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At least 199 records · Page 11

ERK Oscillation-Dependent Gene Expression Patterns and Deregulation by Stress-Response

Studies were undertaken to determine whether ERK oscillations regulate a unique subset of genes in human keratinocytes and subsequently, whether the p38 stress response inhibits ERK oscillations. A DNA microarray identified many genes that were unique to ERK oscillations, and network reconstruction predicted an important role for the mediator complex subunit 1 (MED1) node in mediating ERK oscillation-dependent gene expression. Increased ERK-dependent phosphorylation of MED1 was observed in oscillating cells compared to non-oscillating counterparts as validation. Treatment of keratinocytes with a p38 inhibitor (SB203580) increased ERK oscillation amplitudes and MED1 and phospho-MED1 protein levels. Bromate is a probable human carcinogen that activates p38. Bromate inhibited ERK oscillations in human keratinocytes and JB6 cells and induced an increase in phospho-p38 and decrease in phospho-MED1 protein levels. Treatment of normal rat kidney cells and primary salivary gland epithelial cells with bromate decreased phospho-MED1 levels in a reversible fashion upon treatment with p38 inhibitors (SB202190; SB203580). Our results indicate that oscillatory behavior in the ERK pathway alters homeostatic gene regulation patterns and that the cellular response to perturbation may manifest differently in oscillating vs non-oscillating cells.

carcinogenesis↗

Structure-dependent vibrational dynamics of Mg(BH 4 ) 2 polymorphs probed with neutron vibrational spectroscopy and first-principles calculations

We investigated the structure-dependent vibrational properties of different Mg(BH 4 ) 2 polymorphs (α, β, γ, and δ phases) with a combination of neutron vibrational spectroscopy (NVS) measurements and density functional theory (DFT) calculations, with emphasis placed on the effects of the local structure and orientation of the BH 4 - anions. DFT simulations closely match the neutron vibrational spectra. The main bands in the low-energy region (20–80 meV) are associated with the BH4 - librational modes. The features in the intermediate energy region (80–120 meV) are attributed to overtones and combination bands arising from the lower-energy modes. The features in the high-energy region (120–200 meV) correspond to the BH 4 - symmetric and asymmetric bending vibrations, of which four peaks located at 140, 142, 160, and 172 meV are especially intense. There are noticeable intensity distribution variations in the vibrational bands for different polymorphs. We can explain these differences using the spatial distribution of BH 4 - anions within various structures. An example of the possible identification of products after the hydrogenation of MgB 2 , using NVS measurements, is presented. Our results provide fundamental insights of benefit to researchers currently studying these promising hydrogen-storage materials.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Probing charge transfer characteristics in a donor–acceptor metal–organic framework by Raman spectroelectrochemistry and pressure-dependence studies

The stimuli responsive behaviour of charge transfer donor–acceptor metal–organic frameworks (MOFs) remains an understudied phenomenon which may have applications in tuneable electronic materials. We now report the modification of donor–acceptor charge transfer characteristics in a semiconducting tetrathiafulvalene–naphthalene diimide-based MOF under applied electrochemical bias and pressure. Here, we employ a facile solid state in situ Raman spectroelectrochemical technique, applied for the first time in the characterisation of electroactive MOFs, to monitor the formation of a new complex TTFTC˙+–DPNI from a largely neutral system, upon electrochemical oxidation of the framework. In situ pressure-dependent Raman spectroscopy and powder X-ray diffraction experiments performed in a diamond anvil cell revealed blue shifts in the donor and acceptor vibrational modes in addition to contractions in the unit cell which are indicative of bond shortening. This study demonstrates the utility of in situ Raman spectroscopic techniques in the characterisation of redox-active MOFs and the elucidation of their electronic behaviours.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Salt-dependent properties of a coacervate-like, self-assembled DNA liquid

Liquid DNA droplets, made of self-assembled DNA particles (‘nanostars’), show salt-dependent viscosity, self-diffusion, and surface tension due mainly to basepairing thermodynamics. Yet, certain aspects indicate a heterogeneous liquid structure. These results are compared to other coacervate systems.

Chemistry↗

Surprisingly big linker-dependence of activity and selectivity in CO 2 reduction by an iridium(I) pincer complex

In this work, we report the quantitative electroreduction of CO 2 to CO by a PNP-pincer iridium(I) complex bearing amino linkers in DMF/water. The activity and selectivity of the reduction greatly depend on the choice of linker within the ligand. The complex 3-N is far superior to the analogues with methylene and oxygen linkers, showing higher activity and better selectivity for CO 2 over proton reduction.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Phenomenological extraction of Transverse Momentum Dependent distributions

We discuss phenomenological extraction of Transverse Momentum Dependent Distributions (TMDs) from experimental data. At leading twist spin structure of spin-1/2 hadron can be described by 8 TMDs. TMDs reveal three-dimensional distribution of partons inside polarised nucleon. Experimentally these functions can be studied in polarised experiments using Spin Asymmetries in particular Single Spin Asymmetries (SSAs). We discuss transversity that measures distribution of transversely polarised quarks in a transversely polarised nucleon and Sivers distribution function that describes distribution of unpolarised quarks in a transversely polarised nucleon.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

Two-current model of the composition dependence of resistivity in amorphous (Fe100-xCox)(89-y)Zr7B4Cuy alloys using a rigid-band assumption

Composition dependence of resistivity is studied in amorphous (Fe100-xCox)(89-y)Zr7B4Cuy (0 <= x <= 50, y = 0, 1) alloys. The two-current model proposed by Mott for crystalline materials is extended to a disordered amorphous system where s-d scattering is dominant in electron conduction. A rigid-band assumption is made due to the small atomic number difference between Fe and Co. Band structures with a constant density of states (DOS), parabolic distributed DOS, and Gaussian distributed DOS were investigated to fit experimental data. The Gaussian distributed DOS was found to simulate the resistivity maximum and magnetic moment maximum in the Fe-rich region. The basic concepts presented here can potentially provide insight into the optimization of FeCo-based HITPERM alloys for applications at increased frequencies. (C) 2012 American Institute of Physics. [http://dx.doi.org/10.1063/1.4765673]

Shen, S↗

Note: Alignment/focus dependent core-line sensitivity for quantitative chemical analysis in hard x-ray photoelectron spectroscopy using a hemispherical electron analyzer

X-ray photoelectron spectroscopy is an established technique for quantitative chemical analysis requiring accurate peak intensity analysis. We present evidence of focus/alignment dependence of relative peak intensities for peaks over a broad kinetic energy range with a hemispherical electron analyzer operated in a position imaging mode. A decrease of over 50% in the Ag 2p{sub 3/2} to Ag 3d ratio is observed in a Ag specimen. No focus/alignment dependence is observed when using an angular imaging mode, necessitating the use of angular mode for quantitative chemical analysis.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Yield strength dependence on strain rate of molybdenum-alloy nanofibers

The yield strength dependence on strain rate was studied for molybdenum-alloy nanofibers with varying initial dislocation density at three different pre-strain levels. In-situ tensile experiments at three displacement rates were carried out in a scanning electron microscope. Yield strength and its scatter decreased as a function of the pre-strain level for different displacement rates. A statistical model was used to analyze the results, and a negative strain rate dependence was inferred from the yield experiments. This finding suggests the need for theoretical investigations since classical models such as dynamic strain aging may have limitations at such nanoscales.

36 MATERIALS SCIENCE↗

Solute location in a nanoconfined liquid depends on charge distribution

Nanostructured materials that can confine liquids have attracted increasing attention for their diverse properties and potential applications. Yet, significant gaps remain in our fundamental understanding of such nanoconfined liquids. Using replica exchange molecular dynamics simulations of a nanoscale, hydroxyl-terminated silica pore system, we determine how the locations explored by a coumarin 153 (C153) solute in ethanol depend on its charge distribution, which can be changed through a charge transfer electronic excitation. The solute position change is driven by the internal energy, which favors C153 at the pore surface compared to the pore interior, but less so for the more polar, excited-state molecule. This is attributed to more favorable non-specific solvation of the large dipole moment excited-state C153 by ethanol at the expense of hydrogen-bonding with the pore. It is shown that a change in molecule location resulting from shifts in the charge distribution is a general result, though how the solute position changes will depend upon the specific system. This has important implications for interpreting measurements and designing applications of mesoporous materials.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Interface and thickness dependent domain switching and stability in Mg doped lithium niobate

Controlling ferroelectric switching in Mg doped lithium niobate (Mg:LN) is of fundamental importance for optical device and domain wall electronics applications that require precise domain patterns. Stable ferroelectric switching has been previously observed in undoped LN layers above proton exchanged (PE) phases that exhibit reduced polarization, whereas PE layers have been found to inhibit lateral domain growth. Here, Mg doping, which is known to significantly alter ferroelectric switching properties including coercive field and switching currents, is shown to inhibit domain nucleation and stability in Mg:LN above buried PE phases that allow for precise ferroelectric patterning via domain growth control. Furthermore, piezoresponse force microscopy (PFM) and switching spectroscopy PFM reveal that the voltage at which polarization switches from the “up” to the “down” state increases with increasing thickness in pure Mg:LN, whereas the voltage required for stable back switching to the original “up” state does not exhibit this thickness dependence. This behavior is consistent with the presence of an internal frozen defect field. The inhibition of domain nucleation above PE interfaces, observed in this study, is a phenomenon that occurs in Mg:LN but not in undoped samples and is mainly ascribed to a remaining frozen polarization in the PE phase that opposes polarization reversal. This reduced frozen depolarization field in the PE phase also influences the depolarization field of the Mg:LN layer above due to the presence of uncompensated polarization charge at the PE-Mg:LN boundary. These alterations in internal electric fields within the sample cause long-range lattice distortions in Mg:LN via electromechanical coupling, which were corroborated with complimentary Raman measurements.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

Thickness, humidity, and polarization dependent ferroelectric switching and conductivity in Mg doped lithium niobate

Mg doped lithium niobate (Mg:LN) exhibits several advantages over undoped LN such as resistance to photorefraction, lower coercive fields, and p-type conductivity that is particularly pronounced at domain walls and opens up a range of applications, e.g., in domain wall electronics. Engineering of precise domain patterns necessitates well founded knowledge of switching kinetics, which can differ significantly from that of undoped LN. In this work, the role of humidity and sample composition in polarization reversal has been investigated under application of the same voltage waveform. Control over domain sizes has been achieved by varying the sample thickness and initial polarization as well as atmospheric conditions. In addition, local introduction of proton exchanged phases allows for inhibition of domain nucleation or destabilization, which can be utilized to modify domain patterns. Polarization dependent current flow, attributed to charged domain walls and band bending, demonstrates the rectifying ability of Mg:LN in combination with suitable metal electrodes that allow for further tailoring of conductivity.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

Doping concentration dependence of the photoluminescence spectra of n -type GaAs nanowires

In this work, the photoluminescence spectra of n -type doped GaAs nanowires, grown by the metal organic chemical vapor deposition method, are measured at 4K and 77 K. Our measurements indicate that an increase in carrier concentration leads to an increase in the complexity of the doping mechanism, which we attribute to the formation of different recombination centers. At high carrier concentrations, we observe a blueshift of the effective band gap energies by up to 25 meV due to the Burstein-Moss shift. Based on the full width at half maximum (FWHM) of the photoluminescence peaks, we estimate the carrier concentrations for these nanowires, which varies from 6 x 10 17 cm -3 (lightly doped), to 1.5 x 10 18 cm -3 (moderately doped), to 3.5 x 10 18 cm -3 (heavily doped) as the partial pressure of the disilane is varied from 0.01 sccm to 1 sccm during the growth process. We find that the growth temperature variation does not affect the radiative recombination mechanism; however, it does lead to a slight enhancement in the optical emission intensities. For GaAs nanowire arrays measured at room temperature, we observe the same general dependence of band gap, FWHM, and carrier concentration on doping.

36 MATERIALS SCIENCE↗

Two-metal versus one-metal mechanisms of lysine adenylylation by ATP-dependent and NAD + -dependent polynucleotide ligases

Polynucleotide ligases comprise a ubiquitous superfamily of nucleic acid repair enzymes that join 3'-OH and 5'-PO 4 DNA or RNA ends. Ligases react with ATP or NAD + and a divalent cation cofactor to form a covalent enzyme-(lysine-Nζ)–adenylate intermediate. Here, we report crystal structures of the founding members of the ATP-dependent RNA ligase family (T4 RNA ligase 1; Rnl1) and the NAD + -dependent DNA ligase family ( Escherichia coli LigA), captured as their respective Michaelis complexes, which illuminate distinctive catalytic mechanisms of the lysine adenylylation reaction. The 2.2-Å Rnl1•ATP•(Mg 2+ ) 2 structure highlights a two-metal mechanism, whereby: a ligase-bound “catalytic” Mg 2+ (H 2 O) 5 coordination complex lowers the p K a of the lysine nucleophile and stabilizes the transition state of the ATP α phosphate; a second octahedral Mg 2+ coordination complex bridges the β and γ phosphates; and protein elements unique to Rnl1 engage the γ phosphate and associated metal complex and orient the pyrophosphate leaving group for in-line catalysis. By contrast, the 1.55-Å LigA•NAD + •Mg 2+ structure reveals a one-metal mechanism in which a ligase-bound Mg 2+ (H 2 O) 5 complex lowers the lysine p K a and engages the NAD + α phosphate, but the β phosphate and the nicotinamide nucleoside of the nicotinamide mononucleotide (NMN) leaving group are oriented solely via atomic interactions with protein elements that are unique to the LigA clade. We conclude, the two-metal versus one-metal dichotomy demarcates a branchpoint in ligase evolution and favors LigA as an antibacterial drug target.

59 BASIC BIOLOGICAL SCIENCES↗

Mapping the Temperature-dependent and network site-specific onset of spectral diffusion at the surface of a water cluster cage

We explore the kinetic processes that sustain equilibrium in a microscopic, finite system. This is accomplished by monitoring the spontaneous, time-dependent frequency evolution (the frequency autocorrelation) of a single OH oscillator, embedded in a water cluster held in a temperature-controlled ion trap. The measurements are carried out by applying two-color, IR-IR photodissociation mass spectrometry to the D3O+?(HDO)(D2O)19 isotopologue of the “magic number” protonated water cluster, H+?(H2O)21. The OH group can occupy any one of the five spectroscopically distinct sites in the distorted pentagonal dodecahedron cage structure. The OH frequency is observed to evolve over tens of milliseconds in the temperature range (90-120 K). Starting at 100 K, large “jumps” are observed between two OH frequencies separated by ~300 cm-1 indicating migration of the OH group from the bound OH site at 3350 cm-1 to the free position at 3686 cm-1. Increasing the temperature to 110 K leads to partial interconversion among many sites. All sites are observed to interconvert at 120 K such that the distribution of the unique OH group among them adopts the form one would expect for a canonical ensemble. The spectral dynamics displayed by the clusters thus offer an unprecedented view into the molecular-level processes that drive spectral diffusion in an extended network of water molecules.

Yang, Nan↗