High-pressure structural, elastic and electronic properties of the scintillator host material, KMgF_3

The high-pressure structural behaviour of the fluoroperovskite KMgF_3 is investigated by theory and experiment. Density functional calculations were performed within the local density approximation and the generalized gradient approximation for exchange and correlation effects, as implemented within the full-potential linear muffin-tin orbital method. In situ high-pressure powder x-ray diffraction experiments were performed up to a maximum pressure of 40 GPa using synchrotron radiation. We find that the cubic Pm\bar{3}m crystal symmetry persists throughout the pressure range studied. The calculated ground state properties -- the equilibrium lattice constant, bulk modulus and elastic constants -- are in good agreement with experimental results. By analyzing the ratio between the bulk and shear modulii, we conclude that KMgF_3 is brittle in nature. Under ambient conditions, KMgF_3 is found to be an indirect gap insulator with the gap increasing under pressure.Comment: 4 figure

Magnetic moments of W 5d in Ca2CrWO6 and Sr2CrWO6 double perovskites

We have investigated the magnetic moment of the W ion in the ferrimagnetic double perovskites Sr2CrWO6 and Ca2CrWO6 by X-ray magnetic circular dichroism (XMCD) at the W L(2,3) edges. In both compounds a finite negative spin and positive orbital magnetic moment was detected. The experimental results are in good agreement with band-structure calculations for (Sr/Ca)2CrWO6 using the full-potential linear muffin-tin orbital method. It is remarkable, that the magnetic ordering temperature, TC, is correlated with the magnetic moment at the 'non-magnetic' W atom.Comment: accepted for publicatio

Biophysical Characterization of Fluorotyrosine Probes Site-Specifically Incorporated into Enzymes:

Fluorinated tyrosines (F[subscript n]Y's, n = 2 and 3) have been site-specifically incorporated into E. coli class Ia ribonucleotide reductase (RNR) using the recently evolved M. jannaschii Y-tRNA synthetase/tRNA pair. Class Ia RNRs require four redox active Y's, a stable Y radical (Y·) in the β subunit (position 122 in E. coli), and three transiently oxidized Y's (356 in β and 731 and 730 in α) to initiate the radical-dependent nucleotide reduction process. F[subscript n]Y (3,5; 2,3; 2,3,5; and 2,3,6) incorporation in place of Y₁₂₂-β and the X-ray structures of each resulting β with a diferric cluster are reported and compared with wt-β2 crystallized under the same conditions. The essential diferric-F[subscript n]Y· cofactor is self-assembled from apo F[subscript n]Y-β2, Fe ²⁺, and O₂ to produce ∼1 Y·/β2 and ∼3 Fe ³⁺ /β2. The F[subscript n]Y· are stable and active in nucleotide reduction with activities that vary from 5% to 85% that of wt-β2. Each F[subscript n] Y·-β2 has been characterized by 9 and 130 GHz electron paramagnetic resonance and high-field electron nuclear double resonance spectroscopies. The hyperfine interactions associated with the 19 F nucleus provide unique signatures of each F[subscript n]Y· that are readily distinguishable from unlabeled Y·'s. The variability of the abiotic F[subscript n]Y pK a 's (6.4 to 7.8) and reduction potentials (-30 to +130 mV relative to Y at pH 7.5) provide probes of enzymatic reactions proposed to involve Y·'s in catalysis and to investigate the importance and identity of hopping Y·'s within redox active proteins proposed to protect them from uncoupled radical chemistry.National Institutes of Health (U.S.) (Grant GM29595)National Science Foundation (U.S.) (Grant 0645960

Thermodynamic properties and structural stability of thorium dioxide

Using density functional theory (DFT) calculations, we have systematically investigated the thermodynamic properties and structural stabilities of thorium dioxide (ThO$_2$). Based on the calculated phonon dispersion curves, we calculate the thermal expansion coefficient, bulk modulus, and heat capacities at different temperatures for ThO$_2$ under the quasi-harmonic approximation. All the results are in good agreement with corresponding experiments proving the validity of our methods. Our theoretical studies can help people more clearly understand the thermodynamic behaviors of ThO$_2$ at different temperatures. In addition, we have also studied possible defect formations and diffusion behaviors of helium in ThO$_2$, to discuss its structural stability. It is found that in intrinsic ThO$_2$ without any Fermi energy shifts, the interstitial Th$_i^{4+}$ defect other than oxygen or thorium vacancies, interstitial oxygen, and any kinds of Frenkel pairs, is most probable to form with an energy release of 1.74 eV. However, after upshifting the Fermi energy, the formation of the other defects also becomes possible. For helium diffusion, we find that only through the thorium vacancy can it happen with the small energy barrier of 0.52 eV. Otherwise, helium atoms can hardly incorporate or diffuse in ThO$_2$. Our results indicate that people should prevent upshifts of the Fermi energy of ThO$_2$ to avoid the formation of thorium vacancies and so as to prevent helium caused damages.Comment: 11 pages, 11 figure

High pressure structural study of fluoro perovskite CsCdF3 upto 60 GPa: A combined experimental and theoretical study

The structural behaviour of CsCdF3 under pressure is investigated by means of theory and experiment. High-pressure powder x-ray diffraction experiments were performed up to a maximum pressure of 60 GPa using synchrotron radiation. The cubic $Pm\bar{3}m$ crystal symmetry persists throughout this pressure range. Theoretical calculations were carried out using the full-potential linear muffin-tin orbital method within the local density approximation and the generalized gradient approximation for exchange and correlation effects. The calculated ground state properties -- the equilibrium lattice constant, bulk modulus and elastic constants -- are in good agreement with experimental results. Under ambient conditions, CsCdF3 is an indirect gap insulator with the gap increasing under pressure

Auxin pretreatment promotes regeneration of sugarcane (Saccharum spp. hybrids) midrib segment explants

We have developed a new, simple, quick and genotype-independent method for direct regeneration of sugarcane using novel midrib segment explants. Our protocol involves two steps: the pretreatment of starting material on MS (Murashige and Skoog (1962) Physiol Plant 15:473–497) medium containing 3.0 mg/l 2,4- dichlorophenoxyacetic acid (2,4-D) for 8 days under continuous dark and subsequent transfer of the explants to MS medium augmented with 0.1 mg/l benzyladenine (BA) and 0.1 mg/l naphthaleneacetic acid (NAA) under light-dark conditions. On the regeneration medium, numerous globular structures appeared from the explants and subsequently differentiated into shoots. Regenerated shoots attained 2–5 cm height within 30 days of culture initiation and readily rooted on MS basal medium. Hardened plants were successfully established in the greenhouse. The regulation of sugarcane morphogenesis by auxin pretreatment is discussed

Formal Reduction Potential of 3,5-Difluorotyrosine in a Structured Protein: Insight into Multistep Radical Transfer

The reversible Y–O•/Y–OH redox properties of the α[subscript 3]Y model protein allow access to the electrochemical and thermodynamic properties of 3,5-difluorotyrosine. The unnatural amino acid has been incorporated at position 32, the dedicated radical site in α[subscript 3]Y, by in vivo nonsense codon suppression. Incorporation of 3,5-difluorotyrosine gives rise to very minor structural changes in the protein scaffold at pH values below the apparent pK (8.0 ± 0.1) of the unnatural residue. Square-wave voltammetry on α[subscript 3](3,5)F[subscript 2]Y provides an E°′(Y–O•/Y–OH) of 1026 ± 4 mV versus the normal hydrogen electrode (pH 5.70 ± 0.02) and shows that the fluoro substitutions lower the E°′ by −30 ± 3 mV. These results illustrate the utility of combining the optimized α[subscript 3]Y tyrosine radical system with in vivo nonsense codon suppression to obtain the formal reduction potential of an unnatural aromatic residue residing within a well-structured protein. It is further observed that the protein E°′ values differ significantly from peak potentials derived from irreversible voltammograms of the corresponding aqueous species. This is notable because solution potentials have been the main thermodynamic data available for amino acid radicals. The findings in this paper are discussed relative to recent mechanistic studies of the multistep radical-transfer process in Escherichia coli ribonucleotide reductase site-specifically labeled with unnatural tyrosine residues.National Institutes of Health (U.S.) (Grant GM29595

NIBBS-Search for Fast and Accurate Prediction of Phenotype-Biased Metabolic Systems

Understanding of genotype-phenotype associations is important not only for furthering our knowledge on internal cellular processes, but also essential for providing the foundation necessary for genetic engineering of microorganisms for industrial use (e.g., production of bioenergy or biofuels). However, genotype-phenotype associations alone do not provide enough information to alter an organism's genome to either suppress or exhibit a phenotype. It is important to look at the phenotype-related genes in the context of the genome-scale network to understand how the genes interact with other genes in the organism. Identification of metabolic subsystems involved in the expression of the phenotype is one way of placing the phenotype-related genes in the context of the entire network. A metabolic system refers to a metabolic network subgraph; nodes are compounds and edges labels are the enzymes that catalyze the reaction. The metabolic subsystem could be part of a single metabolic pathway or span parts of multiple pathways. Arguably, comparative genome-scale metabolic network analysis is a promising strategy to identify these phenotype-related metabolic subsystems. Network Instance-Based Biased Subgraph Search (NIBBS) is a graph-theoretic method for genome-scale metabolic network comparative analysis that can identify metabolic systems that are statistically biased toward phenotype-expressing organismal networks. We set up experiments with target phenotypes like hydrogen production, TCA expression, and acid-tolerance. We show via extensive literature search that some of the resulting metabolic subsystems are indeed phenotype-related and formulate hypotheses for other systems in terms of their role in phenotype expression. NIBBS is also orders of magnitude faster than MULE, one of the most efficient maximal frequent subgraph mining algorithms that could be adjusted for this problem. Also, the set of phenotype-biased metabolic systems output by NIBBS comes very close to the set of phenotype-biased subgraphs output by an exact maximally-biased subgraph enumeration algorithm ( MBS-Enum ). The code (NIBBS and the module to visualize the identified subsystems) is available at http://freescience.org/cs/NIBBS

Hypotensive effect and endothelium-dependent vascular action of leaves of Alpinia purpurata (Vieill) K. Schum

The aims of this study were to evaluate the chemical profile, vascular reactivity, and acute hypotensive effect (AHE) of the ethanolic extract of leaves of Alpinia purpurata (Vieill) K. Schum (EEAP). Its chemical profile was evaluated using HPLC-UV, ICP-OES, and colorimetric quantification of total flavonoids and polyphenols. The vascular reactivity of the extract was determined using the mesenteric bed isolated from WKY. AHE dose-response curves were obtained for both EEAP and inorganic material isolated from AP (IAP) in WKY and SHR animals. Cytotoxic and mutagenic safety levels were determined by the micronucleus test. Rutin-like flavonoids were quantified in the EEAP (1.8 ± 0.03%), and the total flavonoid and polyphenol ratios were 4.1 ± 1.8% and 5.1 ± 0.3%, respectively. We observed that the vasodilation action of EEAP was partially mediated by nitric oxide (·NO). The IAP showed the presence of calcium (137.76 ± 4.08 μg mg-1). The EEAP and IAP showed an AHE in WKY and SHR animals. EEAP did not have cytotoxic effects or cause chromosomic alterations. The AHE shown by EEAP could result from its endothelium-dependent vascular action. Rutin-like flavonoids, among other polyphenols, could contribute to these biological activities, and the calcium present in EEAP could act in a synergistic way