits, no Y is detected in the perfect twin parts. On the other hand, Y segregation occurs very locally in the dislocation cores on about four atomic planes perpendicularly to the GB, which in fact corresponds to the step height associated with the interfacial dislocations. By comparison with an undoped bicrystal, both the dislocation distribution and the Y segregation localization confirm the influence of Y on the dislocation mobility. Furthermore, in the Y-rich defects, high spatial resolution analysis of the energy loss near edge structures (ELNES) of the Al-L23 absorption edge brings some enlightenments about the Al3+ cation environment, provided the effects of local radiation damage are fully considered and under control.

Geochemical chaos: Periodic and nonperiodic growth of mixed-layer phyllosilicates

Interstratification—periodic or nonperiodic stacking of two different silicate layers along a c ∗-axis—is common in phyllosilicates. Published evidence indicates that some interstratified minerals precipitate directly from aqueous solutions. In this paper, we have demonstrated, based on chaos theory, that both periodic and nonperiodic interstratification can autonomously arise from simple kinetics of mineral growth from a solution. Growth of a mixed-layer mineral is assumed to proceed layer by layer, and each layer starts with the formation of a base (Si, Al)–O tetrahedral sheet, whose structural configuration in a– b dimensions determines the type of new layer that forms. The sequence of layer stacking can be described by a one-dimensional map (i.e., a difference equation), which accounts for two competing factors: (1) the affinity of each end-member structural component for attaching to the surface of the preceding layer, and (2) the strain energy created by stacking next to each other two silicate layers with different structural configurations. Chaotic (or nonperiodic) interstratification emerges when the contacting solution becomes slightly supersaturated with respect to both structural components. The transition from one interstratification pattern to another reflects a change in chemical environment during mineral crystallization. Our model can successfully predict the occurrence of mixed-layer phyllosilicates and the associated layer stacking sequences observed in both hydrothermal alteration and sediment diagenesis. The model suggests that the diagenetic transition of smectite → nonperiodic illite/smectite → ordered illite/smectite → illite may reflect relative changes in the saturation degree of pore water with respect to two end-member phases as a result of increasing burial temperatures.

An X-ray photoemission study of interfacial reaction during annealing of Mg/GaAs(100) interface

In this paper, we present an in situ annealing study on Mg(15 A)/GaAs(100) interface using X-ray photoelectron spectroscopy (XPS). The core level results indicate that an interfacial reaction starts between Mg and Ga atoms at room temperature and enhances with annealing. However, at a higher temperature of annealing, a mixed layer of ternary Mg–Ga–As phase is formed at the interface. Corresponding Auger spectra of Mg, Ga and As also show considerable modifications in their nature and therefore support the above reaction. The observed results are correlated and interpreted in terms of continuous changes in electronic and chemical environment at the Mg/GaAs interface. Copyright © 2005 John Wiley & Sons, Ltd.

Structural ordering of ultra-thin, amorphous aluminium-oxide films

The structural ordering of ultra-thin (<5 nm) Al-oxide films, as grown by dry, thermal oxidation for various oxidation times within the temperature range of 373–773 K, has been investigated by chemical state analysis using X-ray photoelectron spectroscopy (XPS). To this end, the changes in chemical environment of the Al and O ions in the oxide film during the transformation from amorphous Al-oxide to γ-Al 2O 3 with increasing oxidation temperature and oxide-film thickness has been deduced from the corresponding shifts of the Al and O Auger parameters. It is concluded that the transition from amorphous Al-oxide to γ-Al 2O 3 is realised by a gradual development of long-range order in the dense-random-packing-of-spheres network of oxygen ions, accompanied by a densification of the oxide film. During the transformation, neither a significant short-range ordering of Al cations nor a redistribution of Al cations over tetrahedral and octahedral interstices of the oxygen sublattice is observed.

Dielectric spectroscopy measurements of the sub- Tg relaxations in amorphous ethyl cellulose: A relaxation magnitude study

Amorphous ethyl cellulose exhibits three secondary relaxations at temperatures below its glass transition. The fitted parameters that describe these processes and the comparison with other polysaccharides allow to ascribe the relaxations to lateral groups on one hand and to local main chain motion on the other hand. Their contributions to the dielectric constant overlap and induce a broad dielectric losses peak. The amplitude of one of these relaxations is found to decrease regularly with time. It is believed it comes from a gradual change of the polar groups chemical environment that constrains their motion.

Characterization of intervertebral disc degeneration by high‐resolution magic angle spinning (HR‐MAS) spectroscopy

The goal of this study was to determine the ability of high-resolution magic angle spinning (HR-MAS) NMR spectroscopy to distinguish different stages of intervertebral disc degeneration (IVDD). 17 discs were removed from human cadavers and analyzed them using 1D and 2D (total correlation spectroscopy (TOCSY)) (1)H HR-MAS spectroscopy, and T(1) and T(2) relaxation time measurements to determine the chemical composition and changes in chemical environment of discs with increasing levels of degeneration (Thompson grade). Among the significant findings were that spectra were very similar for samples taken from annular and nuclear regions of discs, and that visually apparent changes were observed in the spectra of the annular and nuclear samples from discs with increasing Thompson grade. Area ratios of the N-acetyl to choline (Cho) regions, and Cho to carbohydrate (Carb) regions of the spectra allowed us to discriminate between discs of increasing Thompson grade with minimal overlap of individual ratios. Changes in T(1) and T(2) relaxation times of the chemical constituents of disc spectra were not significantly correlated to the degree of degeneration. The results of this study support the feasibility of using in vivo spectroscopy for detecting chemical changes associated with disc degeneration.

Breakthrough pain in malignant and non-malignant diseases: a review of prevalence, characteristics and mechanisms

Breakthrough pain or transient worsening of pain in patients with an ongoing steady pain is a well known feature in cancer pain patients, but it is also seen in non-malignant pain conditions with involvement of nerves, muscles, bones or viscera. Continuous and intermittent pain seems to be a general feature of these different pain conditions, and this raises the possibility of one or several common mechanisms underlying breakthrough pain in malignant and non-malignant disorders. Although the mechanisms of spontaneous ongoing pain and intermittent flares of pain (BTP) may be difficult to separate, we suggest that peripheral and/or central sensitization (hyperexcitability) may play a major role in many causes of BTP. Mechanical stimuli (e.g. micro-fractures) changes in chemical environments and release of tumour growth factors may initiate sensitization both peripherally and centrally. It is suggested that sensitization could be the common denominator of BTP in malignant and non-malignant pain.

Magnetic properties of sediment in the Ría de Arousa (Spain): dissolution of iron oxides and formation of iron sulphides

A detailed magnetic study of mineral dissolution has been carried out in order to better characterise the sedimentary environment in the Ría de Arousa, an estuarine-like system in western Spain. There the large number (>3000) of mussel rafts has resulted in a high influx of organic matter causing a change of the original chemical environment. Magnetic measurements of sediment cores (reaching 4.1 m depth) combined with electron microscopy show that there is a distinctive depth trend for the concentration of magnetic minerals. The different iron oxides dissolve with increasing time and depth and at different rates, so that their relative proportions change. At the same time, pyrite is forming, replacing the iron oxides at shallow depths. The magnetic properties of the sediments indicate a high dissolution rate of magnetite (half-life ⩽5 year) and other iron oxides in a strongly reducing environment. Additionally, goethite and hematite in the studied system seem to be less reactive than magnetite.

Investigation of the crystal structure and electrical properties of La3+-doped SrBi2Ta2O9 ceramics

The layered-perovskite ferroelectric ceramics of La3+-doped SrBi2Ta2O2 (SBT), with the chemical formula of SrBi(2 - x)LaxTa2O9 (SBLT), have been prepared by the conventional mixed-oxide method. The effect of substitution of La3+ for Bi3+ in the crystal structure and electrical properties of SBT ceramics was explored with the aid of X-ray diffraction, e(T) curve and ferroelectric hysteresis loop measurements. The electrical properties such as dielectric constant (e) and remanent polarization (Pr) showed a dependence on the crystal structure, and both reached maxima of 243 and 25 μC cm−2, respectively, with 6 at % La3+ substitution, accompanying the greatest structure change. Theoretical considerations were presented to suggest that the atomic displacements and the crystal deformation implied by the crystal structure change are responsible for the improvement of electrical properties. On the other hand, degradation of fatigue resistance was observed in SBLT ceramics, which is believed to be caused by the chemical environment change of the perovskite layers arising from La3+ substitution on Bi3+ sites.